Data!

I have data. We sent off one of my samples for sequencing and got the results back a couple of days ago. Now I need to start learning what to do with this type of data. It is really exciting to have this data because, while it is still very preliminary, it means that I have a springboard to start thinking about what might be going on in the environments that I am studying. It also means that our process of DNA extraction and amplification (from very difficult samples) worked, at least for this sample.

I like that scientific research comes in phases. First you have to plan out your experiments or your sample analyses. This often involves a lot of background research to figure out what other people have done to ask similar questions, and how they did it. Then you have to do the actual lab or field work. In the case of the lab work I have been doing, a lot of this feels like one step forward two steps backward because each time we figure one thing out in our procedure, there is another issue to deal with. We spend a lot of time trying to figure out why our extractions or DNA amplification isn't working, and deciding which of the 20 factors to tweak the next time around. If we get luck and pick the right one, things progress fast. If not, we can spend weeks or even months trying to navigate around some road block that is standing between us and the data we seek. Once samples have been collected, experiments have been carried out, experimental samples have been preserved or analyzed we are ready to proceed to the next phase... data analysis.

Once there is data in the picture the game changes. A new set of challenges arise because the goal in this phase is to figure out what the data are telling you. Sometimes this is frustrating because there is no clear story, and sometimes you realize you need to back up and get more data or slightly different data in order to really understand what is going on. In the world of genetic sequences that task becomes figuring out what hundreds of thousands of A's, C's, T's, and G's mean. There are databases to help you figure out what organisms are in your samples, but in environments like hydrothermal vents where so many of the microbes are uncultured and unknown these databases are of limited use. So now it falls to me to learn a new set of skills that involve computer savvy (using new programs and platforms), a thorough understanding of genetics, and I'm not sure what else. Bioinformatics... here I come!

After preliminary data typically comes more experiments and additional data collection. Eventually you decide you have enough data to tell a compelling story and then the next phase begins... writing. That one is a long way off, but it is the ultimate goal: to write up your results and get them published. In reality these phases often co-occur if you are working on various projects or various aspects of the same project. The way people do science very rarely occurs in the way that middle school science text books describe the "scientific method", but to me these phases represent different mindsets, and the transition from one to the next makes me feel like I have accomplished something.

I am excited because this data provides a peak into the next phase of my science... data analysis. It will be fun to not just be doing lab work for a while. It is intimidating and exciting to have a whole new set of skills (bioinformatics) to begin learning. This whole process has been one steep learning curve after another. It keeps you busy, and transition between phases prevents boredom.

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 350^oC (662^oF), 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 (2^oC, 36^oF) 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.

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

lots to learn and loving it!

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.

© S. Lowry—University of Ulster—Stone/Getty Images - http://tinyurl.com/5u2fkg

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.