Friday, April 17, 2020

Never published Alfred Treibs medal speeches

Dana's Graduation from Evergreen State Univ., 2011

Typically the speech of the Alfred Treibs medal winner is published with a photo in one of two journals: Geochimica Cosmochimia Acta or Organic Geochemistry. Mine wasn't for some reason. I have no photos from the presentation. So, here it is along with Susan Lang's introduction--now "published" on the blog. Susan spent a summer in my lab when she was a postdoc. She fixed an older finicky gas chromatographic system and managed to get some nitrogen isotope data. While she was at the Geophysical Lab, I was enormously impressed with her knowledge and creativity. She's now an Associate Professor at the Univ. of South Carolina studying the biogeochemistry of hydrothermal vents at the bottom of the oceans. I suspect when she reaches full professorship, she'll be a candidate, herself, for the Treibs award!

Susan Lang's Citation for the presentation of the 2013 Alfred E. Treibs Award to Marilyn Fogel

"It is my great pleasure to introduce this year’s recipient of the Alfred E. Treibs Award in Organic Geochemistry, Marilyn Fogel, long time Senior Scientist at the Carnegie Institution of Washington, and current Professor and Chair of the UC Merced Life and Environmental Sciences Group. The Treibs medal is awarded to an individual for major achievements in organic geochemistry over a period of years, and Marilyn is the first female recipient.
Susan Lang, center, is a biogeochemist studying deep ocean hydrothermal vents

It is not unusual for isotope geochemists to contribute to wide variety of disciplines, but a particular trademark of Marilyn’s has been her focus and depth of engagement in multiple fields. It is a breadth of interests that is certainly evident today; during a visit to her laboratory you would be just as likely to encounter a portion of a banded iron formation as you would a well preserved set of bird feathers. Throughout her career she has contributed major advances by applying isotope geochemistry to ecology, ecosystem science, paleoecology and paleoclimatology, astrobiology, biogeochemistry, and marine science.

This depth of interest in multiple disciplines began early in her career, when she earned a Ph. D. in both Botany and Marine Sciences at the University of Texas at Austin Marine Science Institute. It is worth noting that one of her dissertation advisors was Dr. Patrick Parker, himself a Treibs medalist in 1996. In fact, Pat Parker was already a second generation Medalist as his own advisor, Tom Hoering, received the honor in 1986. After receiving her PhD, Marilyn was able to work closely with Tom when she moved to the Carnegie Institution’s Geophysical Laboratory as a Postdoctoral Fellow. These early pioneers in isotope organic geochemistry must have recognized in Marilyn a kindred spirit who could continue their legacy. Marilyn’s position as a Postdoctoral Fellow quickly transitioned to a permanent position as a Staff Scientist, and she remained at the Geophysical Laboratories for an extremely productive 30+ years.

I have to imagine that those early years were an exciting time. Isotope geochemistry was still a relatively new field, and the community at the Geophysical Laboratories was central in demonstrating how high-precision measurements of natural abundance isotopes could be applied in new and innovative ways. In conjunction with Tom Hoering, Marilyn made some of the first D/H isotope measurements of organic biomarkers, a subject that has again come to the forefront of isotope geochemistry, as is evident from the schedule of this IMOG conference.

Marilyn’s wide ranging work over her career describing the transformations of carbon and nitrogen in ecosystems has epitomized this approach. In business, people would describe it as a cradle-to-grave philosophy. In a series of papers with colleagues such as Noreen Tuross, Jonathan Sharp and Ron Benner, and postdoctoral fellows such as Stephen Macko and Mark Teece, she described the isotopic fractionation associated with the microbial uptake of ammonium and nitrate; the isotopic signatures imparted during the synthesis of biomarkers such as amino acids, fatty acids, and lignin; and how the breakdown of organic matter alters these isotopic compositions. She then applied the knowledge gained by these detailed and controlled approaches to investigations of the transformations of carbon and nitrogen in real world environments such as the Delaware estuary, Antarctica, the ocean’s water column, and meteorites. This body of work laid the groundwork for our understanding of how nitrogen and carbon enter the food web and are altered in complex ecosystems. It further provided a roadmap of how to extract similar information of past environments from the small portion of organic chemical fossils that survive over geological time.

The full extent of Marilyn’s research is impossible to cover in such a short time, but two specific projects are particularly worth highlighting. During a sabbatical from the Geophysical Laboratories, Marilyn returned to her botany roots and traveled Carnegie Institution of Washington’s Department of Plant Biology at Stanford. There, she, Joseph Berry, and colleagues were the first to characterize the large isotope fractionation that occurs during the uptake of O2 in photorespiration. This work was particularly important because it provided, for the first time, an explanation for the “Dole Effect,” or the observation that atmospheric oxygen is anomalously enriched in 18O. This had been one of the earliest conundrums in stable isotope geochemistry.

A second major highlight during her time at the Geophysical Laboratories was her work with Beverly Johnson on the impact of humans on the large mammals of Australia. Through a series of papers that exploited organic biomarkers within the remains of ancient megafauna such as emu and wombats, they demonstrated that the diets of these mammals shifted coincident with the arrival of early humans approximately 50,000 years ago, and that widespread extinctions quickly followed. They attribute these signals to massive fires that were set by the first humans, causing a shift in the Australian ecosystems from one of shrubs, trees and grasses to the desert shrubs of today. This is a major line of evidence that human-induced vegetation changes – as opposed to changes to the global climate – were ultimately responsible for the extinction of Australia’s megafauna.

Of course, counting papers and marking research advances is only one measure of scientific influence. Another is the role that scientific leaders play in the training of the next generation, and here again Marilyn has had an outsized influence. A large portion of the current generation of isotope geochemists was first introduced to the subject as Postdoctoral Fellows in her laboratory, during visits for their Ph. D. research, or as undergraduate or high school interns. These folks can now be found on the faculty and in the administration of universities across the country, running private companies, and arguing on the isogeochem listserv. No doubt this record of mentorship will continue with a new crop of students and postdocs as Marilyn transitions into her new position at UC Merced. I know I am not alone in looking forward to the new and exciting research that will continue from the laboratory of this outstanding scientist, and 2013 recipient of the Alfred E. Treibs Award, Marilyn Fogel."

Marilyn's Treibs Acceptance Speech
 September 16, 2013
Ladies and Gentlemen:

Having served several times on the committee to select Treibs Medalists, I worked both behind the scenes and upfront to broaden the demographic of the organic geochemist chosen for this award. I was surprised to find out that although I was unsuccessful in my committee work, I had myself attained what I believe is important for all the under-represented scientists in organic geochemistry. Thanks to Roger Summons, Walter Michaelis, Susan Ziegler, Paul Koch, and Noreen Tuross for nominating me and writing my letters of support, and to the Geochemical Society for making this happen.
The actual medal--in silver

As a child growing up in New Jersey, plants, insects, weather, and NASA’s space program fascinated me.  At the age of 12, I wrote an essay stating that when I grew up I wanted to have a chemistry lab, 6 children, and 10 dogs. (I’ve got the Lab, 2 children, and a few dogs over time). In 1970, I started at Penn State University as a Biology major just before the molecular genetic revolution hit biology and found myself taking a couple of extra classes in earth science. Penn State, being a big sports university, required their students to take 4 classes in physical education. I was enrolled in a bowling class three days a week at 8 am, when a friend of mine excitedly reported to me a class that I absolutely needed to take. In my senior year, I took a class taught by a British professor, a slightly disheveled man with a tie that told of his last few meals, a white beard, and dignified countenance. Peter Given, organic and coal geochemist, taught Organic Geochemistry to a handful of students. The class conflicted with my bowling course, however, so I begged my bowling teacher to let me take Organic Geochemistry and miss bowling once a week. The interdisciplinary nature of Organic Geochemistry was exactly what I was searching for: biology, chemistry, and earth science rolled into one.
I believe Pierre Albrecht is next to Given

At the completion of my B.S. degree, I was faced with a choice: a position as a plant physiologist for the Campbell’s Soup Company, in Camden, New Jersey, or a slot at the University of Texas’s graduate school at the Port Aransas Marine Science Laboratory. I chose graduate school where I went to work with “Chief” Patrick Parker (Treibs Medalist 1996). When I arrived, though, I worked in the lab of Chase Van Baalen, an algal physiologist, who decided that I needed a microbial physiologist (Robert Tabita) on my advising team as well. My studies were funded by a NASA Exobiology grant to Parker, Van Baalen, and Tabita to study carbon isotope fractionation by the enzyme ribulose 1,5-bisphosphate carboxylase, the protein responsible for fixing CO2 during photosynthesis. NASA was interested in this research because at the time scientists like John Hayes and Ian Kaplan were measuring the carbon isotope compositions of Earth’s oldest rocks. It was important then, as it is now, to understand whether carbon isotopes in organic matter in ancient rocks are biosignatures or whether their patterns are the result of multiple abiotic reactions such as diagenesis and thermal processing. I learned enzymology, algal and microbial physiology, and isotope biogeochemistry, all skills that I have used during my 35 years as an independent organic/Biogeochemist.
I was offered a job at $5,000 per year in 1973. The factory is now closed.

Every summer in Port Aransas, a small town on an island of the Texas Gulf Coast, Thomas C. Hoering (Treibs Medalist 1987) would take his vacation. Hoering was Parker’s major professor and postdoc advisor during Hoering’s tenure at Univ. of Arkansas and the Geophysical Laboratory in Washington, DC. As I was wrapping up my Ph.D. in 1977, Hoering approached me, slouching in his way against the wall in the hallway of the Port Aransas Lab, and asked if I was interested in applying to come up to Washington and work with him. I was taken aback that such a “famous” scientist was interested, so my answer was a mumble, a tentative “certainly”. I was offered two postdocs: the Geophysical Lab or a postdoc in plant physiology at the University of Georgia. Again, the choice—straight biology or go the interdisciplinary route. The decision was an easy one, and a fun, exciting 35-year career at the Carnegie Institution of Washington followed.
Tom (center); Abelson (right)
Our field, organic geochemistry, allows us to explore Earth’s entire fascinating history from the origin of life at 3.8 billion years ago to yesterday’s methane production. We take advantage of chemistry’s most novel instruments detecting fragments of molecules that once formed living organisms. And, if we dream big enough, we can use what we know about early Earth and apply our knowledge to answering one of our biggest scientific questions “Are we alone in the universe?”  During my career I have taken three pathways: 1) understanding modern ecosystems using stable isotope tracers at the natural abundance level, 2) applying this knowledge to studying Earth’s past ecosystems, climatic changes, and evolution, and 3) understanding how to determine whether organic and inorganic materials in meteorites originated from biotic or abiotic reactions.  Taken together, I have been privileged to work with many brilliant, creative scientists.
Geophysical Lab, circa 1987; Marilyn front row right

At the Geophysical Laboratory of the Carnegie Institution of Washington, where I spent 35.5 years as a staff member, I started my “science family”, an eclectic group of young and not so young bio-geo-chemists who brought their best ideas to the lab and we tried our best to make new discoveries, usually with stable isotopes. My 1st postdoc, Steve Macko, was another Univ. of Texas import to the Carnegie. During his brief time at the Lab, he managed to get all three Organic Geochemists (Ed Hare, Tom Hoering, and me) to work together with him as a team to master compound specific isotope analysis of amino acids well before gas chromatography methods came on line. Luis Cifuentes, a student at the University of Delaware, came to work with Tom and ended up forging an early collaborative career with me and started my involvement with oceanography. In fact, “Tom Hoering” was the original draw for postdocs and students who were interested in learning the stable isotope craft, including an undergraduate student, Kate Freeman, who once washed glassware in my lab as a summer intern.

I have yet to tell the story of the 1st Gordon Conference in 1982. Here is a story about my 1st IMOG meeting in the Hague and how is was to be a female back in the day at IMOG:

With time, however, I was fortunate enough to have the track record to attract young scientists, like Paul Koch, Matthew Wooller, Matt McCarthy, Mark Teece, James Scott, and Seth Newsome, who were interested in working with me on more biological problems, particularly in marine, estuarine, and archeological sciences. Long-term colleagues that I have worked with for 20-30 years include Ron Benner, Ken Nealson, and Giff Miller. George Cody and Andrew Steele joined the Lab as staff members replacing Ed and Tom. The three of us forged new pathways in the study of Astrobiology for the Carnegie, getting involved in meteorites, Mars, and the origins of life. It was not an easy path for the three of us to be respected in a sea of petrologists and mineral physicists, but triumph we did attracting NASA funding for almost 20 years.
For over 30 years, I was the only woman on the Geophysical Lab’s staff of senior scientists. I learned to negotiate through a male-dominated world through mentorship by Carnegie’s leaders, Charlie Prewitt, Wes Huntress, Vera Rubin, and Maxine Singer. I grew outspoken as a result about the opportunities for women, particularly at the higher levels. I developed the reputation of a somewhat of a viper, with thick skin of a rhinoceros, when in reality, I am as thin skinned as an amphibian. As I got older, and somewhat wiser, I had the privilege of mentoring many sharp, young women, who were interested in learning the art of science along with the challenge of how to balance a family and a career- Beverly Johnson, Carmen Aguilar, Sue Ziegler, Jen Eigenbrode, Penny Morrill, Roxane Bowden and other women (like Susan Lang and Valery Terwilliger), who I did not directly advise. These women are strong, funny, and devoted to their lives as females and scientists. In 1988 with Noreen Tuross then at the Smithsonian Institution, we pioneered stable isotopes as tracers of human nutrition, particularly breast-feeding, with a study of nursing infants and their mothers. I was one of the mothers in the study, and my daughter served as a “subject” for about a year. Noreen is now at Harvard University, and to this day we have the “weirdest isotope” contest every time we get together.
In 2009, I spent 16 months as Director of the Geobiology and Low-temperature Geochemistry program at the U.S. National Science Foundation, where I was proud to try to help our community write and submit successful, competitive proposals. During this time, I held workshops to promote women in science through the Earth Science Women’s Network. It was rewarding to me to mentor not only on a personal level, but also at a national and sometimes international level.
Recently, my interests in under-represented minority involvement in science have taken me to a last grand adventure. In January of 2013, I started a position as Professor in the School of Natural Sciences at the University of California at Merced. UC Merced is the newest U.S. research university, founded in 2005. The student body has a majority of 1st generation students, from Hispanic and Asian backgrounds, who are getting their first chance at a college education. The University campus was started just prior to the major recession in 2009, which has slowed its growth, but remains committed to promoting interdisciplinary science. Half of the faculty in the Life and Environmental Science department that I now Chair, are women! Now at the ripe age of almost 61, I am starting completely over with an empty room, barely qualified to be called a laboratory and a fledging group. Coming from the conservative, old-school Carnegie Institution to UC Merced is providing me with an opportunity to forge new collaborations and learn new things.
I would not have been able to reach this accomplishment without the help and encouragement of my husband, Christopher Swarth, an animal ecologist and wetland scientist, who coaxed me out of a shy, self-effacing start to my career and helped me stand up for myself and assume leadership positions. My children, Dana and Evan Swarth, now young adults, constantly remind me that we women can have almost all, if not all. They traveled the world on field trips with me, trekked to the Lab on school holidays, weighed samples, cleaned glassware, and in general participated in my career.
Ladies and Gentlemen, I am honored to accept the Treibs medal and to stand with my distinguished colleagues who have had this honor before me. Thank you for giving me this honor.

Monday, April 13, 2020

Isotope Biogeochemistry of Viruses?

Maureen Coleman, Jake Waldbauer, Chris and Marilyn, Newsome's wedding 2008

“Viral infection drives microbial mortality and nutrient recycling in many ecosystems. Despite the importance of this process, little is known about how viruses obtain the resources they need to produce progeny.” Jake Waldbauer et al., Proceedings of the National Academy of Science, 2019.

I’ve often been asked what I think the next big thing in stable isotope biogeochemistry will be. I’m not very good at predicting the Big Trends. I think I do best with small, possibly important things that we don’t know much about. I’ll not have the time remaining in my active career to delve into this idea, so here goes some early ideas about studying the stable isotope patterns in viruses.

I was riding on the late night bus back to my hotel from the conference banquet of the International Meeting of Organic Geochemists (IMOG) in 2013 with a group of slightly inebriated fellow geochemists. The conference that year was held on the Canary Islands, remote volcanic islands off the coast of Africa. It was the typical blow out banquet with too much booze and never enough food. This wasn’t the super late bus with the out of control folks, but we were suitably loosened up. I found myself seated across the aisle from Jaap Sinninghe-Damste, ( ordinarily a bristly fellow who has been our field’s Young Turk for more than two decades. Earlier in the conference I received the Alfred Treibs Medal for my career in organic geochemistry. I was the first woman to receive the award. The normally cliquish community opened up to me, when I joined the elite, small group of 27 Treibs medalists.
Tenerife, site of IMOG 2013

Jaap leaned over in the bus and asked, “So what do you think the next big thing in Organic Geochemistry will be?”

I recognized this as an opportunity. “Let me think,” I answered. After a minute or two, I answered, “Viruses. We don’t know much about their biogeochemistry and nothing about their stable isotopes.”

He thought for a few seconds, “But they don't have lipids. What would we study?”

Lipids, essentially fats, are the molecules that last the longest in the fossil record—possibly even a billion years or so. Jaap’s career was built on finding new, novel, and rare lipid molecules in living organisms and ancient rocks. At Gordon conferences, small meetings held in rural New Hampshire, Jaap and his Dutch colleagues from NIOZ (Royal Netherlands Institute for Sea Research) often held court as young kings and princes of the field. With the exception of stable isotope God Jacob Bigeleisen, he’s the only one I’ve ever seen stand up in the middle of someone’s talk and essentially tell the speaker they were full of s*$%, such that the speaker ended his talk without finishing and sat down. One year when the IMOG meeting was held in the Netherlands, Jaap, a character personally as well as professionally, dressed in a white suit and disco danced imitating John Travolta in Saturday Night Fever.

Before the bus ride, I’d never had a serious conversation with Jaap. His persona was such that I didn’t necessarily want to get too close. But, I’d talked with many of the young people who had worked with him in his lab over the years. They gushed about what a good mentor he was. I was pleasantly surprised.

After telling him my thoughts on viruses, I asked him a question, “How do you guys identify all those complex lipid structures? I can barely figure out simple molecules.” “We have a manual,” he shot back. His lab group, easily 20 people at any one time, assembled a system for looking for diagnostic patterns. Everyone who worked there used the manual. It hadn’t occurred to me to do such a thing.
Marilyn and Kate Freeman, IMOG, Canary Islands, 2013

Viruses and their impact on ocean biogeochemistry are now a hot topic. Recently, friends and colleagues Jake Waldbauer ( and Maureen Coleman, University of Chicago, have been putting out some very intriguing papers on how viruses affect ecosystems at the very basic level. I’ve known Jake since he was in kindergarten. He worked in my lab as a college intern one winter, collecting fish and crabs in mangrove ecosystems with me and Mat Wooller. He’s gone up in the world since then and is a pioneer in using proteomics—the study of individual protein molecules—in geochemistry!

Viruses not only cause death and mayhem for humans—they may be controlling the most important processes in the ocean.

 Ecosystems are controlled by ‘bottom-up’ (resources) and ‘top-down’ (predation) forces. Viral infection is now recognized as a ubiquitous top-down control of microbial growth across ecosystems but, at the same time, cell death by viral predation influences, and is influenced by, resource availability…First, viral infection transforms host metabolism, in part through virus-encoded metabolic genes; the functions performed by these genes appear to alleviate energetic and biosynthetic bottlenecks to viral production. Second, viral infection depends on the physiological state of the host cell and on environmental conditions, which are challenging to replicate in the laboratory. Last, metabolic reprogramming of infected cells and viral lysis alter nutrient cycling and carbon export in the oceans, although the net impacts remain uncertain.” A. E. Zimmermann et al., Nature Review Microbiology, 2019.

Viruses are made up primarily of a protein outer “coat” with inner nucleic acids, either DNA or RNA. Animal viruses are more complex and often include an outer membrane built from fragments of the host’s cell membrane and a special type of protein that is linked to sugar molecules—glycoproteins. When a virus infects a cell, they coopt the cell’s biochemical machinery to make many copies of the protein coats. During this biochemical highjacking, the cell’s central metabolism is changed.

Changes in the fundamental biochemical pathways of living organisms cause major metabolic disorders. Think cancer, for example. The simple pathways all students learn in high school biology flow in different directions and at different speeds. When things like this happen, we know that the stable isotope patterns in amino acids, and maybe lipids, will be altered. For a brief, but fun period, I collaborated with Fabian Filipp and Christina Bradley on comparing melanoma (skin cancer) cell cultures with healthy human tissue. We found major differences in the isotope patterns of amino acids synthesized in the central pathways. There’s something to this work, but we weren’t able to follow up. I think it would be a very fruitful avenue of research.
Unpublished data of Bradley, Filipp and Marilyn

What if viruses ruled the amino acid biosignatures of organic matter in the ocean? Brian Popp, Hilary Close, and Matt McCarthy’s labs are devoting serious efforts at understanding what happens to organic matter once organisms die and sink to the bottom of the ocean. Perhaps viruses are playing a key role. Given their newfound importance, that very well might be.

What about in mammalian or animal tissues? Could the lipids in viral membranes survive in the fossil record? What if they could be found in some of Earth’s earlier rocks in the Cambrian?

And what if something like a virus, a primitive biogeochemical “secret agent,” might be a good model for searching for evidence of life on Mars or other icy moons? Many have thought about this including the first NASA Astrobiology Institute Director Barry Blumberg, who won a Nobel Prize for his work on hepatitis virus and its vaccine.

I think there’s some good geochemistry and biochemistry to do with viruses. If we were able to study the stable isotope patterns of those viruses that are causing major pandemics, could they reveal something about how they impact cell metabolism? Can those proteins and amino acids provide fodder for studying marine food webs?

I think it’s worth a closer look.

Rounding Third Base and Heading Home

Cards from Franny and Flowers the Rumbles   My daughter Dana is marrying George Goryan on June 25 at our home in Mariposa...