Archive for: December, 2010

Green Christmas Trees

Dec 13 2010 Published by under Biology & Environment

This weekend was the annual Christmas tree lighting in the small  park in front my local City Hall.  As you can see from the picture, the decorations aren't the most inspired - nothing but white lights, large ornaments (which you can't see after dusk) and a broad white garland that unfortunately looks a bit toilet paper-like when viewed from a distance.

I personally prefer more brightly colored holiday decor. But one of the nice things is that no tree was killed to decorate our civic center. It grows there year round, providing greenery even in the hottest part of summer. Very ecologically sound, that.

Of course a living tree isn't a usually a practical option when you put up a Christmas tree in your living room. It's not just that a tall potted fir is difficult to move. You also need someplace to put the tree when Christmas is over and the decorations have been removed – planting it in your yard requires a lot of space, considering that firs and spruces and pines can grow as tall as 100 feet.

But I was interested to read about another option in the LA Times this weekend.  The Living Christmas Co. rents potted Christmas trees for the season. You just pick out your tree, and it will be delivered to your home - assuming you live in western LA County, then picked up again after Christmas.  You can even adopt a special tree of your own to be delivered year after year. It's both easy and "green".

The company's owner,  Scott "Scotty Claus" Martin explains his philosophy:

"How, on one hand can something mean new hope, new joy, new love, and on the other hand be so easily discarded? And is that really Christmas?" he said.

The company's mission is not just to be sustainable but "regenerative," he said. Beyond saving trees, that means using all recyclable materials, running delivery trucks on biodiesel and employing adults with disabilities to maintain the trees around the year.

There are similar companies in San Diego, San Francisco, Portland and many other cities.

The down side is that it seems a bit pricey. A 6 foot tree costs $80 to rent, plus another $40  for delivery and pickup.   Adopting a specific tree costs another $50 per year, only offset a bit by a $20 credit towards the next year's rental. And of course a living tree requires more TLC than one that's going to end up on the curb come January.

Despite the cost and extra care required, I find the idea pretty appealing. It just seems so wasteful to cut down a tree, only to toss it out after a couple of weeks. We usually don't spend Christmas at home, so the past few years we've only put up a token little artificial tree.  But if tree rental becomes popular enough to spread way out the the 'burbs where we live, maybe we'll give it a try.

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There's an App for that! Free Biology Mobile Applications

Dec 10 2010 Published by under Biology & Environment

I was surfing around for sciency holiday e-cards, when I came across this cute albino alligator looking for a kiss from the California Academy of Sciences.  You can choose one of several e-gifts, including polar bear wallpaper, a catchy tune,  or a Golden Gate Park field guide mobile application .

If you download the Golden Gate Park Field Guide iPhone app this month, you can just show it at the ticket window for $5 off admission through December 24th. That's a great deal if you happen to be in the San Francisco area.

That inspired me to see what other biology-related free iPhone/iPod Touch applications I could find.  I haven't had a chance to try them out yet, but the ones below looked the most interesting. I've noted which ones are available for Android devices as well.

Wildlife and Nature

While the Audubon and Petersons field guides will cost you, there are several apps that allow you to find, record and share wildlife sightings for free.

Golden Gate Park Field Guide (iPhone App store): Field guide, park map, self-guided activities, share your wildlife sightings.

Project Noah (iPhone App store):  Field guide, share wildlife sightings. They have a special project to document the impact of the Gulf oil spill on wildlife.  You can your Google account to sign in and share your sightings and photos.

WildObs Observer (iPhone App store; Android Market): Record  and share wildlife encounters. Has companion apps: WildObs Lookup (iPhone App store) field guide;  WildObs Lookout (iPhone App st0re) to find out what others have observed around your location;  and WildObs Naturalist (iPhone App store) to "keep your encounters and re-use them". WildObs is a partner of the National Wildlife Federation's Wildlife Watch. A free WildObs account is required.

NatureFind (iPhone App store):  This app allows you to search for nature spots and events near your ZIP code.

Science News

Get science-related news.

Scientific American Advances (iPhone App Store): Scientific American news and in-depth reporting. Requires registration at Nature.com to view content.

Nature.com (iPhone App Store): Science news stories and the latest published research in Nature and the other journals from the Nature Publishing Group. News articles, abstracts and some research articles are free.

Science Mobile (iPhone App Store, Android): news from ScienceNOW, abstracts from the journal Science. This doesn't look as useful as Nature's app.

Molecules and Anatomy

For exploring the bits that organisms are made of.

Molecules (iPhone App store): 3-dimensional rendering of molecules that you can manipulate.  You can download molecules from the RCSB Protein Data Bank or elsewhere online.

BioCourseWare: Apps developed by the University of Nottingham, aimed at students in the biological sciences. Their free offerings include a Biology Dictionary, History of Genetics, and  Genetic Decoder.

Nature Human Genome Special Edition (iPad App): Nature's Human Genome at 10, repackaged into an interactive app for the iPad.  It looks pretty neat, but it's not available for the iPhone.

BrainTutor 3D (iPhone App store) : Explore a three-dimensional model of the  human brain.

Paleontology Apps

For learning about animals that no longer walk the Earth.

Dinosaurs (iPhone App Store): This app from the American Museum of Natural History allows you to explore their amazing dinosaur fossil collection.

MEanderthal Mobile App (iPhone App Store, Android):  This app from the Smithsonian Museum of Natural History allows you to morph yourself into a Neanderthal.  I suspect the novelty of this wears off pretty quickly.

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If any of you use one of the wildlife spotting apps,  how well does it work for you? Is there a better free option?

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The Christmas Bird Count

Dec 07 2010 Published by under Biology & Environment

For over a century the Audubon Society has organized a massive citizen science undertaking: The Christmas Bird Count. Tens of thousands of volunteers help take a census of the bird populations of Canada, the United States, Mexico and Central and South America.

Data from the annual surveys has provided biologists and conservationists a picture of long term changes in the distribution of North American bird populations.

For example, analysis of data collected over the past 40 years shows that the the winter range of many bird populations - 177 of the 305 species examined -  has shifted north, in some cases hundreds of miles. The shift correlates with an increase in mean January temperatures of almost 5 degrees during that period, and it's likely that climate change is at least partially responsible. Based on that data, the Audubon Society's report on birds and climate change (pdf) concludes that "ecological disruptions that threaten birds, other wildlife and human communities [due to climate change] are likely already in motion".

The Christmas Bird Count has also helped identify common bird species - from  meadowlarks to hummingbirds -  that "have taken a nosedive" over the past 40 years.

On the other hand, doves and pigeons have expanded their ranges along with growing urban and suburban development.

It's data that would be difficult to collect without an army of volunteers.

If you'd like to participate, this year's Christmas Bird Count begins on December 14th and runs through January 5th.  You'll need to register for a count:

There is a specific methodology to the CBC, but everyone can participate. The count takes place within "Count Circles," which focus on specific geographical areas. Each circle is led by a Count Compiler. Therefore, if you are a beginning birder, you will be able to join a group that includes at least one experienced birdwatcher. In addition, if your home is within the boundaries of a Count Circle, then you can stay home and report the birds that visit your feeder once you have arranged to do so with the Count Compiler. There is a $5 fee to participate in the CBC for all field participants aged 19 or older.

Find a count circle near you (unfortunately only searchable by state or province).

Even if you can't participate in the Christmas Count, you might be interested in similar bird observation projects:

Images from  from Our Winter Birds: How to Know and How to Attract Them by Frank M. Chapman (1918).  Chapman, an ornithologist with the American museum of Natural History and officer in the Audubon Society, proposed the first Christmas Bird Count in 1900. Top image: Tree Sparrow. Bottom Image: Northern Shrike.

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A virus walks into a bar . . .

Dec 03 2010 Published by under Humor

A little geeky humor for Friday night: science comedian Brian Malow at the 2009 WonderFest at UC Berkeley.

Go to ForaTV for a larger video or to download the audio track.

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Sudoku-solving bacteria

Dec 01 2010 Published by under Biology & Environment

One of the goals of synthetic biology is to engineer bacteria into biological "machines" that can be used to produce energy, deliver drugs, or synthesize materials. If the engineered bacteria could selectively communicate with each other, would expand their possible uses.

A team of students from the University of Tokyo decided to create E. coli bacteria that could selectively communicate with each other for this year's Internationally Genetically Engineered Machine (iGEM) competition, held last November 6-8 at MIT.

Sudoku Puzzle

Sudoku Puzzle

As a proof-of-principal for their bacterial communication system, the Japanese team created microbes that could solve a Sudoku puzzle.

Sudoku puzzles are usually made from a 9x9 grid made up of nine 3x3 squares. The numerals 1 through 9 can only be used once in each row, once in each column, and once in each 3x3 square. The puzzles start out with some of the numbers already filled in, and the goal is to fill in the blanks. You can see an example of a starting grid over on the right -->

Even though a Sudoku puzzle uses numbers, it's not a math puzzle - no adding, subtracting or other number manipulation is required. It's a logic puzzle. It could work just as well with nine different pictures or nine different letters or nine different colors.

The simple logic rules of the game were an ideal way to demonstrate the ability of the modified bacteria to communicate.

The Japanese team's modified bacteria were designed to solve a 4x4 Sudoku grid.  They engineered 16 genetically different bacteria, one for each spot on the grid. Each of those strains of bacteria has the ability differentiate into one of 4 types. Each of those types can then direct "detection bacteria" to produce a corresponding fluorescent color.

Just like any Sudoku puzzle, the grid begins with some of the squares already solved, like this:

E.Coli Sudoku Puzzle

The differentiated bacteria produce signals that tell the other bacteria their type. The undifferentiated bacteria are able to detect which of the 4 types are already present in the same "row",  "column" and "block", while ignoring information from irrelevant "squares". For example, undifferentiated bacteria representing square 4 would need to detect which differentiated types were already present in squares 1-3 (the same row), squares 8, 12, and 16 (the same column), and squares 3, 7 and 8 (the same block).  They would have to ignore the bacteria in irrelevant squares 11 and 13.

Here is their video of how the system works, which is a bit clearer than my explanation:

The students already have figured out - at least theoretically - how to modify their system so that bacteria would be able to solve a 9 x 9 Sudoku grid.

But that isn't the only use of such engineered microbes. Bacteria that can differentiate between relevant and irrelevant communications could ultimately be used to design bacterial logic circuits for parallel calculation devices. Maybe someday we'll be able to use bacteria to plug away at difficult computing problems.

You  can read the technical details to learn more about the biochemistry of the system.

And if you want to test your own Sudoku skills, I recommend the daily puzzle here.

(Project via New Scientist)


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Top image: A Sudoku layout generated by the GNU programSu Doku Solver and contributed in the public domain by Lawrence Leonard Gilbert. From Wikipedia.
Bottom Image: "16 kinds of E. coli corresponding to each cell" by the UT Tokyo iGEM team, shared under a Creative Commons Attribution-ShareAlike license.

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