Minggu, 27 Desember 2009

Who Were the Hobbits' Ancestors?

In 2004 scientists unearthed a partial skeleton and other bones on the island of Flores in Indonesia. The scientists postulated that the skeleton belonged to an extinct species of primitive humans that had descended from Homo erectus ancestors. They named the new species Homo floresiensis, but the press dubbed them the hobbits because of their diminutive size.

Almost immediately the new find created a controversy. If Homo floresiensis descended from the much larger Homo erectus, how did they come to be so small, and in particular, how did their brains become smaller, too? Some scientists postulated that the skeleton was just a diseased modern human; others argued that the new species had undergone a phenomenon known as “island dwarfing”.

Analysis of the morphological features of Homo floresiensis has led to a new theory, summarized recently by Kate Wong in Scientific American – that Homo floresiensis descended not from Homo erectus, but from older (and smaller) ancestors, such as Homo habilis. That would explain LB1’s small size and diminutive brain, but it raises more questions than it answers. For example, if Homo floresiensis diverged from other known human lines nearly two million years ago, why haven’t other skeletons of this species been found? Did Homo floresiensis emigrate from Africa even before Homo erectus did? Where did they go before arriving in Indonesia?

It’ll be interesting to see how our thinking about Homo floresiensis evolves as new information comes in.

Reference: Wong, Kate. Rethinking the Hobbits of Indonesia. Scientific American, Nov. 2009, pp. 66-73.

Jumat, 18 Desember 2009

Underserved medicine seminar series

I've heard great things about this seminar series in the past.

One of the 6 programs of Doctors Without Walls is the underserved medicine seminar series at UCSB. We have a great line up of speakers this year! The class has 35 enrolled students but is held in a large lecture hall so we can accommodate attendance by others and invite faculty and staff to attend when they can.
Dr Mimi Doohan MD PhD
PS There is always a lively Q and A session at the end of every presentation.

Scheduled Speakers:

Underserved Medicine Course (MCDB 194MD):
UCSB Molecular, Cellular and Developmental Biology (MCDB) Department
Thursdays 6-7:50pm, Winter quarter 2010
Location: Broida 1640
Course Instructor: Dr Mimi Doohan, MCDB adjunct faculty

Jan 7
Course Introduction
Dr Mimi Doohan MD PhD
Family physician
Doctors Without Walls-Santa Babara Street Medicine-founder/medical director

Jan 14
Modern Day Slavery and Human Trafficking in the 21st century
Thomas F. Burke MD
Chief, Division of Global Health and Human Rights, MGH
Faculty, Departments of Emergency Medicine and Pediatrics
Massachusetts General Hospital
Harvard Medical School

Jan 21
Medicine in Crisis Zones
Jason Prystowsky MD
Doctors Without Borders
Faculty, Department of Emergency Medicine Loma Linda University
Faculty, Department of Emergency Medicine UCLA

Jan 28
Health Care Reform
Congresswoman Lois Capps
23rd district of California

Feb 4
Womens Health:
Alice Levine CNM
Womens Free Homeless Clinic at Transition House
Scotti Warren, Americorp Member
Annette Perez, Transition House, Director of Operations
Jennifer Ferraez, LCSW
Morgane Naveau, UCSB student volunteer

Feb 11
Surgical Care of the Underserved
David Thoman MD
Director of Trauma and Associate Director of Surgical Education

Santa Barbara Cottage Hospital Charity Thoman MD, MPH
Resident Physician, Internal Medicine

Santa Barbara Cottage Hospital

Feb 18
LGBT Health (Lesbian, Gay, Bisexual, Transgendered)
David Selberg
Executive Director
Pacific Pride Foundation, Santa Barbara CA

Feb 25
Medical Tourism
Eric McFarland MD PhD
Robert Gayou MD

March 4
Care of Veterans
Robert Gaines MD
Medical director, Santa Barbara County Veterans Administration Clinic

March 11
Care of the Unshetlered Homeless
Jim Withers MD
Founder and director, International Street Medicine Institute
Founder and director, Operation Safety Net, Pittsburgh P


Senin, 14 Desember 2009

That's One Small Step for Gene Therapy...

French researchers report that they have successfully used gene therapy to treat beta-thalassemia in a 19-year-old male patient. Beta-thalassemia is a genetic blood disorder in which a defect in the gene coding for the beta-globin chain of hemoglobin results in persistent and life-threatening anemia and dangerously high blood iron levels. Two years after the treatment, according to the researchers, the young man no longer needs regular monthly blood transfusions and appears to be in good health.

The French team has the approval of French authorities to treat more patients with the same inherited disorder. The hope is that someday they’ll be able to successfully treat one of the most common of all genetic blood disorders – sickle cell anemia.

Sabtu, 12 Desember 2009

H1N1 Flu Deaths Update

The Centers for Disease Control and Prevention estimated this week that between 7,000 and 14,000 people have died of swine flu in the U.S. through mid-November, out of the 34-67 million people who had the swine flu so far.

Deaths caused by the flu are notoriously hard to estimate because most people are not tested for the flu when they have it and because people may die of a combination of causes, including the flu. The usual estimate is that the regular seasonal flu causes about 30,000 deaths each flu season (the winter months), so these latest swine flu numbers aren’t too bad. In fact they’re well below the government’s estimate back in August of 30,000 to 90,000 deaths from swine flu this season.

The big question is what will happen in January/February – will swine flu reassert itself in a third wave, as happened in the pandemics of 1918 and 1957? Will the H1N1 virus change to become more lethal, or more resistant to the vaccine? If either of these things happens the situation could change quickly. Most people in the U.S. are not yet immune to the swine flu because they have not had it yet and they have not been vaccinated against it.

Apparently many people think the danger is passed. We’ll hope they’re right. But if you still haven’t gotten your swine flu shot, it’s not too late. The vaccine supply seems to be pretty good these days.

Kamis, 10 Desember 2009

Prion-like Activity in Neurodegenerative Disorders

Could misfolded human proteins with prion-like activity contribute to the progression of certain chronic diseases such as Alzheimer’s, Parkinsons, and Huntington’s disease? A common feature of all three of these diseases is the presence of abnormal accumulations of certain misfolded proteins in or around nerve cells in the brain. Eventually these protein accumulations become so extensive that they choke off nerve cell function.

No one is saying that these diseases are infectious, like mad cow disease. But according to the latest thinking, once an endogenous protein "goes rogue" and misfolds, it might then cause nearby normal proteins to misfold as well. Once the process starts it could become self-propagating, from one region of the brain to the next.

Rabu, 09 Desember 2009

Summer research opportunity #2

Caitlin passed on this reminder:

I thought it might be important to note that REU deadlines are usually between the second week of January and early March.

REU stands for Research Experience for Undergraduates and is an NSF funded program that is one of the largest sources of funding for undergraduate summer research. You apply to the individual REU sites for the funding so you need to do your homework.

Access the full list of REU sites here for Biological Sciences and here for a wider list of subjects.
Click on the individual sites to find full details and application details.

Winter internship opportunity

Bruce Tiffney passed this one on:

CCBER has several Coastal Fund-supported restoration intern positions (~ 6 hr/week) available this winter as well as several paid student worker positions (~10hr/week) available for students interested in developing their hands-on restoration skills. Lots of planting, plant identification, site maintenance, nursery work and camaraderie in the field!
Please send e-mail of interest including mention of relevant experience, winter schedule and an indication of the amount of time you want workduring the work week to Lisa Stratton: stratton@lifesci.ucsb.edu

Thank you very much,


Lisa Stratton, Ph.D.
Cheadle Center for Biodiversity & Ecological Restoration (CCBER)
Harder South, Rm 1005
UCSB, MC 9615
Santa Barbara, CA 93106

Office: (805) 893-4158
Fax: (805) 893-4222


Summer Research opportunity #1

Kathy Foltz passed this one on:

Dear Colleague:

We would appreciate you sharing the following opportunity with your students.

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.


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

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 13, 2010.

For more information, please visit www.murf.caltech.edu


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 16, 2010.

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

Kamis, 03 Desember 2009

Show Your Working

From the BBC: 'Show Your Working': What 'ClimateGate' means.'

The "ClimateGate" affair - the publication of e-mails and documents hacked or leaked from one of the world's leading climate research institutions - is being intensely debated on the web. But what does it imply for climate science? Here, Mike Hulme and Jerome Ravetz say it shows that we need a more concerted effort to explain and engage the public in understanding the processes and practices of science and scientists.

Selasa, 01 Desember 2009

Ecological Consequences of Natural Oil Contamination

Heather Coleman
PhD Candidate Wednesday, Dec. 2, 2009
2:00 p.m.
Bren Hall Dean's Conference Room (2436)
"Ecological Consequences of Natural Oil Contamination"
Faculty Advisor: Hunter Lenihan

Rabu, 25 November 2009

Faculty Research Interests

Faculty in EEMB and MCDB sorted by Research Interests

Molecular genetics
Plant molecular biol
Microbial Pathogenesis
Neurobiology (molecular/cellular neuroscience)
Developmental Biology
Virology and Immunology
Cell Cycle/Cell Biology
Stem Cell Biology see also UCSB center for Stem Cell Biology and Engineering
Nanomedicine see also Center for Nanomedicine

    Biological oceanography
    Freshwater ecology
    • James Case Professor Emeritus
    • David Chapman Professor Emeritus
    • Peter Collins
    Physiological ecology
    Plant ecology
    Marine ecology
    Plant genetics/evolution
    Marine Pharmacology
    Parasitology and Infectious Diseases
    Mathematical ecology
    Microbial ecology
    • Allan Stewart-Oaten Professor Emeritus

    Origin of disease seminar

    BMSE and Biochemistry Seminars

    MRL 2053 at 11 am on Wednesday December 2nd

    Dr. Jamey Marth, Dept of MCDB and BMSE, UC Santa Barbara

    Seminar Title: "A Unified Approach to Discovering the Origins of Disease"

    Breast Self Examination

    Women; have you been feeling guilty because you haven’t been doing regular breast self-examinations to make sure you aren't developing breast cancer? Well, here’s good news for you. The U.S. Preventive Services Task Force (USPSTF), which makes recommendations about preventive care services for people who do not yet have any signs or symptoms of disease, is now recommending against breast self-examination (BSE) as a way to detect breast cancer. (The USPSTF’s previous position on the usefulness of BSE was “insufficient evidence” either for or against).

    The USPSTF systematically reviews of the benefits and harms of a preventive care services, and then tries to come up with a net assessment. In the case of BSE, the USPSTF reviewed the latest published data and concluded that; a) regular BSE does not lower the mortality rate from breast cancer, and b) women who perform BSE tend to have more imaging procedures and biopsies than women who don’t. These procedures are expensive and are themselves associated with minor health risks, such as infection and increased exposure to radiation. Overall, the net risk/benefit ratio for BSE is on the side of net risk.

    The recommendation against BSE is only for women who are not at increased risk for breast cancer. Women who are at increased risk should consult their physician.

    Reference: U.S. Preventive Task Force. Screening for Breast Cancer: U.S. Preventive Services Task Force Recommendation Statement. Ann. Int. Med. 151:716-726, 2009.

    Senin, 23 November 2009


    Gerick Bergsma will be presenting his PhD work on how direct and indirect effects of a coral mutualist propagate through a reef community.
    4pm today in the MSI auditorium.

    Dan Reed will be speaking at the Monday night CCBER Conservation and Restoration Seminar Series tonight, Nov. 23rd, 6-7pm, Rm 1013 Harder on
    The use of artificial reefs to mitigate the loss of kelp forest habitat caused by the operation of a coastal power plant.

    Sabtu, 21 November 2009

    Stress Reduction and Heart Attacks

    It has long been suspected that a risk factor for heart attacks, in addition to lack of exercise, poor diet, high cholesterol, genetic makeup, and so on, is the level of stress in one’s life. Scientists have hypothesized for years that relaxation techniques such as yoga and meditation might have a positive effect on disease outcome, but it’s been difficult to prove.

    Now a team of researchers claims to have proved it, according to a news article. They report that just 20 minutes of transcendental meditation per day significantly lowers the risk of heart attack by 47% in a group of high-risk patients (African American patients with narrowed coronary arteries.)

    The results have not yet been published in a peer reviewed medical journal, the point at which they generally are accepted by the scientific community. Personally, I’d feel better if one of the researchers were not from the Maharishi University of Management, an institution founded by the Indian guru who popularized transcendental meditation back in the 1960s. In addition, it’s not clear whether the results in this one group of high-risk patients would translate to other types of high-risk patients, or to persons at lower risk. Time will tell whether the findings can be duplicated by other researchers and whether other stress relaxation techniques have a similar effect.

    Kamis, 19 November 2009

    No such thing as a free lunch (or book)

    Copies of the Origin of Species, complete with a brand new and scientifically dodgy introduction by evangelist Ray Comfort, are being handed out by the Arbor right now(across from main library entrance). If you want a free copy of the Origin make sure you pick up, or print out, this bookmark courtesy of the National Center for Science Educations 'Don't Diss Darwin webpage.'

    Minggu, 15 November 2009

    Caffeinated Alcoholic Beverages Under Scrutiny

    This week the Food and Drug Administration (FDA) notified 27 manufacturers of caffeinated alcoholic beverages that they must either explain to the FDA why they believe that the addition of caffeine to alcoholic beverages is “generally recognized as safe” (GRAS) or take their products off the market. According to the FDA, for caffeine to be allowed as an additive to an alcoholic beverage “there must be evidence of its safety at the levels used and a basis to conclude that this evidence is generally known and accepted by qualified experts.” If the companies cannot provide such data within 30 days, the FDA will “take appropriate action” to ensure that the products are taken off the market.

    Caffeinated alcoholic beverages are marketed primarily to young people under such names as Max Vibe, Torque, and Evil Eye. Some promotional campaigns depict consumption of multiple drinks in conjunction with high-risk sports such as snowboarding and motocross biking. The action by the FDA comes after the agency received a letter from 18 state Attorneys General asking that the FDA use its authority to see that the products are removed from the market. The Attorneys General argue that caffeine can mask the effects of alcohol and could lead to increased risk-taking behavior.

    The two largest manufacturers have already agreed to remove their products from the marketplace. It would not be surprising to see the others follow suit within 30 days.

    Jumat, 13 November 2009

    Energy Sustainability in 20 years?

    Would it be possible to get 100% of our energy needs from renewable resources such as wind, water, and the sun in just 20 years? In theory, yes, but for practical reasons it's not likely to happen that soon. With current technologies it would require almost 4 million wind turbines, nearly 90,000 concentrated solar and photovoltaic power plants, and rooftop photovoltaic systems on nearly every rooftop – 1.7 billion, to be exact. Other challenges include a projected critical shortage of certain materials that would be needed, including rare earth metals (found primarily in China), lithium for lithium-ion batteries (half of the world’s reserves are in Bolivia and Chile) and platinum for fuel cells. In addition, we’d have to shift to shift to electric vehicles for transportation.

    Fortunately, the technologies for harnessing energy from renewable resources continue to improve each year. It may take some time and effort, but what choice do we have? At current rates of consumption, known reserves of the non-renewable energy resources (coal, oil, and gas) will run out in less than a century.

    Reference: Jacobson, Mark Z. and Mark A. Delucchi. A Path to Sustainable Energy by 2030. Scientific American pp. 58-65, Nov. 2009.

    Kamis, 12 November 2009

    The Green Initiative Fund

    The Green Initiative Fund (TGIF), a student-governed committee awarding grants for sustainability projects on the UCSB campus, is currently soliciting project proposals for the 2009-10 grant cycle. Any UCSB student, staff, or faculty member is eligible for funding for projects that reduce the university's impact on the environment. Ideal projects will show a quantifiable change (energy, waste, water reduction, etc.) while also educating the campus community.

    Do you work in a campus department that could use a little money to create a program that leads to behavioral change - turning off lights, purchasing Environmentally Preferable Products, purchasing reusable coffee cups, etc.? Are you a faculty member that would like to perform a small research project on a sustainability issue affecting UCSB? Are you a student member of a campus group that could use a little seed money to start that environmental initiative? All of these are perfect projects for TGIF funding!

    If you have an idea for a project, but need some help fleshing it out, please contact the TGIF Grants Manager, Jill Richardson at jill.richardson@vcadmin.ucsb.edu.

    Applications are available now and due on Monday, January 25, 2010.

    For more information on previously funded projects or to download the application, please visit the TGIF web site: http://sustainability.ucsb.edu/tgif

    We look forward to reading your proposals!

    The TGIF Grants Committee

    Selasa, 10 November 2009

    How bacteria talk

    Not a substitute for attending a talk on campus but as an additional treat check out this TED talk by Bonnie Bassler on how bacteria talk.

    If you haven't discovered the TED talks yet then you should check out the website - the world's most fascinating thinkers and doers, are challenged to give the talk of their lives - in just 18 minutes.

    Once you start watching it's hard to stop and it beats watching another cat playing piano on YouTube.....

    Senin, 09 November 2009

    I Don't Hear You...

    How does the public respond when a published scientific report shows that a dietary supplement is ineffective, or even worse, potentially harmful? To find out, scientists at the National Institutes of Health examined the sales trends of five different dietary supplements before and after the publication of negative research results. There were no significant declines in sales for four of the five supplements (saw palmetto, Echinacea, glucosamine, and St. John’s wort) after published reports that the supplement was ineffective. But sales of the fifth supplement (Vitamin E) declined about 33% after a report suggested that high doses of Vitamin E might actually be harmful.

    Why did consumers ignore the reports that supplements just didn’t work, but responded to a report of potential harm? Researchers speculate that reports of harm might have higher impact because of greater news coverage, or that some supplements (such as Vitamin E) might be recommended more often by physicians who are more likely to read and understand scientific reports, or even that it depends on the type of person who takes a particular kind of supplement, the purpose of the supplement, and the availability of alternatives.

    Still, it must be discouraging for public health officials to learn that consumers aren’t getting the message, don’t believe the message, or just don’t care whether their supplements work or not.

    Kamis, 05 November 2009

    Bren Research seminar

    Jeffrey McDonnell
    Richardson Chair, Watershed Science
    Distinguished Professor of Hydrology
    Oregon State University

    Thursday, Nov. 19, 2009
    12:30 - 1:30 p.m.
    Bren Hall 1414

    "The two water worlds paradox: Isotope evidence that trees and streams
    return different water pools to the hydrosphere"

    Anatomy of Viral Persistence

    Don't forget the seminar assignment for the Biology Colloquium. There's lots of good seminars going on right now but the pickings may get slimmer as we head into Thanksgiving week and the end of the quarter.

    Today's MCDB Seminar:

    “The Anatomy of Viral Persistence”

    Michael B.A. Oldstone, M.D.
    Department of Immunology and Microbial Science
    The Scripps Research Institute, La Jolla

    Thursday, November 5, 2009
    3:30 p.m. - 4:30 p.m.
    Rathmann Auditorium, LSB 1001

    Rabu, 04 November 2009


    Special thanks to Mac Cowell for posting links to these videos on the DIY Bio mailing list.
    One important note that I have mentioned before. The use of biohacking in the biology community simply refers to working with DNA. The word hack has been given a bad rap by the internet era, but this in no way refers to any malicious activity. Hack in this sense simply refers to genetic engineering.

    Water versus Ethanol

    In 2007 the U.S. Congress passed the Energy Independence and Security Act, which calls for a five-fold increase in fuel-grade ethanol production by 2022. Most of the ethanol would come from corn produced in the Corn Belt states of the Midwest. It sounds good for the economy of those states, but there’s a catch; growing the corn and producing the ethanol would require nearly 100 gallons of water per gallon of ethanol, by some estimates. Eventually we might have to choose between water and ethanol, or between ethanol and higher food prices.

    There would be winners and losers in an ethanol-based biofuels economy, because water generally must be used locally, whereas ethanol is more easily transported. Agricultural communities with plenty of irrigation water and the ability to grow corn would benefit from an ethanol-based biofuel economy. Agricultural communities with marginal water supplies would be forced to choose how best to use their dwindling water supplies – for agriculture or for people? City dwellers generally would be in favor of ethanol production for fuel by others; they don’t use much water for agriculture anyway and so have nothing to give up. However, they are likely to react negatively to a run-up in food prices.

    What do you think about producing ethanol from corn?

    Senin, 02 November 2009

    Understanding Cultured Meat (also called in vitro meat)

    Cultured meat is a hot topic that everyone should start learning about. Essentially most of the products we eat are just a collection of cells that have been programed to work together in a certain way. That means that animal meat can be programed up from single cells and will be made of the exact same ingredients as traditional meat. But, by producing meat in clean controlled environments the product would no longer carry the environmental, ethical, and health concerns it faces today.

    Here is a quick top line summary of those concerns:
    • Environmental: Meat production is a major cause of green house gas - more than transportation and is inefficient to produce as much animal feed is wasted. Current methods are not sustainable.
    • Ethical concerns: Factory farming and other forms of animal suffering. Anyone who has paid attention to the recent investigations into the food industry can see just how immoral the industry has become.
    • Health: Numerous illnesses, diseases. and health concerns arise from animal husbandry and packing animals close together. Avian flu, swine flu, mass antibiotic use leading to antibiotic immunity, and bacterially infected meats are just some examples.

    In Vitro Meat Nova ScienceNOW episode, aired on PBS January 10, 2006, discussing in vitro meat.

    Discusses the environmental impact of meat and in vitro meat production - from August 09 - 2009.

    Quoted from Mick Hartley who attended the 2008 In-Vitro Meat Symposium (http://mickhartley.typepad.com/blog/2008/04/at-the-in-vitro.html)

    "...Here's the low-down on how we'll be getting our meat in the future:

    In five to 10 years, supermarkets might have some new products in the meat counter: packs of vat-grown meat that are cheaper to produce than livestock and have less impact on the environment.
    According to a new economic analysis presented at this week's In Vitro Meat Symposium in Ås, Norway, meat grown in giant tanks known as bioreactors would cost between $5,200-$5,500 a ton (3,300 to 3,500 euros), which the analysis claims is cost competitive with European beef prices. With a rising global middle class projected by the UN to double meat consumption by 2050, and livestock already responsible for 18 percent of greenhouse gases, the symposium is drawing a variety of scientists, environmentalists and food industry experts. "We're looking to see if there are other technologies which can produce food for all the people on the planet," said Anthony Bennett of the United Nations Food and Agricultural Organization. "Not only today but over the next 10, 20, 30 years." Rapidly evolving technology and increasing concern about the environmental impact of meat production are signs that vat-grown meat is moving from scientific curiosity to consumer option. In vitro meat production is a specialized form of tissue engineering, a biomedical practice in which scientists try to grow animal tissues like bone, skin, kidneys and hearts. Proponents say it will ultimately be a more efficient way to make animal meat, which would reduce the carbon footprint of meat products. "To produce the meat we eat now, 75 to 95 percent of what we feed an animal is lost because of metabolism and inedible structures like skeleton or neurological tissue," Jason Matheny, a researcher at Johns Hopkins and co-founder of New Harvest, a nonprofit that promotes research on in vitro meat, told Wired.com. "With cultured meat, there's no body to support; you're only building the meat that eventually gets eaten." Researchers can currently grow small amounts of meat in the lab, and have even been able to get heart cells to beat in Petri dishes. Growing muscle cells on an industrial scale is the next step, scientists say. "That's the goal and it seems pretty clear from this conference that it's achievable," said Matheny on Thursday by telephone from the symposium. Scientists are working on a variety of cell culture procedures. The cutting edge of in vitro meat engineering is the attempt to get cells to grow as if they were inside a living animal. Meat like steak is a complex combination of muscle, fat and other connective tissue. Reproducing the complexity of muscle is proving difficult. "An actual whole muscle organ is not technically impossible," said Bob Dennis, a biomedical engineer at both North Carolina State University and the University of North Carolina, who attended the conference. "But of all the tissue engineering applications it is by far the most difficult one." While scientists are struggling to recreate filet mignon, they anticipate less trouble growing hamburger. "The general consensus is that minced meat or ground meat products -- sausage, chicken nuggets, hamburgers -- those are within technical reach," Matheny said. "We have the technology to make those things at scale with existing technology."

    Jumat, 30 Oktober 2009

    Monday's eemb seminar

    Hanna Kokko will be giving the EEMB departmental seminar next week. Dr Kokko is a behavioral ecologist and theorist and will likely discuss her work on the evolution of sex roles, population dynamics, and sperm parasites (Amazon mollies).

    Title:From individuals to populations ... and back
    Date: Nov 2
    Time: 4:00 pm
    Location: MSR Auditorium

    Kamis, 29 Oktober 2009

    Fantastic opportunity

    Part Time Research and Curatorial Assistant

    Opportunity for Biology student with excellent computer and statistical skills to assist with curating of entomology collection, statistical analysis of collection data and creation of collection data-base. Hours are extremely flexible and can be adapted to your schedule, ideally averaging about 10 hours per week. Some work can be performed at your home, some where the collection is located about 15 minutes from campus. Potential exists for junior author status on future scientific papers.

    Initial projects will include analysis of 20 years of flight period data for evidence of local impact of global warming, and comparison of post-wildfire collecting data with 10 years of base line records to evaluate habitat recovery.

    This large (60,000 specimen) collection is in need of a good computerized data-base using File Maker Pro or other data base application on Mac OSX that will be compatible with data systems at two Natural History Museums. Other curatorial and collection organization tasks are also needed. This is could be a two year or even longer opportunity for the right student. There is additional potential for studies of the student's own design utilizing the collection.

    Compensation: $10 per hour.

    For further information or to apply contact Paul Russell, 805 682-6960, maliboo@verizon.net

    Selasa, 27 Oktober 2009

    We love you Cynthia Kenyon! A new video! (July 10th 2009)

    Thank you, thank you, thank you for all your hard work Cynthia! So many diseases are caused by aging. Keeping people younger longer makes our society healthier, more experienced, and wiser. Oh this is so exciting!

    Professor Cynthia Kenyon (University of California, San Francisco, USA)
    Summary: Scientists have long thought that aging just happens. Yet because of their genes, different species have different lifespans. From the roundworm C. elegans, we now know that aging is regulated, by specific genes. These genes also influence life span in mammals, including humans. This system, and its evolution, will be discussed.

    Drew Endy Wired Magazine Video (posted on Wired on 10/26/09)

    iGEM 2009 K.U.Leuven: Essencia coli, the fragrance factory. Promo video

    Video about how Essencia coli, the fragrance factory works. Visit their project's webpage at http://2009.igem.org/Team:KULeuven for more information.

    IGEM 2009- Washington U Sunglasses for Sphaeroides

    This is an overview of the project done in 2009 by undergraduate students at Washington University in St. Louis participating in the iGEM competition. For more information, please visit: http://2009.igem.org/Team:Wash_U

    Minggu, 25 Oktober 2009

    Scientists Discover Gene That 'Cancer-proofs' Naked Mole Rat's Cells

    Quoted from: http://www.sciencedaily.com/releases/2009/10/091026152812.htm#at
    ScienceDaily (Oct. 27, 2009) — Despite a 30-year lifespan that gives ample time for cells to grow cancerous, a small rodent species called a naked mole rat has never been found with tumors of any kind -- and now biologists at the University of Rochester think they know why. The findings, presented in The Proceedings of the National Academy of Sciences, show that the mole rat's cells express a gene called p16 that makes the cells "claustrophobic," stopping the cells' proliferation when too many of them crowd together, cutting off runaway growth before it can start. The effect of p16 is so pronounced that when researchers mutated the cells to induce a tumor, the cells' growth barely changed, whereas regular mouse cells became fully cancerous.
    "We think we've found the reason these mole rats don't get cancer, and it's a bit of a surprise," says Vera Gorbunova, associate professor of biology at the University of Rochester and lead investigator on the discovery. "It's very early to speculate about the implications, but if the effect of p16 can be simulated in humans we might have a way to halt cancer before it starts."
    Naked mole rats are strange, ugly, nearly hairless mouse-like creatures that live in underground communities. Unlike any other mammal, these communities consist of queens and workers more reminiscent of bees than rodents. Naked mole rats can live up to 30 years, which is exceptionally long for a small rodent. Despite large numbers of naked mole-rats under observation, there has never been a single recorded case of a mole rat contracting cancer, says Gorbunova. Adding to their mystery is the fact that mole rats appear to age very little until the very end of their lives.
    Over the last three years, Gorbunova and Andrei Seluanov, research professor of biology at the University of Rochester, have worked an unusual angle on the quest to understand cancer: Investigating rodents from across the globe to get an idea of the similarities and differences of how varied but closely related species deal with cancer.
    In 2006, Gorbunova discovered that telomerase -- an enzyme that can lengthen the lives of cells, but can also increase the rate of cancer -- is highly active in small rodents, but not in large ones.
    Until Gorbunova and Seluanov's research, the prevailing wisdom had assumed that an animal that lived as long as we humans do needed to suppress telomerase activity to guard against cancer. Telomerase helps cells reproduce, and cancer is essentially runaway cellular reproduction, so an animal living for 70 years has a lot of chances for its cells to mutate into cancer, says Gorbunova. A mouse's life expectancy is shortened by other factors in nature, such as predation, so it was thought the mouse could afford the slim cancer risk to benefit from telomerase's ability to speed healing.
    While the findings were a surprise, they revealed another question: What about small animals like the common grey squirrel that live for 24 years or more? With telomerase fully active over such a long period, why isn't cancer rampant in these creatures?
    Gorbunova sought to answer that question, and in 2008 confirmed that small-bodied rodents with long lifespans had evolved a previously unknown anti-cancer mechanism that appears to be different from any anticancer mechanisms employed by humans or other large mammals. At the time she was not able to identify just what the mechanism might be, saying: "We haven't come across this anticancer mechanism before because it doesn't exist in the two species most often used for cancer research: mice and humans. Mice are short-lived and humans are large-bodied. But this mechanism appears to exist only in small, long-lived animals."
    Now, Gorbunova believes she has found the primary reason these small animals are staying cancer-free, and it appears to be a kind of overcrowding early-warning gene that the naked mole rat expresses in its cells.
    When Gorbunova and her team began specifically investigating mole rat cells, they were surprised at how difficult it was to grow the cells in the lab for study. The cells simply refused to replicate once a certain number of them occupied a space. Other cells, such as human cells, also cease replication when their populations become too dense, but the mole rat cells were reaching their limit much earlier than other animals' cells.
    "Since cancer is basically runaway cell replication, we realized that whatever was doing this was probably the same thing that prevented cancer from ever getting started in the mole rats," says Gorbunova.
    Like many animals, including humans, the mole rats have a gene called p27 that prevents cellular overcrowding, but the mole rats use another, earlier defense in gene p16. Cancer cells tend to find ways around p27, but mole rats have a double barrier that a cell must overcome before it can grow uncontrollably.
    "We believe the additional layer of protection conferred by this two-tiered contact inhibition contributes to the remarkable tumor resistance of the naked mole rat," says Gorbunova in the PNAS paper.
    Gorbunova and Seluanov are now planning to delve deeper into the mole rat's genetics to see if their cancer resistance might be applicable to humans.
    This research was funded by the National Institutes of Health and the Ellison Medical Foundation.
    Adapted from materials provided by University of Rochester.

    Sabtu, 24 Oktober 2009

    Infertility Patients Favor Stem Cell Research

    Most couples that have had to resort to in vitro fertilization (IVF) techniques in order to have a child are in favor of stem cell research. When asked in a national survey what they might choose to do with their frozen embryos left over after they have successfully had a child, 60% reported that they were “somewhat likely” or “very likely” to donate them for stem cell research. In contrast, less than a quarter of the respondents planned to discard their frozen embryos, or expressed a desire to donate them to another couple.

    Infertility patients are especially aware of the advances in science that have made it possible for them to have children. Perhaps they are just more grateful than most, but apparently most of them have resolved any internal moral dilemma over what to do with their leftover embryos. It is interesting, however, that most of them would rather donate their embryos to research than to know that their biological child was being raised by another couple.

    Kamis, 22 Oktober 2009

    Phosphate Recovery From Sewage

    In this blog (June 1, 2009) I talked about the world’s dwindling phosphate supplies, and how the key to sustainability of phosphate supplies would be recycling. But who among us has even thought about how we might recycle the gram and a half of precious phosphate we excrete in urine every day?

    Well, a researcher at the University of British Columbia did, and then he set out to do something about it. Today, a phosphate recovery system based on his design is producing about a ton of slow-release phosphate fertilizer every day from a sewage treatment facility serving Portland, Oregon. The fertilizer is in such high demand that the recovery system will pay for itself in less than five years. Other recovery plants are planned, including larger ones to recover the waste from dairy and pig farms.

    So if you live in Portland, Oregon, count yourself lucky; you already ARE recycling your phosphate! (Or at least somebody is.)

    Reference: Tweed, Katherine. Sewage’s Cash Crop. Scientific American Nov. 2009, p. 28.

    Senin, 19 Oktober 2009

    Tasting the Bubbles

    It used to be assumed that the tingling sensation of carbonated beverages was due to stimulation of mechanoreceptors by bursting bubbles of CO2. In fact, researchers now know that we also have chemoreceptors for CO2, and that they are located on the same taste cells that detect sour taste. The receptor molecule is the enzyme carbonic anhydrase, which converts CO2 (plus a water molecule) into bicarbonate and a proton. Protons activate the taste cell, which in turn activates the sensory neuron that synapses with it.

    Why don’t carbonated beverages taste sour, given that the carbonic anhydrase is located on the sour-detecting taste cells? No one knows for sure, but researchers speculate that the brain interprets CO2 receptor activation plus mechanoreceptor stimulation as primarily a tingling sensation.

    Minggu, 18 Oktober 2009

    Mesa Community College Biology 181 Fall 2009 Course Videos

    Dr. Dennis Wilson

    COURSE - Biology 181 - August 26, 2009

    COURSE - Biology 181 - August 28th, 2009

    COURSE - Biology 181 - September 2nd, 2009

    COURSE - Biology 181 - September 4th, 2009

    COURSE - Biology 181 - September 9th, 2009

    COURSE - Biology 181 - September 11th, 2009

    COURSE - Biology 181 - September 16th, 2009

    COURSE - Biology 181 - September 18th, 2009

    COURSE - Biology 181 - September 23rd, 2009

    COURSE - Biology 181 - October 7th, 2009

    COURSE - Biology 181 - October 9th, 2009

    COURSE - Biology 181 - October 14, 2009

    More Lectures will be posted in the future: To see them go to http://www.youtube.com/user/mesacc#grid/user/DC901D5F2BFF60A9

    Sabtu, 17 Oktober 2009

    Voyage of the Beagle finger puppets

    Brilliant. Check out the three finches with three different beaks.....

    You know you want to make them....

    There's a template available here along with patterns for various other crocheted items (octopus, squid, jellyfish, prawn and mustaches (?))

    Stem Cell Therapy for Parkinson's?

    Researchers in Europe are about to begin a long and expensive series of experiments to determine if transplantation of fetal brain cells into the brains of patients with Parkinson’s disease will improve the patients’ condition. The study is raising some eyebrows in scientific quarters. Two similar experiments carried out in the U.S. in the 1990s, admittedly when the techniques were less well developed, failed miserably.

    If they get final approval to go ahead, the researchers will harvest fetal brain cells from 6-9-week-old human fetuses and then inject the cells into the brains of patients with Parkinson’s disease. Up to six fetuses will be needed to obtain the 8 million cells to be transplanted into each Parkinson’s patient, according to a news article in Science. The first patients will receive the injections in 2012 as part of a safety study. If all goes well, a double-blind trial complete with sham surgeries will be carried out to see if the procedure actually benefits patients.

    Controversial? Yes. Worthwhile? You decide.

    Jumat, 16 Oktober 2009

    Charles Darwin - The True story



    Dr. John van Wyhe
    Christ's College, Cambridge
    Director, The Complete Work of Charles Darwin Online

    2:00 PM, Webb Hall 1100

    This year is the 200th anniversary of the birth of Charles Darwin and the 150th of the publication of Origin of Species. Yet much of what is commonly known about Darwin is wrong. He did not discover evolution on the Galapagos, Darwin's finches were not the turning point, he did not keep his theory secret for 20 years, he was not trying undermine religion and he was not an atheist. This talk reveals the real Darwin and outlines what he really did and said in a clear and entertaining way.

    Selasa, 13 Oktober 2009

    RISE - Research Internships in Science and Engineering

    This looks like a great opportunity to pursue summer research activities in Germany in the fields of biology, chemistry, physics, earth sciences & Engineering.

    Undergraduate students work with research groups at universities and top research institutions across Germany for a period of 1.5 to 3 months during the summer. RISE interns are matched with doctoral students whom they assist and who serve as their mentors. The working language will be English. All scholarship holders receive stipends from the DAAD to help cover living expenses, while partner universities and research institutes provide housing assistance. In 2010 we hope to have 300 interns.

    The application period for undergraduate students from the US, Canada, and the UK, who wish to take part in an internship during summer 2010, is:
    December 7, 2009 to January 31, 2010.

    Sabtu, 10 Oktober 2009

    The DIYbio Community - Presented at Ignite Boston 5 (2009)

    The DIYbio Community - Presented at Ignite Boston 5 (2009) from mac cowell on Vimeo.

    "We founded diybio.org, a community for amateur scientists, last year in May, just in time to present at ignite boston 2008. Since then, the community has grown. In this talk, I spend 5 minutes giving a lighting overview of the community and the current hot projects members are working on: new, cheap, diy-hardware, distributed science experiments (think flashmobs for science), a biohacking coworking space, and some molecular biology experiments (including making genetically engineered fluorescent yogurt, a melamine biosensor, and a biological counter)." - Mac Cowell

    Safety First!!! If you are a student working in a lab here are some additional safety videos to go along with your formal training

    This video series provides guidance and instruction on how to control risks associated with protocols and practices used in the modern biology laboratory. The series will make laboratory personnel aware of the intrinsic hazards associated with biomedical research and provide instruction in safe techniques that will enable workers to protect themselves from these hazards. The information will introduce new staff to good laboratory practices and provide meaningful technical review in safety for the more experienced laboratory worker.

    Produced by Schumann Productions Inc. for the Howard Hughes Medical Institute Office of Laboratory Safety
    © Howard Hughes Medical Institute

    Chemical Storage Hazards from benny on Vimeo.

    Glassware Washing Hazards from benny on Vimeo.

    Centrifugation Hazards from benny on Vimeo.

    Chemical Hazards from benny on Vimeo.

    A list of iPhone apps every biologist needs

    Peruse a PhD student's top 10 smart phone applications that boost his efficiency and speed his research

    By Balachandar Radhakrishnan

    Although the desktop computer has long been the workhorse for modern scientists, it is high time for academics to embrace the next technological wave that is mobile computing. We have all been comforted by the efficiency with which today's computers allow us to process data and information. Now, emerging mobile computing platforms will allow researchers to access and manipulate information no matter where we are. The iPhone is a good example of a mobile device that can yield a substantial productivity boost for scientists. If you are an academic and use the iPhone or iPod Touch, here are the 10 apps that will benefit you most. Feel free to add apps that you like and use for your work in the comments.

    1) Molecules
    Molecules is an application for viewing 3D protein structures. Need to quickly look up a protein structure? Just pull up the Molecules app and browse through the Research Collaboratory for Structural Bioinformatics database, download the structure, and you're good to go.
    Price: Free

    2) Solutions
    Solutions is an app from the programmers atMekentosj, who make nifty software tools for the "mac-a-demic." It's a must have calculator for making quick calculations required to prepare stock solutions and buffers. The app is very well designed, keeps lists of recently entered chemicals and their molecular weights, and has the ability to search for chemicals and their molecular weights in online databases.
    Price: $2.99

    3) Promega
    Promega is a bundle of useful stuff from the Promega website thrown together as a handy iPhone app. This is mostly a web app, which means the application itself just provides an interface to the content on the Promega site. The BioMath calculators are the best part of the app. They help you handle conversions like μg to pmol, molar ratios of insert:vector concentrations, melting temperature calculations and more.
    Price: Free

    4) iCut DNA
    Molecular biologists can typically remember the restriction sites of a couple of enzymes, but it's tough to memorize the sites for more than 10 or so. That's where iCut DNA comes in. This app brings New England Biolab's Restriction Enzyme Database (REBASE) of around 2000 enzymes onto your mobile device, allowing you to look up the recognition sequence of any type II restriction enzyme available on REBASE. The interface is seamless, and tracking down any enzyme is a snap. The app also lets you to select molecules based on enzyme name (with a handy auto-suggest drop down menu that narrows down enzymes based on your text input) or recognition sequence (again with auto-suggest drop down entries).
    Price: $4.99

    5) PubSearch Plus
    PubSearch Plus gives you the ability to search PubMed from the comfort of your iPhone or iPod Touch, and lets you read and email selected publications. Though the iPhone screen isn't ideal for viewing high resolution images in research papers, it definitely helps when you're looking up a specific piece of information from a particular paper. The app also supports EZProxy so you can connect to journals that are available only through institutional access.
    Price: $1.99

    6) Papers
    Papers is iTunes for research literature. Just as iTunes lets you sync your music with your iPod - the Papers app now has a companion app for the iPhone/iPod Touch that allows you to sync your collected journal papers. You can keep copies of all or some of your research papers on your mobile device for quick reading and reference. The built in pdf reader on the Papers app does the job comfortably and can be handled with versatile touch gestures. Papers also features "beaming" where users can send a pdf to another user or sync their library with a desktop wirelessly.
    Price: $9.99

    7) The Chemical Touch
    The Chemical Touch is an app that brings a souped-up periodic table to the iPhone and iPod Touch. An additional table of amino acids is one of the most useful parts of the app. The 20 amino acids appear with their single letter and three letter codes, isoelectric point, RNA codons, etc.
    Price: $0.99

    8) Labtimer
    Labtimer can be as useful in the lab as in the kitchen. As the name implies, it's a timer app that provides the feel of a conventional lab timer. There are four individual timers that can be set with corresponding text labels. The alarms on the app also play over any music that you may be listening to, making it useful even when you have your headphones in at the bench.
    Price: Free

    9) Evernote
    Evernote, which started out as a simple note taking tool, is now a solid information manager that can handle everything from voice notes to clippings pulled from the web. The beauty of Evernote is its versatility. I frequently use Evernote to collect notes from meetings and whiteboards directly to my mobile device, adding voice memos for better clarity. It has helped make me more efficient, especially with its ability to sync with all the different devices on which I'm running Evernote. I take a note on my iPhone, and it gets automatically synced to my desktop at home, my notebook, my netbook, and my work PC.
    Price: Free

    10)RSS Reader
    RSS feeds are essential tools for anybody who deals with information overload. As researchers we are always looking for information online, be it research publications, news articles, Journal TOCs or blog posts. A mobile RSS reader helps cut down on information clutter, and several are available for the iPhone and iPod Touch. I would recommend an app that can sync with an online service where your feeds are handled so that they can be accessed via the computer as well as your mobile device. Newsstand and Byline are two wonderful RSS reader apps that you should try.
    Price: Byline $4.99, Newsstand $4.99

    Balachandar Radhakrishnan is a PhD student at the University of Kassel, Germany, working on RNAi in the slime mold Dictyostelium. Bala has always been fascinated by technology, especially mobile technology and how it can help researchers in their endeavors. You can find more of his tips and advice here"

    How high-throughput sequencing technologies are transforming biomedical research. Presented at UCLA CNSI, July 2009.

    Why High-Throughput Sequencing is Changing Almost Everything from Christopher Lee on Vimeo.

    Jumat, 09 Oktober 2009

    Thomas A. Steitz, 2009 Nobel Prize in chemistry winner, discusses his work.

    2009 Nobel Prize in chemistry winner Thomas A. Steitz, Sterling professor of Molecular Biophysics and Biochemistry and Professor of Chemistry at Yale.

    Steitz is one of three winners for his work describing the structure and function of the ribosome, the protein making factory key to the function of all life.

    Steitz, a Howard Hughes Medical Institute investigator, shares the $1.4 million award with Venkatraman Ramakrishnan of the MRC Laboratory of Molecular Biology, Cambridge, United Kingdom and Ada E. Yonath, Weizmann Institute of Science, Rehovot, Israel.

    All three used a technology called X-ray crystallography to map the position for each and every one of the hundreds of thousands of atoms that make up the ribosome. While the work began as a quest to answer basic questions about the makeup of ribosomes, knowledge of its structure has created targets for a new generation of antibiotics.

    Writing, Reading, and Reviewing Scientific Articles

    This coming week in the bio colloquium we're reading an article from the primary literature. To provide general background on the elements of a scientific paper we also handed out "guidelines for writing a scientific paper". To help you think about it from the other end (reviewer vs. writer) you may want to see what guidelines the scientific journals provide their reviewers, that is, what helps us decide whether a paper is "publishable" by a given journal. This is useful in writing (and reading) a paper to see what the "critics" are looking for.

    Here is the link for reviewers for the journal, Ecology:

    Also informative is the "Reviewers Information Pack" (http://www.nxtbook.com/nxteu/elsevier/reviewersinfopack/) for everything you might want to know about the review process for journal articles. This is provided by Elsevier, which publishes Developmental Biology, and hundreds of other journals (http://www.elsevier.com/wps/find/journal_browse.cws_home)

    Here's their reviewers' home page:
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