Saturday, December 30, 2006

Deep Sea Welcome

The link I included to the Deep Sea News blog a few posts ago has been noticed by the scientists who run it and have officially welcomed our class via a blog entry there. You should check it out and take advantage of the spirit of cooperation and interactivity that these blogs give us.

Here's their link again:

Deep Sea News
(scroll down a bit to find the 'Welcome Attleboro' post)

Friday, December 22, 2006

(most of) Your Gels

Not my best photographic work, but here you go. I tweaked them a bit in Photoshop to better bring out the set of second bands. Click on the photos for a larger image.

Where do plants come from?

We've been discussing in class a bit how we as a society are able to genetically engineer organisms - a technology that has taken hold over the past 30 years or so. But the natural world has been genetically engineering for millenia - not with anything technological or with that high a success rate, but effective nonetheless. We've mentioned earlier in the year how chloroplasts and mitochondria are believed to have evolved from prokaryotes that were engulfed by larger single-celled organisms - a process called endosymbiosis. Quite an amazing feat - esssentially harnessing the genetic power of one organism to help you survive. It was long believed that the evolution of algae and plants all stemmed from a single endosymbiotic event and that all chloroplasts share a common ancestor some 500 million years ago. But new research has shown that this may not be the case. By sequencing and comparing the genomes (full genetic makeup) of various chloroplasts (remember that chloroplasts and mitochondria have their own DNA) researchers have discovered that there were likely at least two independent endosymiotic events that lead to chloroplasts. This has many implications, including the idea that if this sort of thing can happen twice, why not more. And if it has happened more than once, what does this mean about the origin and evolution of the various photosynthetic organisms around today?

As a side note, this article/research is a good example of a branch of biology that studies the very early branches of the tree of life - basically delving back 100s of millions of years to examine how life emerged. Interesting, but difficult work.

Delving Into Chloroplasts' Past

Wednesday, December 20, 2006

Sea of Life: part II

For those of you interested in marine biology check out the following blog on the deep sea. I especially like the "25 things you need to know about the deep sea" series.

Deep Sea News

(actually, a lot of the blogs housed over at are pretty good)

Tuesday, December 19, 2006

Genetically Modified Organisms

Genetically modified plants and animals are becoming more and more common in our lives. Some are purely designed to help scientists more easily study some aspect of biology while others are important for their medicinal or food value. The image here is a picture of grains of golden rice - the rice strain that has been genetically engineered to produce beta-carotene presumably to make it more nutritious, though others argue that it is nothing more than a marketing scheme. There are a lot of concerns around Genetically Modified Organisms (GMOs) and like just about anything there are pros and cons that need to be considered when deciding whether we should proceed in a certain direction with GMOs. To help you learn more about GMOs and the science behind them here are a few links:

WikiPedia article on genetic engineering - a good general article

New Scientist - this section of this website is dedicated to all things concerning GMOs. Scroll down to see an list of about a billion news articles on GMOs (well, maybe only a million).

Monday, December 11, 2006

Sea of Life

Here's an interesting article that highlights some of the marine research that was done this past year. It's amazing how much we still have to learn about the natural world - just when people think we couldn't possibly discover anything more, up pops a shrimp thought extinct for 50 million year or schools of fish 20 million strong. Amazing stuff.

Census of seas reveals amazing forms of life

Friday, December 08, 2006

Solutions to Genetics Problems

Here are the answers to the handout of genetics problems.:


Tuesday, December 05, 2006

Virtual Fly Lab

For those interested in playing around in the virtual world of fruit fly genetics, here's the link:

Virtual Fly Lab

I'm also interested in hearing whether or not you found the site and the activities interesting and/or helpful.

UPDATE: want to order your own Drosophila? Check this out.

Monday, December 04, 2006

Is That a Fungus In Your Brain?

this video is really just too cool - a parasitic mushroom that takes control of an insect's brain.

video here

Friday, December 01, 2006

Inner Life of Cells - Part II

Here's the link to the extended version of The Inner Life of Cells. This is the full-length version that does not have the cool music, but does have a narration explaining everything. It is really rather dry - even I am am having a hard time watching the whole thing - but is it interesting to hear the various components explained.

Inner Life of Cells
(when you follow the link you'll need to wait a few seconds before the Harvard copyright warning gives way to the video)

Thursday, November 30, 2006

Online Genetics Problems

Just a couple of links to some practice problems with explanations from the Biology Project website:

Mendelian Genetics

Human Genetics Problems

Tuesday, November 28, 2006

Quizzes - good for your head

Just thought some of you might like to see this brief article on the effects of testing on memory...maybe I should start giving pop quizzes...

Testing Boosts Memory

Thursday, November 16, 2006

Rise of the Neanderthal

Two groups of scientists have announced that they have just sequenced DNA from a Neanderthal fossil. This is a huge breakthrough as it shows that scientists are making progress in their ability to detect, extract, and work with ancient DNA. Technological improvements are a big part of this advance. This is also huge in that it allows us to now begin looking for genetic answers to some questions that researchers have wondered about - when did modern humans and Neanderthals split from a common ancestor? did they interbreed? do we have traces of Neanderthal DNA in us? If so, what does this DNA do? Note: the idea that Neatnderthals were our ancestor has long been abandoned - it is now understood that humans and Neanderthals coexisted for a short while.

I am sure this will raise the question of cloning and whether or not we should/could/would "make" a Neanderthal, but for now I think it is exciting that we are pushing the envelope of genetics.

Neanderthal DNA Comes to Life

Thursday, November 02, 2006

Sing-A-long Cellular respiration

So, as the cool kid i am i was surfing the web and i totally found some sick biology songs and figured id share them with you guys. Mostly theyre a little over the top and geeky but i found them amusing. My favorite is the glucose one but i put some others up as well. Hope you enjoy :) Glucose, Glucose - Come on Down the Electron Transport chain The Krebs cycle

Monday, October 30, 2006

Geo Ducks or shall I say "Gooey Ducks"?

Has anyone ever heard of Geoducks. Pronounced gueyducks. They are these really amazing clams that live for an average of about 146 years. Pretty amazing life span I would say. I happen to see them on a show called Dirty Jobs and figure I would make a blog about them. I enjoyed the segment of Dirty Jobs on the discovery channel where Mike Rowe (Host of the show) jumps into a shore that had millions of Geoducks planted in it. It was also pretty entertaining when he actually got to see what they were used for. He visits a chinese restaurant and finds out that they use Geoducks for making sashimi. Anyway, I thought it was pretty entertaining so if you want to learn more about them check em' out.

Monday, October 23, 2006

Sodium Potassium Pump

Here are a couple of animations for you - the first one is a bit over-the-top, especially with the sound effects; the second a bit boring, but more complete:

Na+/K+ pump animation #1
Na+/K+ pump #2

Extremophiles...on Mars?

Well, those pesky little extremophiles can't seem to leave us alone. They're in the news again - this time by giving credence to the idea that life may be possible on Mars. Apparently some microbes collected from Antarctic lakes are able to survive AND reproduce at temperatures as low as minus 28 degrees Celsius - comparable to some Martian subsurface temperatures.

Speaking with no expertise on the matter, I honestly doubt that life exists elsewhere in our solar system, but if it does, extremophiles are sure to be the life-forms found out there. You just can't get rid of those little buggers.

Life on Mars?

Tuesday, October 17, 2006

One of Biology's Great Mysteries

As New Englanders we are particularly in tune with the changing colors of deciduous tree leaves during autumn. It is one of those seasonal cues that warns us of the approaching winter, reminds us of a new school year, and makes us think of jack-o-lanterns, apple-picking, and fall harvests.

Scientists have long know how the leaves change colors. As leaves prepare to fall off the tree (an adaptation for the colder temperatures approaching), they stop producing chlorophyll, the pigment that makes leaves green. Without the green pigmentation, other pigments are produced, and thus, other colors "shine through". We even know the molecular makeup of these pigments. However, biologists have yet to figure out why trees bother to produce these other colors. Why spend energy on creating a red or yellow or orange pigment?

Carl Zimmer has a post on his blog that discusses some experiments that investigate changing leaf color. There are some intriguing ideas there, but, in the end, we still do not know why leaves change color.

Autumn Leaves

Monday, October 16, 2006

Membrane Transport Animation

Here's a rather nicely done animation that takes you through the various types of transport through the cell membrane - simple diffusion, facilitated diffusion, osmosis, and various active transport mechanisms. We haven't (yet) convered all this in class, but the animation is worth a look.

Membrane Transport

Thursday, October 12, 2006

online cell models

Not sure if this will be helpful, but here's a link to "interactive" plant and animal cells and their contents. I haven't explored the rest of the site, but it may also contain other useful tools as well.

Cells Alive

Thursday, October 05, 2006

Inner Life of Cells

As we get ready to begin our exploration of the cell and its processes, here is a very cool computerized "music video" for you to take a look at. I don't have a lot of info about it except that it was made at Harvard and that it contains a lot of computerized video of the inner workings of cells and macromolecules. If nothing else it is an amazing example of the intersection of art and science. I will try to find out if this is a small example of a larger piece or if there is a "scene list" somewhere. But for now, sit back and enjoy.


(you should probably have a high speed connection for this one - and you'll need the Flash player to view it)

update: I just found an unofficial explanation of the video by someone named Andrew Sobala

Monday, October 02, 2006

Coldly goes the sloth

James' question in class about sloth body temperature made me curious, so I ran a quick search and came up with a couple of links for your enjoyment. Indeed, sloth body temperature is lower than most mammals. Whether they're slow because their body temperature is low or their body temp is low because they're slow is another question. And I have no idea how this effects the relative activity rate of slothian enzymes....though I am sure you all can make some hypotheses about the optimal temperature of them...maybe even something about the range of temperatures they function over.
Wilderness Classroom


Nothing too exciting, but here's a rotating, 3D model of catalase...

Catalase model

Sunday, September 24, 2006

Check this out! Wicked cool . . . I suppose it gives new meaning to when a person says he or she is "all knotted up inside."

Friday, September 22, 2006

Lucy and Bigfoot

ugly baby...jeeeez

my sister was telling me about that Lucy character. I guess she took this class on bigfoot. Yeah, that's right...a whole class on bigfoot. She knows all there is to know. She knows about Lucy too.

Pretty interesting.
k byeeee!

Thursday, September 21, 2006

Lucy's "Baby"

This isn't really relevant to stuff we're talking about in class, but I thought it was an interesting discovery.

Scientists have unearthed the world's oldest human child - an amazingly complete fossil that dates to beyond 3 million years ago. Human evolution is not a topic we will cover much (if at all) in class and is something I wish I knew more about simply because I find it intereting to think about. If anyone is interested in this topic I have a pretty good book you could take a look at and there are a few websites out there I am sure we could dig up.

Anyways, here's the link to the National Geographic story:

World's Oldest Child

Tuesday, September 19, 2006

This is wicked cool!

Just testing to see if I signed up the right way. See y'all tomorrow. : )

Saturday, September 16, 2006


You may remember from class that one of the three domains of life is the Archaea (the other two are Bacteria and Eukarya). Members of Archaea are prokaryotic organisms that are usually found in extreme environments - in fact they are often called 'extremophiles'. They are found in areas of high salinity, temperature, acidity, or alkilinity. Others are found where oxygen levels are extremely low or non-existant (anoxic environments). Some very cool and very different biology going on with them (but not THAT different, which makes them even more interesting). Here are a few websites if you are interested in learning more about them:

Triumph of the archaea (an older article by Carl Zimmer, an exceptional science writer)

Intro to the Archaea

WikiPedia article on Archaea

Some biologists think that the Archaea are the base of the tree of life - that the earliest living things were Archaea (or Archaea-like) and that all other living things evolved from them. Recently there has been some debate over this sentiment as DNA evidence has come out to suggest that this may not be the case. Biology is full of mysteries and unsolved puzzles and the Archaea are one of them.

AP Bio Blog

Hi all -

Not sure how this site will work, but I thought it would be a good "central" online home for any news and events, interesting websites and info, and otherwise helpful stuff for the AP Biology class and exam. There is so much to cover in this class that sometimes the really fun details get pushed aside (like the ecology of the Archaea). Hopefully this blog will allow us to explore and discuss some of these things.

I've never run a blog like this before so I am unsure exactly how it works - you may be able to start new posts as well as comment on them, but I don't know that for sure. Only the members of our class are members of this blog so we are not a completely open community ("outsiders" can read this, but can't comment on it). I'll let you know about any particularly useful info posted here during class.

Some ground rules for posting/commenting:
1) keep it clean
2) keep it relevant
3) keep it respectful
4) keep it fun/interesting/useful

Major violations to the above rules will result in walking the plank into an Archaea-infested pool of water.

Finally, I'm sure that the structure of this blog will evolve over time to better suit its function (which I am also sure will evolve). Remember, science is a process and is constantly moving and changing. Scientists need to be like sailors - ready to change course when necessary. We can't change the direction of the wind, but we can adjust the sails.