CreatureCast – Tangled String

posted by Sophia Tintori / on December 31st, 2010 / in Cell Biology, Podcast

This video is about the enzymes that, for me, first turned cells into little toy chests full of delightful tiny gadgets.

All of the mechanical things that our bodies do, like keeping other things out, or seeing, can be described by somewhat abstract functions. For example, ‘the skin makes a protective sheet’ or ‘the lens focuses light’. But then all of those abstract functions can be broken down again into mechanical motions of the small molecules inside the cells, complete with hinges and springs, making them seem tangible once more, at least to my mechanism-oriented mind: The outside of each skin cell is littered with little molecules that hold on to the same types of molecules on the next cell in a strong handshake, forming a tight, grime-proof layer, while lens cells pack hundreds of copies of a single type of protein up tight against each other, forming almost a crystal, and then jettison all of things in the cell that would scatter light, like DNA or mitochondria, in order to let light pass cleanly through the cell.

This story in this video is about a problem that all living things have — how long and thin DNA is, and how easy it would be to get it all tangled. Not only is there a huge amount of DNA in each cell (around two meters in each human nucleus, for example), but also every time a cell divides into two, the two strands of all of that DNA have to be untwisted from each other to be copied. Think about pulling the fibers of a length of twine apart; the wound end gets tighter and tighter and then twists up on itself, making it impossible to move forward. Thankfully there are these little enzymes, called topoisomerases, that are there to iron out the wrinkles.

Video and narration by Sophia Tintori, with an original score generously provided by Amil Byleckie. The video is released under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 license.

Waiting for the bus (…in the wild)

posted by Stefan Siebert / on December 22nd, 2010 / in Birds

A couple of days ago when waiting for the bus at Kennedy Plaza near Burnside Park in downtown Providence, I witnessed an episode of urban wild life. Luckily I had my camera at hand. While waiting at the bus stop I started looking into the trees and suddenly spotted a proud red-tailed hawk which just had caught a pigeon and was about to start its meal. I was not the only one who was amazed by the scene. While trying to find a good angle, I bumped into Peter Green, who was also on the hunt for good shots. As I learned, Peter devotes a great part of his free time to the hawks and falcons of the city. Beside the red-tailed these also include Cooper’s hawks and Peregrine Falcons, arguably the fasted animals on the planet, with speeds over 200 mph. If you want to see more of raptor life in Providence visit Peter’s website (or visit Burnside Park). I ended up missing my bus, and the next two as well, but I will definitely keep my eyes open the next time I am downtown.

Pictures by Stefan Siebert

Practical Computing for Biologists

posted by Casey Dunn / on December 7th, 2010 / in Books, Technology

I’m happy to announce the release of Practical Computing for Biologists, a book I wrote with my friend Steve Haddock. Here is a flyer with more information. The book is available directly from the publisher, Sinauer Associates, and from Amazon.

We wrote this book because computational tools are becoming increasingly important across all of biology, but few biologists have training in general tools for handling and analyzing data. There are many reasons for the growing role of computers in biology, even in fields that were adequately served by an Excel spreadsheet and a piece of scrap paper just a decade ago. First and foremost, datasets are now just too large to reformat or analyze by hand, and there is increasing interest in analyzing different types of datasets in combination. Both tasks require custom tools.

Biologists are facing larger datasets for a couple reasons. There is a growing number of public data archives where biologists can deposit raw data from their studies, and these archives enable large analyses across datasets. In addition, instruments now generate far more data than they used to. Improved imaging tools scan organisms at very high resolution, DNA sequencers generate 100,000 times more data than they did a few years ago, environmental sensors can log temperature and humidity at sub-second intervals for months, and physiological instruments are growing more precise. Gone are the days when a young scientist can find refuge from statistics, mathematics, and computer programming in the basement of a Natural History museum, the forests of Halmahera, or a developmental biology lab.

But the changes are happening so fast right now that university curricula haven’t kept up, and biologists that were trained even a few years ago now find that they need to learn computer skills that weren’t covered in any of their coursework or prior research training. There is wide recognition that these are critical problems in biology. There are a couple of possible solutions. First, biologists can work to get computer scientists interested in the problems they face and collaborate with them on solutions. Second, biologists can become more proficient with computational tools. Both need to happen.

Many interesting problems in biology are also interesting computational problems, and there is a strong history of close collaboration that has produced software tools that biologists can use even if they don’t have a computer science background. Many of the day-to-day computational challenges that biologists face, however, are not particularly interesting to computer scientists. These include reformatting the output of one program so that it can be used as the input to another program, automating the download of weather data from several field sites, and writing a script to automatically shuttle data through a series of analyses that require multiple programs and some novel calculations. It is highly unlikely that computer scientists would solve these many routine problems for many biologists, and the challenges are so varied that no one piece of software could take care of them all.

This is where our book comes in. We provide a grounding in time-tested general-purpose tools for handling data, including regular expressions, the Unix command line,  Python, and  image editing tools. An emphasis on general-purpose technologies rather than particular analysis programs enables biologists to build a skillset that can be used to face a far larger set of problems. We hope that the book will be useful to established scientists, as a companion book in courses that have a computational component, and as a stand-alone textbook.

The bird sculpture on the cover is by Ann Smith.

CreatureCast – The Stomatopod Strike

posted by Sophia Tintori / on December 7th, 2010 / in Arthropods, Biomechanics, Podcast (Student Contribution)

This podcast comes from Nati Chen, a sophomore in Casey Dunn‘s Bio 0410 Invertebrate Zoology class here at Brown University. In this video, Nati describes how this crustacean is able to move its appendages faster than could possibly be accounted for by muscles alone.

All of the artwork and edited was done by Natividad Chen, and many of the sound effects are real recordings of stomatopods, provided graciously by the Patek lab at University of Massachusetts at Amherst. The video is released under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 license.

CreatureCast – Moray Eel

posted by Sophia Tintori / on December 1st, 2010 / in Podcast (Student Contribution), Vertebrates

Here is the first of this semester’s creaturecasts from the students in Casey Dunn‘s Bio 0410 Invertebrate Zoology class here at Brown. Students in this class have the option of making a creaturecast episode for their final project. This one from Phil Lai introduces the Moray Eel and describes the amazing way they eat.

This video was drawn and edited by Phil, and  is released under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 license.