Saturday, February 22, 2020

Iso-mistakes OR Learning from doing



Marilyn and hydrogen isostope glass vacuum line, circa 1980

Isotope camps are good for people who want to learn the very basics about isotope chemistry. But for those of us who build a career on this technique, training is a life-long process. In every major university in the United States, for example, there will probably be one, if not two, stable isotope ratio mass spectrometers at each one! Typically, it’s in a geoscientist’s laboratory, rather than in chemistry, anthropology, or biology, but that’s only a general observation. I estimate that in California alone, there are 70 of these instruments at universities. I am sure there are others in business and government laboratories. If there are 70 instruments in California’s academic labs, there are probably at least 25 professors whose research programs use stable isotope techniques at the heart of their work. How did these 25 academics get their training? They’ve mastered their work by learning from their professors, trial-and-error, reading and studying others.

The trial-and-error period never seems to end. Every week, I hear about something someone tried that resulted in some form of “failure” or “error” or just plain “disaster.” I’ll be the first to say that I’ve learned a significant amount through this method, as have others. We learn a lot from our mistakes. Following are some good examples of trial-and-error that I’ve personally experienced as well as some good stories from my colleagues.

Today, many of the stable isotope methods that we use are fully automated. Some students think that they’ve accomplished something major after weighing 40 some samples into little tin capsules. We older generation isotopists roll our eyes at this. Read on for some isotope entertainment.
Marilyn's son Evan preparing samples for isotope analysis; he was in high school, 2009

Even before samples are analyzed in mass spectrometers, they all need to be dried, then often chemically extracted to either remove potential contaminants or to concentrate a portion of the sample that is of interest. In my laboratory, we are interested in examining the protein fraction of organisms in order to understand metabolism or an animal’s diet. The first part of getting at the protein is to heat the sample in a special test tube with strong acid. Our analyses are very sensitive and we can pick up very small amounts of contamination—perhaps from a test tube. Accordingly, we take great pains to make sure all of the tubes, spatulas, and anything that touches the sample are extremely clean.
One colleague put in samples in reverse order; another forget a plastic cover was in place.

All of our glassware is “muffled” in a hot furnace at 500-550°C for 1-2 hours before we use it. For the United States folks, 500-550°C is about 1,000°F, well above anything a commercial kitchen oven can reach. Most of us realize that only glass and metal can survive such high temperatures. But, some of us, usually those in training, don’t really know what 500°C means.

The test tubes we use have caps—made of plastic with Teflon liners on the insides of the caps. Plastic and Teflon can’t survive at 500°C and melt around 250°C, then at higher temperatures start to combust!

One well-meaning postdoc was instructed on how to muffle his test tubes to analyze protein in fossil bones. I assumed he understood that he was to muffle the glass tubes, not the caps. The next day, he started the process. It wasn’t long before the lab was filled with an acrid smell. I rushed into the room with the furnace and was confronted with a wall of smoke.

            “Who has stuff in the muffle furnace?” I shouted into the lab.
            “I do,” the postdoc answered.
            “What’s in there?”
            “The hydrolysis tubes,” he answered.
            “Did you put the caps in there?” I shouted back.
            “Yes, but they have Teflon on them,” he said.

I grabbed a metal bucket filled it with water, ran into the furnace room, and switched off the furnace. The door was opened carefully, and using a heavy-duty oven mitt, grabbed the smoldering caps out and into the bucket.

            “Get this outside,” I shouted to the trembling postdoc. Fortunately, I have a sensitive nose and found the problem before a real disaster happened.

The same scenario happened three more times! The second time, a very senior colleague of mine made the same mistake—he did not figure that plastic and Teflon could not withstand high temperatures. We were prepared with the metal bucket nearby, the thick mitt, and a calmer response having gone through this once before. The third time it happened was probably due to a language issue. A Japanese postdoc did not fully understand all the potential sources of plastic. In that instance, the building was filled with acrid smoke and evacuated. Fortunately, my nose smelled this before the smoke set off the fire alarms.

That was not the case the fourth time. I had already moved from UC Merced down to UC Riverside, but my lab in Merced was still being used. My nose was useless 300 miles away. 

            A text message: There is a funny smell in the lab.
            Me: Sometimes truck exhaust comes through the ventilation system.
            Response: It’s getting stronger.
            Me: What room is it in? Main lab or chemistry lab?
            Response: Seems to be the chem lab.
            Me: Anything going on in the hood?

My phone now rings.
            “There’s smoke in the lab.”
            “Is there anything in the muffle furnace?” I asked.
            “I’ll call you later.”

The smoke alarms went off in the Science and Engineering 1 Building housing over 75 labs with professors, students, and staff. The building was evacuated. Firemen arrived to find the smoldering furnace with plastic caps inside.

Plastered on the front of the furnace was a big sign: NO PLASTICS!

One of the firemen smugly said, “Someone can’t read.”

The furnace was put on a cart and hauled out to the center of the campus Quad for all to see. Finally, my phone rang again.

            “I muffled the caps,” the guilty person admitted.
            “And what is that about?” I asked.
            “I guess I wasn’t thinking at the time.”

All four of these folks have gone on to become competent in their fields—some of them perhaps relying more on technical assistants. Lessons were learned.

Other problems happened when we used liquid mercury in our glass vacuum lines. A visiting graduate student at the Geophysical Laboratory insisted on working at night. We arrived one morning to find Steve Macko’s glass vacuum line in pieces and a sheepish student with an injured hand.

I learned—no working alone at night!

Another visiting postdoc, a cocky fellow, broke my hydrogen isotope line that included hot uranium along with hot mercury. It was a big mess that Tom Hoering and I had to clean up. He was not invited back.
One of Doug Rumble glass vacuum lines with mercury, 2001

One of my best postdocs (well, they’ve all been great) was experiencing some personal family issues. We shared an office in the old Geophysical Lab with a mass spectrometer that used a mercury-based glass vacuum line to admit nitrogen gas into the instrument. He was performing a very delicate part of the analysis with liquid mercury surging carefully up into a small fragile opening into the mass spectrometer. His phone rang and he sprang for it—momentarily forgetting the mercury.

I was in the adjacent lab at the time and heard the glass explode and the vacuum pump chug loudly. There was the postdoc with the phone still in his hand and his mouth open staring at the destruction. I moved swiftly to turn off the vacuum pump and the ion source on the mass spec. Both of us were shaking—no one was injured.

Eventually, Tom Hoering came down to view the damage. He shook his head. Later in the day he met with the postdoc.

            “I think you’re destined for administration,” he said, a verdict that was akin to research failure for us technically savvy folks.

It took several weeks to fix the instrument and was a mess to clean up all the mercury in our office. The postdoc, indeed, did go into administration later in his career and turned out to be a very successful science research administrator.

Another postdoc had a scare on that same mass spectrometer with its frightening mercury pistons. She had been working in Australia and had put some plants into plastic bags while they were still fresh. Long story short, the plants molded by the time they came to the lab. Were they any good for isotope analysis? A resourceful person, the postdoc decided to conduct an experiment with molded Ramen noodles that one of my other colleagues left in a bowl in my office sink. She knew the noodles would have very little nitrogen in them, so she weighed out more than twice the normal amount. When she put the noodle sample into the mercury-piston glass vacuum line, her heart leapt! The mercury piston shot down perilously bubbling out the bottom. Turns out she had produced a substantial amount of carbon monoxide from all those carbon-rich noodles. Fortunately, nothing was broken.
Postdoc Jeff Silfer, Marilyn, Postdoc Bev Johnson in front of isotope line, circa 1995

Other innocent mistakes happened that I would never have thought of. This story is a bit different.  Once, during travel, my colleague had a graduate student who was quite strong in the lab, meaning the student could be trusted not to harm the expensive equipment. He felt confident that this student could keep things running while he was attending a meeting.  At some point the mass spectrometer needed to be turned off, vacuum pumps off and vented to the atmosphere. Eventually the student was able to turn the instrument on again. Using the vacuum pump system, the student starting evacuating the instrument.

“The student realized that it was taking too long and panicked – torn between patience (during which maybe the leak would turn out to be water degassing, or perhaps the turbo would heat up and stop functioning) and immediately shutting everything down to wait for my return, the student decided to call me on my cell phone and ask for a video call.  I was pretty sure I knew what the problem was, I just needed to see the screen on the control computer. A quick video call would get the student going again.  Sure.  We connected.  We had 30 seconds of small talk, laughed at the faux pas, and the student apologized. 

I smiled, and said, 'OK let’s get to work.' 

The student started to walk over the mass spec. I recognized with satisfaction as he swung his laptop computer on the brief transit to the mass spec that the components in my lab were still roughly in place while I was gone.

There was a quick spin, a lift of his laptop, and my student said, 'OK, let me put this down and show you…' 

Before I could scream, 'NOOOOOOOO!!!!!!' the screen went blank--disconnected.

I knew my student didn’t intentionally hang up on me. I also knew it was not worth calling back. The mass spec would have to await my return. My very bright and capable graduate student had put the laptop computer on top of the mass spectrometer’s magnet.”[thereby destroying its hard drive.]

Two other senior isotopists shared an experience I had with a postdoc—mixing up the gases we use for transferring our samples into the mass spectrometers. Helium—the gas that fills birthday party balloons—is used in many of our instruments as a “carrier gas”—a gas that propels the gases that we analyze, carbon dioxide, nitrogen gas, and hydrogen gas, into the mass spectrometers. Helium, an ultralite gas, flows through our mass spectrometers swiftly. One of my lab folks put a tank of argon on our mass spectrometer because the tank had been mistakenly painted the same color as a helium tank. A rookie mistake!
Mark Woodworth: master of fixing complicated instruments, UC Merced 2014

Another very senior isotopist reports tearing his hair out over why he was mysteriously only able to measure vastly reduced amounts of hydrogen gas than he thought he should have.  He’d checked everything and it all seemed fine.  Eventually, with less hair on his head, he remembered having purged all of his carrier gas lines with ultrapure nitrogen gas to remove moisture and contamination. Nitrogen gas is much heavier than helium and hydrogen—of course.  Helium wasn’t strong enough to push through the nitrogen, thus preventing any hydrogen from making its way through.

Turns out that helium, although rare and expensive does the trick for our analyses. Another bright isotope geochemist had a “better idea.” He intentionally used argon gas on purpose. He thought other scientists with similar but different instruments use it all the time. He did some fine-tuning and was able to find nitrogen and carbon dioxide gases. Precision was not as good as he was used to. He briefly thought he was going to save the research field from helium shortages!

A week later, the delicate ion source—the heart of the mass spectrometer--blew and was filthy when he opened it up to see what had happened. Oh, the colors he saw when he disassembled it. And it smelled horrible. That ended his “experiment,” and he switched back to using helium as a carrier gas. That didn’t end the “experiment” completely, however. Even with helium, there were still residual effects and the new source blew again shortly thereafter and needed to be cleaned again. We’re stuck with using helium.

A dirty ion source with colors

Those not in the stable isotope chemistry field might think we’re a bunch of cowboys—but that is not the case. Our work demands, not just needs, but demands 100% concentration. Sometimes, for whatever reason, we operate at 95%. For the tens of thousands of isotope analyses I’ve made with my lab group over 40+ years, we’ve done a pretty good job of keeping within the rigorous boundaries of safe and sensible lab practice.
When we needed to channel intelligence we donned the Arkansas razorback Pig Hat. It worked!

Monday, February 17, 2020

Camps for learning about Isotopes OR Getting from Isodope to Isopope


Woods Hole Isotope Camp, 1986: Brian Fry, Marilyn, Bob Michener front row center
2nd row: Marion O'Leary (center) next to Chuck Douthitt, then Ron Benner (2nd from right)
3rd Row: Kate Lajtha, Terry Chapin (left), Tom Jordan, Brad Tebo (right)

When you’re a kid, if you’re lucky, your parents might send you to camp in the summer to learn new skills or just have fun. My children attended nature camps, art camp, horseback riding camp, and sports camps, as well as a “just be silly and have fun” camp. My childhood friend Franny Stein (Kasen) excelled at doing camp first as a camper, then a counselor in training, and eventually a counselor. She held court every summer at overnight camps that lasted months. The friends she met there sustained her throughout the rest of the year. And in fact, she met her husband at camp when she was a lifeguard at the Jewish Community Center day camp in South Jersey. Good things can and do happen at camp. Similarly, students interested in the field of stable isotope biogeochemistry meet peers and network at what is becoming very popular—isotope training camps.

To learn the “Ins and Outs” of stable isotopes these days, graduate students and postdoctoral scholars often attend Isocamps—week(s)-long training sessions with lectures by experts (Isopopes) and laboratories led by the technically savvy (Isocopes). The first workshop that I organized for students to learn about stable isotopes was in 1982 on the more general topic of “Biogeochemistry.” Sponsored by the American Geophysical Union (AGU), about 25 young scientists came to the Geophysical Laboratory for 2 days of lectures from microbiologist Ken Nealson, organic geochemists John Zumberge and Bernie Simoneit, my Geophysical Lab colleagues Tom Hoering, Ed Hare, Steve Macko, Michael Engel, and me.  We were educating a new group of people who wanted to think outside of their disciplinary boxes. Some of the students who attended that workshop went on to become leaders in biogeochemistry. We didn’t include a laboratory component, but I learned how to bring senior scientists on board, show enthusiasm to people outside my field, and develop lecture skills.

I learned enough from this experience to do a much better job for the isotope “camp” I organized in 1986 with my colleague Brian Fry, then a scientist at Woods Hole Marine Biology Lab in Massachusetts. Brian Fry and I had worked together as graduate students at the University of Texas Marine Science Lab in Port Aransas. Essentially, we’d “grown up” together going from being “Isodopes”, learning our way to becoming young “Isopopes”. We planned our workshop with lectures in the mornings and evenings with laboratories in the afternoons. For the lectures, we brought in some big names at the time—John Hayes, Marion O’Leary, and Leo Sternberg. Each of us had a full day to give our lectures that concentrated on the basics in the morning followed by more specific examples in the evening.

Brian and I worked with his lab manager Bob Michener to set up six glass vacuum lines for processing samples for isotope analysis. This was a feat that required much planning and thought. Each vacuum line needed its own vacuum pump, metal support frame, liquid nitrogen flasks, clamps, and sample bulbs. Fortunately, we were able to make a simple design that worked well and purchased six lines from a local glassblower. Our students worked three to a vacuum line so that they became intimately familiar with how they worked. 
Isotope camp students and lecturers, Patagonia, 2013


Each group of students designed a simple research project on Monday, collected samples, prepared them, and analyzed them by Thursday. They presented their results on Friday. Bob needed to make sure all the fragile vacuum lines held a vacuum and didn’t break. He also needed to make sure the isotope ratio mass spectrometer was in tip-top condition so he could finish all the analyses by Thursday night. Nothing was automated at that time, so each and every sample required hands on careful attention to details.

The class was a raging success!! It was a great sense of accomplishment for me to carry this off, including showcasing my abilities to important Isopopes like John Hayes, a decided leader of stable isotope biogeochemistry. Brian, Bob Michener, and I really enjoyed working together. Even today, I believe the shared experience from holding this workshop almost 35 years ago remains a fond memory for the three of us. Many of the students from this class went on to use stable isotopes to solve scientific problems in their specific disciplines. 
Brian Fry's cartoon on isotopes-masterpiece!


Brian Fry used this experience to write the first textbook on Stable Isotope Ecology, a somewhat folksy rendition of an otherwise serious subject. I’ve used parts of this book for teaching Isocamps and full on classes during my career. Brian made up cartoons of people with their hands, body, head, and feet as stable isotopes. He drew an illustration of “light” and “heavy” isotopes paddling a canoe with the heavy isotope’s figure tilting the canoe dangerously. Brian’s cartoons of isotopes are classics in our field of isotope scientists and convey to even the most chemically-adverse student the basic rules of stable isotope chemistry and physics.
From Brian Fry's book, Stable Isotope Ecology


Chemistry and physics—two subjects that strike fear and loathing in the hearts of many who eschewed science and studied the liberal arts. In fact, even science majors have a certain dread about taking organic chemistry classes.  To get a deeper understanding of the stories in Brian’s book, bear with me and consider a couple basic rules first articulated by Marion O’Leary, a physical chemist who was very influential in the 1970s and 1980s.

Recall—atoms are made up of protons (P), neutrons (N), and electrons.

Rule #1: Lighter isotopes go through chemical reactions faster than heavier ones.

This makes sense to just about everyone. For example, thinner, lighter people typically can run up hills faster than thicker, heavier people like me.

 The lighter isotopes that have one or two less neutrons like 12C (carbon atoms with 6P:6N), 14N (nitrogen atoms with 7P:7N), 16O (oxygen atoms with 8P:8N), and 1H (hydrogen atoms with just 1P), form chemical bonds easier and faster than the heavier isotopes: 13C (6P:7N), 15N (7P; 8P), 18O (8P; 10N), and 2H (1P;1N) that have an extra neutron or two.
From: Brian Fry's Stable Isotope Ecology book

Rule #2: Heavier isotopes form stronger chemical bonds than lighter ones.

This concept is harder to grasp, but let’s work through it. Chemical bonds hold together important molecules like sugars in which hydrogen and oxygen atoms are bound to carbon atoms.

The heavier isotopes stick to other atoms more strongly. While the lighter isotopes will form chemical bonds more easily according to Rule #1, they also break apart more quickly later on. The heavier isotopes need more energy to form a bond initially and they require more energy later to break these bonds.

Rule #3: Beware of over interpreting small isotope differences or patterns.

Although we can break the chemistry and physics down into a couple of simple rules, the natural world is much more complicated than that! A living organism carries out thousands of biochemical reactions every second. Comprehending the shuffling of stable isotopes at that scale is impossible! We rely on knowing which reactions are the most important and understanding those in greater detail. Even geological reactions, which can take place over millions of years and at extreme temperatures, take some time to understand fully.

Rule #4: You are what you eat—plus or minus a little bit.

The isotopes we eat—yes, we eat them folks—are in our food and end up in our tissues. You shouldn’t be surprised.

When we analyze animal tissues we do this to figure out what animals have been eating when no one is watching. Imagine trying to determine what a whale is eating as it cruises 100 meters below the surface of the ocean. Our work measuring stable isotopes in Australia on extinct species allowed us to figure out what animals now long gone ate! This approach enabled us to understand prehistoric ecosystems.
Baja Mexico--Isotope camp 2012


After a week of in-depth isotope camp, we expect students to fully grasp Rules #1 and #2, to see the utility of Rule #4 and to come to appreciate Rule #3.

Every year Isocamps are held in Salt Lake City, New Mexico, Michigan, Germany, Italy, and Chile or somewhere else in the world. Jim Ehleringer and Thure Cerling at the University of Utah held one of the most popular and longest running Isocamps for over twenty years. They branded the name “IsoCamp”, attracted a worldwide student population, and provided lecturers from around the globe the opportunity to spread their knowledge to a diverse audience.

I worked with my colleague Seth Newsome holding isotope ecology short courses in Argentina (2009 and 2013) and Baja Mexico (2012). When we held our first isotope camp in Argentina in 2009, there was only one isotope mass spectrometer in the entire country.  Because there was no available mass spectrometer for us to use, we trained students in how to design ecosystem level isotope studies and how to formulate laboratory experiments to understand more complex species level isotope questions. When serious isotope ecologists like me look at a landscape, we see isotope patterns in the plants, the soil, and in the tissues of animals. It’s a talent akin to how a naturalist might examine an ecosystem identifying plant communities, stream flow, tallying species diversity, and listening for the sounds of birds and insects.  It takes years to get good at imagining and speculating about the isotope patterns in an ecosystem, but with many of my postdocs, Seth and Matt Wooller for example, we have “mass spectrometer” eyes that assess a plant’s photosynthesis pathways, the influence of climate and water availability, water sources, and potential prey items.
Luciana, Marilyn, and Seth, 2009


In 2009, Seth and I flew to Argentina to work with Argentinian grad student Luciana Ricciardelli on presenting our first Isocamp. Earlier she had visited the Geophysical Lab to analyze samples of dolphins and porpoises found stranded on the coast of southern Patagonia. Seth and I landed in Buenos Aires with duffle bags filled with sample gear and technical books. After a short stay in Buenos Aires, we drove south along the La Plata River with Luciana to the city La Plata where we conducted our short course at the University de la Plata, a sizeable university of more than 30,000 students.

In general, Argentinians of a certain age aren’t fans of Americans. During their Dirty War in the mid 1970s to early 1980s, the CIA tacitly ignored what was happening in Argentina. In the US, we rarely learn the history of countries outside of Europe, so I was almost completely ignorant of what happened at that time. I became educated by staring in shock at the photos of “missing” students, who would have been my age (18-22) at that time. It’s now well known that dissident students were rounded up by the fascist government, murdered, then dumped off shore. It was a horrible time for Argentina. Seth and I worked hard to engender good relationships, and I think it worked.
Seth giving informal lecture, 2009

On the first day of the camp thirty eager students arrived. My Spanish is rudimentary to non-existent. Fortunately most students knew some English so that lectures could be conducted in English as were our question and answer periods. Argentinians drink coffee in the evening, but prefer yerba matte, a hot drink with lots of caffeine, throughout the day. Matte bowls were passed around the room during the long lecture periods. Students used a shared special metal straw to take a hit off the strong brew. In the evenings, we went out for pizza, steaks, and ice cream often meeting up with a few students in the class.

Seth and I worked nearly round the clock preparing lectures, lab practicums, and interacting with students who were thirsting for knowledge. By the time it was over we invited several of the most promising students to come to the United States as interns, and we were able to provide modest support for them.
Students working on sample strategies, 2009


This year, Seth and his colleagues at University of New Mexico will take over the next phase of IsoCamp as Jim and Thure have passed the torch. There are 60 applicants to fill 25-30 available slots. Clearly we had created a unique and powerful way of educating the next generation of stable isotope scientists. Working on these camps was one of the most satisfying educational opportunities of my career and a strong testament to the power of using isotopes as important tool in scientific research.

For this year’s IsoCamp in Albuquerque, New Mexico, I have been asked to give an evening lecture on a topic of my choice, not the nuts and bolts lectures that others will cover. I’ve got plenty of stories to tell—many of them good, all of them educational.

People want to learn about stable isotopes! I hope that this memoir reaches an even greater audience and when you hear the word “isotope” you’ll think of all the cool things about them.
Marilyn (foreground) teaching isotopes, 2013



Winter in the "Olden Days"

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