Archive for the 'Biology' Category

Sparse and large-scale learning with heterogeneous data

Saturday, March 6th, 2010


Google Tech Talks September 5, 2006 Gert Lanckriet is assistant professor in the Electrical and Computer Engineering Department at the University of California, San Diego. He conducts research on machine learning, applied statistics and convex optimization with applications in computational biology, finance, music and vision. ABSTRACT An important challenge for the field of machine learning is to deal with the increasing amount of data that is available for learning and to leverage the (also increasing) diversity of information sources, describing these data. Beyond classical vectorial data formats, data in the format of graphs, trees, strings and beyond have become widely available for data…

5th ISCB Student Council Symposium

Sunday, February 28th, 2010


This video is a short summary of the 5th ISCB Student Council Symposium which was held in Stockholm on June 27, 2009. More information on the symposium website symposium.iscbsc.org

Physics Meets Biology

Sunday, February 28th, 2010


If scientists could take advantage of the awesomely complex and beautiful functioning of biologys natural molecular machines, their potential for application in many disciplines would be incalculable. Nobel Laureate and Director of the Lawrence Berkeley National Laboratory Steve Chu explores Possible solutions to global warming and its consequences. Series: Lawrence Berkeley National Laboratory Summer Lecture Series [2/2006] [Science] [Show ID: 11023]

High End Computing and Scientific Visualization at NASA

Thursday, February 25th, 2010


Google techtalks January 25, 2006 Dr. Rupak Biswas and Dr. Chris Henze Dr. Rupak Biswas is currently the Acting Chief of the NASA Advanced Supercomputing (NAS) Division at NASA Ames Research Center. Dr. Biswas received his Ph.D. in Computer Science from Rensselaer Polytechnic Institute in 1991 and has been at NASA ever since. Chris Henze is the lead of the Visualization Group in the NASA Advanced Supercomputing (NAS) Division at Ames Research Center, in which capacity he supervises research and development activities in data analysis and visualization. Dr. Henze received his Ph.D. in computational biology from the University of Arizona in 1993.

Bruce Lipton – Biology of Perception 5 of 7

Thursday, February 25th, 2010


see info for first part more audio/video at channelzero.multiply.com

Running Large Graph Algorithms: Evaluation of Current State-Of-the-Art and Lessons Learned

Monday, February 22nd, 2010

Lec 8 | MIT 7.014 Introductory Biology, Spring 2005

Monday, February 22nd, 2010


Biochemistry VI (cont.) DNA as Genetic Material (Prof. Graham Walker) View the complete course: ocw.mit.edu License: Creative Commons BY-NC-SA More information at ocw.mit.edu More courses at ocw.mit.edu

Einstein Faculty, 5 of 6

Friday, February 19th, 2010


Aviv Bergman, Ph.D., founding professor and chair of systems & computational biology at Einstein, discusses the clinical applications of his work on head and neck cancers; the characteristics of his ideal recruit; the importance of collaboration; and shares why he chose to work at Einstein.

iGEM – Drew Endy Defining Synthetic Biology (video)

Saturday, February 13th, 2010


Description of

Lec 1 | MIT 7.014 Introductory Biology, Spring 2005

Wednesday, February 10th, 2010


Introduction (Prof. Graham Walker) View the complete course: ocw.mit.edu License: Creative Commons BY-NC-SA More information at ocw.mit.edu More courses at ocw.mit.edu

A lab the size of a postage stamp

Monday, February 8th, 2010

Traditional lab tests for disease diagnosis can be too expensive and cumbersome for the regions most in need. George Whitesides’ ingenious answer, at TEDxBoston, is a foolproof tool that can be manufactured at virtually zero cost.

Creative Commons Attribution 3.0 Unported This work is licensed under a Creative Commons Attribution 3.0 Unported.

Firas Khatib – FoldIt

Thursday, February 4th, 2010


twitter.com – twitter.com – The University of Washington are investigating whether the brainpower of humans worldwide can be brought to bear on critical problems posed in computational biology. The long term goal of this project is to utilize the combined power of humans and computers in order to build accurate models of disease-related proteins by introducing a new approach: distributed computing driven by human intuition. www.gnomedex.com – http

Practical Life Extension Results

Monday, February 1st, 2010


Google Tech Talk October 9, 2009 ABSTRACT Presented by Gregory Benford. Genescient is the world’s first computational biology company founded on the use of artificial biological selection to cure the diseases of aging. Our laboratory animals have been selected for longevity through 750 generations for the equivalent of 15000 human years. I will describe Genescient’s multiple pathways toward accelerating human longevity, with parallel enhancements of vigor and function. Genescient applies 21st century genomic technology to identify, screen and develop benign therapeutic substances at precise doses, to defeat the diseases of aging. Our singular approach addresses the complex genomic networks that underlie aging and aging-associated diseases such as cardiovascular disease, Type II diabetes and neurodegenerative diseases. I shall display some results and our first product, due in 2009. Gregory Benford is a Professor Emeritus at the University of California, Irvine, where he was a Professor of Physics. He is a Woodrow Wilson Fellow, a Fellow of the American Physical Society and was Visiting Fellow at Cambridge University and the Universities of Turin and Bologna. In 1995 he received the Lord Prize for contributions to science. With more than 200 scientific publications, his research encompasses both theory and experiments in the fields of astrophysics and plasma physics. His research has been supported by NSF, NASA, AFOSR, DOE and other agencies. He is an ongoing advisor to NASA, DARPA (Defense Advanced Research Projects Agency) and the CIA. Dr. Benford is also the author of more than thirty books, nearly all still in print. His work has won many awards, including the Nebula Award for his novel Timescape. His non-fiction Deep Time received much praise in 1999 and he won the United Nations Medal in literature in 1994. Gregory Benford became Emeritus form the University of California, Irvine, in 2006 in order to found and develop Genescient.

Dna Molecular Biology Visualizations – Wrapping And Replicat

Friday, January 29th, 2010


Dna Molecular Biology Visualizations – Wrapping And Replication.mpg

Synthetic Biology: Drew Endy

Tuesday, January 26th, 2010


Long Now Synthetic Biology Debate: Drew Endy Drew Endy is a biological engineer at Stanford University and a leading voice in the field of synthetic biology.

Integrative Biology 131 – Lecture 02: Skeletal System

Saturday, January 23rd, 2010


Integrative Biology 131: General Human Anatomy. Fall 2005. Professor Marian Diamond. The functional anatomy of the human body as revealed by gross and microscopic examination. The Department of Integrative Biology offers a program of instruction that focuses on the integration of structure and function in the evolution of diverse biological systems. It investigates integration at all levels of organization from molecules to the biosphere, and in all taxa of organisms from viruses to higher …

Computational Biology Field Trip-2

Wednesday, January 20th, 2010

Improving Biology Education

Wednesday, January 20th, 2010

Everybody agrees that education is important. Likewise, it has become a commonplace to say that we aren’t educating the nation’s children as well as we should. Improving education is an exceptionally complex task, but one part of the problem is that we’re having trouble as a society defining what a “good education” actually is. This is a particular problem in subjects that are politically and emotionally charged. One of the most acrimonious areas of education is the one that is also nearest to my own heart: biology. Allow me to lay out some thoughts on what a sound education in biology ought to look like, and what the benefits of this might be on both the individual and the societal level.

First, and perhaps most importantly, it is critical that all sciences, including biology, are taught as a process and a way of thinking, rather than a set of facts that are “true” and must be memorized. For example, one of the more startling ideas in biology is that much of the weight of an oak tree has actually been pulled out of thin air. If someone just told me that, and I had no idea where the information came from, I’d think they were a bit loopy at best or trying to sell me a bill of gods at worst. Equipped with an actual understanding of the scientific inquiry that went into this discovery, I not only believe it, but more importantly I understand and remember it as well. Now, replicating even the simplest of the experiments scientists used to unravel the question “How do plants gain weight?” would be difficult in the average classroom and probably not the best use of precious time. But looking into case studies like this one is a fabulous way to learn about both scientific facts and scientific thinking.

Once we start thinking about biology as a process of acquiring knowledge about living things and biology education as an opportunity to understand that process and hone critical thinking skills at the same time, we will be in a much stronger position to improve science education than we are in now. At that point, we’ll be well placed to reliably turn out scientifically literate high school graduates and also to tackle teaching more politically charged aspects of biology education.

Without question, the most politically charged aspect of biology is evolution. It is also among the very most important scientific ideas ever elucidated. If we present evolution in the classroom as “great man, Charles Darwin, discovered evolution, and now we know that people descended from apes without the help of God” we have only ourselves to blame if 65 % of American citizens are creationists . Evolution education might not be quite that bad in most schools, but I’ll warrant that it’s not too much better. What do we lose if evolution is understood by only a minority of Americans? Well, from an aesthetic point of view, it seems a shame that so many of us don’t understand one of the big ideas about how the world works. From a practical perspective, it’s just plain scary that most of the farmers who use antibiotics to help their livestock gain weight and most of the patients who don’t follow their doctor’s instruction when it comes to taking antibiotics don’t understand the role they are playing in promoting the evolution of antibiotic resistant bacteria.

One frequent complaint I hear from students in high school biology classes is that there is so much memorization. This is more closely linked to the failures of our educational system than you might think at first. True, there is a significant amount of new vocabulary that students must learn if they are going to be able to speak, think, read, and write about new concepts. However, a biology class should never feel like a pile of memorization to slog through. The most important thing we can do to change this is to focus on the how’s and why’s of biology rather than just the conclusions that biologists have drawn over the years. In this way, students will be making connections and developing big picture concepts rather than just memorizing niggling little facts.

An important result of this type of education is that years after high school is over, a student who actually developed a genuine understanding of biology is far less likely to be the person frivolously abusing antibiotics.

Another way to greatly improve this situation is to eliminate pure survey classes and require students to study one or two areas in much greater depth. One model that I have seen work quite well at the introductory high school level is to have a traditional survey-style class supplemented by two significant research projects. One of the research projects was a hands-on experiment (or series of experiments), much like a traditional science fair project. The other was an in-depth library-based research project, much like a term paper more traditionally seen in history classes. These types of projects are not without costs. Most notably, they are very hard on the teacher. It takes a tremendous amount of time and energy to coordinate a hundred (or usually more) projects, each on a different topic. This is daunting for a teacher even under the best of circumstances and can be impossible in more difficult situations. Nevertheless, the benefits are clear and significant. Not only do these types of projects give students an opportunity to develop a real understanding of scientific thinking, but they also give the students a library of interlinked facts to refer to when they are trying to make sense of the big picture in biology.

For example, a student who chooses to do a research report on handedness and brain asymmetry in humans will undoubtedly learn about neurology, evolution, and epilepsy as well. As an added bonus, if the projects are structured properly, students get much needed practice making visual and oral presentations and writing non-fiction papers. Rather than just throwing up our hands and saying that this type of education is too difficult to organize, we need to structure our schools (and exert peer-pressure on parents) so that this type of higher-level learning becomes feasible.

A good education in biology should be a routine part of the education that every American student receives. We need to structure curriculums and classrooms so that science is taught as a process and method rather than some sort of received truth. This type of science education is an important part of teaching students to have strong critical thinking skills and for ensuring that they have the tools to not simply negotiate the modern world, but also thrive in it.

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Monty Carlos’ Saga

Sunday, January 17th, 2010


and Nathan Kane. Special thanks to the men of Triangle Fraternity (Devin Koba, Mark Lu, Arnold Yeung, Oliver Zhu and Alex Cheng). Extra special thanks to Teresa Head-Gordon and Aaron Kaluszka of the Bioengineering Department at the University of California at Berkeley. Finally, thank you to the BioE 143 – Methods in Computational Biology Class for Spring 2009. … “Monty Carlos’ Saga” “computational biology” comedy parody funny awesome Nerd Nerds Computers “best movie ever” BioE 143 Spring …

biology – nuclear transfer (clone creating)

Sunday, January 17th, 2010


Nuclear Transfer is a form of cloning. The steps involve removing the DNA from an oocyte and while(unfertilized egg), and injecting the nucleus which contains the DNA to be cloned. In rare instances, the newly constructed cell will divide normally, replicating the new DNA while remaining in a pluripotent state. If the cloned cells are placed in the uterus of a female mammal, a cloned organism develops to term in rare instances. This is how Dolly the Sheep and many other species were cloned …