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.