| Related sites for http://biocurious.com/ |
| Dotdotdot Fun at the science disco - a light-hearted look at science and life as a microbiology researcher. | | Dura_Mater__Odd_Bits_From_a_Distracted_Scientist\'s_Brain Reflections on science and technology news and its influence on society. | | Epigenetics_News News and opinions on research and developments in the field of epigenetics. | | The_Flame_Trench Dispatches on all things space from the Florida Today blockhouse at the Kennedy Space Center. | | FuturePundit Future technological trends and their likely effects on human society, politics and evolution. | | The_Geomblog Ruminations on computational geometry, algorithms, theoretical computer science and life. | | Gooz_News Pharmacology writer Merrill Goozner comments on science, health and the public interest. | | Gyre_org Gyre.org is an attempt to track the breakthroughs and implications of the next military and technological revolutions. | | Henry\'s_Webiocosm_Blog Observations and photography in biology, botany and zoology. | | Impact_Lab The DaVinci Institute present scientific breakthroughs and innovative technologies. | | In_The_Pipeline Weblog about developments in pharmacology and chemistry by a working researcher at a drug company. | | Life_Studies_Blog Discussion about philosophy of life, death, nature, science and technology, and their impact on contemporary culture & society. | | The_Loom Commentary and edification on evolution, biology and more by science author Carl Zimmer. | | Lubos_Motl\'s_Reference_Frame News, opinion and political commentary relating to string theory, mathematics and physics. | | Migrations Cells, birds and musings from a biologist. | | Mr_Science Features information about a science TV show, summaries of news articles, and podcast links. Page includes photos. | | NASA_Orion_Spaceship_Blog News relating to NASA's Orion Spaceship and it's mission to take astronauts to the Moon and Mars. | | Nature_Newsblog News weblog of Nature periodical, allowing readers to comment on recent developments in science and technology. | | Nodalpoint Newsfeed from this community of bioinformaticians and biotechnology researchers. | | Not_Even_Wrong Physics and mathematics discussion from the author at the front line of the string theory controversy. | | The_OpenScience_Project_Weblog Weblog of a collaboration encouraging the production and release of open source scientific software. | | Philoneist A digest of technology and health stories. | | RealClimate Commentary on climate science news by working climate scientists, with discussion. | | RobBlog__Science_News_and_Opinion Digest of science news from a wide range of sources, with commentary. | | The_Sceptical_Chymist New and exciting developments in chemistry and chemical biology from the editors of Nature and associated journals. | | SciAm_Observations Opinions, arguments and analyses from the editors of Scientific American. | | Science_Blog General science and technology news blog. | | Science_in_Action Explorations of science and math in the real world, with topical comments, unexpected connections and weird facts. | | Science_Musings_Blog A regular meditation on humankind's quest to understand the universe. | | Science_Surfing Topic-specific overviews of free-access online scientific sources. | | ScienceBase_com Science news and features plus commentary by science journalist and writer David Bradley. | | ScienceBlogs A community of 40 selected science bloggers, set up as an experiment in scientific communication. | | ScienceNewsBlog_com Provides coverage of space and science news. | | SciScoop Community edited science blog and discussion forum. | | Short_Sharp_Science A science news blog from New Scientist. | | So_I_Want_To_Be_An_Astronaut A Kuwaiti girl dreams of being an astronaut, and becoming the first Kuwaiti, Arab, Muslim female to go into space. | | Space_Spin News and technological innovations in space exploration. | | spacebar Commentary on science and general interest news stories, plus art and photography postings. | | Stem_Cell_Research_Process_Blog Weblog charting developments and discussing current opinions in this field. | | theWatt News and discussion about energy, fuels and the environment. |
|
Biocurious
Biocurious/ a biophysics blog
Main
About
Archive
Contact
Colophon
Feeds: RSS / Atom
About Biocurious
Biocurious is a weblog about biology through the eyes of physicists. More...
Recent comments
Biophysical Journal moves to Cell Press (3)Josh, PhilipJ, JoshPZ Myers: "Science is not Important" (9)Ben, Andre, Massimo , ...Traditional lectures don't work (1)AlexMolecule of the Month: Glucose Oxidase (8)P.C.Chen, Joseph , _Arthur, ...The Most Exciting Future Biophysics Tool (3)Andre, PhilipJ, Alex
Molecule of the Month
Tobacco Mosaic Virus
Browse by section
AcademicsAndre's ResearchBiocuriositiesBooksGraduate SchoolHistory of ScienceHot off the PressIgor's ResearchInterdisciplinarityMolecule of the MonthOpen AccessPhilip's ResearchPhilosophy of SciencePhysicsPhysicsworld.com
Other blogs
BackreactionCeclia's Blog at PHD ComicsCocktail Party PhysicsCosmic VarianceThe Daily TranscriptEasternblotEveryday ScientistThe Evilutionary BiologistEvolgenFreelancing ScienceThe Futile CycleGood Math, Bad MathiMechanicain singuloIncoherently Scattered PonderingsJuniorprofKlara StefflovaLife of a Lab RatThe LoomMalletriviaMetadattaMixed StatesMorning Coffee PhysicsNot Even WrongNotes from the biomassNotional SlurryOpenScience ProjectPharyngulaPLoS BlogPonderings of a foolRecombinantsThe SandwalkSciAm ObservationsScienceBlogsShtetl-OptimizedThree-toed SlothUncertain PrinciplesWhat's New by Bob Park
Powered by
Hosted by
Molecule of the Month: Tobacco Mosaic Virus
Posted 7 January 2009 by PhilipJ under Molecule of the Month
Tobacco mosaic virus (TMV) has been at the center of virus research since its discovery over a hundred years ago. TMV was the first virus to be discovered. Late in the 19th century, researchers found that a tiny infectious agent, too small to be a bacterium, was the cause of a disease of tobacco plants. It then took 30 years of work before the nature of this mysterious agent became apparent. In a Nobel-prize-winning study, Wendell Stanley coaxed the virus to form crystals, and discovered that it was composed primarily of protein. Others quickly discovered that there was also RNA in the virus. Then, many prominent structural researchers (including J. D. Bernal, Rosalind Franklin and James Watson) used x-ray diffraction and electron microscopy to probe the structure of the virus. Finally, as part of his Nobel-prize-winning work, Aaron Klug determined the atomic structure of the virus.Several structures of the whole tobacco mosaic virus are available in the PDB, including one solved by x-ray diffraction of fibrous crystals (shown here from PDB entry 2tmv) and a more recent structure solved by analysis of many electron micrographs (PDB entry 2om3). The virus is composed of one strand of RNA (shown in red) wrapped inside a sheath of protein (shown in blue). The protein coat is composed of about 2130 copies of a small protein, which stack like bricks in a cylindrical chimney. The RNA strand encodes four proteins, which together orchestrate the life cycle of the virus. These include two proteins that replicate the viral RNA, a protein that transports the RNA from cell to cell, spreading the infection, and the capsid protein seen in the PDB structures. Read the rest from David Goodsell at the PDB, here.
 Comment
Biophysical Journal moves to Cell Press
Posted 6 January 2009 by PhilipJ under Hot off the Press
The Biophysical Journal is now published by Cell Press, so point your browsers (and change your RRS feeds) once you’re redirected to the new site automatically. From the horse’s mouth:Cell Press is proud to become responsible for publishing the Biophysical Journal with the first issue of 2009. To facilitate the transition from the journal’s previous web site, all content will be freely accessible for the first three months. Members of the Biophysical Society will receive an email in late March explaining how to set up their online access to the journal. Emphasis mine. For the next three months, we can all enjoy free access to Biophysical Journal. Get reading!
Comment [3]
Traditional lectures don't work
Posted 2 January 2009 by PhilipJ under Academics
As will be no surprise to anyone who has ever sat through a lecture, traditional lecturing doesn’t work, or at least, not as we wish. The most recent discussion of how traditional lecturing is failing students is from physicist Eric Mazur, who writes in the most recent edition of Science in Farewell, Lecture? (pdf, closed access):The traditional approach to teaching reduces education to a transfer of information. Before the industrial revolution, when books were not yet mass commodities, the lecture method was the only way to transfer information from one generation to the next. However, education is so much more than just information transfer, especially in science.* New information needs to be connected to preexisting knowledge in the student’s mind. Students need to develop models to see how science works. Instead, my students were relying on rote memorization. Reflecting on my own education, I believe that I also often relied on rote memorization. Information transmitted in lectures stayed in my brain until I had to draw upon it for an exam. I once heard somebody describe the lecture method as a process whereby the lecture notes of the instructor get transferred to the notebooks of the students without passing through the brains of either. That is essentially what is happening in classrooms around the globe. The traditional lecture method ignores the fact that lots of people learn in lots of different ways, and when it comes to things like calculation, watching someone else do them does little for one’s own understanding. It might make sense to you for the brief moment while watching, but it is not a substitute for doing it yourself to really master something. I think the relative lack of utility of the traditional lecture has been masked by the fact that students are (usually) in a university program out of choice, and will pick up the slack and teach themselves as is necessary to succeed in the course. It is also my philosophy that the quicker a student realizes they should (and can!) be teaching themselves the material, the more enjoyable the learning process and the better they do. So what are we going to do with all these professors who still need to teach courses? Mazur’s take is to change the way the classroom is run:[…] I have begun to turn this traditional information transfer model of education upside down. The responsibility for gathering information now rests squarely on the shoulders of the students. They must read material before coming to class, so that class time can be devoted to discussions, peer interactions, and time to assimilate and think. Instead of teaching by telling, I am teaching by questioning. I’ve had a couple of profs over the years who have taken this approach, and I have always felt it works so much better than the traditional method. The only problem is that it is most effective in the small class setting such as upper-level undergraduate courses. It can be implemented in a large introductory class through the use of so-called “clickers”, but the implementation is key. Quoating Mazur again:I often meet people who tell me they have implemented this “clicker method” in their classes, viewing my approach as simply a technological innovation. However, it is not the technology but the pedagogy that matters. Unfortunately, the majority of uses of technology in education consist of nothing more than a new implementation of old approaches, and therefore technology is not the magic bullet it is often presumed to be. Are any of our readers using clickers and changing their teaching methodology (I think Rosie has used them in her courses)? If so, I’d love to hear your feedback on how they were received by students, and whether it was more or less work to prepare for the course. I fear (but appreciate) that the effort involved will be a deciding factor on whether these new teaching tools (implemented properly!) will be embraced. * I don’t agree that science is somehow different from other subjects when it comes to traditional lectures and their relevance to learning. No subject is just a collection of facts to be regurgitated on an exam.
Comment [1]
Edge World Question 2009: What will change everything?
Posted 1 January 2009 by PhilipJ under Biocuriosities & Interdisciplinarity
The 2009 Edge World Question is What game-changing scientific ideas and developments do you expect to live to see?. It seems like a lot of people ignored the question, but most were still an interesting read. As per previous years, here are a few of my favourites. Alun Andersen thinks simple, engineered organisms that can soak up energy in a vat in any sunny spot and turn that sunlight straight into a precursor for fuel, preferably a precursor that can go straight into an existing oil refinery that can turn out gasoline are the solution to our energy problems. Jesse Bering thinks we’ll come to realize that God needn’t actually exist to have evolved. Mihaly Csikszentmihalyi argues that it is more important to understand events, objects, and processes in their relationship with each other than in their singular structure, which I would argue has been obvious for a long time already. Keith Devlin thinks the mobile phone will reach nearly 100% of the human popluation. Freeman Dyson, because he is already 85, changes the timescale of the question, and concludes radiotelepathy. David Eagleman thinks we’ll give computers our consciousness. Kenneth W. Ford thinks we’ll be able to read your mind. Richard Foreman, quite sensibly, thinks everything won’t change. James Geary agrees with Eagleman that we’ll see brain-machine interfacing. Sam Harris thinks we’ll have a true lie detector, some kind of mind-reading device. Roger Highfield thinks we’ll finally build fusion reactors. Eric Kandel hopes we’ll achieve a biological understanding of mental illness. Stuart Kauffman thinks that much of the universe stands partially free of physical law. Andrian Kreye is also big into synthetic fuels. Clifford A. Pickover things we’ll see a proof of the Reimann hypothesis. Ed Regis brings up the (thanks to things like synthetic biology) now-passé idea of nanotechnology. Carlo Rovelli, being open-minded, imagines no big changes coming. Gino Segre thinks we’ll find additional space-time dimensions. And while neither André nor I are part of the Edge crowd, I might imagine both our answers would be along the lines of The Most Exciting Future Biophysics Tool, as the implications of such an instrument go far beyond biophysics. Happy New Year everyone!
Comment
The Most Exciting Future Biophysics Tool
Posted 18 December 2008 by Andre under Interdisciplinarity & Physics
If you could wish for any capabilities in an instrument to help you with your research, what would they be? It might not be hard to come up with a useful super power that’s way out of reach of current or near-future technology, but what about something you might actually have in the next 10 or 20 years? One of my interests is high resolution imaging, either by scanning probe or fluorescence microscopy, and I’ve seen and taken advantage of some great electron microscopy as well (although I haven’t done any myself). Each of these methods in their current most common form has advantages and disadvantages: scanning probe microscopies tend to be slow but offer high resolution with little sample preparation, fluorescence microscopy suffers from lower resolution but has pretty good acquisition rate and molecular specificity, and electron microscopy involves more complicated sample preparation that can distort the sample and only provides a snapshot, but it can provide truly exquisite images at a range of spatial scales. These methods are all providing new insights into every area of cell biology and biophysics—fluorescence microscopy especially is now a staple of almost every lab in these fields—but it’s the ways that these methods are being pushed beyond their current limits that are truly exciting. New tools have always provided new insights, but I think cell biology is poised to be completely revolutionized in the next few decades.  Take atomic force microscopy. High resolution in water, but painfully slow. Wouldn’t it be nice if it were faster? It is. The animated gif on the right is an AFM movie taken at 12 frames per second in Toshio Ando’s lab at Kanazawa University in Japan. You’re seeing a single myosin molecule undergo a conformational change in real time. Single molecule fluorescence methods have provided a lot of insight into the mechanism of molecular motor motion (they walk) but there are still finer scales to investigate and high-speed AFM may prove to be the tool of choice in the very near future. That’s very nice for in vitro work, but ultimately cells are where the action is. I want an instrument that will reduce the vast majority of cell biology to computer science. That will “only” require the convergence of three existing technologies: cryo-electron tomography, environmental scanning electron microscopy, and femtosecond electron diffraction. The ultimate fantasy or course is an atomic scale femtosecond movie of a living cell over hours. That would give you a complete genetic, proteomic, biophysical, and biochemical picture of cell function. You would still need interesting perturbations to ask questions, but all the answers would be provided by a single instrument and clever data mining. Even relaxing the goal by orders of magnitude in every direction to 10 nm spatial resolution and millisecond time resolution in a one minute movie would be radical.  Sounds far-fetched, but don’t forget that we’ve already got Wolfgang Baumeister talking about the molecular sociology of the cell and visual proteomics and people like Philip’s advisor doing femtosecond electron diffraction. Environmental scanning electron microscopy works in water vapour. At a talk at the College of Physicians, Ahmed Zewail spoke about an instrument his group is developing for electron diffraction and imaging. He showed a picture of a cell they took with it and he says their goal is to do a single particle version of electron diffraction in a cell within a few years. Maybe he wasn’t even exaggerating… While on the topic of things that might be possible in the future, nanotech enthusiasts might be interested to know that Eric Drexler now has a blog called Metamodern.
Comment [3]
Molecule of the Month: Hsp90
Posted 4 December 2008 by PhilipJ under Molecule of the Month
 When cells are challenged with extreme heat, they build a collection of protective proteins called heat shock proteins (typically abbreviated as “Hsp” with the approximate molecular weight afterwards). Many of these proteins are chaperones that work to keep cellular proteins folded and active when conditions get bad. They also play important roles in the normal life of the cell, helping proteins fold and limiting the dangerous aggregation of immature proteins. Some of these proteins, such as Hsp70 and Hsp60 are general chaperones. Hsp90, on the other hand, plays a more specific role.Hsp90 is a specialized chaperone that assists in the maturation of a select clientele of proteins. These proteins include over a hundred transcription factors and kinases, such as steroid receptors, mutant p53 protein, and the HER2 protein involved in breast cancer. So far, researchers have not discovered a unifying theme for this growing list of proteins, just that Hsp90 is essential for maintaining active forms of these proteins. To find out more about Hsp90, click through to the PDB.
Comment [1]
Previous
This work is licensed under a
Creative Commons Attribution-Share Alike 3.0 License.
|
|
