Tag Archives: career

Young David steps out of his comfort zone

Sometimes, a look through the scrapbook can be a very humbling experience.  I resolved this month to finish a project I launched in 1994.  At last I am publishing the journal I recorded during my first trip to Europe!  For the first time, I am bringing together the forty-two journal entries, my photographs, and the video camera footage that I recorded during my clockwise circuit around the continent.  Before you jump right into the journal, though, could I ask you to read a few thoughts?

More time has passed since I wrote that journal (23 years) than I had lived at that point (I was 20 years old).  The experiences of the last two decades have certainly left their mark.  Since that time, I’ve graduated from two degree programs; I’ve filled my passport with stamps; I’ve built my career in academia; I’ve achieved some level of comfort in finance; I’ve married and divorced.  All of these changes make it hard to recognize the person who wrote those entries as the same person writing this blog!

Setting the scene

19941002-Lyon photo01

I’m sitting by “Le Crayon,” the tower of Credit Lyonnais.

The David who wrote this journal was experiencing profound discomfort.  As a fellow in the University of Arkansas Sturgis Fellows program, I was strongly pushed to spend at least a semester of my junior year abroad.  My undergraduate advisor, Doug Rhoads arranged for me to visit the laboratories of Jean-Jacques Madjar at the University of Lyons, where Thierry Masse mentored my project.  The fact is that I did not enjoy “wet bench” research, and I was becoming concerned that my Biology degree could equip me for a career I did not want!  To complicate the matter further, we never formalized my visa to work in the laboratory for a year-long stretch, and so I needed to leave France well before even a semester had passed.  Scheduling this journey through many countries was my fall-back plan, and my mother was working with the University of Arkansas to get a formal plan in place for the spring of 1995.  In short, I felt that I was failing in this first real test of applying my academic skills.

If you mainly know me as a globe-trotter who uprooted his career and moved to South Africa, you might be surprised to know that as a young man I disliked travel, and I feared change.  Ask the members of Yates Lab how huge a step it seemed to me to move from Seattle, Washington to San Diego, California in the year 2000.  I spent six months poring over maps and dawdling over last details in Seattle.  To go back further in time, I was always the first member of the family to feel it was time for us to return to Kansas City when our family took long road trips in the summer time.  If you read the journal, you will see a David feeling perpetually out of place and coping badly with exhaustion and self-induced malnutrition because I wasn’t willing to spend enough money on food.

The most redundant feature of the journal is that the 20-year-old me was completely agog at the young women I encountered on my travels.  Although a disproportionate number of my friends since elementary school have been female, I must say that I was essentially undateable until my mid-twenties.  I would summarize by saying that I routinely put women on a pedestal and couldn’t see myself as desirable.  This aspect of the journal is high on my list of cringe-inducers.


I had already given up cursive in college.

What should we call the nexus of judgmental, puritanical, dismissive, and obsessed with money?  I am reminded in this journal that the person I am today was distilled from common mud.  Today I am not immune from these traits, but I do try to improve myself with time.  I have been tagged with the label “stubborn” more times than I would like to admit, but I hope that I can manage open-mindedness and respect for others at least from time to time.  In particular, I struggled to read the passages I wrote about the Turks in Budapest or the drive-by racism I dumped on Latin culture.  At least I realized that smug American chest-thumping was not preferable.  My memories of myself from that time have been substantially white-washed, but my text makes it clear I had a long way to go.  In my memories of that time, I mostly remember that the international relations scholar from Turkey taught me that a bishop or a castle is generally more reliable than a knight in the chess end-game.

From 1994 to now

Travel in Europe today is considerably simpler than it was in 1994.  Moving from country to country is considerably easier because of the Schengen agreement that eliminates customs at borders between countries and the Economic and Monetary Union that makes the Euro the only currency you need for much of the continent.  The traveler’s checks that fueled my travel are not needed in Europe; instead, you feed your bank card into an ATM, and out pops money.  My single telephone call home from Vienna would be likely replaced today by Skype; I could use my phone or computer in the WiFi of any hostel to chat right away with folks at home.


My account book, in many currencies

I wrote my journal narrative in a spiral-bound notebook, and I kept strict accounts of every franc, Deutschmark, schilling, crown, etc. in a separate small notebook, both of which I acquired while living in Lyon.  I was very fond of Pilot rolling ball pens at the time, and so each page is filled with cramped blue writing.

While my parents used 35mm slide cameras to capture my early years, I carried a 126 film cartridge camera made by Vivitar with me to Europe.  As you will see, many of the images I mention never made it to print when I developed those films, and the term “focus” does not really apply.  In three cases, I used Microsoft’s Image Composite Editor to stitch together multiple photos into a single panorama.

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The two most visible cathedrals of Lyon, France

Computer video has come quite some distance since 1994.  I originally recorded the video on an analog Sharp “Video8” camera.  When I subsequently upgraded to a miniDV camera, I was able to transfer the video from the old camera to a new one via an S-video cable; this process recorded the video in a digital format on the new tape.  I was able to transfer that digital video without loss to a desktop computer with a FireWire card.  To deinterlace and compress the section of video I’ve posted to YouTube, I used the “yadif” filter of FFMPEG:

ffmpeg.exe -ss 00:00:09 -i input.avi -vf yadif -t 00:45:05 -c:v libx264 -preset slow output.mov

With those comments in place, I hope you enjoy reading the journal, a project 23 years in the making!


The song of the circuit bioinformaticist

The joys of Circuit Informaticist
(The pro who with your data will assist)
Are many, though my schedule leaves me tired.
I’m “circuit” since I travel near and far;

My duties run to UCT each week,
With Blackburn Lab and SATVI each to seek,
And twice a month we run to Stellenbosch,
Biology and chemists, oh my gosh!

The questions range from DNA to stats.
For each problem we try to come to bat.
I’m learning lots of flow cytometry,
In hopes of helping immunology.

Some projects I touch lightly, if at all,
But some require that I must move the ball.
I’m proud that I can help some of these folks,
Though they must field the worst: my jokes!

Dave goes back to work: the Colorado State connection

I have been very fortunate to spend this week at Colorado State University in Ft. Collins, CO.  The university agreed to temporarily appoint me as a Visiting Scientist in the Department of Microbiology, Immunology, and Pathology, starting on October 1st and continuing through the end of 2015.  As a result, my short-term “retirement” is at an end.  One may reasonably ask just what I am doing that justifies my appointment as temporary faculty.  In this post, I will try to explain our goals for this appointment.

The research at Colorado State is a natural bridge between the work carried out in my prior laboratory and the work in which I will be engaged in South Africa.  In the last couple of years, my team has begun work on algorithms for lipid identification.  My last graduate student at my former institution produced results that enabled him to give an oral presentation at the 2015 American Society of Mass Spectrometry meeting.  We are now completing the publication of his innovations.

Lipid mass spectrometry is a very big deal at Colorado State.  Research teams here have interrogated the lipids associated with infectious disease, with a particular emphasis on the Mycobacteria.  M. tuberculosis has drawn their attention because of its impact on human health.  Bacteria are far more diverse in the biochemistry that they deploy than are animals.  Many of the lipids produced by M. tuberculosis are specific to this organism, and understanding the functional role played by these lipids can help us to understand better how the bug interacts with human tissue.

Colorado State has been making considerable headway in deploying tandem mass spectrometry to yield inventories of bacterial lipids (their lipidomes), and my lab has developed software to identify major classes of lipids from tandem mass spectra.  If we can extend our software to handle the glycosylated lipids of M. tuberculosis, we will greatly improve their ability to translate data into knowledge.

Perhaps the best irony of my appointment is that the graduate student who wrote the lipid identification software spent much of his life living right here in Colorado!

John Belisle, Dave Tabb, and Nurul Islam take a break in the Research Innovation Center.

John Belisle, Dave Tabb, and Nurul Islam take a break in the Research Innovation Center.

How to adult, from The Little Prince

Despite my training in French and penchant for reading, I had somehow missed The Little Prince until last week. It’s not a very long book, and I read most of it while enjoying a sandwich rather than dealing with rush-hour traffic in Madison, TN. I found it whimsical and even a bit fey.  When I read the sections detailing the Little Prince’s journey to earth, though, I felt sure I should write about it here.  The Little Prince has quite a lot to teach new professors, and I’m sure the message would be adaptable for anyone else taking a position of responsibility!

The Little Prince starts on his own little asteroid and visits six other asteroids before making his way to Earth.  On each of the other asteroids, he meets an adult who befuddles him (see the official page for delightful images).  Let’s look at each one to see what we can learn about “adulting.”

The King
Upon sighting the Little Prince, The King immediately greets him as his subject. The King makes every act of the Little Prince one that The King has ordered or forbidden, and his robes cover almost every bit of terrain on the asteroid, leaving little room for anyone else. New professors can fall in the same trap. A friend once advised me that I should stop introducing a programmer with my research team as “my programmer.” I’ve tried hard to follow that advice. Certainly a professor will have opinions on how a task should be carried out by a post-doc or graduate student, but if he or she persists in micro-managing every act by people in the group, he or she will have little time for anything else! Every professor needs to find the right balance between independence and prescription for the members of his or her team.
The Conceited Man
The Conceited Man has only one kind of interaction with the Little Prince; when the Little Prince applauds, the Conceited Man briefly salutes with his hat. When the Little Prince questions this relationship, the Conceited Man ignores the question. Few people become faculty members without winning considerable praise along the way, whether that comes in the form of grants, trophies, or just lots of papers. Sadly, we can become dependent upon receiving that praise; a large part of my struggle in graduate school was emerging into an environment where excellence was expected and was not considered comment-worthy. We must always remember to empathize with others, and that goes double for those whom we supervise.
The Tippler
The Tippler was a prime example of a self-defeating cycle (a leitmotif in The Little Prince). A tippler is a habitual drinker of alcohol. When questioned about his behavior, he responds that he drinks because he wants to forget. He wants to forget that he is ashamed. He is ashamed because he drinks. Plenty of people, of course, have gone through phases where this is literally true for them. Not every self-defeating cycle involves alcohol, though. In the latter stages of my faculty position in Nashville, I felt depressed about research funding. Because I was depressed, I could not write grants with the same sense of excitement that I once felt. Because I was less excited, I wrote grants that were less engaging. As a result, I did not do well with study sections. The first step to breaking out of such a cycle is to recognize that we are in one!
The Businessman
I think I enjoyed the Businessman more than any of the others. The Businessman persists in speaking of numbers, computing literally astronomical sums. The Little Prince discovers that he is attempting to enumerate the stars so that he can claim ownership of them. The Businessman can also clearly enumerate the number of times he has suffered an interruption in his task. I particularly appreciated this claim: “Then they belong to me, because I was the first person to think of it!” Being the first person to learn something new can confer real prestige in science. Our grants, for example, are reviewed to determine the degree of novelty that they incorporate. A scientist can get downright tetchy if someone fails to recognize that he or she was the originator of some knowledge. A great many of us feel quite swamped with work, and interruptions (even pleasant ones) can really grate on a full day. It was nice to have a laugh at the Businessman’s expense, knowing that I was laughing at myself.
The Lamplighter
In times before we had electronics to detect the light levels of the sky, cities would employ lamplighters to light the streets at nightfall and douse the flames at sunrise. Unfortunately for the Lamplighter, the asteroid on which he works is rotating more quickly with time, so that he must continuously light and douse the flames of his lamp. When the Little Prince tries to give him an alternative path (walking along the asteroid surface so that he is always in light), the Lamplighter refuses. Again we see the self-defeating cycle, but the Little Prince at least admires him for his devotion to his duty. Most adults encounter periods where they are “stuck in a rut.” It sometimes happens that we resist alternative paths that others lay out for us. I am sure that my path out of my own personal rut is a bit more extreme than many would take!
The Geographer
The Geographer sits as his desk waiting for an explorer to serve as a source of information for his big book. He has clear notions about what merits inclusion in the book; mountains and oceans are fine, but flowers are ephemeral, a word that dismays the Little Prince, remembering his favorite flower. The Geographer also displays his skepticism, noting that the moral character of the explorer must bear investigation and expecting explorers to provide proofs of their claims. In reading of the Geographer, I was reminded of scientists who become so encumbered with grant writing and academic visits that they have little time to conduct research with their own hands. More directly, I am reminded of how long it has been since I last wrote software in something other than a statistical environment! Professors must remember to engage our own hands in the lab from time to time, if only to be able to understand the data that our teams produce more completely.

If you have not read The Little Prince, I hope you will be able to give it a try. It’s a sweet and imaginative look at friendships and responsibility. I think you will be glad you gave it a look!

Dave discusses the prospect for a manuscript with a CPTAC working group

Shepherding a paper with many authors to publication

Twice in my career, I have been asked to take the lead in creating a manuscript to represent the labor of a large working group.  Both times, the effort has posed a considerable challenge and chewed through a significant amount of time.  I wanted to share the strategies that led to my eventual success in publishing a paper for a working group.  Hopefully they will let me succeed in my current manuscript, as well!

My first paper of this type was “Repeatability and reproducibility in proteomic identifications by liquid chromatography-tandem mass spectrometry” on behalf of the National Cancer Institute’s Clinical Proteomic Technology Assessment for Cancer (CPTAC) program.  A network of five lead institutions, their partner institutions, along with NCI and National Institute of Standards and Technology, had conducted a variety of multi-site experiments to evaluate the stability of technologies in proteomics.  Our group was intended as a response (technology assessment) to many challenges that had been raised about proteomics; funding agencies needed to know that if they made grants in the area of proteomics, they weren’t simply throwing their money away.  My second manuscript of this type is in its final stages of preparation for the successor to CPTAC, now renamed the “Clinical Proteomic Tumor Analysis Consortium.”

Large grant programs face a lot of pressure within the National Institutes of Health.  A single CPTAC network may cost ten times as much as an individual R01 grant, and so expectations are quite high for productivity.  The working group papers, then, have special significance; they are perceived as “points on the board” for these teams, and generating the most impact possible from the data is the order of the day.  These are the guidelines that helped me navigate through to a published paper.

Choose a purpose important to your group
The energy people apply to supporting you in your manuscript goal reflects their individual interest in seeing its key question answered. It also reflects the support they will receive from their own leaders to get it done. At several points during the authorship of the repeatability paper, I felt that others did not have the sense that this topic was worth a publication of its own. In fact, at one low point in its preparation (after rejection by the initial target journal), other authors sought to move some analysis from my manuscript to others in preparation. The manuscript might have sundered altogether if I and some senior investigators in the program hadn’t been able to hold the line.
Accept that the paper critically depends upon you
The paper may, in the end, list upwards of thirty authors, but almost every successful group paper effort I have ever seen depended critically upon one person who championed the publication effort from start to finish. I am not referring solely to the effort of writing the text, although my experience suggests that 80% of the words on the page come from one person. Nor am I talking about the data analysis or other experiments, though I’ve never seen a case where the lead author didn’t perform a serious amount of that work, too. The task of the paper champion is to build and maintain the momentum in contributing authors toward the common goal of publication. If you don’t feel enthusiastic about the effort and convey that enthusiasm to others in your teleconferences and in-person meetings, your paper will probably sink in a mire of ho-hum.  The appreciation you lavish on your contributors privately and publicly will help to set a tone for the project.
Know when to fold ’em
This line from Kenny Roger’s “The Gambler” is very good advice! There are certainly times when the data simply aren’t good enough or the analysis you have constructed does not tell the story you sought to relate. There will be times when your flagship manuscript needs serious reformulation before its time will come. Don’t force it. It’s far better for you and your co-authors to decide to mothball your work while additional data or analyses can be assembled than it is for the journal’s peer-reviewers to tell you to start over. I know from personal experience that a bad peer-review (whether or not you think it is unfair) may threaten to scuttle a manuscript effort altogether.
Pick a target journal appropriate to your reach
Many large consortia take the perspective that multi-lab experiments must obviously be published in high-impact journals. Some researchers even take the perspective that a field-specific publication (like Journal of Proteome Research) would be a failure or a disappointment. If you throw all your effort into high publication, be aware that you are rolling the dice. You may throw your manuscript to peer-reviewers who are peeved because they didn’t receive funding from the program that is sponsoring your paper. You are nearly certain to meet serious restrictions in figures and word counts to format your manuscript for the journal, leading to more material in supporting information than in the manuscript itself.  High-profile publications must also meet political criteria outside your control; acceptance will not be based on the science alone. For my part, I know that I can write a really solid manuscript for a journal like JPR above, but my skills at formulating research for Nature Biotechnology have not been as good. I also know that I generally afford more credibility to a paper that explains its methods well, and that causes me to look at the “lower-impact” journals first for something I can trust. In the end, if your project has produced results that the whole world needs to see, you will have to target the big journals, and best of luck to you.
Work, work, and work some more
The heads of the program have called upon you to take on this project. You know how to tackle a fair bit of the analysis, and you identify a core group of other researchers who can fill in for the parts you do not know how to do. Some of them even provide a couple of pages of text to explain their work! Now you will shove aside other tasks that are begging for your attention to give your time and effort to the analysis and the write-up. You will sail the dangerous waters of framing a full author list! You will seek approvals from leadership for including that bit of data or for limiting your scope to one of several lines of analysis. In the end, you cast your manuscript upon the waters, letting all the authors see a nearly-finished manuscript, and after a week or two of begging, the comments will begin to trickle back. Some of them will be useful. With those objectives satisfied, you can seek final approval from program leadership for submission.

Remember, it is an honor to be asked to write a manuscript on behalf of a group.  Smile!

Between jobs

Yesterday was my last day as an Associate Professor at a major university in Tennessee.  I do not yet know the day on which I will become a professor in South Africa; I need to get a visa before I can begin my new position.  As a result I am, quite literally, between jobs.

It has been quite a long time since I had an extended interval without major responsibilities.  Between my post-doc appointment and my faculty post, I had essentially no time beyond what I needed to move.  The same was true between graduate school and my post-doc.  My last free interval was between my undergraduate commencement (May, 1996) and starting graduate school (September, 1996).  I began that summer at home in Kansas City, and I took a temporary job as a Fox Pro database programmer at a local transportation company to acquire a bit more work experience (the company went out of business shortly thereafter).  During the tail end of that summer, my parents and I drove our cars in a caravan to Seattle, where I purchased and equipped my first home.  All in all, the summer of 1996 was a busy one, despite the freedom from coursework.

The summer of 2015, by contrast, feels quite empty, at the moment.  I should be careful saying “summer,” though, because Cape Town is currently enduring winter.  I envision at least two months before starting my position in South Africa, so my 2015 will form this sequence: winter, spring, summer, spring, summer!  Ten weeks would be quite a lot of time to fill.

Even though I’m off the payroll at my former institution, you can be sure that I have some tasks that remain on my desk from it.  The most pressing is a manuscript on behalf of a working group from a major grant.  Yesterday I committed myself to finishing that manuscript by the middle of September.  Frankly, it will probably be a good thing to have a solid deadline to motivate the completion of that project.  I’d feel very guilty about promising my friends a manuscript if I didn’t complete it.  That task, then, is about relationships rather than money.

The new job will certainly have responsibilities in advance of the move, as well.  Simply completing all the visa paperwork will be quite substantial, and there are workshops and collaborations to plan, too.  For a while, I expect to be riding two horses at once (may I have the grace of the pictured stunt rider)!  Happily, this open time will allow me some opportunities for travel, and I look forward to producing albums of photos from these trips.

I hope to waste some of the time, too.  Perhaps I can develop my skills for sleeping late, and surely I can find some time to return to Civilization III, the finest video game ever produced.  I also hope to immerse myself in Starcraft II, since I loved the original so much.

Who knows when my next chance to relax will come?

Winning the Conference Lottery

While talking with graduate students about the upcoming conference for the American Society of Mass Spectrometry, I realized that I could help tell the story of how speakers are chosen for this conference each year.

ASMS is a large assembly, with a yearly attendance in excess of 6500.  That might seem huge, but keep in mind that the recent National Rifle Association meeting in Nashville drew 78,865 people.  Many graduate mentors require their students to submit an abstract to the ASMS meeting as the “price” of attendance.  These abstracts generally lead in one of two directions: A) the abstract is chosen for an oral presentation, or B) the abstract is chosen to be presented as a poster.  Oral presentations are organized into 64 different sessions; ASMS 2015 will be a “multi-track” conference, with eight different sessions taking place at the same time, morning and evening, over four days (8x2x4=64).  Each session includes six oral presentations in 120 minutes (20 minutes for each slot, split between lecture and questions).

At first blush, it might seem like it would be challenging to fill the schedule, since it includes a total of 384 lectures!  A look at the cavernous poster hall, however, tells a very different story.  According to this year’s final program, a total of 2762 posters will be presented (plus a couple allowed to be displayed on multiple days).  If we assume that each poster was also considered for an oral presentation (we know that some are not, at the request of the authors), we see that 7.2 abstracts are pushed to posters for every one that becomes an oral presentation.

I have twice served as a panel organizer for ASMS.  The first time, I played a role in defining the topic for the panel, but the second time I was asked to chair a panel that already existed.  In each case, I remember being faced with around sixty abstracts to fill the six speaker slots for my panel.  A similar number of abstracts had listed my panel topic as a second-best fit.  This is the rough process I used to organize the task:

  1. Glance through the abstracts to sample the gestalt.  My idea of what the panel includes may not match what the submitters thought it should.  When I chaired a panel most recently, the “informatics of protein identification” faced an onslaught of abstracts in proteogenomics (essentially the combination of proteomic and genomic data).  The subject clearly possessed a lot of momentum, so I needed to shift my expectations in that direction.
  2. Triage, triage, triage!  Some researchers do not market their work well, burying the lede rather than explaining what is important right up front.  Some researchers make claims that are downright silly, such as claiming an infinite improvement with their algorithm because the competing software produced zero hits.  Sometimes the results are rather ho-hum, while others are so implausible as to be dismissed outright.  I produce a shortlist from my set of abstracts that includes around half the original number.  Frequently that set is split into categories; I might decide to “spend” two presentations to be drawn from a set of six possibilities on a particular topic.
  3. Balance the speakers.  If your panel includes only senior investigators in your field, you will send a discouraging message to junior researchers who are trying to make a dent.  In my experience, graduate students and post-docs are more likely to present high-risk material.  If you include only males in your speaker roster, you risk winning the Hasselhoff award.  Sometimes a phone call to a colleague can be helpful in assessing the presentation skills of a potential speaker.
  4. Second-guess your friendships.  By the time you are selected to make these decisions, you will have developed a rich network of relationships with investigators in your field.  If we all selected only speakers from labs that we know, however, our fields would become cliques and we would stagnate.  In the past I have intentionally selected someone I did not know well over a long-time friend  just to ensure the audience got the chance to see someone new.

What can you do to increase your chance of selection?

  • Make the selector’s job easy: if I must invest serious time into an abstract to determine why it is important, I will simply assume it is not important.  Borrow strategies from our friends in journalism to put the most significant findings first.  I frequently see scientific writing from junior investigators that assumes prior knowledge of their work; you should explain your work as though the selector has never heard of it.
  • Be concrete: abstracts generally provide enough information to let the selector determine whether an idea is pie-in-the-sky or has substantial data behind it.  If you are working in bioinformatics, you will be expected to show the algorithm enables new biological insight, not just lower run-times.
  • Be visible: when you ask a question at a conference, introduce yourself, and give your affiliation.  Make productive contact with leaders in your field; most investigators are willing to answer well-formed questions that reflect knowledge of our work.  When a high-profile speaker visits your institution, ask to be part of a lunch meeting.
  • Do valuable work: in my field, “YA” is an abbreviation for “yet another,” as in “yet another database search algorithm.”  Novelty is your friend.  Work to resolve a long-standing barrier in biotechnology is generally useful.  Of course, your chance of selection is better if your experiments work out beyond your wildest dreams.

May your efforts lead to amazing science!