Sunday, January 24, 2010

Super Exciting Microscopy (SEM)

The scanning electron microscope (SEM) is my new favorite toy. Ok fine, its not really mine, and I guess its not a toy, but I have to admit that I was just as giddy as a chile with a brand new Ticke Me Elmo (or whatever is cool these days) on Friday afternoon, when I got to play with one of these amazing tools. A light microscope is limited in resolution by its optics, but also fundamentally by the properties of light. The microscope uses light reflected off of the subject to see it and then the optics focus and magnify the image generated by that light. Basic physics proves that any object or feature that is smaller than the wavelength of visible light (380-750 nm) will not be detected by a light microscope. That is where the SEM comes in. An electron beam has a much smaller wavelength than visible light, and when it is used to scan an object the resulting image has much higher magnification than is possible with a light microscope.

The image below is the fungus Acremonium strictum.

This next image is a Stibella fungus growing on Manganese.

The next image is from the same sample (Stibella growing on Mn). I think we are looking at bacteria growing next to fungal hyphae (on the right side of the image) but I am not entirely sure. It is interesting that when looking at something familiar under a new level of magnification, it can be difficult to tell what you are actually looking at.

Below is another image of the fungus Acremonium strictum, but at lower magnification.

I am pretty sure that everyone in my group thought I was a total nerd when I excitedly exclaimed "yes!" upon hearing that one of our samples was dinoflagellates. These are some of my favorite marine plankton, and leave behind beautiful shells that accumulate in sediments and allow scientists to reconstruct past climate based on which species (or really morphotypes) are present. Here is one image that I thought was especially nice. The UFO shaped object is a dinoflagellate, but I dont know what species or type.

Here is an image from the same sample that I was able to make into a 3D image by taking a picture of the same thing on a stage tilted 3 degrees in either direction and then merged with a special program. Unfortunately unless you have 3D glasses, it wont be that exciting.

Fun with light microscopes

Composite image of bovine endothelial cells created with fluorescense microscopy.

I spent three days last week participating in a microscopy workshop organized through a microbial sciences initiative at my school. It was interesting to meet others who different aspect of the micro-world. While I work with specific types of environmental samples, most microbiologists work on a specific model organism trying to figure out a specific process or part of that organism's physiology. Microscopy provided a common tool of interest to all of us!

This is an image of filamentous algae taken out of a Winogradsky Column, which is a great way to grow a lot of bacteria and other microbes in one location with very little work. We looked at many samples (compost, fungi, cultured organisms) under light microscopes but this sample was the most interesting to me to me because it was easy to find lots of cool microbes to take pictures of.
This is another image from the same sample. Here there are at least two different types of organisms, but I don't know what they are. The green is an alga of some sort, and the red could be a colony of purple sulfur bacteria.

After playing around with the basics of light microscopes and trying to perfect our focus, we tried our hand at fluorescence microscopy. This technique uses specific wavelengths of light to excite certain molecules within cells that emit light when they are excited. It is typically used for looking at samples that have been pre-stained with fluorescent dye (like the one at the very beginning of this post), but many of the organisms in the Winogradsky were auto-fluorescent so we were able to get some cool images by looking at them under specific colors of light. This green image is the same image as the one above, but with the red filter on. The organisms absorb red light, and reemit green light.

I looked at this exact part of the sample under red, green, and blue light. Each light excited different organisms, or different parts of the same organism. When you capture an image of each and merge the image you get something pretty cool!

Here is another example, but this time looking at a filamentous algae (shown in red) and a round one (shown in blue).

Stay tuned for even more exciting images from a Scanning Electron Microscope (SEM)!

Wednesday, January 6, 2010

On class and race issues, and their relevance to my scientific career, or not.

This image provides an appropriate setting for the daydream described below.

Warning: the following post contains ramblings and daydreaming. Please comment if anything needs clarification.

I just finished watching a 4 part PBS/BBC documentary called
America Beyond the Color Line, by Henry Louis Gates Jr. It brought me back to things I haven't thought about as much as I used to since my current graduate program. This film examines the state of black Americans 100 years after W.E.B. DuBois said that the problem of the 20th century would be "the problem of the color line". Gates travels through black America in this film (from Hollywood to wealthy black neighborhoods in Atlanta, to inner city Chicago housing projects and much more) and elegantly communicates a very complicated situation - race relations in America having come incredibly far since the beginning of the Civil Rights movement, but still having far to go. The film identifies a growing gap between inner city disadvantaged African Americans, and the growing African American middle class (and very wealthy) that have "made it". Much of the film asks questions about where to we go from here and how do we bridge this growing gap. There is no easy answer (obviously) and many interconnected approaches ranging from political changes, to localized mentoring and education programs, to a need for bigger dreams and belief that better is possible are all discussed.

So what does this all possibly have to do with me, a white graduate student studying deep sea microbiology? I am not totally sure, but the segments of this film that interviewed educators and high school age students resonated with me, and reminded me why I went into teaching rather than more grad school 3.5 years ago. It is easy to get sucked in to the world of research and academia and never look out. This is understandable given the amount of work and time required of a career as a professor or even life as a grad student.

I have worked with underprivileged students of various ages in a few different mentoring/inspiring/extra help/outdoor experiential ed programs, and it is something I love doing. I sometimes wonder whether I would have a bigger impact doing the science I am doing now (and whatever comes out of that) or through a career of teaching. I am honestly not sure I could hack it as an inner city teacher, and I sometimes feel guilty about that. I do know that I love working with kids, and really enjoy talking to them about how cool science is, and would like this to be part of what I do when I "grow up" (I like to live in a bit of denial-land where I am not yet an adult). I had so many wonderful opportunities growing up that inspired me to study science, and I would love to be able to provide similar experiences for youth who won't get them otherwise.

Back in October I wrote about a workshop I attended about how scientists communicate with The Public. One of the things that got brought up is how outreach-type activities are typically not valued in academia (at least not when it comes to hiring and/or tenure decisions) and that this is a reality that scientists like me (who think it is our responsibility to communicate not just with peer reviewed scholarly papers) have to deal with. Maybe I am cut out for academia and maybe I am not, but here is a day dream of a program that Future Me has started...

Located in the woods somewhere with water (maybe a lake or a river, but ideally a rocky sea shore) on a large tract of pristine land, but within a couple hours drive from a major metropolitan area (read - bad inner city school system) lies a campus that looks part farm, part school, part summer camp, and part laboratory. There is a ropes course, kayaks and/or canoes, camping equipment, cabins, and maybe a big fire ring. There are lab facilities with plenty of salt water tanks and touch tables housing a rotating selection of organisms and a good set of microscopes, and plenty of room to set up experiments. There is a garden that provides local organic produce and maybe even chickens for out kitchen and also provides educational opportunities. This is a property that I (or some very wealthy and dear friend) own and have built up. Hey, its my day dream so maybe I even built some of the buildings.

This campus is home to a variety of programs that have the following goals 1. bring urban youth into the wilderness, 2. get youth excited about science, 3. preach academic excellence, and 4. provide underprivileged kids with role models and connections that last a long time. I can many different types of programs occurring in this facility from a college semester or summer program to weekend or day trips for school groups. The coolest program offered is some type of collaboration with a program in the nearby city that targets a group of youth in elementary school and works with them through their college years on tutoring and mentoring and uses my facility for regular (annual? Monthly?) gatherings or mini-courses… who knows?

There are many programs that do things like this. Someone I know started a program of this type on his own that is particularly impressive. Some day I hope to go visit and learn how he pulled it off. I guess the point is that I am going to eventually want/need to be doing something other than pure science. This film reminded me of things that were definitely a priority at one point in my life that have become more of a passing interests/side project over the last few years.

In some ways it is all about your perspective. Being a geologist taught me to see things in very long time scales, time scales at which global catastrophic climate change might matter, but probably wont change Earth itself all that much. From this perspective, environmental issues are not about saving the planet, but about preserving our ability to live on it, and the environmental issues are the most pressing for humanity to tackle because all the social issues will be irrelevant if we are dead. ON the other hand that type of perspective can allow many of us (ie me) to ignore social issues that just seem too difficult to tackle.

I can’t help comparing two potential contributions that I could make to humanity: one being the creation of a wonderful program that is some fraction of what is described in the day dream above and the other being whatever cool scientific tidbits I might discover along the traditional track lying ahead of me in Academia. Depending on the perspective I look at these options with I can make arguments that either is somehow better. It is hard to know where I would have a greater impact (which is how I like to think of success). I remember as a child having very definitive opinions about just about anything (ask anyone who knew me before I was 18), but much of that certainty has vanished as I have seem a plethora of possible roads to travel (I have written about this before too). Maybe clarity will come, or maybe opportunities will arise, or not, and that will determine where life takes me.

Sunday, January 3, 2010

Resolving not to resolve... sort of

I hate New Year's Resolutions. I never keep them, or even remember what they were. I always feel dumb resolving to do something like "get in shape" or "make more time for me". I am curious what percentage of American women resolve to lose weight each year, and don't do it. That said, I really do like the process of reflecting on the year and trying to consciously make changes to improve the next year. I was thinking that setting goals might be a better thing to do than make a formal, intimidating, year-long RESOLUTION.

I have worked with numerous groups of students on goal-setting. I like to use a quaint little acronym (S.M.A.R.T.) that I became familiar working for NOLS. Good goals are Specific, Measurable, Attainable, Realistic, and Timely. I figured this was a good time to start practicing what I have preached. I sat down this evening with grand plans to make some goals for the year, but had trouble thinking about the whole year. Years that are now past seem to be very short, but the one ahead of me seems very long right now, and therefore hard to plan for or thing about as a unit. However, I did have plenty of things I wanted to accomplish on a shorter time scale. So, I made a list of 10 goals for January, and decided that monthly goal setting would be a pretty good activity. So after my initial decision not to make resolutions this year, I actually have one after all... I hear by resolve to make goals at the beginning of each month, and to revisit them at the end of each month.

For January I have 10 goals. One is to accomplish a lab safety project that I have been avoiding. One is getting to the next phase on a paper I am trying to write. Two have to do with physical fitness, specifically making time for climbing, and getting out on the ice at least once. One is to make sure I see a friend I haven't seen in a while. One is to visit family members a few hours away. One is about sticking with a new hobby of mine (scrap booking). One is to go hear local live music at least once. One is to make at least 6 blog posts.*

Each of these goals is doable, but I don't think I will accomplish all of them. I have a long history of telling myself I am going to do things, and then not doing them. Maybe this process can break me of that habit. I am hoping that thinking about what I get done and what I don't each month will help me figure out my priorities, and whether or not I am allotting them enough time, and, subsequently, better manage my time the following month. Make goals...evaluate...repeat... this might even lead to a spreadsheet and graphs! Now I just need to remember to reevaluate come the end of January, and each month thereafter. Reminders will be greatly appreciated!

*Yes, I know I only described 9 of my 10 goals. The 10th is complicated, personal, and takes place entirely inside by brain, so it stays private.