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.

"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.

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?

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.

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.

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.

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.

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
1^st 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
1^st 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. 

Science Education is a National Defense Issue: A Call to Action

One of the most successful programs sponsored by the National Science Foundation is on the chopping block and we need your help to save it. The program is called GK-12 or the Graduate STEM Fellows in Education. This program matches science, technology, engineering and mathematics (or STEM)graduate students with a mentor teacher at a local elementary, middle, high school to assist with improving the science content and serving as a science role model in the classroom. Over the course of the fellowship scientists learn to communicate their research to the kids in the classroom and translate their improved science communication skills to communicating with the public throughout the course of their careers. According to the Save GK-12 website, since its inception in 1999, the GK-12 program has changed the lives of:

7,400 Graduate fellows

5,000 Schools

9,000 Teachers

600,000 K-12 students

This direct line of communication between the education system in the United States and the scientific community is critical in our increasingly technological society. Our children need better math, science and critical thinking skills in order to be prepared to address our coming societal challenges. Having a GK-12 Fellow that is already on the technological front lines facing these challenges provides a unique perspective on the intersection between science and society. The GK-12 fellows are doing cutting edge research that affects almost every aspect of daily life. Energy policy, climate change, species diversity, earthquake science and engineering,  water quality and urban development, astrophysics, agriculture, development of unmanned aircraft, and AIDS vaccine development are just a few of the content areas GK-12 fellows are researching. Many fellows research develops technologies and addresses challenges that Adm. Mullen has cited as critical to National Defense. The true breadth of their research could not be summarized in a blog post and possibly not even in a book.  This program doesn’t imagine the power of having kids being mentored in research by cutting edge scientists, it’s doing it and your children are benefiting from it.

The rationale given for slashing the program from the National Science Foundation’s budget was that Fellows do not spend enough time in the classroom to bond with the students and really influence them in a significant way. I would respectfully beg to differ on this point. As a 2^nd yr Fellow in the GK-12 program, I can honestly tell you that my fellowship is all about relationships. Kids often tell me things that they do not tell anyone else. When I sit down to work with a kid, my first question is always, “Tell me what you’re passionate about.” The answers vary: skateboards, music, etc. Inevitably any of these interests can be turned into a science lesson. For example, if your kid loves skateboards, then I try to help him investigate the physics of skateboarding, which will hopefully lead to fewer trips to the doctor for him and his parents. This past year, 9 of the 11 students I work with have entered science fair having completed individual research projects that are largely of their own design and execution.

What you need to ask yourself is whether you would rather your child learns science as a series of facts and worksheets, or whether you want your child to be educated by the strong partnership of a mentor teacher and graduate STEM fellow under GK-12. Then we, the GK12 program ask you to contact your Congressman, Senators, and the Senate and House Appropriations Committees and ask them to save the most successful science education program at NSF from being cut from the 2012 budget.

 You can contact your Congressman and Senators through Congress.org by typing your zip code.

At the end of the day, what makes our country great is our individual ability as citizens to petition our government for redress. We shape the American democracy and we determine what things the government should spend money on.  Our nation’s future is now and it rests in the hands of our children in the educational systems. Every dollar spent to improve the quality of science education is an investment in your child, in our nation and in our ability to compete successfully today and tomorrow. Please stand up and support the GK12.

For more information on my experience with GK-12, please go here. A former fellow has also posted her experience. Numerous You Tube videos showing the hands-on work in the classroom abound.

National Science Foundation cancels the GK-12 Fellowship program

This year during the State of the Union Address, the President stated that science education was a priority in the national interest. He made it clear that we need more scientists to deal with an increasingly technological world.

Fast forward to today and imagine my surprise when someone forwards me a Science article that explains that the GK-12 fellowship program, which allowed graduate students to be placed in school classrooms around the country to assist kids and teachers in conducting scientific inquiry in the classroom, was cancelled. Color me shocked. Actually, I think horrified is a better approximation of my emotions. Let me explain.

I am a current NSF GK-12 Fellow. This is my second and final year on the fellowship. I was awarded the fellowship in the second semester of my first year of my PhD program. This was about the same time I was working on writing my proposal for my research. I found that working through explaining the research process to middle school children really helped me focus down on my own research topic and finish my proposal by the end of the summer of my first year. This really helped me to move forward in my research over the summer and get the better part of one paper finished my by my second year of graduate school.

The following school year, I was moved to a high school where I worked with sophomores, juniors and seniors on water quality research.  In the high school where I work, the seniors conduct a year long science research project as a capstone course. Helping the kids work through the inevitable "mandatory floundering" of research toward those moments of enlightenment we all experience as scientists was incredibly rewarding. It also had the unintended benefit of giving me something positive to hold on to when my anxiety caused me to fail my oral comprehensive exams last year. GK-12 gave me a sense of purpose that helped me to keep pushing forward on my research when I felt pretty bleak.

This fall, working with a new set of kids, explaining the research process again, and helping them move through the research process, helped me to get my confidence back and improve my public speaking skills to the point where I could pass my comprehensive exams. I also have students this year who are really interested in geomicrobiology, which has given me the opportunity to shape projects and advise students on all kinds of research questions I find interesting, but otherwise don't have the time to pursue. Additionally, I have been working with a class of undergrads at BIG U who intend to be teachers, performing the same type of advising  on their projects. I feel like I have a better handle on what it takes to be faculty at a R1 institution than some of my compatriots who don't have the opportunities my fellowship has provided. I also do not believe that the GK-12 fellowship has negatively impacted my research skills as suggested in the science article, as I intend to graduate in 4 years with 5 publications, including a methods paper.

The GK-12 fellowship really inspired me to do more and to be better. It made me realize how important it is for me to talk about my science with everyone I meet. A lot of my job in the classroom isn't just to help the kids develop research questions and find ways to answer those questions. My job is first and foremost to listen to the kids, to find out their interests, and to help them see how science and math plays into EVERYTHING, whether it's skateboarding or biofuels. Carl Wieman, associate director in the White House Office of Science and Technology Policy asserts that one reason the program was cut is that:

  “"The reality is that, under GK-12, the time available for kids to interact with grad students so that both sides could develop a relationship …was probably not enough to achieve the impact that one would have liked to see.."

I really question this assertion, because it is the antithesis of my experience. I have comforted the military child in one of my classes who needed a good cry because she hadn't heard from her Dad who was in Iraq. I felt her pain as only someone in a military family could. She didn't need a scientist that day; she needed a friend who understood what she was going through. We worked on managing her stress so that she could focus on her school work. I have listened to many a kid who is growing up every bit as poor as I was as a kid and I have shared with them my success story and the tools that I found worked to escape poverty. I love those kids and I have celebrated every success and mourned every heartache with them for 2 years now. The truth is that unlike what Mr. Wieman supposes, you cannot teach someone unless you have a trusting relationship with them.

Most Americans don't even know a scientist. They still describe scientists as old, white men in lab coats. They think science either is 1) all figured out already (i.e. science is taught as a series of facts) or that 2) scientists change their minds all the time for no reason. Neither of these views are accurate representations of the truth. Each of these misconceptions affects whether or not young people will consider a career in science. Having a young woman (i.e. me) or a person of color, or someone like my friend Ilya there discussing science and engaging in explaining how and why science is a process has meaning and value.

I am deeply disappointed by this decision. I encourage each and every one of you, whether you are a scientist or not, to write your Congressman and the President and tell them that these programs are critical to our ability to grow future scientists and maintain our preeminence in the scientific arena. I really believe that the GK-12 program is one of the most important things I have ever participated in as a scientist and it is a shame that the relationships GK-12 fellows have built aren't recognized or appreciated by our government, even as they stress the need for better science education.

Lab work as a meditation

This weekend I had a student working in the lab with me. He seemed interested in the project initially, went out and collected the samples himself, came to my lab to run them and then seemed bored out of his mind the entire time he was here.

I know sequential extractions cannot be described as a non-stop thrill-ride adventure, but I have to say that I really enjoy working in the lab. That’s quite a statement for a former field geologist to make, I think. Don’t get me wrong; I still love hanging off the sides of cliffs and starting out over a vast plain from the top of a mountain. There is a unique beauty, peace, solitude, and perspective that field work brings.

Lab work has a different vibe to it. Whether it’s picking grains for analysis or performing a sequential extraction, there is a beauty to the slow methodical rhythm of lab work. Pipetting liquids from one tube to another doesn’t sound like a serene experience, but it really is. It forces me to focus on the moment, the way my hands are moving, getting the pipette as close to the sediment interface as possible without touching it. There is little room for all the other stresses in my life. Without those stressors cluttering my mind, I find myself more prone to joy and deep satisfaction with my life.

I also find that moments of clarity are easier to come by in these routine lab bench moments. The majority of my consciousness if focused on doing the job at hand, but part of it has uncluttered time to think. In these long lab work days, I find I can focus on one issue at a time that needs dealt with.  It has made me realize that for me lab work can have the same emotional/mental/spiritual effect as my tai chi practice.

 I wonder if all scientists feel this way or if lab work is something you have to get through on your way to something else (i.e. publication).  I wonder what I can do to explain or share with students the intrinsic power of laboratory meditation or if it is something people have to find out for themselves. 

Graduate School: What happens if you get shown the door. Part 2

Part 2: So you don't think your graduate student is working out, now what?

***DISCLAIMER: For the record, I am not a faculty member, so this post is an opinion based on my years working in industry.***

Not every person you hire is going to be a great fit with your company or your brand. It happens. Some people look great on paper when they aren't. Some people are really nice and would be a great fit in some one else's company, but they just don't fit with yours. The reasons people get fired run the gambit from personal to professional reasons depending on federal, state, and local laws. The real question is: what do you do when things aren't working out?

The first thing you need to do is stay calm. The graduate student-advisor relationship can be stressful on both sides. You've invested in this person and things aren't going as planned. It can be every bit as stressful as being a parent. This is why calm has to be the first order of the day. You need to separate your feelings about the person from his or her performance. Sometimes writing things down helps clarify things. If nothing else, it will help you clarify whether the issues can be resolved.

Secondly, let your student know early on in the process where they stand. Most graduate students want to be successful. Letting them know where they are doing well and where they need to improve can be beneficial. My current advisors are really amazing in giving us yearly evaluations and usually we have an end of semester sit-down where we talk about what worked, what didn't, and benchmark goals for the next semester. When things go poorly, we all talk about it right away and get things back on track. When they go really well, we celebrate and I walk away feeling like I can conquer the next step we've laid out. Under no circumstances should you just pretend your student doesn't exist until you fire them. It's a waste of your money and both parties time.

This leads into my third point: Keep it professional. At some level, graduate school is an apprenticeship and the graduate student does need to be evaluated. This is an evaluation of his/her performance, not who they are as a human being. Personal attacks and discussion of personal life (except where it bridges into professional life) are off-limits. It doesn't matter if you think your graduate student is a horrible excuse for a human being or whom your graduate student is dating/sleeping with, unless it is relevant to their position as a graduate student or TA. 

If you have a problem with your student, talk to your student about it. I knew a faculty member who had huge divisions in his lab group because he would tell his favorite students all about the students he didn't like as well. These favorite students would then tell other people and it would eventually get back to the student who was the subject of the gossip. I told my current advisors when they hired me that I expected that if they had a problem with me, I would hear about it from them directly and not anyone else. I respect them because they have always come to me directly when I've made a mistake.

Most importantly, providing feedback early and often is really positive for you and for your graduate student. When I failed my comps the first time due to anxiety issues, my advisors told me to write them a one page corrective action plan that I would follow over the next semester to address the issue. It was enormously helpful, because I had an opportunity to figure out what went wrong and how to fix things. I laid out goals, including mini-comps with my advisors, that helped me get used to speaking in front of people. I got help from people on campus as well. I still was nervous the second time around, but I was able to hold it together enough to pass and I knew that I had done everything I could to fix my problem. If I hadn't, well, they could have shown me my plan, how I didn't follow it, and I wouldn't have been able to blame them if they booted me. I think this is the way things should work.

I am stressed out like most graduate students, but I admit that having advisors who run the personnel end of the lab like a company has really been a blessing. I feel more confident because I know where I stand. When I got booted from my previous PhD attempt, it was a bolt out of the blue. I never knew my advisor was unhappy with me until it was too late to do anything about it. I really don't think I have become more brilliant in the years between being kicked out of school and coming back. I think having great advisors who understand the mentoring process was what I needed to be successful. They aren't perfect and there are things I would do differently, but they have been just great. I also have a great committee who has been there every step of the way with me too.

Of course there are exceptions to these guidelines, like academic misconduct. That is a whole other ball of wax. Most universities have defined rules on how such incidents are handled. This is why I did not touch on such behaviors. I feel like the guidelines I have written are more for instances that are more routine such as when your student is slacking, or has an issue like anxiety, etc.

Graduate School: What happens if you get shown the door.

Every graduate student fears being voted off the graduate school island. There are always vague rumors of people who have been down that road. It is almost always implied, if not directly stated, that whatever happened was 100% the graduate student’s fault and that it was because s/he was a horrible excuse for a graduate student and perhaps even a human being.

This week, a dear friend, a brilliant friend, was voted off the island. He’s crushed. I can’t blame him, since I was once voted off the graduate student island myself.  It was one of the most soul crushing moments of my life and something that I have never talked about in great detail with anyone except my husband. Hearing my friend relate his experience to me brought back the conversation I had with my old advisor several years ago. It made me realize that some of the things I have struggled with this second go-around at the PhD are a direct result of how I feel about myself as a result of that horrible, horrible day when I was voted off the island. The words from my old advisor’s lips are things I need to move beyond. That is harder than it sounds. I have thought that maybe describing my experiences will help me move beyond this and help my friend understand he isn’t alone. I thought I would break my thoughts into a couple of different posts to address both the advisor and the student side of this issue.

Part 1: What you’ll feel right after the break-up w/ your advisor

The very first thing you have to remember, should the worst happen, is that you are still a good person. It sounds cliché, but when you are told to pack sand by your advisor, it’s hard to remember that you are a valuable human being, graduate degree or no. All I had ever wanted was to be a geology professor, so when I was told “your passion isn’t enough” and that I wasn’t any good as a scientist, I was devastated. Like my friend, it happened early enough in the semester that I couldn’t just skulk off into that good night. I had to show up to my classes the next day. When you feel like a worthless human being, it is hard to get out of bed and shower, let alone go to class.

This desire to dissolve into a wall somewhere is intensified in graduate school, because most departments are more gossipy than most high schools. Everyone seems to know everyone’s business and depending on how discreet you, your advisor and/or the faculty is, the news may or may not spread like wildfire. Once is does, everyone seems to start treating you differently, more distantly, maybe questioning your performance in other areas. It compounds the depression and worse still, makes you question your judgment about yourself, your career and whatever was said when the break-up between you and your advisor occurred. Whatever you do, do not give into the depression and do not assume that perception is reality. There are still a lot of people who think well of you and are willing to help you into a soft landing. You need to keep putting in the effort to make this a reality.

The first couple of days are going to be the worst, so give yourself some time to grieve, because you will grieve. Do not make all of your life’s decisions in this time.  Once you are feeling better, it is time to polish your resume. Every school has career services, so you should check with them for help if you need it. Then, you will need to look for a job. It’s important to find/create a positive spin on what happened. I happened to have been dealing with a breast cancer scare when I was shown the door. That wasn’t the whole reason, but it is a solid sympathetic reason for leaving my old job (graduate school) was key in getting a new job. Take your resume and shop it around. Ask people in the department if they can help you and if you are interested in environmental, contact Aerotek Engineering. They do a lot of environmental recruiting and I’ve always had good luck with them. Find a space where you can envision this as a positive step in your life and go get that job. Remember, the best revenge is living well.

Then, once you know you’ve secured a roof over your head and food on your table, you need to take time to evaluate what happened. Some proportion of being fired IS your fault. No one is perfect. We all make mistakes. Recognizing your own mistakes and changing is vital to overcoming this setback, especially if you want to make a second academic run later. That said, it is NOT ALL your fault. Some proportion of what went wrong was likely beyond your control. Recognizing that other factors played a role in your setback will help you accept what happened and maintain a positive self-image. Sometimes the advisor is part of the problem. Sometimes financial, health or other factors may have played into the situation. These are not your fault.

Ultimately, I found that leaving graduate school was a good experience for me. I don’t like to talk about it, because I do worry that people will still view me as a loser. That’s  my problem. Honestly, working 8-5 at a couple of good companies with good people gave me an opportunity to see that I am a good scientist. I learned how to manage my time better. I learned to be happier. When I came back to graduate school the second time, as worried as I was that old advisor was right, each success showed me that I wasn’t that person and I didn’t have to accept anyone’s opinion of me as gospel. Getting fired from graduate school ultimately made me a better graduate student and employee.

I don't expect that everyone has had the same experience I have had and I welcome any comments about how you have dealt with being fired as a graduate student and how you made your come back.

Science Baby Steps: What can we learn from a sitting outside?

I want to start writing about easy science inquiries and activities parents can do with kids, but I feel that before I can do that, I have to address the ins and outs of embracing a scientific mindset. To that end, I am going to try to write a series of science baby steps to help share some of the things that I think help me as a scientist.

For the past two years I have been an NSF GK-12 fellow. Each of those years our fellowship advisor and a few of the School of Education faculty put on a Middle School Science Academy for local middle school teachers. Some of these teachers then work with the GK-12 fellows over the course of the following year after the academy.
One of the first activities for the teachers is to go outside, find a shady spot and write 50 questions about what they see. After about 15-25 questions, people start getting frustrated and that's when the magic happens, because Brad Williamson pulls a leaf off of a tree and asks them to think about it. The questions just begin to pour out of them.

A ginko leaf.

This lesson has taught me two very important things. First, good questions often result from changing the scale or scope of observation. Second, when we engage in scientific inquiry, we are brought back to that magical time in childhood when we asked questions about everything. Why is the sky blue? Why do birds sing? Why do trees grow up, instead of sideways? Everything was magical and therefore open to question, observe, touch, play with and enjoy.
When most people think of scientists they think of us as stodgy white men in lab coats carrying on about some obscure principle. After two years of watching and participating in the middle school science academy, I have come to view scientists like myself as children still caught in that magical time where we feel free to push the limits of everything.
This week the weather in the Midwest is warming up. The snow will melt. The sun will shine. It's a perfect time to shake off the doldrums of winter and step outside, find a quiet spot and reconnect with the kid inside all of us who is free to dream, imagine, and most importantly, question everything around us.
The first step in being a scientist is to let your mind explore all the things you normally pass without truly observing or interacting with them and be open to all the questions that those observations bring, even if you don't know or can't find the answers to them. Some of those questions will capture your imagination and you'll keep thinking about them. That is what thinking like a scientist is like.

Why twitter is an awesome tool for scientists

I am so thoroughly excited by social media. It has literally opened up a whole new world of science for me. I learn so much by perusing people's blogs, their tweets, and retweets by scientists they know. It's kind of amazing.
I was trying to explain this to my Dad, a non-scientist, last night on the phone. Twitter is the new town square in some regards. Now my Dad is getting a twitter account, so he can follow all of my new science friends.
In addition to that, I have made new friends and acquaintances on Twitter. These people are catalysts for all kinds of good ideas, because they answer questions I ask or throw ideas out there that I can run with. One important twitter relationship I have developed is with @Colo_kea. She helped me prepare my blog design and first post, which was a massive help. Another is @ugrandite who has been a huge help with all sorts of random questions and problems I have. She's my cheering section. I think I may talk to these two more than I see my advisor (He has a lab group of 14 people, so I am not criticizing him).
I've gotten lots of good advice about my career from these ladies and @ArmedwScience who gave me the low down on American Association for the Advancement of Science (AAAS) fellowships. He also gave me the idea, albeit indirectly, to contact AAAS and see if they could have one of their fellows chat with the members of our NSF GK-12 fellowship when we are in DC for a conference next month. I can't believe that AAAS took me seriously when I tweeted them and asked them about the possibility. I am really excited that they seem interested in spending some time with our graduate students. This is especially important because I am considering applying for an AAAS fellowship when I graduate. Honestly, if it weren't for Twitter's ability to reduce the activation energy required to make contact with people, I am not sure I would have had the ability to put this together in a matter of days. It's really exciting.
I know there are a lot of scientists out there who see social media as a waste of time. I guess, I hope that in writing this, I might convince one scientist out there to take a chance on social media. There is real value in social media tools when you use them correctly, both for scientists and non-scientists alike. Soon @ugrandite, @armedwscience, and @colo_kea will be followed by my Dad, a non-scientist who is interested in all the cool stories I tell him about my science and the scientists I meet in this global marketplace. Then these wonderful people will be able to reach out and inspire him, the way they inspire me and that is the real power of social media. We can reach out and interact with all sorts of people we might never otherwise intersect and thus create ideas that otherwise might go unarticulated.

Did silica prevent the phosphate crisis in the Archaean ocean?

**Please note: I wrote this for a class 2 yrs ago, and I know it needs updated with more recent references. It will be, but I wanted to get something other than a placeholder up for you in the meantime.**

Controversy is a defining characteristic of Precambrian geologic studies, in part as a result of the lack of preservation of many rocks and environmental indicators as a result of rapid tectonic cycling during this earliest period of Earth’s history. This controversy extends to debates over the nature of formation of banded iron formations (BIFs), which were deposited during two main time periods ca. 3.8–2.2 Ga and ca. 1.8 Ga and have no modern analogs. At the heart of this debate is the question of what, if any, role biota played in the formation of BIFs. Bejerrum and Canfield (2002) have argued, based on modeling of phosphate concentrations preserved in banded BIFs, that the deposition of iron oxides preserved in BIFs would have created a phosphate crisis in the Archaean and early Proterozoic oceans. Because phosphate strongly adsorbs onto iron oxides, the high iron content of the oceans would have actively scavenged phosphate from the water column. This would lead to an overall reduction in biota because phosphate is a limiting nutrient; this suggests that perhaps abiological models for the formation of BIFs have more standing. However, Konhauser et al. (2007) present contrasting evidence that silica out-competes phosphate adsorption, forming stable complexes that inhibit anion adsorption under conditions similar to the Archaean ocean. They argue that rather than a phosphate crisis, phosphate availability was similar to today’s oceanic concentrations, giving the argument for biologically mediated BIF deposition standing. 

Inherent within these hypotheses regarding the debate over the microbial role in BIF deposition is the subsidiary debate over the timing of the rise of atmospheric oxygen. Brocks et al.’s (1999) publication of biomarker evidence for the presence of cyanobacteria  ca. 2.7 Ga has given strength to the argument that free oxygen must have been present in limited quantities at or near the sea surface during BIF deposition. This has been used to suggest that photo-oxidation of iron in conjunction with the production of free oxygen by cyanobacteria could create a large enough pool of oxidized iron to form BIFs. However, Rasmussen et al. (2008) called this into question based on analysis of the Pilbara Craton kerogen from which the Brocks’ biomarker was extracted. At present, the rise of cyanobacteria and the oxygenation of the oceans appears to have occurred later. In fact, while cyanobacteria were likely operant before the rise of atmospheric oxygen  ca. 2.45 Ga, a stratified, largely anoxic ocean is recorded by biomarkers (Brocks et al., 2005), as well as molybdenum (Anbar et al., 2004) and sulfur (Farquhar and Wing, 2003) isotopic evidence at 1.64 Ga, after the majority of BIF deposition had ceased. These data have been used to infer that anoxygenic photoferrotrophs may have been responsible for oxidized iron present in BIFs, which was supported by Kappler et al.’s (2005) experimental model that showed that purple sulfur bacteria oxidize iron under anoxic conditions similar to those present in the Archaean ocean. More recently, field data from Lake Matano, Indonesia, suggests that green sulfur bacteria may oxidize iron photoferrotrophically under anoxic conditions (Crowe et al., 2008). This provides additional evidence that suggests a causal link between microbial metabolisms and the presence of large quantities of oxidized iron found in Precambrian BIFs.

Johnson et al. (2008) attempted to distinguish between microbial oxidation in the near surface environment and microbial reduction of FeOH₃ at depth, which was proposed to have occurred based on carbon isotope data (Walker, 1984) and is believed to be a necessary step in the formation of BIFs based on the oxidation state of iron in the deposits (e.g. ^Fe2.4+). However, because the fractionation of iron is so small, these different processes appear to have ranges of fractionation values that overlap (Johnson et al., 2008; Severmann et al., 2008), making their use problematic in modern as well as ancient environments.

The biological origin question was further addressed by Posth et al. (2008) who sought to go beyond simply discussing the nature of iron oxidation in the Archaean, but to also couple microbial activity to the alternating iron-silica banding that is a defining characteristic of many BIFs. Their experiment suggests that temperature fluctuations in an iron and silica rich ocean could cause the banding observed. At low temperatures microbial oxidation of iron is inhibited, but it resumes when temperatures increase. While this study may be useful for the rare BIFs associated with Proterozoic glaciations, the relevance of this study to Archaean BIFs is limited because it is unlikely that the Archaean ocean reached such low temperatures. Nevertheless, the cyclic deposition of silica and iron raises questions about the source, roles, and relationships of silica and phosphate in the depositional system, a question not addressed by Posth et al. (2008). Thus, the origin and mechanism of formation of BIFs remains unknown.

BIFs have been divided into two types of deposits (Algoma and Superior). These groups are determined by what the geological relationships infer about the putative origin of iron . However, positive εNd and negative Eu anomalies reported by Jacobsen and Pimentel-Klose (1988), as along with oxygen isotope data, have been used to suggest that the source of iron for all BIFs is related to mid-ocean ridges (Hayashi et al., 2007). This is of interest and importance because much of the silica (and shale in the case of the Hamersley Basin, Western Australia) has a suggested continental source, although the continental signature decreases upsection (Hayashi et al., 2007). Since the majority of phosphate input in to the oceans is controlled by continental weathering (Schlesinger, 1997), and the source of silica has also been suggested to originated from a continental source, it is likely that their input to the system would be coeval. These different sources for the compositional bands in one way complicate the story of the depositional environment of BIFs, but on the other hand provide a potential rationale for why phosphates, while found in BIFs (Bejerrum and Canfield, 2002), may have been effectively out-competed by silica on a large scale, especially if silica and phosphate inputs into the system were not entirely coeval with iron inputs. Moreover, these different component sources suggest that a nascent oceanic rift may be a probable primary tectonic setting of formation for BIFs, because iron mobilized from hydrothermal alteration is not present in the water column in large concentrations at great distances from the ridge axis.

While ridge axes in the Precambrian may have been broader structures and may have been associated with greater hydrothermal fluxes to higher heat flows than those of modern fast-spreading ridges, like the East Pacific Rise, it is difficult to imagine high iron concentrations persisting many kilometers away from the ridge axes. Moreover, the association of Algoma BIFs with greenstone belts suggests that preservation of at least some BIFs is directly associated with ophiolite emplacement mechanisms, because most ophiolites are now considered to have formed in marginal basins in the upper plate of subduction zones (Phillips-Lander and Dilek (2008)Robinson et al., 2008). These settings would provide broad continental slopes due to crustal loading as a result of the intrusion of mafic dikes during rifting, which would in turn provide ample area for anoxygenic phototrophs to thrive within the photic zone.

Nascent rift settings would put microorganisms in direct association with a light energy source, phosphate nutrient sources, as well as iron and silica sources—all the components believed to be necessary for BIF deposition during the anoxic environment during the Archaean and early Proterozoic. This creates a plausible circumstantial case for the mode, nature, and setting of BIF deposition; however, significant additional research needs to be done in order to prove that the iron-rich oceans present during BIF deposition did not create a phosphate crisis and that BIF deposition was inherently biologically mediated.

Future research should include (1) investigations into the rate at which anoxygenic photoferrotrophic microbial metabolisms mobilize and oxidize iron in analogous field settings; and (2) the relationship of this metabolism to nutrient availability—including phosphate—a point well articulated by Crowe et al.(2008). This should provide a means for better estimating the minimum amount of phosphate required for microbially mediated BIF deposition, which can be correlated with existing data regarding phosphate concentrations preserved in BIFs. Phosphate concentrations preserved in BIFs likely record minimum phosphate concentration for the Precambrian oceans; these data may shed additional light on whether or what extent there was a phosphate crisis in the Archaean ocean.

References
Arnold, G. L., A. D. Anbar, J. Barling and T. W. Lyons, 2004, Molybdenum isotope evidence for widespread anoxia in the Mid-Proterozoic oceans. Science, 304, 87-90.

Brocks, J. J., G. A. Logan, R. Buick, and R. E. Summons, 1993, Archaean molecular fossils and the rise of eukaryotes. Science, 285, 5430, 1033-1036.

Brocks, J. J., G. D. Love, R. E. Summons, A. H. Knoll, G. A. Logan, and S. A. Bowden, 2005, Biomarker evidence for green and purple sulphur bacteria in a stratified Palaeproterozoic sea, Nature, 437, 866-870.

Crowe, S. A., C. Jones, S. Katsev, C. Magden, A. O’Neill, A. Sturm, D. E. Canfield, G. D. Haffner, A. Mucci, B. Sundby, and D. A. Fowle, 2008, Photoferrotrophs thrive in an Archaean ocean analogue. Proceedings of the National Academy of Sciences, 105, 41, 15938-15943.

Hyashi, K., H. Naraoka, and H. Ohmoto, 2007, Oxygen isotope study of Paleoproterozoic banded iron formation, Hammersley Basin, Western Australia. Resource Geology, 58, 1, 43-51.

Johnson, C. M., B. L. Beard, C. Klien, N. J. Beukes, and E. E. Roden, 2008, Iron isotopes constrain biological and abiological processes in banded iron formation genesis. Geochimica et. Cosmochimica Acta, 72, 151-169.

Kappler, A., C. Pasquero, K. Konhauser, and D. Newman, 2005, Deposition of banded iron formations by anoxygenic phototrophic Fe(II)-oxidizing bacteria. Geology, 33, 11, 865-868.

Phillips-Lander, C. M. and Y. Dilek, 2008, Structural architecture of the sheeted dike complex and extensional tectonics of the Jurassic Mirdita ophiolite, Lithos, Special Issue: Balkan Ophiolites, in press.

Posth, N. R., F. Helger, K. Konhauser, and A. Kappler, 2008, Alternating Si and Fe deposition caused by temperature fluctuations in the Archaean oceans. Nature Geoscience, 1, 703-708.

Rasmussen, B., I. R. Fletcher, J. J. Brocks, and M. R. Kilburn, 2008, Reassessing the first appearance of eukaryotes and cyanobacteria. Nature, 455, 1101-1104.

Robinson, P. T., J. Malpas, Y. Dilek, and M. Zhou, 2008, The significance of sheeted dike complexes in ophiolites. GSA Today, 18, 11, 4-10.

Scott, C., T. W. Lyons, A. Bekker, Y. Shen, S. W. Poulton, X. Chu, and A. D. Anbar, 2008, Tracing the stepwise oxygenation of the Proterozoic ocean. Nature, 452, 456-460.

Severmann, S., T. W. Lyons, A. Anbar, J. McManus, and G. Gordon, 2008, Modern iron isotope perspective on the benthic iron shuttle and the redox evolution of ancient oceans. Geology, 36, 6, 487-490.

Walker, J. C. G., 1984, Suboxic diagenesis of banded iron formations. Nature, 309, 340-342.

Acknowledgments

Thanks to @Colo_Kea for editing help.