Monday, December 28, 2009
Tuesday, December 22, 2009
Wednesday, December 16, 2009
Thursday, December 10, 2009
Do any of you readers have suggestions for things you would enjoy seeing on such a cartoon?
Friday, December 4, 2009
Hydrothermal Vents 101
Hydrothermal Vents are chimney like structure that form along with new sea-floor at divergent plate boundaries in the middle of oceans. They form because an oceanic plate is being pulled from two opposite sides where it meets continental plates and subducts below. The oceanic plate splits apart in the middle, under miles of water. This splitting process allows sea water to come in contact with hot magma from below Earth’s crust. This hot magma forms new sea floor in the form of basalt. Basalt is a rock that is low in silica, unlike granite which makes up the continental crust and is much more buoyant. The water that comes in contact with the magma becomes super-heated and therefore able to dissolve lots of minerals that water doesn’t otherwise contain. Heat adds energy to a system which causes chemical reactions to speed up, and so many reactions happen in the presence of hot water that wouldn’t be noticeable otherwise. These hydrothermal fluids can be up to 350oC (662oF), which means that they would be gas (water vapor) under pressures that we are used to on Earth’s surface. However, because pressures at the sea floor bottom can be up to 345 times what they are at sea level, these liquids remain just that. As soon as the heated fluid comes in contact with cold seawater (2oC, 36oF) the minerals it was holding on to immediately precipitate out of solution (in a process that is the opposite of dissolving) and form solid rock structures. These sulfides make up the chimney-like structures that are characteristic of these environments. Minerals such as pyrite (fool’s gold) and chalcopyrite (a crusting mineral often confused with fool’s gold) coat the inside of these chimneys with shimmering golden crystals. Hollow tubes remain in the center of these structures, and the chimneys grow taller as more hydrothermal fluid flows through them adding its minerals as it is suddenly chilled by the surrounding seawater. Eventually the cracks in the underlying rocks fill in with new rock, or small earthquakes occur forming new cracks. When this happens one chimney “dies” and others begin to form. A single chimney might last 20 years.
The mysterious producers referenced above that were found to inhabit this extraordinary window into the deeper Earth are microscopic bacteria and archaea. Archaea are a relatively recently defined ancient group of microscopic organisms as genetically different from bacteria as animals or plants. These microrganisms, referred to as microbes or “bugs” (affectionately by microbiologists) garner energy from the dissolved minerals in the hydrothermal fluids described above. Some of these microbes thrive in the pore space of the sulfide rocks and are constantly bathed by incredibly hot, mineral-rich water.
The rocks that make up the chimneys, as well as the basalt crustal rocks that they grow on top of, provide a network of cracks and pore spaces in which the heated, mineral-rich waters mix with cold overlying seawater. The result is a warm and hospitable area called a diffuse flow zone that supports most of the life (animal and microscopic) in these ecosystems. The microscopic producers that convert this geological energy into energy that other organisms can use are called chemosynthesizers, chemoautotrophs or sometimes chemoautolithotrophs! While the terminology can seem like jargon it is actually very specific and explanatory. Chemo- means chemical, auto- means self, litho- means rock, and troph- has to do with feeding. By the same naming conventions plants and certain plankton are considered photoautotrophs, while we are considered heterotrophs, because we require organisms other than our self (hetero means different) for food.
Scientists do not know how life appears seemingly out of nowhere at new vents. Some have proposed that the carcasses of dead whales (whale falls) or sunken logs (wood falls) provide an intermediate nutrient source. Others have found evidence that there is an underground reservoir of microbes (the Deep Subsurface Biosphere) that survive in mantle material and come up as new vents are formed. Scientists have identified seven different biogeographical provinces of vents that all share similar species assemblages. Two of these provinces are dominated by the charismatic white and red tubeworms, but the others are dominated by various combinations of giant mussels, enormous clams, amphipods, shrimp, crabs, polychaete worms, huge barnacles, snails and anemones.
Wednesday, December 2, 2009
A Discovery of Significance
In 1977 geologists made a discovery that changed the way we think about life on this planet. On a geologic research cruise to find places on the deep sea floor where the Earth’s crust was pulling apart (divergent plate boundaries) and study newly formed sea floor they found unbelievable assemblages of species. In this environment, thought to be devoid of life due to the lack of sunlight, they found diversity and richness that rivaled the tropical rain forests. There had been previous indications of life in these deep wastelands, but no one had expected that a significant amount of life could exist in the deep. Huge clamshells had appeared on videos of the deep taken by a robotic camera guided. This camera was attached to a Remotely Operated Vehicle (ROV) but the footage was dismissed as an anomaly. It wasn’t until scientists themselves physically went down to the deep in mini-submarines called submersibles, and saw thriving communities with their own eyes, that the concept of significant life on the sea floor became a reality.
People who have been down to see the vents in submersibles describe it as a totally surreal experience. A slow and erie descent through darkness punctuated by layers of neon light shows, much of which can not be caught on film. Dr. Bob Ballard was one of the scientists on the 1977 expedition that discovered the vents. He described it as follows
“We didn’t know we were going to make this discovery. I mean, my god, thats what makes it so amazing. We thought we’d find a crack in the ocean with water coming out. Big deal: that’s what surprised us. We didn’t know this was going to be as gigantic a deal as it was.”
These communities were something people had to experience in order to believe because it was contrary to what we thought we knew about life. The vast majority of exciting Eureka! moments in science happen in a lab. This discovery was so fundamental that it happened out at sea on a ship, rather than after samples had been processes and analyzed. The thrill the geologists on board felt at encountering something so novel, must have been something like what Charles Darwin felt when he came across creatures in the “new world” unlike anything he had seen before. There are few places on land where this type of encounter can still being had. The deep sea represents one of the last environments on Earth where the scientists can still be considered Explorers.
Prior to the discovery of deep sea hydrothermal vents, it was understood that all life on Earth was dependent on the sun, and could not survive without it. Period. It may seem that the existence of these verdant deep sea communities is little more than a bizarre exception to this rule. However, their existence forced a scientific re-evaluation of life and its evolutionary history on this planet (and potentially others) on par with the re-evaluation of the planet that occurred when early scientists realized that the world was not flat.
Living things are primarily divided up into producers (who make their own food), consumers (who eat other organisms), and decomposers (who break down dead organisms). It had been assumed and taken for granted that all producers made their food by converting the sun’s energy into sugars such as glucose through photosynthesis. Maple tree sap that becomes maple syrup is a clear example of this process. Producers form the base of all food chains and they tend to be present in ecosystems in far greater amounts (either in terms of numbers or overall volume of organisms) than the consumers. In a simplified view we can think about a single carnivore like a bald eagle. It feeds on animals such as snakes or fish which in turn might feed primarily on insects. If all of those insects fed only on grasses, you could imagine that a huge grassy field would be necessary to form the base of the food pyramid supporting a singe eagle. In the ocean it is much the same except instead of plants the surface waters are full of microscopic plankton that perform photosynthesis (phytoplankton) as well as slightly larger animal-like plankton (zooplankton) that eat the plant-like phytophankton and in turn feed smaller fish who feed larger fish and so on and so on. The one glaring exception to this is can be seen in the largest organisms on the planet. The baleen whales (such as Humpbacks) who filter unimaginable numbers of krill (shrimp-like invertebrates who feed on plankton) from the ocean on a daily basis. The blue whale is the largest animal that has ever lived on the planet, and it is able to grow as large as it does because it feeds low down on the food chain on organisms that are found in great abundances. If it had to swim quickly after fish it would not be able to eat enough to meet its energy demands.
The sun’s light energy does not penetrate more than a few hundred meters below the ocean’s surface, and because of this it was assumed that producers would not be found in any abundance at depth in the ocean. Up until the early 1980’s it was thought that the only creatures in the dark mysterious world covering most of our planet’s surface were solitary strange fishes that feed on each other or the organic debris that continuously rains down from the upper layers of the ocean where it was generated (directly or indirectly) from the sun’s energy. These alien organisms (and they really do look like aliens!) with their own lights to lure in prey, or jaws able to open far wider than their head to consume large prey were known, but they are few and far between. The world that people imagined at the bottom of the sea was a desolate one inhabited by rare monsters, completely dependent on nutrients from above.
The discovery of dense communities of tubeworms, crabs, snails, mussles, clams, shrimp and even fishes at these vents in concentrations that rivaled the rain forests meant that there had to be a totally new class of producer forming the basis of these bizarre ecosystems. There simply couldn’t be enough organic matter drifting down from above to support them otherwise. A fundamentally new type of energy pyramid had to be understood! The organism forming the basis of that pyramid had to be using a source of energy other than the sun to create sugars that in turn provided energy for the rest of the animals that otherwise would never be able to exist in such high numbers. It turned out that geology was the key. These perplexing organisms were tapping into energy from inside the earth, rather than 93 million miles away from it, in a process that remained undiscovered for the first 10,000 years of human civilization.
The Mysterious Ocean
From space Earth is a glass marble swirled blue and white. The white cloud cover shows change and active weather processes, while the blue announces to onlookers million miles away the single most important defining characteristic of our home planet: it is covered with water. The seas cover roughly three quarters of Earth’s surface. The oceans also contain the majority of places on the planet where things can live. This is because the depth combined with the area covered provides a much more three dimensional habitat than the land. Rain forests have three dimensionality in the various layers of tree canopy, but the scale of that (tens of meters) is minor compared to the ocean depths. 80% of the biosphere (the portion of the planet where living things are found) is actually in the ocean below 1000 meters.
These deep sea environments are very challenging to study because we can't see them. The Hubble space telescope can see galaxies 15 billion light years away, but satellites can not take pictures of the bottom of the ocean because “seeing” through the water is difficult, since light only penetrates the top 50 meters. We have ways of sensing the topography of the ocean floor using satellites and sonar aboard ships, but we can not see whats there without sending down a some type of camera. This means that there are many snapshots, and make guesses about what’s between them. How many photographs would you need to understand what it was like on another planet? How many would you need to see before you felt like you had seen it all? We have more detailed maps of the surface of the Moon or even Mars than we do the sea floor. Anyone with internet connection can go to Google Mars and see images of individual craters canyons and mountains on Mars, but Google Earth can only take us under water in specific areas that have been well documented.
One way to think of how well we know what’s at the bottom of the ocean is this: If aliens found earth and wanted to see what it was like without leaving their space ship, they might take a sample from the surface but lowering some sort of bucket or jar and seeing what they pulled up. If they sampled somewhere over the United States and pulled up a bucket of corn, their best guess might be that the whole U.S. is one big cornfield. That is a silly analogy, but roughly illustrates how well we understand the deep ocean know. We know where the major under sea mountain ranges are, and we know that 80% of the worlds volcanic activity happens underwater, but the specific details are few and far between, literally. Scientists are constantly discovering new species in the deep sea, and they regularly find types of organisms that are very unique and that we know almost nothing about (this type of discovery happens only rarely on land). They are still discovering dramatically different types of ecosystems that were unimaginable only a few years ago. One discovery in particular stands out...
Monday, November 30, 2009
Monday, November 23, 2009
Wednesday, November 18, 2009
Tuesday, November 17, 2009
Thursday, November 12, 2009
I dont have much time tonight, because I have 8 papers to read for my 9:30am class. However, I had a good day and wanted to share part of it. Some folks in my lab and I are working on a project that involves trying to get DNA out of rocks that microbes are (presumably) living in. The rocks have been frozen, and the first step is to grind the rocks into a powder so that we can get at all the microbes that might be present within the rock's pores. The way we did this was very basic - mortar, pestle, and elbow grease. However, the key was not to let the rocks thaw out because we wanted to preserve the microbes as they were when the rocks were collected. In order to accomplish this we were pouring liquid nitrogen over the samples as we were crushing them in the stainless steel. Nitrogen is a gas at room temperature (~80% of what you breath in with each breath is dinitrogen, or N2). Nitrogen is a liquid at very cold temperatures, so when you put something in it, it freezes almost instantly. This makes it great for biology because you can freeze tissue samples before molecules start to react and change. LN2 (as liquid nitrogen is called) boils at -196 C (-321 F). When you pour it over something at room temperature it immediately starts to boil. I will bring my camera in next time I do this type of work (the above image is not mine, but gives the general idea) because it looked like a witches brew with nitrogen steam spilling over and down onto the floor as we worked. This is a similar (but more pronounced) effect to that created by dry ice (frozen N2). I really felt like I was in a Hogwarts potions class rather than a microbiology lab... awesome!
Tuesday, November 10, 2009
Monday, November 9, 2009
Saturday, November 7, 2009
Saturday, October 31, 2009
Tuesday, October 27, 2009
Monday, October 19, 2009
I spent a day this weekend in the woods of north-central Massachusetts. It was cold and crisp... perfect end of fall weather. I looked for bugs and found very few. I flipped over rocks in a small (freezing!) stream and didn't find any, and was equally unsuccessful under bark of a rotting log, and digging in the soil. I suppose it is to cold for them, but I am curious where they go to. I was reminded that fall is my favorite time in New England, and that (even though it is currently snowing... in mid-October) I am thrilled to be back living in the land of the wonderful Fall.
Saturday, October 10, 2009
Saturday, October 3, 2009
Being relatively new to blogging, I am taking my first stab and writing for a Blog Carnival. Here goes...
The Road Not Taken
While I am fairly, ok very, early on in my “career” (having just started graduate school) the idea of alternate paths is one that I have mulled over quite a lot in the last year. I often feel torn between science and wilderness. While these are obviously not mutually exclusive, and often (wonderfully) go hand in hand, for me science had meant less wilderness. Specifically, it has meant no more teaching in the wilderness... at least not for a while. I used to lead backpacking trips for students of various ages, and the idea of being a hands on experiential educator is one that I toyed around with for a long time. When I was a classroom teacher I was very involved with our school’s wilderness program, and had I continued down that path I might have had the opportunity to craft new ways for young men of Dallas to connect with the natural world. I think this is incredibly important given our increasing disconnect with Nature (PLEASE read "Last Child in the Woods" by Richard Louv) and as the climate and conservation issues become more and more profound.
I remember as a NOLS (National Outdoor Leadership School) leading my group of 10 16-18 year olds down a steep rocky slope in the Wind River Mountains after an arduous 12 day of day of traversing a 3 mile (yes, 3 miles in 12 hours = immense frustration) scree slope full of house-sized boulders. We were rushing to beat a building storm. Our group got into camp and set up tents just in time for us to tell our students to get out of their tents and assume lightning position in the rain and hail (to avoid proximity to metal poles). Then, as hypothermia became a greater risk than the lightening (roughly 30 minutes later) telling our students to get back in the tents. It was a very difficult day physically, and emotionally. Clearly, my memories of wilderness education are not all wonderful, but after spending a month taking care of themselves and each other in the wilderness those students were more confident, more capable, better leaders, and were certainly Wilderness advocates for life. I learned more about myself, and my leadership style working for that organization group than i will in any other job... I’m certain. The flip side is that I was not doing science, and I missed it.
I decided to leave both classroom teaching (middle school life and earth/space science and high school marine science) and wilderness education behind when I applied to graduate school. I loved teaching about science, and especially talking about what scientists that I knew were up to, but I really missed actually doing science. The classroom teaching had allowed me the schedule to do wilderness based experiential education in the summers, but I am fairly certain graduate school will not.
There are things I already miss... now that I am a whopping 2 months in. Primarily I miss my my colleagues and students. I miss coaching, and watching skills and confidence grow outside of the classroom. I miss my former students running into my room to say hi (or possibly trying to disrupt my classes). I miss having a wonderful group of educators around to collaborate or commiserate with. I miss the fun and silliness that comes with middle school. I miss my after school climbing club.
However, I am somewhere that is almost overwhelming in its vibrancy. The almost tangible swirling energy and idea make it an incredibly exciting and energizing place to be. I had missed doing research while I was teaching, and now I am picking projects and taking classes, and learning a huge amount. Getting paid to learn is quite the luxury, and I consider myself very lucky for the opportunity! I don’t know where exactly the PhD route will take me, but I know that I will always be an educator of some sort. In some foggy crystal ball vision I can almost see the path not taken and the chosen route converging down the line a ways where I create a wilderness-based science school in some beautiful location, maybe overlooking the sea on the Maine coast.
Monday, September 21, 2009
A beautiful moment (winter 07?)
As the chapel doors opened out to the main green after the service today, one of the most wonderful moments of my thus far very short teaching career occurred. There door I was looking through framed the lit Christmas tree, and as the chilly air rushed in, we all saw the first snow flurries swirling around the tree. This was accompanied by the excited gasps of about 250 thrilled young men all in unison while trying to maintain the composure required of chapel. The older ones forgot for a second that they are no longer little boys. I hate to admit it but I almost teared up. Maybe it was because a teacher had just finished talking about his son who passed away 10 years ago. There was just something about the tangible kid energy and the visual expression of innocence and enthusiasm that really was beautiful. A colleague also noticed this, and said that it was a moment you would never experience if you weren’t a teacher, and that you couldn’t really explain it. I guess this was my attempt.
Sunday, September 20, 2009
This weekend I caught up with a few friends I left behind in Texas. Some former co-workers had a get together and they thought enough about me to give me a call! It meant a lot to feel remembered and missed, because I have certainly been missing them. I promised one friend a new blog post this weekend. I was psyched to hear that someone was actually reading my blog down there, but now there is pressure to write something interesting... thanks Nick!
Sunday, September 13, 2009
title: "Drinking from a fire hose" - originally published 2/5/2007
I have found a new way to procrastinate (just what I needed). This website (www.phdcomics.com) is a hilarious look into the life of a grad student. I thought this one was especially appropriate given my post yesterday!
Saturday, September 12, 2009
Bacteria are unicellular microorganisms that have, despite their extremely small size, significant beneficial and harmful effects on humans. This scanning electron micrograph shows the bacteria known as Streptococcus pyogenes, which causes strep throat, a common illness in humans.
In my first weeks in grad school I have felt like a sponge, learning new things just about everywhere I go... from just about everyone I talk to. Part of this is due to the fact that I have signed up to study microbiology knowing just about nothing about that subject. I am more of a geologist by training. I really feel like the proverbial kid in a candy store though. The more I learn about microbes, and their study, the better I feel about my choice of subjects. It also helps that just the other evening I heard my #1 science idol Ed O. Wilson speak and he said that if he were starting out as a scientist now he would study microbes and microbial diversity! Woohoo!
Did you know that your body holds more microorganisms than your own cells? Did you know that crazy drug resistant staph infections killed more people in the US last year than the Aids virus did? Did you know that there are about 5,000,000,000,000,000,000,000,000,000,000 (that’s 50^30) microbes on the planet? Did you know that there is more carbon stored in microbes living deep under the sea floor than there is in all the plant and animal life on land? Did you know that you have an entire ecosystem within your intestines (probably about 500 species of microorganisms) that is key to keeping you healthy, and that we have only begun to investigate how that ecosystem functions, and that your internal ecosystem is very different from that of the person sitting next to you (unless that person is your sibling or mother, then it might be similar)? The vast majority of these species are unknown and many of the ones that we have seen we know virtually nothing about. Talk about drinking from a fire hose! (I know, I am just full of cliches tonight...sorry)
Microorganisms were the only living things on the planet for roughly 2.5 billion (thats 2,500 million) years. Animals have been around for .5 billion (500 million) years, while mammals appeared 220 million years ago. Human beings only showed up roughly 200,000 years ago! I think what gets me the most excited is how little we know about these organisms, other than that they are hugely important for the function of ecosystems (imagine all the trash and dead stuff if there weren’t decomposers!), the function or organisms, and for understanding the evolution of life on Earth. My task for the next 6 years or so... discover something awesome about these organisms... more specifically the ones that live in and around hydrothermal vents! I had better get to work.
Friday, September 11, 2009
Wednesday, September 2, 2009
Thursday, August 27, 2009
Tuesday, August 25, 2009
Mountain top yoga... it is my new goal to do this as often as possible. I went hiking with friends the other day in New Hampshire. It was a bit overcast, and we were rain soaked on the way down. This was actually a nice break from the heat and humidity of Boston. It was wonderful to be in the White Mountains again. These forests feel familiar and safe to me in a way that the plans, scrubland, and vast open areas of Texas never did. I guess that is part of what makes many of us have such strong attachments to the regions where we grew up.
Friday, August 7, 2009
We went out on a whale watch yesterday with the class. I was excited, but didn’t have many expectations. I figured we might see a few shadowy figures in the distance and be convinced that they were whales. I could not have been more wrong! We must have seen 50 different whales, and we saw some incredibly close. Not only did we see whales up close, but we saw some really amazing behavior.
We blew past some Minke whales on the way out because the captain had been told about Humpbacks a ways out. We stopped to see some Finbacks chowing down on a huge bait ball. This also allowed us to see enormous numbers of Shearwaters and Wilson’s Storm Petrils sharing in the whales feast. After being thoroughly amazed by these examples of the planet’s second largest organism we went off in search of Humpbacks.
We came across a mother and calf and they shocked us by getting right up close to the boat and doing partial breaches. We were able to see the massive head if the young Humpback right next to the boat. We watched the two eat and dive for a while and then went in search of other whales. For a while we were all on sensory overload because in any direction you could see spouting or diving (showing us their tail). There were plenty of Finbacks around as well and even a few Minkes.
The grand climax came just about as we were getting ready to head back. We came across a group of 3 humpbacks that, after gorging themselves on baby herring, were incredibly playful. We were treated to flipper slapping in unison, synchronized dives, and lots of breaching! Seeing a humpback whale come all the way out of the water is not something I will forget, ever. One particularly feisty animal breached 5 times in a row. It really seemed like they were performing just for us. When we finally had to pull ourselves away two of the whales began to tail-slap the water repeatedly, as if waving goodbye to us. This continued until we were out of view. Truly amazing!
Check out the video that I put together about the trip: Whale Watch Film
Saturday, August 1, 2009
Written at 11:30pm last night...
Time moves fast on the island. The new course has been here for 5 days now, so the course is more than 1/3 over. It was a good, very busy day. We started with a survey lecture about ocean vertebrates, then had time for group project work (students are designing their own experiments in groups). We ate lunch quickly and half of the class went on a seal-viewing boat trip to a nearby island. They saw Harbor Seals and Grey Seals displaying many interesting behaviors. The rest of us did a second round of transects. This involved gathering chemical, biological, and physical data about tide pools on the exposed side of the island for later comparison with similar data collection from the sheltered side. Organisms on the exposed side tend to be dwarfed, and there is less biodiversity. It is a wonderful venue for discussing environmental factors that affect intertidal life. It was pouring rail during this collection, but the intrepid young scientists were not deterred. There were very few complaints despite all of us being thoroughly soaked, and morale was high throughout!
At 4pm the now dry students came to the lab for their lab practical. They had to memorize the Latin names of 30 intertidal organisms as well as different adaptations that each organism had that helps it succeed in the rocky intertidal zone. They also had to key out a mystery algae using a dichotomous key. After this we had a delicious dinner of risotto, Arctic Char, and sauteed spinach. After dinner the class mad a sculpture out of the non-recyclable marine debris that they collected yesterday. They created a “monster” that they “slew” with a lobster buoy sword. I was very impressed. Following this creative time there was a lecture from the other TA about experiments in Cephalopod cognition. During this lecture there was one of the most beautiful sunsets I have ever seen. There were vibrant reds and oranges and some patches of blue right in the middle of it all. The blue patches I don’t understand, and they didn’t come out in the pictures that I snuck out of lecture (I heard it last course) to take. This all ended about 9pm, and the students had their first (and maybe only) real free night. They had nothing to study for, and no major projects to work on so they were free to hang out and watch movies or go to bed as they pleased. This was a relatively relaxing day, believe it or not. Tomorrow we clean up oil spills, echolocate, do more transects and seal viewing, talk about marine fisheries, and watch presentations from students in the Genetics of Marine Diversity class. It should be another good one.
Thursday, July 23, 2009
Let me preface this by saying that not only do photos not capture the reality of a beautiful sunset (duh!), but the colors in this image seem dull and muted compared to how they look in my iPhoto.