Monday, December 28, 2009

More holiday ruminations

Two bloggers that I follow (FSP and Karina) have inspired me to write this post because we all share Christmas time birthdays. I wrote a bit about this before the holidays happened, but now that they are almost over I can say that it really was wonderful. My birthday was great because exams and such were over, and I was able to spend it with a few important people I don't see very often. In the past I have spent my birthday working and hectically trying to finish up before winter holidays, or at college when friends were either taking exams or gone already for break. As a child I celebrated my birthday in the summer because my mom wanted nothing to do with planning a winter party that close to Christmas (quite a brilliant move on her part I must say). This year my housemate threw me a party, I had no work to do, and my advisor told me not to come into work (lab policy: no coming in on your birthday)! These festivities really got me in the spirit for Christmas with the family.

While living away from my family for the last few years, these winter holidays were always a bit stressful because I struggled to fit in seeing everyone I wanted, and doing everything I felt I needed to do during the few days I was there. This year was different. I made the 20 minute trip to my parents house and stayed there for a few days. There were no out of town guests, and no trip to be made out of town. There was no dressing up, and no fake formality with people I am not totally comfortable with. Instead it was really relaxed. This is the first truly stress free holiday that I can remember!

I went back into the very empty lab today for a productive day's work, and now sitting on my couch there is no work to do... it is a strange feeling, and one that I am trying to enjoy and not feel guilty about because I know it wont last long. I had a long meeting with my advisor about my project today, and things are about to get busy! Here's to a cheerful ringing in of 2010!! Bring it on, I am ready to get down to work.

Tuesday, December 22, 2009

Internet Love (get your mind out of the gutter!)

I love the internets... I know this is trite, but I really don't know how people functioned before it. I am specifically thinking about how people did science (the whole social aspect of the internet is another issue altogether). Forget how much more difficult it was to create a document (paper, thesis, dissertation) without word processing... I can't imagine trying to do research and find articles without academic search sites like ISI, Science Citation Index, PubMed, or GeoRef. I know that most universities have large paper journal collections for this reason, and that things took longer. Maybe people actually got more out of the articles they looked up because if you took the time to actually go find an article you might do more than just read the abstract, look at the figures, and maybe skim the conclusions. I wonder (and this is something that would be easy to look up... in all my free time) if papers published pre-internet, or even pre- lots of stuff on the internet, had fewer citations. I wonder if there were fewer papers published. If there were fewer papers published I wonder if the average quality was the same, or if all the e-resources have increased, or decreased the average quality of papers. How one would assess average quality of papers, I have no idea. I do wonder about how many new journals have been put out in the last 5, 10, 15 years as compared to the 15 years before that. Clearly, it is too early in the morning for completely comprehensible thought (I had to drop someone off at the airport at 5am), but maybe this January when things are quieter I will look up some of these things.

Thoughts... predictions.. more interesting questions?

Oh, I completely forgot to mention what spurred this: Yesterday I was able to google-chat with a friend who is currently in Antarctica doing research on glacial movements and change over time. She (as I understand it) pours bright red dye into cracks in glaciers and her colleagues, positioned in boats in various bays along the coast, wait to see if they see the dye come out. Sometimes nothing happens and they feel like they have waisted time and resources, but other times they learn incredibly cool stuff about the way water moves through large glaciers (rates, volumes, speeds, distances), which is very difficult to measure any other way. I think this trip is actually taking ice cores, but they may be doing multiple things. Anyhow, the fact that I was able to chat with her while she is in Antarctica doing all this full on burley fieldwork really struck me as amazing which started the "i heart internetz" train of thought.

Wednesday, December 16, 2009

Semester's end brain dump

The academic semester has ended. I somehow thought that the pace of things would calm down once classes were over. I feel as busy as ever. Partly it is general holiday time hectic, but it is also the pressure to start cranking out the lab work, now that I have "more time". I find it hard to explain to people out side the university that, unlike in undergrad, I am not actually "off" now that classes are over. I am beginning to understand (although not yet agree with) the advice I have received multiple times - that classes are just a waste of time and get in the way of all your work.

I am not complaining. The fact that I have lots of lab work to do is good. I am getting more comfortable with molecular biology techniques. Now I just need to work some PCR voodoo and start getting some results! I also need to figure out if I will have time to volunteer in a local classroom again next semester. I should clarify... by "figure out if I have time" what I mean is decide whether or not to make time. I am beginning to realize that "when I have time" will never happen, and postponing things until then is pointless. I am the most productive when I decide that things have to happen now, even if there isn't really enough time for all of them. I think that part of being successful in academia (and certainly many other careers as well) is knowing that you are able to do more than you think you have time for.

All of this makes me feel guilty of course for not prioritizing family and friends at this time of year. It has always been my favorite time of year because I get Thanksgiving, My Birthday,Christmas, and New Year's Eve all in succession.

Thanksgiving is my favorite holiday because it is all about family for me. When I was younger and the world was blacker and whiter Thanksgiving represented hypocrisy and white oppression/extermination of native peoples. However, I have come back to truly loving it at its face value... a time to think about how lucky we are, and be with the ones we love, and cook! Cooking is huge in my family, and making thanksgiving dinner with my mom, and recently brother is something I look forward to all year.

The reasons for loving my birthday are obvious... its all about me! While I am feeling a bit of the "OMG I'm almost 30 where has my life run off to", mostly I am excited for a party, a visit from my boyfriend, and more friends and family time.

Christmas, (for me a secular holiday), is like a combination of Thanksgiving and my birthday... good food, family, and of course presents (giving and receiving). It is always a whirlwind, but (at the risk of corny-induced eye rolling) it is the time of year when I feel the most loved, and I when I think the most about how much I love my friends and family.

New Year's Eve is sometimes exciting, some times dramatic, some times disappointing, but always spent with friends. This year I will be spending it with some friends I no longer see regularly, and I am particularly excited about that.

Since classes ended, I have become absorbed in a time consuming, but very fun project that I have a feeling is going to become a hobby. I am making a Christmas/birthday present for a friend, and since they occasionally read this blog, I don't want to spill the beans as to what the project is quite yet!

This year I am feeling the holiday spirit quite a lot for two reasons. One, I have a particularly festive lab-mate who has been playing Christmas carols, baking cookies for the lab, and wearing cute cheesy holiday earrings and somehow pulling it off in a totally endearing way. Second, I am back in the Northeast, and it is cold! Winter never really felt like winter to me when I was living in Texas.

Thursday, December 10, 2009

warning: completely random...

A friend and I were instant messaging (ok fine, procrastinating) today, and somehow we started thinking how amusing it would be if the ocean was made of wine. This conversation turned into a discussion of what a great cartoon this fantasy world could make. Drunken crabs and fishes stumble-swimming all over the place... Yes, I am a biologist, and I realize that this is not actually feasable, but neither are talking sponges or deep sea fast food chains, and that cartoon has managed to take off and might have even taught some kids a bit of science along the way! If only I knew how to animate. This is what happens when exams start turning my brain to mush!

Do any of you readers have suggestions for things you would enjoy seeing on such a cartoon?

Friday, December 4, 2009

The mysterious love child of geology and biology: Hydrothermal Vents - Part 3

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

The mysterious love child of geology and biology: Hydrothermal Vents - Part 2

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.

Stay tuned for Part 3: Hydrothermal Vents 101

The mysterious love child of geology and biology: Hydrothermal Vents - Part 1

I have been working on an essay for a writing contest for the last few weeks, and thinking about it for a month or so prior. Last night I realized that I had been looking at last year's submission deadlines, which means that I completely missed the deadline for this year. D'oh! Needles to say, I was very frustrated with myself for this. I suppose it is better than missing the deadline for something important like the fellowship applications I have also been working on. I am going to post the unpolished essay, in sections, here. My overall goal was to express to a wide audience how exciting it is to study the oceans, and in particular hydrothermal vents.

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...

Stay tuned for Part 2: A Discovery of Significance