Category Archives: Podcast

Podcasts, webcasts, online video and audio on science and engineering topics.

YouTube+ for Science from PLoS

SciVee is a new site by the great people at PLoS, with support from NSF and San Diego Supercomputer Center. It is very early in the launch of this effort but it looks very promising.

SciVee allows scientists to communicate their work as a multimedia presentation incorporated with the content of their published article. Other scientists can freely view uploaded presentations and engage in virtual discussions with the author and other viewers. SciVee also facilitates the creation of communities around specific articles and keywords. Use this medium to meet peers and future collaborators that share your particular research interests.

Of course plenty of great videos are already online but this looks like another great effort at helping improve communication of scientific ideas by the Public Library of Science. And there are advantages to a community lead by scientists that not only posts videos but encourages scientific discussion on the related matters. I am hopeful (and confident) this will become a great resource.

Related: Science and Engineering Webcast Directory – Stanford Linear Accelerator Center Public Lectures – Google Engineering and Technology Webcasts
Originally I posted this to my employers blog: Engineering and…. It turns out it was made public prematurely – SciVee update.

One Species’ Genome Discovered Inside Another’s

Video describing genome inside genome Watch video of Professor Werren describing the genome-in-a-genome at the University of Rochester.

More incredible gene research. Scientists at the University of Rochester and the J. Craig Venter Institute have discovered a copy of the genome of a bacterial parasite residing inside the genome of its host species. The research, reported in today’s Science, also shows that lateral gene transfer—the movement of genes between unrelated species—may happen much more frequently between bacteria and multicellular organisms than scientists previously believed, posing dramatic implications for evolution.

Such large-scale heritable gene transfers may allow species to acquire new genes and functions extremely quickly, says Jack Werren, a principle investigator of the study. If such genes provide new abilities in species that cause or transmit disease, they could provide new targets for fighting these diseases.

The results also have serious repercussions for genome-sequencing projects. Bacterial DNA is routinely discarded when scientists are assembling invertebrate genomes, yet these genes may very well be part of the organism’s genome, and might even be responsible for functioning traits.

“This study establishes the widespread occurrence and high frequency of a process that we would have dismissed as science fiction until just a few years ago,” says W. Ford Doolittle, Canada Research Chair in Comparative Microbial Genomics at Dalhousie University, who is not connected to the study. “This is stunning evidence for increased frequency of gene transfer.”

Continue reading →

Great Speech by Marissa Mayer on Innovation at Google

Marissa Mayer speech at Stanford on innovation at Google (23 minute speech, 26 minutes of question and answers). She leads the product management efforts on Google’s search products- web search, images, groups, news, Froogle, the Google Toolbar, Google Desktop, Google Labs, and more. She joined Google in 1999 as Google’s first female engineer. Excellent speech. Highly recommended. Google top 9 ideas:

(inside these are Marissa’s thoughts) [inside these are my comments]

Ideas come from anywhere (engineers, customers, managers, executives, external companies – that Google acquires)
Share everything you can (very open culture)
Your Brilliant We’re Hiring [Google Hiring]
A license to pursue dreams (Google 20% time)
Innovation not instant perfection (iteration – experiment quickly and often)
Data is apolitical [Data Based Decision Making – common errors in interpreting data – read the related links too]
Creativity loves Constraints [process improvement and innovation]
Users not money (Google focuses on providing users what they want and believe it will work out)
Don’t kill projects morph them

So far every time I hear one of Google’s leaders speak I am happier that I own a bit of stock – this is another instance of that.

Harvard Course: Understanding Computers and the Internet

Harvard Extension School – Computer Science E-1: Understanding Computers and the Internet

This course is all about understanding: understanding what’s going on inside your computer when you flip on the switch, why tech support has you constantly rebooting your computer, how everything you do on the Internet can be watched by others, and how your computer can become infected with a worm just by turning it on. In this course we demystify computers and the Internet, along with their jargon, so that students understand not only what they can do with each but also how it all works and why. Students leave this course armed with a new vocabulary and equipped for further exploration of computers and the Internet. Topics include hardware, software, the Internet, multimedia, security, website development, programming, and dotcoms. This course is designed both for those with little, if any, computer experience and for those who use a computer every day.

Nice job. via: Learn How The Darn Thing Works … from Harvard

YouTube Architecture

This very interesting post by Todd Hoff gives an overview of the YouTube Architecture and thus some interesting ideas on large scale web application architecture.

Each video hosted by a mini-cluster. Each video is served by more than one machine.
* Using a a cluster means:
– More disks serving content which means more speed.
– Headroom. If a machine goes down others can take over.
– There are online backups.
* Servers use the lighttpd web server for video:
– Apache had too much overhead.
– Uses epoll to wait on multiple fds.
– Switched from single process to multiple process configuration to handle more connections.
* Most popular content is moved to a CDN (content delivery network):
– CDNs replicate content in multiple places. There’s a better chance of content being closer to the user, with fewer hops, and content will run over a more friendly network.
– CDN machines mostly serve out of memory because the content is so popular there’s little thrashing of content into and out of memory.
* Less popular content (1-20 views per day) uses YouTube servers in various colo sites.
– There’s a long tail effect. A video may have a few plays, but lots of videos are being played.

I have noticed a large increase in significant delays (taking 10-20 seconds to start playing) with YouTube in the last few months.

Evo-Devo

Sean B. Carroll discusses the science of evolution and the field of evo-devo in this New York Times Video. Learn more in this extensive article – From a Few Genes, Life’s Myriad Shapes:

evo-devo is the combined study of evolution and development, the process by which a nubbin of a fertilized egg transforms into a full-fledged adult. And what these scientists are finding is that development, a process that has for more than half a century been largely ignored in the study of evolution, appears to have been one of the major forces shaping the history of life on earth.

For starters, evo-devo researchers are finding that the evolution of complex new forms, rather than requiring many new mutations or many new genes as had long been thought, can instead be accomplished by a much simpler process requiring no more than tweaks to already existing genes and developmental plans. Stranger still, researchers are finding that the genes that can be tweaked to create new shapes and body parts are surprisingly few. The same DNA sequences are turning out to be the spark inciting one evolutionary flowering after another. “Do these discoveries blow people’s minds? Yes,” said Dr. Sean B. Carroll, biologist at the Howard Hughes Medical Institute at the University of Wisconsin, Madison.

via: Justin Hunter (Justin and me in Madison) 🙂 Related: Opossum Genome Shows ‘Junk’ DNA is Not Junk – science webcast directory – Learning About the Human Genome – Curious Cat Science and Engineering Search

Educating Engineering Geeks

Yossi Sheffi, Professor of Civil and Environmental Engineering and Engineering Systems, Director, MIT Center for Transportation and Logistics, presents his thoughts on engineering education changes at MIT in this webcast.

So MIT must shift gears, and embrace two basic missions: continuing to produce world-class experts (geeks) – practicing engineers who design complicated systems – and generating world-class leaders (chiefs), who will deploy their technological expertise in the real-world. “My hypothesis is that the great leaders of the next century will have to have a technological background, because we’re going toward a technologically innovative society.” These leaders will be problem definers as much as problem solvers, and, says Sheffi, “either we or China will educate them.”

Sheffi suggests a School of Engineering-wide undergraduate program, where all the fundamentals courses are rethought and taught differently. This means sacrificing problem sets for case studies, and “learning how a subject fits into the grand scheme of things.” MIT should integrate humanities with engineering subjects, ensuring undergraduates understand business, ethics, legal language, environmental concerns, organization and process design. There should also be a formal leadership workshop, required time in a foreign culture and along the lines of the European Union, a five-year educational model. If MIT builds it, others will follow, assures Sheffi.

via: Geeks and Chiefs: Engineering Education at MIT

Inner Life of a Cell: Full Version

This is an extremely cool 8 minute movie on the inner workings of a Cell. The earlier version we posted about back in September of last year has been one of our most popular posts – see our most popular posts. They have added the scientific explanation that I mentioned I would love to see in the last post.

update: Unfortunately Harvard seems to want to prevent people from seeing this educational webcast. Why they don’t want to promote science education is beyond me. I guess they have better uses for their $35 billion endowment than promoting science. I sure wish they would hurry up and realize this isn’t the 18th century. They say their mission is “The advancement of all good literature, arts, and sciences; the advancement and education of youth in all manner of good literature, arts, and sciences; and all other necessary provisions that may conduce to the education of the … youth of this country…” (Jun 2008). You don’t have to just educate a few privileged soles in ivy covered buildings. You can do that any provide great education material for others around the globe.

Animation created for Harvard’s Molecular and Cellular Biology program:

Harvard University selected XVIVO, LLC, a Connecticut based scientific animation company, to customize and develop an animation that would propel Harvard’s Molecular and Cellular Biology program to the next level of undergraduate education. XVIVO’s recently completed animation, titled “The Inner Life of the Cell”, has already won awards. The eight minute animation transports Harvard Biology students into a three-dimensional journey through the microscopic world of a cell.

Communicating Science to the Public

Webcast above: Speaking Science 2.0 by Matthew Nisbet, School of Communication, American University, and Chris Mooney, Washington Correspondent, Seed Magazine, speak at the AIBS annual meeting, May 2007, in Washington DC. They discuss how to improve the transfer of science knowledge to the public (an important topic and one I am interested in). More on The American Institute of Biological Sciences conference: Evolutionary Biology and Human Health.

via: Framing Science

Water Buffaloes, Lions and Crocodiles Oh My

Pretty amazing video. A look at real wild life with lots of excitement, a bit violence and some surprising turns. On my trip to Kenya I saw an interaction between lions and one water buffalo but it was without much of this action. Basically there was a standoff for like half an hour with half charges and the like. Even that was very interesting.