Reflections

Hello everyone! I apologize for my long absence on the blog. I hadn't intended to let the blog go for so long. But it is time to get back on the horse, as the saying goes. I have been doing a lot of that lately.

At the beginning of September I took a much-needed vacation to northern Michigan, visiting Sleeping Bear Dunes National Lakeshore. Oh yes, and Short's Brewing Company as well! It really was a long and busy summer, and I felt much more ready to come back to work after some hiking, swimming, sleeping, and good company! We are actually very spoiled here in Michigan--it is a beautiful state.

In mid-September I passed the one year mark as a postdoc in the GEM lab. To mark the occasion, I felt that I needed to reflect a bit on the last year and take stock of what I have learned. This was actually a little more difficult than I anticipated. I think it is hard to analyze a situation when you are still in the middle of it. Nevertheless, here is what I came up with.

The most obvious change is that I feel fairly comfortable in my job now. I know the lab, I know the people, and I have a decent handle on my project. In fact, I am wrapping up a project right now with the aim of submitting a paper early next year. I have often heard that it takes 6-12 months to settle in to a new job, and I certainly feel that this was true for me. The tragedy is that my postdoc appointment is only two years in total, so I have spent half of that time settling in! I know that I am the type of person who likes being comfortable in her job. Some people love starting new jobs, but I see myself staying in a job for a long time. So far life has not allowed me to do that, and I know that I am adaptable enough to move around when necessary, but I do hope that my next job will be more permanent.

I also feel that I have gained a greater sense of independence in the last year. I know how to take on a new project and how to tackle it. It still amazes me how big things are built from small pieces. Writing my dissertation drove this home for me more than anything else. I watched then as the sentences became paragraphs, which became chapters, which somehow became a 200-page document describing my accomplishments of the last five years. Every small piece had enormous value. I think the same is true for any project. I am no longer afraid that the small pieces (i.e., the things I do day to day) will not be enough. For example, at this very moment I am running standards on the ion chromatograph to define elution times for various known compounds and to create calibration curves using a series of samples having different concentrations. None of this is ground breaking or difficult. But it does give me confidence in running the instrument and lays the foundation for the things I will try next that have not been done before. (Although right now this one sample is taking forever to come through the column--I hope everything works out!!)

I have also started to think of myself more as a colleague than as a student. I recognize that science is a process of lifelong learning, but I do have a certain amount of knowledge and experience. I noticed at the Goldschmidt conference that I approached more people, and with the intention of exchanging knowledge and possibly collaborating. Someone close to me once told me that some promotions are intended to be grown into. Perhaps the PhD is the same way.

The million dollar question on everyone's mind is, "What next?" I don't know yet. I do want to stay in science, but in what capacity I don't know. My career will probably also be driven by the job market. So stay tuned: In less than one year, I expect to be starting a brand new adventure. Happy weekend!

Money Makes the World Go 'Round

The other day I was talking to a friend of mine who is an attorney. (Read: not a scientist.) One of her many great qualities is that she asks very good questions, and lots of them. During this particular conversation, we got to discussing how science is funded. This is something that apparently most non-scientist Americans have little concept of, despite the fact that the federal government—meaning taxpayers—funds a good deal of the basic and applied research that happens in this country. I believe this lack of knowledge about how research dollars are spent is demonstrated especially clearly by the (false) charge from so-called climate skeptics that climate researchers are just lining their pockets. So today I thought I’d offer a short primer on science funding in the United States, with some stylistic touches borrowed from xkcd.com.

There are a number of agencies and departments within the federal government that fund science. For example, the Department of Defense and the Department of Energy spend billions of dollars on research every year. However, a good deal of the research performed in academic laboratories is funded by two agencies: the National Science Foundation (NSF) and the National Institutes of Health (NIH). Currently, NSF has a budget of about $7 billion per year, and NIH has a budget of about $30 billion per year—not exactly small potatoes. As a geologist, I don’t work on problems at all related to health or medicine, so my experience with funding is through NSF, and the rest of this post will refer to the NSF process of applying for and receiving grants.

In order to receive any kind of grant money, the principal investigator (PI, often known as a professor) first needs to write a grant proposal. Within the grant proposal, the PI details his/her research ideas, why they are important, what he/she will accomplish, and provides a budget necessary for completing the work. Other scientists in the field then review the proposal, and their input helps to determine whether the proposal is funded. Applying for grant money is highly competitive, and the majority of grant proposals are rejected for funding. Let’s assume that our PI has written an absolutely stellar proposal and has gotten funding. Typically for my field, I have seen budgets in the hundreds of thousands of dollars range for a three-year project. Perhaps our plucky PI receives $500,000 to be spent over a three-year period.

First, the university takes a cut of the grant money to fund overhead costs such as keeping the lights on in the buildings. Typically, this is close to 50%. Our PI’s university takes 43% of the grant money, leaving him/her with $285,000 for three years, or $95,000 per year to spend. 

Salaries for graduate students, postdocs, undergraduates, and laboratory managers or technicians must be paid, and perhaps even part of the PI’s salary as well. 

The grant money may also pay for consumable supplies such as chemical reagents, centrifuge tubes, and pipettes; field work; travel to conferences; and publication costs. Last but not least, the cost of laboratory analyses must be paid, which can run into the thousands of dollars. Every instrument costs money to run and maintain, and some, like the ICP-MS, consume expensive supplies like argon gas. At the end of the day, our PI has no money left for his/her trip to Bermuda. TANSTAAFL—There Ain’t No Such Thing As A Free Lunch. Besides, the PI must regularly report on his or her progress to NSF, and there are rules governing how grant money may be spent. Many academic departments at research-intensive universities have a grants manager whose sole job is to administer faculty grants. 

Although as a geologist, it is always a bonus when your research simply must take you to beautiful far-off lands!

That so many professors manage to fund and run their own research labs is remarkable. Most professors spend inordinate amounts of time writing grant proposals, many of which will not even be funded. So for anyone thinking of using science as a get-rich-quick-scheme, they will be sorely disappointed. Play the lottery instead.

"Algae" video

Just a quick midweek post. Here is a very cute video produced by Michigan Radio:

http://www.youtube.com/watch?feature=player_embedded&v=PubDuWiUh84

See you tomorrow!

Fun with rocks, more fun with mud

Happy Friday to all again! I don’t know where the weeks go—they just fly by. I am still feeling pretty worn out from all the travelling we’ve been doing this summer, but I am feeling better than last week. Thankfully, I am taking a much-needed vacation at the beginning of September.

In my last post, I described our chief scientist training cruise on Lake Superior. Anthony and I collected a number of sediment cores, and one feature of the last set of cores we collected near Isle Royale intrigued me: sand-sized black spots. Now, I think up to this point I have neglected to mention why we are even interested in mud from the bottom of lakes. Sediments (mud) record the chemical, physical, and biological history of oceans and lakes. As geochemists, Anthony and I are most interested in discovering the current and past chemistry of natural waters. However, natural systems are unlike nice, neat laboratory experiments in that they are complex, and none of these processes (chemical, physical, and biological) is unaffected by the others. My approach to my science is to consider these systems as a whole as much as possible. Within sediments, there are mainly lithogenic, biogenic, and authigenic components. Lithogenic material is derived from rocks; biogenic material comes from living things; and authigenic material precipitates from the water. My suspicion was that the black spots were lithogenic material weathered from the surrounding land, but I didn’t know much about the local rocks. I was aware that the Upper Peninsula of Michigan and northern Minnesota are somewhat geologically special in the United States in that there are some very old rocks exposed there. Here is what I found out.

I will start with a disclaimer that traditional geology is not my forte, but I have been trying to learn as much as I can since I started graduate school. So be kind to me, and I will do my best to summarize the information. I looked into both the geology of the Upper Peninsula and northern Minnesota, ignoring the most recent rocks. About 1.1 billion years ago, the Midcontinent Rift formed. This rift is similar to what is currently happening in the Afar region of Africa, where a new ocean is forming from the Red Sea through East Africa. As the continental crust opened, basalt lava flows filled the Midcontinent Rift. However, rifting ceased after a few million years, and a new ocean failed to form. The rift was filled with sediments and compressed as the supercontinent Rodinia formed. Younger sediments later covered these rocks but they were exposed as the Pleistocene glaciers scoured the landscape. Along the western shore of Lake Superior, some of these rocks are known as the Duluth Complex. During the period of compression, hydrothermal fluids moved through the faults created during rifting, depositing native copper and other metal ores. Iron and copper mining have been sources of major economic activity in the Upper Peninsula. I found a much more detailed geologic history of the region in this fantastic field trip guide for those who are interested.

The result of all this is that I think my suspicions that the black grains in my core are igneous rock weathered from the area are correct. The other hypothesis about the grains was that they were bugs, but I don’t think so. Now that I know something about the local geology, I know what kind of contribution the local rocks can be making to the trace metal concentrations that I will measure. Hurrah for geology! See you next week.

End of summer

Hello everyone, I am working on a new blog post but have been fighting being exhausted after this busy summer. We'll talk soon.

Meghan

A Superior Cruise

We are back! For the last week and a half Anthony and I have been participating in a UNOLS Chief Scientist Training Cruise on Lake Superior. On a research cruise, one person is designated as the chief scientist. This person has responsibility for balancing the research needs of various groups against the time available at sea. Sometimes this is called herding cats. The chief scientist also interfaces between the science party and the ship's crew. Our training cruise took place aboard the R/V Blue Heron, which is owned by the Large Lakes Observatory (LLO) at the University of Minnesota-Duluth. The Blue Heron is the smallest research vessel that I have been aboard, at 86 feet long. Nonetheless, the ship got the job done and the crew lived up to its reputation for being incredibly helpful and accommodating in getting the scientists' work done.

The Blue Heron in port.

The scientific party included Doug Ricketts, the marine superintendent at the LLO; a geomicrobiologist from Michigan State University; a geophysicist from the University of Wisconsin-Milwaukee; a biological limnologist from Michigan Technological University; and Anthony and me. (Note: limnology is the study of inland waters, including lakes.) I truly enjoyed meeting all these new people and getting a peek at their research. Without a doubt, this was a great group of people.

We set sail last Friday, passing under Duluth's lift bridge as we exited the harbor.

So long, Duluth!

The lift bridge

Under the bridge

We spent the next five days collecting water and sediment samples, and conducting experiments aboard ship.The story is probably easier told through pictures. We had fantastic weather throughout the cruise. The lake was almost perfectly calm the entire time. This is very helpful for getting good samples.

Some pictures of the ship:

The "clean room tent" we made in the dry lab.

Inside the tent--ready to process samples

The wet lab

Dining area

Galley

Science in action:

Collecting water samples from the rosette

Foad being all science-y

Jason, the marine tech, next to the CTD. CTD stands for conductivity, temperature, and depth. There are electronics underneath the bottles that measure these characteristics as the CTD is lowered to the bottom of the lake or ocean. There are also other sensors that measure things like oxygen, pH, and fluorescence.

CTD going down

Jason hard at work (or hardly working?)

Hauling the CTD on board after it has returned to the surface

Having fun while at sea is an absolute requirement! We took some time to enjoy the sights on this beautiful lake, and we sent some poor styrofoam cups down to the bottom of the lake. Pressure increases in any body of water as you go deeper, so the cups returned to the surface a bit shorter than they started.

Bald eagle!

Cups tied to the CTD inside a pillowcase, ready for their journey to the bottom.

Two squashed cups on the left, and a new cup on the right for comparison.

Getting silly with the cameras

We returned to port on Wednesday and made the long drive home on Thursday. Now the real work begins as we analyze our samples, and share our data and learning with one another in the months to come.

After our cruise I also have a new found appreciation for Lake Superior and a few outstanding questions about it. I will try to look into this in the coming week and post about some of the local geology next time. There are some very old rocks in the area so it should be quite fascinating.

Superior Research

Hello everyone! This week I am writing from Lake Superior on board the R/V Blue Heron, which belongs to the University of Minnesota-Duluth. We are on a research cruise as part of a UNOLS chief scientist training course. The internet is very slow on board the ship so I will explain all of this next week and post some pictures.

Yesterday we arrived at our first sampling location near Duluth. We collected water column, sediment, and pore water samples. The sediments appear to show evidence of some well-documented dumping of waste from an iron ore processing facility close by. The dumping ended perhaps 30 years ago but there is a very prominent iron oxide layer near the top of the sediments. Today we are doing a multibeam bathymetric survey near Isle Royale for the geophysicist on board. This is my first time ever participating in this kind of data collection so I am learning a lot.

The lake is amazingly flat and calm this time of year. It is really helping us to get good data and good samples. And the crew on board is also fantastic. Really couldn't ask for more.

Have a great week!

Hodor!

Happy Friday, everybody! It has been a tiring week although I don't know that anything out of the ordinary happened. Next week Anthony and I will be heading to Duluth to the Large Lakes Observatory to participate in a chief scientist training cruise (more on this next Friday). This last week I spent some time putting together all of our field work supplies. I think we are almost ready to go. But I certainly have to give some credit to our lab manager, Aurelie Dhenain, and our undergraduate students for their help in preparing. It is wonderful to have other people around to double check you, and to do all the little tasks. Thank you! On another note, yesterday two of our undergrads braved the Chippewa River and collected some more DOM samples. I think they had fun!

But the main subject of today's post is Hodor. Yes, I have now revealed myself as a big nerd--if you didn't know that already. Just for my own amusement, I named our glove box Hodor.

Trying to get a full view of the glove box. The room is very narrow so it's not easy to take photos. The gloves provide a way for the scientist to manipulate items inside the glove box (hence the name). This also means that the only dancing that can be done while working in the glove box is the Macarena. But the 90-degree turn is impossible.

You know what's coming: Hodor!

I spend a fair amount of time doing experiments in the glove box. A glove box is an enclosed chamber that maintains an atmosphere different from the ambient, or normal, atmosphere. Typically, researchers want to exclude oxygen and/or water, and in our case we have an anaerobic (oxygen-free) atmosphere. The atmosphere inside the glove box is a mixture of hydrogen and nitrogen. The gas analyzer is our main source of information about the maintenance of the glove box atmosphere.

The gas analyzer

Samples and equipment are moved in and out of the glove box through the airlock. The airlock goes through three cycles of vacuum followed by refilling with nitrogen before any materials are introduced into the glove box. This ensures that most of the oxygen from the atmosphere outside the glove box is removed before we open the door to the glove box chamber.

The airlock

Gas supply connected to the airlock

However, a small amount of oxygen will always enter the chamber, and it is the job of the catalyst inside the glove box to remove this oxygen. Inside the glove box are two more boxes containing a palladium catalyst. In the presence of hydrogen, the palladium reduces the oxygen to water, which is then retained on the catalyst, keeping an oxygen-free environment.

The glove box is useful for conducting experiments that simulate conditions on early Earth--when there was no oxygen in the atmosphere--and conditions in deeply buried, reducing sediments from lakes and the ocean.

See you next week in Minnesota!

Try, try again

For today's post I just have a few thoughts on failure. As a scientist, my life is full of it. I constantly have to dust off and try again. It's how science is done and how we are all successful. If you can't learn from failure and bounce back from it, then science is not for you. I say this having been brought pretty emotionally low by failure at times. Here are three failure stories for you:

Story #1
I haven't introduced the glove box yet, but perhaps I will do that on Friday. For the moment, I will ask you to imagine a large, enclosed chamber that is free of oxygen so that we can do experiments with air-sensitive materials. We use sulfide in the glove box, which will destroy the electronics inside unless we scrub the sulfide from the glove box atmosphere. To do this, we constantly bubble the glove box atmosphere through a solution containing dissolved silver. The sulfide reacts with the silver, forming black, highly insoluble silver sulfide. Recently we got a new source of silver, silver nitrate. Having worked with silver during my PhD, I know what a pain in the neck this element can be because it is photosensitive. This means that upon exposure to light, dissolved silver is reduced to silver metal and precipitates from solution. Not so good for scrubbing sulfide from the glove box. One way to keep the silver in solution is to add hydrochloric acid. However, I wasn't sure that I wanted hydrochloric acid floating around the glove box destroying the electronics either, so I left it out. I made the silver nitrate solution in water, covered the glass bottle with foil to keep out as much light as possible, stuck the bottle in the glove box, and hoped for the best. Here is the result:

Yeah, that didn't work. So my job tomorrow is to find another way to make the silver nitrate solution. This is just a small example, but it illustrates nicely that many times, there is no recipe for me to follow. There is no formula or predetermined answer to a problem. So we (scientists) try things, make it up as we go along, and when something doesn't work, we back up and try again. On a creepier note, I discovered as a graduate student working with silver that colloidal silver is touted on the internet as a magic cure-all. People actually drink it, which leads to argyria. The pictures are pretty weird. And by the way, the condition is not reversible. Don't drink colloidal silver.

Story #2
I have submitted three papers as first author. They've all been rejected at some point. My first paper took two years to get published. I am still working on revising the other two so that I can resubmit them. Now, getting rejected is par for the course--it happens to everyone. But I am getting tired of having my papers rejected. However, there is nothing else that I can do except revise and try again. Eventually they will get published.

Story #3
I confess that I dropped out of graduate school the first time. I thought I wanted to be a chemist. But after two years, things weren't going well and I didn't like the work I was doing. Dejected, I took a leave of absence for a year to consider my options. After much thought, I decided that I did want to finish graduate school, and that I had truly enjoyed the geology class that I had taken a year earlier. Why not switch departments? So I threw myself 100% into getting into the geology PhD program and somehow it all worked out. It was the best career decision I ever made and I have never looked back. I love my work as a geochemist now. But deciding to quit graduate school the first time was agonizing and left me with a lot of uncertainty in my life. It also amounted to losing a job and I have spent years grappling with the financial consequences. Moreover, it stretched out my time in graduate school from 5 to 8 years.

I wouldn't recommend this path through graduate school to anyone. For me it couldn't have happened any other way, and if it's the right decision then you have to go for it. My dual life as a geologist and a chemist has been an academic strength. Life seems not to move in straight lines and you have to keep getting up and trying again.

ICP-MS Training

Happy Friday again! This week ended up being a little bit intense because I attended three days' worth of training for ICP-MS and IC. I know--more acronyms. ICP-MS stands for inductively coupled plasma-mass spectrometry, and IC stands for ion chromatography. We are going to use both of these techniques in our lab and have new instruments to love. In order to keep this post from getting too complicated, today I'll focus mostly on the ICP-MS.

A good part of our training actually took place in front of the instruments, which are in the clean room. A clean room is exactly what it sounds like: a place that is very clean! Clean rooms can be designed for a variety of purposes. Our clean room has very low concentrations of particles and essentially no metal. Even the paint on the walls is not normal paint; it is specifically designed for use in a clean room. These conditions allow us to measure trace metals and other elements at very low levels, in some cases in the sub-part per billion (ppb) range. Without the clean room, the background concentrations would completely overwhelm the concentrations in our samples, and we would not be able to get any useful data. To enter the clean room, I have to get dressed up in my very clean, fancy duds.

I think the hair net is sexy.

Our ICP-MS instrument. It is an iCAP Q quadrupole mass spectrometer.

The autosampler. This allows the user to set up a run which the computer then executes automatically. It means that I could let a very long run go overnight and collect the data in the morning. Sleep! Zzzzz...

The sample inlet system. This is how the sample gets from the racks in the autosampler into the instrument. In the back is the peristaltic pump. On the lower right is the system that injects the sample, and on the lower left is the nebulizer (glass piece).

We will use our mass spectrometer to measure the concentrations of trace metals and other elements in natural water samples from lakes, rivers, etc.; sediment porewaters; and sediments.

A mass spectrometer separates and detects components of a sample having different masses.Technically, what the instrument measures is the mass-to-charge ratio (m/z), but mostly what reaches the detector has a +1 charge, so we are in effect looking at the mass. What this implies is that the sample must be ionized. There are several different ways of ionizing a sample, but ICP-MS uses an argon plasma to accomplish this. Fun fact: The argon plasma has a temperature approximately equal to that at the surface of the sun. The U.S. Geological Survey has a nice explanation of some of the more technical aspects of how an ICP-MS works here.

One of the important points about ICP-MS (or any other analytical technique, for that matter) is that the sample preparation and experiment design must be thoughtfully considered before putting a sample on the instrument. I think most scientists crack up and shake their heads at all the detective/cop shows on tv where the investigators grab the nearest instrument with an impressive-sounding name, put their sample in it, and two minutes later, the identity of the sample is printed out for them! Voila!

I can't believe it! I think it's dihydrogen monoxide!

In the real world, it doesn't work like that. First of all, the identity of the sample is almost never just given to the scientist. For example, with the mass spectrometer, all the user gets is the mass and the intensity of the signal at that mass. That's it. After that, it's up to the user to do something with it. However, most of the time the scientist already has some information about the sample--where it came from, what compounds or elements might be in it, etc. But to get good quality data from our mass spectrometer, I will have to dilute my samples to an appropriate concentration range, set up the method, prepare the correct calibration standards, optimize the instrument parameters, and a few other things. At the end of the day, it's fun. I enjoy listening to the hum of the instrument. Getting and analyzing data is like watching a story unfold.

Phytoplankton Friday: Part 2

Happy Independence Day to my fellow Americans! Today I am off for the holiday but I am sitting in my nice, quiet office to write this blog post. Holidays are often wonderful times to get work done because the office and lab are quiet. But it is also important to enjoy life, and so later this afternoon I am heading out of town to do just that!

This week I mostly spent my time getting caught up in the lab--remembering where I'm at with experiments, doing general maintenance, and catching up with email and paperwork. As with any job, as a scientist I end up doing some work that is not strictly research but has to be done anyway (administrative paperwork, etc.). Next week I will be ready to get back to doing experiments, although we have some training for the ICP-MS that I have to attend, and I'll report next week on that.

As promised, today is Phytoplankton Friday Part 2. In my very first blog post, I alluded to the fact that organisms require trace metals as micronutrients, including phytoplankton and people. Trace metals are needed as cofactors in metalloenzymes. Let's break that down: Enzymes are proteins that catalyze, or greatly speed up, biochemical reactions. Metalloenzymes, as the name implies, have a metal (the cofactor--sort of a helper) at the active site. One example of a metalloenzyme that most people are familiar with is hemoglobin. Hemoglobin is used to transport oxygen in the blood and contains iron (Fe) at the center of a porphyrin (the ring containing the nitrogen (N) atoms). Phytoplankton also require Fe, although obviously for some different enzymes, such as those associated with performing photosynthesis. In addition to Fe, phytoplankton require zinc (Zn), copper (Cu), cobalt (Co), manganese (Mn), and molybdenum (Mo), plus a few other metals. Often, the job of a metal in an enzyme is to move electrons.

Phytoplankton must acquire trace metals from their surrounding environment. In some oceanic regions, such as the Southern Ocean, Fe limits phytoplankton primary production. Because trace metals are precious resources, some phytoplankton have the ability to store Fe and other nutrients for later use (luxury storage), and phytoplankton can also change their metal uptake rates depending on ambient metal concentrations. Interestingly, coastal diatoms--where nutrients are abundant--have higher micronutrient requirements than diatoms that live in the open ocean--where nutrients are much scarcer. Phytoplankton are truly well adapted to their environments.

On a side note, some bacteria play a very important role by transforming atmospheric nitrogen (N₂) into biologically useful forms of nitrogen, starting with ammonium (NH₄⁺). This is a rather difficult reaction, and it is catalyzed by an enzyme called nitrogenase. Notice that this enzyme requires molybdenum. So here is yet another reason to study molybdenum and how it is related to the evolution of life on earth.