Friday, July 15, 2011

Microorganisms and Hydrothermal Weathering

Weathering refers to in situ physical (mechanical), chemical, and biological breakdown of a mineral or rock and it's replacement with secondary minerals.


Until ~30 yrs ago when microorganisms were discovered living in and around deep sea hydrothermal vents more than 2.5 km beneath the sea surface where no light penetrates, all life was though to be dependent on light energy directly or indirectly. Weathering in these systems was believed to be solely the result of chemical reactions due to the differences between the cold oxic ocean water and the hot reduced rocks that had recently erupted. 
from: http://bit.ly/pqpQTd 
The discovery of microogranisms that could utilize chemical reactions to gain energy propelled a reexamination of weathering in seafloor hydrothermal systems to determine what role, if any, microorganisms play in weathering in these systems.


Early studies focused on textural and chemical analysis of basalt collected from the seafloor (Thorseth et al, 1995; Fisk et al, 1998; Torsvik et al, 1998; Furnes et al, 1999). These studies suggested that microorganisms might play a significant role in the alteration of seafloor rocks, particularly volcanic glasses. More recent studies have called this into question. Templeton et al (2009) incubated cleaned slabs of basalt in hydrothermal fluids at the Loihi seamount for a year and then used scanning electron microscopy (SEM) coupled with a focused ion beam (FIB) to slice through metal encrusted microbial biofilms to observe the basalt surface underneath.  They observed very little weathering of basaltic glass beneath the biofilm and suggested that the heavily encrusted biofilms were the result of microbial interactions with the metal rich hydrothermal fluids alone. As a result of these contradictory findings, the role of microorganisms in dissolution reactions, or the break down of promary mineral phases, in hydrothermal systems remains an open question.


Despite this, microorganisms have been shown to play an important role in precipitation of secondary minerals in hydrothermal systems. For example, Fouke et al (2000) showed that microorganisms increase the rate of precipitation of carbonates at Angel Terrace in Yellowstone by an order of magnitude. Lalonde et al (2005) showed that microorganisms mediate siliceous sinter formation and Konhauser et al (2002) similarly showed they mediated clay formation in volcanic systems.


While the full role of microbial influence in hydrothermal systems is not yet quantified, it is clear that they do influence some weathering reactions, particularly the rates of formation of some secondary phases.


References:

Fisk, M., Giovannoni S. J., and  Thorseth , I. H. (1998). Alteration of Oceanic Volcanic Glass: Textural Evidence of Microbial Activity. Science, 281 (5379), 978-980.


Fouke, B. W., Farmer, J. D. , Des Marais, D. J. , Pratt, L. , Sturchio, N. C., Burns, P. C., and Discipulo, M. K. (2000) Depositional facies and aqueous-solid geochemistry of travertine-depositing hot springs (Angel Terrace, Mammoth Hot Springs, Yellowstone National Park, U.S.A.). Journal of Sedimentary Research, 70, 565-585.

Furnes, H., Muehlenbachs, K., Tumyr, O., Torsvik, T. and Thorseth, I. (1999) Depth of the active bio-alteration in ocean crust: Costa Rica Rift (Hole 504B). Terra Nova, 11, 228-233.

Konhauser, K. O., Schiffman, P., & Fisher, Q. J. (2002). Microbial mediation of authigenic clays during hydrothermal alteration of basaltic tephra, Kilauea Volcano. Geochemistry Geophysics Geosystems, 3(12), 1-13. doi: 10.1029/2002GC000317.


Lalonde, S. V., Konhauser, K. O., Reysenbach, A.-L., & Ferris, F. G. (2005). The experimental silicification of Aquificales and their role in hot spring sinter formation. Geobiology, 3(1), 41-52. doi: 10.1111/j.1472-4669.2005.00042.x.

Templeton, A. S., Knowles, E. J., Eldridge, D. L., Arey, B. W., Dohnalkova, A. C., Webb, S. M., et al. (2009). A seafloor microbial biome hosted within incipient ferromanganese crusts. Nature Geoscience, 2(12), 872-876. Nature Publishing Group. doi: 10.1038/ngeo696.


Thorseth, I. H., Torsvik, T., Furnes H. and Mulenbachs, K. (1995). Microbes play an important role in the alteration of oceanic crust. Chemical Geology, 126, 137-146.

Torsvik, T., Furnes, H., Muehlenbachs, K., Thorseth, I. H. , and Tumyr, O. (1998). Evidence for microbial activity at the glass-alteration interface in oceanic basalts. Earth and Planetary Science Letters, 162, 165-176.

Wednesday, June 1, 2011

"It's not a safety issue; people are being inattentive"

This was a splice of conversation I overheard recently between co-workers in a friend's lab. At issue was the fact that several of the PhD students were continually bringing up safety issues that occur in the lab, which offends some of the other graduate students who work in it.
I have sat on this for some time, because I don't like to put my nose in such issues. I am more of an "avoid the issue until I feel forced to confront it" type. This comment, however, has stuck in my head for sometime and truly worried me.
Before going back to graduate school, I worked for an environmental emergency response company. For a while it had some safety problems. We had many small "accidents", until one day, we had a major incident that resulted in someone's skull getting fractured as a result of a fall. It was the result of a routine inappropriate action that we all knew wasn't the safest thing ever, but had always worked before and saved time. I remember arriving on scene seconds after the ambulance arrived. It was a sad day indeed. It ruined one man's life. I have never forgotten how I felt at that moment, how awful the safety shutdown that followed it felt. I never want to experience anything like it again.
The contributing factors to this near-fatal fall included poor assessment of the risk of lifting 55-gal steel drums over the railing on the 2nd floor down to the people working on the first floor of the shop, as well as the inattentiveness of everyone involved that they did not observe the potential hazard. Inattentiveness is perhaps one of the most serious safety issues, because it is so difficult to overcome. It is easy to fall into the trap, as our crew did, and believe that  because unsafe actions have not previously had a negative outcome they never will.
How do we overcome inattentive actions within lab groups and thereby increase the safety levels in our labs?
The first step is to simply bring attention to the issues at hand. This does not mean being accusatory or negative. No one need be singled out in public, but any and all safety issues should be, at a bare minimum, brought to the lab manager/supervisor immediately for correction and discussed in a group meeting from the perspective of "this is the right way to do things."  Every member of the lab should feel comfortable to mention  to their fellow lab mates that, for example, they need to wear safety glasses when reaching in the acid bath if they have forgotten. Every member should trust his or her lab mates to act in his/her best interest.
Creating a culture of safety requires that every member of the lab "buy-in" to the health and safety program and practices of the lab. It requires them being instructed on proper safety, as well as having it modeled by their peers and their superiors. It means taking some emphasis off safety being important only in terms of cross-contamination, and instead emphasizing that we work with chemicals that are every bit as dangerous, if not more so, than those encountered in my emergency response job.
Many students in  most University labs will NOT go on to be tenure-track faculty. Many may decide to pursue careers in industry, where they will be expected to follow proper safety protocols. These are not protocol that they should first learn when they get that first industry job. Proper safety training and good lab etiquette are things that should be ingrained in them long before they ever get their degree.
The first lesson of any safety program should be as simple as "Inattention can be deadly." It very nearly was at my old job.

Sunday, May 22, 2011

Science Heroes

Back in January, I attended a NSF Science Communication workshop entitled "Becoming the Messenger," hosted by Chris Mooney and Joe Schreiber. Very early on in the first morning session, Chris Mooney stated that most people could not name a scientist. Were they to describe one, they would speak of an older white man in a lab coat, probably with crazy hair. Very few, if any, would list a scientist as one of their heroes. This got me to thinking about my science heroes.
I really didn't have one when I was little. Albert Einstein and Issac Newton weren't names I knew. Even if I had, I don't think I could have really related to them. They both have vastly different experiences from me. My first science hero came into my life as I was finishing my master's degree. Everyone kept telling me how wonderful the books Simon Winchester wrote about earth science were. I picked up "The Map that Changed the World" quite randomly as a reading choice. I am not going to tell you I thought the writing in the book was amazing. It was an arduous book to read for pleasure. I was, however, captivated by the story of William Smith who was a surveyor for many coal companies. He went around and meticulously cataloged the rock types and fossil distributions of rock formations above and below coal seams. Eventually, he began to connect the dots and realize that the bodies were laterally contiguous, leading to his construction of the first geologic map. Here was this humble guy who did what many scientists of his era could not, because he was interested, detail oriented and tenacious. His map was stolen and published by someone else, ahead of  Smith's own publication. This ruined him financially and he was sent to debtor's prison. While the geological society later rectified their mistake, he spent a lot of years being looked down upon because of his background. He was unflinching in adversity that would have made most of us quit. This trait, coupled with his humble beginnings, is why he was my first science hero.
My more recent science hero was brought into my living room via, of all things, The Colbert Report. I watch this show in large measure because I am fascinated by Colbert's interviewing technique. You have to be on your toes to stand up against that man and get your message across. One night, he announced his guest would be Dr. Neil deGrasse Tyson, an astrophysicist. I admit, I sat there fully expecting to watch an old, crazy-haired white guy get sliced and diced by Colbert. Imagine my surprise when not only was this not a crazy old white guy, but he also gave a really good interview and got his message across. Then, as so often happens, I forgot all about it until I saw him on the Colbert Report again and I became a fan, despite his Ivy League education. You can tell from his interviews that he is incredibly bright and very well educated, but he also has heart. He cares about people as well as science. That's important to me, because I am very interested in helping people engage in science.
Now that I have told you about my science heroes, it's time for me to ask, who are yours? Did they come into your life early and encourage you to be a scientist? Or did they come later and provide critical encouragement when you needed it, to help you stay on the science path when you feel like you've hit the wall? Is it incumbent upon us as scientists to become science heroes? What are the risks associated with doing that?

Monday, May 16, 2011

Icarus I am not

My Dad loves to remind me of Icarus every time he thinks I am working too hard or pushing too hard.  While it is true that I have always worked somewhat single-mindedly, there has always been a reason to do so. When I was younger, I had to work hard because every day I didn't was one more student loan I had to take, one more day of poverty. Now, I feel compelled to work hard every day because each day here is a day away from my husband, who is my family.

Lots of people present arguments to me to try to convince me that I need to slow down, take the scenic route through graduate school. Once again, a faculty member compared me to Icarus. After all, I will never have this time again.

That's true. I will never have this time again.

Every morning when I wake up alone, every orders change, every evening when I hope we have time to skype and I think about the fact that I will never have this moment in time again. I am beset by what ifs. What if Senior Jefe's number is up for an IA again? What if it comes up and I can't be there to support him as he prepares? What if it happens and for some reason he doesn't come home? What if our last kiss was skyped?

If any or all of these what ifs occurred, would it make sense to know that I missed them because I was too busy doing an extra side project or going on a field trip or simply kicking back and smelling the roses and having a beer?

I realize most people are trapped by the paradigm they live in and that the faculty member who said this to me probably thinks he gave me great advice. After all, he went and did all kinds of neat things in graduate school., things I won't experience if I keep trying to stay on course. But he also went through graduate school with his girlfriend (eventual wife) by his side. That makes a huge difference. And now, she stays at home with the kids, so he doesn't have the pressures on him as an academic that I will face (i.e. raising a family as a single-parent, possibly geographically separated from my spouse for extended periods, or worrying that he will walk out the door and it will be the last time I see him).

I just worry that all my hard work will be for naught, because of the serious disconnect between America and it's military. It was a disconnect I found offensive before because it leads to people comparing my situation to something akin to my husband being gone on a business trip. The last time your spouse left for business, I bet you didn't worry that he would lose his leg in an IED attack as he meandered back to his hotel after the conference he was attending. There's a big difference between a business trip and what my husband does. Now this disconnect is spilling over into my job prospects, where academics are suggesting I am not serious about my work because I am trying to finish in a reasonable amount of time. What exactly is wrong with wanting to finish on time? What is more important, that you spent 6 yrs in graduate school to publish 5 papers, or you spent 4 to publish 4?

Maybe neither of those things are. Maybe the most important thing is perspective, which is something Icarus didn't have. I know that I can fall back any time I need to in my degree program and take a scenic route if I start burning out. I also know that to choose that course up front is potentially a case of being so invested in doing good things that I fail to do the really important ones. I don't want to fail at the most important things in life, like having a solid family and building a strong next generation of it. Spending time with my spouse is really important, because if he dies and I neglected our relationship for another publication, I will have made a really poor decision. I am pretty sure Icarus never thought far enough ahead to thing about what is important in life. More to the point, if turning your back on the people who are important to you is what you have to do in order to be a successful academic, I am not sure I want to be one.

Therefore, Icarus I am not.

Friday, April 29, 2011

Suicide

It might seem like this blog, which was set up for geoscience is talking about an issue that is so utterly unrelated to geology. Yet, as I have reflected on the events of the past several weeks and tried to categorize them and come to understand them, I have realized that social issues and science go hand in hand.
A few weeks ago a friend attempted suicide. She isn't a scientist. She's a military spouse. To say that this event rocked our community to its very core would be an understatement. While my friend is in the hospital getting the treatment she needs in order to repair the psychological damage she has experienced, we have begun to have a national conversation about military service members and their family members rates of suicide.

How does this affect the Ivory Tower and science?

Well, more and more men and women are returning from war and moving on to exercise their educational benefits. They arrive at college still sporting some of the hidden wounds of this war including depression, anxiety and PTSD, not to mention traumatic brain injuries. These people are students in our courses. They have been trained to think that asking for help is a sign of weakness, and so they may not be able to articulate to faculty members that there is a problem beyond the subtle symptoms of withdrawn behavior, poor attendance, slipping grades, what may seem like inappropriate anger, mood swings, fatigue, changes in eating habits or personal appearance, etc. Despite their desire to be strong and carry on, they may not be able to do so.
It might feel unfair to place the burden of being first responders on the faculty of our Universities, but in some instances you may be the only person who sees the signs. So, I am going to have to ask each of you to look after your students now and in the coming years, for the symptoms of depression, anxiety and PTSD, so that your students don't get so lost that they think suicide is the only option. You don't have to know what it is like to stand on the front lines, survive a mortar attack, or spend your nights worrying that your loved one is dead in order to be able to help out. You just have to be willing to take people aside and talk to them and give them the opportunity to talk and the opportunity to learn about the resources your University has to help them. Often times, the therapists covered by military health insurance are overrun with patients, making it difficult to get necessary treatment. This was in part what I experienced my first year of graduate school.

In order to raise awareness of these issues and their coming impact on the American public, as well as their continuing impact on military families, Blue Star Families in conjunction with Health Net,  TAPS, and the Creative Coalition have put together a couple of PSAs that directly address these issues. I am sharing them here, because I realize this is an uncomfortable subject to broach, but these messages may help reduce American's anxiety about raising the discussion with their friends, neighbors, students and employees who may be suffering. Please take a look:




 I was not getting help until my advisors, who I hated at the time for doing so, sat me down and told me they were requiring me to go get help from our on campus psychological services for the anxiety I was experiencing due to my husband's circumstances at the time. I think part of the reason my friend and fellow military spouse's suicide attempt has been especially sorrowful for me is that looking back, now that I have help, my husband's circumstances have improved, and I am sailing through school, I realize that but for willingness of my advisors to be the bad guys, I may not have ended up all that differently from my friend. I was really pretty close to the edge. As much as I am sometimes frustrated with my advisors, as I assume any graduate student is, I have to admit that they may well have saved my life. I don't know that the University gives out awards for that, but if they don't, they should.

So please, whether you're a faculty member, staff member, teaching assistant, postdoc, friend, etc of a veteran, servicemember, National Guard member or Reservist, or a spouse of a service member please take a moment to check in with them and make sure they're okay. Who knows, you might just save a life.

Thursday, March 31, 2011

Maui: Honokalani Black Sand Beach

I just got back from Maui on Friday, but I wanted to share some of our adventures. I got really lucky that I was able to go geo-trekking with another nerd who humored me getting my nerd on. We hiked all over Haleakala and last Wednesday, we trekked out to the 7 Sacred Pools (more on these adventures later).

On our way back along the infamous "Road to Hana", we stopped at Waianapanapa State Park to visit the black sand beach. It's one of those things on my bucket list, 'cause I'm a nerdy geologist. The black sand is actually more like black pebbles with a little sand in between. What really struck me was watching the waves from the lava tube turned sea cave. I even made a video for you. BTW, for those who choose to visit, they mean it when they say strong surf.

video

I made a little offering to Pele, since she has inspired my desire to be a scientist ever since I was in 4th grade. It occurred to me that my 4th grade teacher went to Maui and brought me back a T-shirt that I wore until it fell apart, literally. She knew I loved volcanoes. I wanted so much to visit HI based on her trip. I hope Pele accepts my offering and knows how much she inspires me.

I hope this video of the waves from the point of view of the lava tube inspires you as well.

Wednesday, March 30, 2011

GK12: How's this for results?

I can't help myself. I need to brag a little. Of the senior class of 11 students I work with, 9 entered the science fair. More importantly all 9 came home with awards. Two of them won 1st place honors, one in Botany/Zoology for her project on flightless birds and the other won in 1st in Earth Science with his project on the effects of sea level rise associated with global warming on different nations. While I am blanking the personal information for obvious reasons, here's the list:



JC
1st Place Senior in Botany & Zoology division
Pioneers in Science Award
Linda Hall Library Display award
XX State Fair Award

RE
Gold Achievement
Write up entered into Society for Technical Communication Writing Contest

BJ
Silver Achievement
Linda Hall Library Display Award
XX City Garden Club
Greater XX City Association of Family and Consumer Sciences
Write up entered into Society for Technical Communication Writing Contest



KL
Bronze Achievement
American Society for Photogrammetry & Remote Sensing (ASPRS)
XX City Garden Club
Offered a future internship with Environmental Company


MM
Silver Achievement

HN
Bronze Achievement
Write up entered into Society for Technical Communication Writing Contest
Offered a future internship with Environmental Company

CP
1st place Senior in Earth and Space Science division
Gold Achievement
American Meteorological Society - XX City Chapter
American Society for Photogrammetry & Remote Sensing (ASPRS)
[University] Advanced Certificate Program in GIS
Earth Science
Association For Women Geoscientists
XX State Fair Award
Write up entered into Society for Technical Communication Writing Contest

DP
Bronze Achievement
ASM International - XX City Chapter
Write up entered into Society for Technical Communication Writing Contest

NS
Silver Achievement
Write up entered into Society for Technical Communication Writing Contest

I intend to help JC get her paper published in a scientific journal and help CP and DP present their work at GSA (fingers crossed) this year. Please congratulate them on all their hard work and remember to write your Congressman and Senators and ask them to save NSF's GK12 program, so that we can springboard many other students to such lofty science heights.