Given I live in a desert which -- for the most part -- lacks colorful deciduous trees, the one way that I know it's fall is a flurry of activity concerning grad school applications. Since I teach an upper division core class for microbiology majors, I often get questions from students about what to do after undergrad. The first thing I tell them is this: The one burning memory that I have from graduate school is from sometime in the spring of 2004. It was my third year and I distinctly remember getting hit with the combination of relationship problems (long distance girlfriend and I finally broke up) and the 3rd year grad school treat of having a bunch of experiments with no hope of any successful results. Everything was so confusing. It was 2am, I was in the lab on a Saturday, the only car in any of the parking lots outside was my own, what the hell was I doing with my life? I sat there on the floor of the lab and cried. Seriously...even went fetal position a couple of times. With the perspective I have now, and looking back on all of my 5 years in graduate school, I can honestly say that getting a PhD sucked. It was a slog, a war of attrition. There were so many times I wanted to quit...BUT it was also one of the greatest experiences in my life. I don't regret any moment of it, and would do it again and again and not change a thing.
Why did I stay with graduate school? I had other options, I was a decently compensated intern at a pharmaceutical company all throughout undergrad and had gotten offers to remain on but turned them down. The 9 to 5 life and a daily routine wasn't for me. Sure I was turning down a good job, but I knew deep down that I'd be much more happy as a university researcher. I just always knew that I got bored with routines, with dealing with the same problems over and over again. Industry jobs seemed like scenes from the movie Groundhog day (I'm not entirely right or wrong about this). It seemed as though a job in academia would bring different challenges every day (and it certainly does). I wanted to be challenged, constantly, always from different angles. I knew that that kind of changing landscape of problems is what satisfies my brain.
It was during my time as an intern that I realized I really enjoyed asking questions, finding out how the world worked. I knew I didn't want to go to medical school, and graduate school just seemed like a good way to continue learning about the world. I remember being amazed that I could actually get paid (not a lot by comparison to other things, but enough) to go to school!!! I still can't believe that there are actual jobs that pay me to learn about the world and share what I learn with others. During my first of second year in grad school, my view of life solidified completely. It was at this point that one of the experiments I had thought of and designed actually worked. There I was, the only person at that moment in time that knew a new fact about how the world worked. It was thrilling, it was addictive...there is simply nothing like the rush you get when you get new experimental results. Sure, the paper that came of this experiment was pretty niche, but I was hooked. It's a combination of all of those feelings that helped me stay the research course even when things looked so incredibly bleak.
So should you go to grad school? It's definitely not for everyone, and as I say above, it really really sucks sometimes. It's simply a personal decision that I can only provide one perspective on. Every department and lab is different, and it's up to you to find a place to thrive. You have to find ways to motivate yourself to keep putting one foot in front of the other, to continue performing experiments even though 95% of them fail. Starting in grad school -- and continuing throughout academic careers -- you are surrounded by rejection. Rejection is never fun or easy, but over time it becomes easier to deal with.
I didn't think I'd make a ton of money with a PhD, I didn't even know if I'd eventually have a job. To this point there are a couple of things I can say now that I didn't know before 1) it's much easier to get an industry job with a BS or Masters than a PhD (companies can hire people and train them the way they want) and 2) it's easy to start out as a Masters student (or PhD) and upgrade to Phd (or downgrade to Masters) so your path isn't set the moment you start grad school. I didn't know what I wanted to do with my PhD when I started grad school (in the beginning I didn't think I'd actually be good enough at research to be a PI), but I knew that I enjoyed learning. My love of learning kept me motivated.
You don't finish grad school, you survive grad school. Your job as a graduate student is to make mistakes and to learn how to avoid making mistakes in the future. Your job as a graduate student is to consume every possible piece of information you can and learn to filter out good from bad. Grades really shouldn't matter to you anymore (in fact, if you can, take every class Pass/Fail). Classes are there not to prove that you can get an A, but to give you an opportunity to truly internalize relevant information. As a grad student you are much more likely to figure out some very small thing about the world that only a handful of people really care about, and that leaves your mom to question why you aren't a REAL doctor, than you are of actually making difference to human health. That's OK, it's all about building a foundation for the future wherever that may lead.
Looking back, there is one extra unexpected bonus that made graduate school worthwhile. Apart from the rush of science and research, grad school happened at a time in my life when I was truly becoming who I actually am as a person. I had moved across the country from NY to Oregon, and had started a life completely on my own away from the training wheels that undergrad life can bring. Some of my best friends to this day are people from my grad school cohort. People who were always up for a beer or pizza, people who shared similar experiences to me growing up as a bit of a science nerd. People from all walks of life, with very different perspectives, who nonetheless all found ourselves diving headfirst into research. I would be a very different person if I did something other than graduate school, because that was the moment in time when I really ventured out from the nest.
Grad school is one of the most difficult things I've ever done, and it's not for everyone, but for me it was completely worth it.
Wednesday, November 13, 2013
Friday, November 1, 2013
Replication and Studies of Host-Pathogen Relationships
There has been a buzz around the interwebs (and on actual paper too, so I guess it must be real!) lately about how difficult it can be to replicate published results. Much of the popular press has focused on a couple of articles from The Economist called "How Science Goes Wrong" and "Trouble at the Lab". There have also been a variety of well thought out posts from the likes of Jerry Coyne, Ian Dworkin, Chris Waters among others.
Some of the chatter has been along the lines of "BUT...REPLICATION IS A PILLAR OF THE SCIENTIFIC METHOD. THERE IS A SERIOUS PROBLEM IF MOST STUDIES CAN'T BE REPLICATED. WASTE OF THE MONEYZ!!! GRUMBLE GRUMBLE..."
At the top of this post I'm hoping to add a slightly more nuanced opinion here, followed by some unpublished results at the bottom to serve as a cautionary tale. I don't really disagree with worries about the state of science. Replication is of the utmost importance for research, and if results aren't robust there must be a way to keep track. Perhaps post pub peer review and comments will fill this particular niche. Experiments now are built on a foundation of experiments and models pioneered over years and decades. If you are interested in getting involved in a new research direction, one of the most important things to do is actually see if you can replicate foundational results in your hands in your own lab. That being said, biology is hard. Replication of single experiments under well controlled conditions can easily be thrown off by Rumsfeldian unknown unknowns. I remember hearing from someone (I want to say it was Paco Moore and that there is a paper somewhere on this which I can't find with quick google searches) that measurement of fitness in the context of Rich Lenski's long term E. coli experiment can be slightly altered by University water quality. In grad school I remember Patrick Phillips describing an experiment with nematodes where the assay would only work for about two weeks a year because the stars and sun and temperature aligned to yield the perfect experimental environment. It turns out that physiology and behavior of living organisms can be extremely sensitive to just about everything if you measure closely enough.
This problem is compounded even more when you are dealing with multiple living organisms, for instance, when your research area is host-pathogen (host-symbiont, same diff) relationships. I can't speak for anyone that works with animal models, but I can definitely attest that plant immune responses are EXTREMELY sensitive to pretty much every stimulus you can think of. Since plant immune responses are dependent on cross-regulation across multiple hormonal pathways, even the slightest change in some environmental factors can completely shift the likelihood of infection. This is exacerbated by having to grow plants for multiple weeks before you can actually do the experiments, all the time worrying that some random lab malfunction (3am growth chamber overheating anyone?) will render batches of host plants unreliable. Different labs will have different water, soil, temperatures, humidity (low humidity in Tucson is the bane of my lab existence sometimes!), etc...When I started working on P. syringae and plants as a postdoc, I would get very frustrated at my inability to replicate other peoples published experiments. The more time I spent in the lab, the more I realized that that's just the way it is sometimes. Don't get me wrong, there are a variety of other reasons that replication may fail, but when you're crying into your lab notebook at 3am keep in mind that it's incredibly hard to control both the host and pathogen growth in the exact way that the published experiments were performed.
I'm guessing that every PI that works with phytopathogens and plants has a story where there was an interesting phenotype which couldn't be replicated when they moved to a different lab/University. As a postdoc I remember screening through 50 or so very closely related isolates of P. syringae pv. phaseolicola to look for subtle differences in virulence on Green (French) bean. The goal here was to minimize random genomic variability between strains, by choosing very closely related strains, so that I could hopefully quickly pin down genotypic differences underlying interesting phenotypic differences simply by looking at the genomes. Basically GWAS for microbes to use a looser term. This was one of the experimental directions I started as a postdoc and was hoping to continue as PI in my own lab. One of the most solid results I had was a subtle difference in growth between two strains on French bean cultivar Canadian wonder. Canadian wonder is the universal susceptible cultivar to P. syringae pv. phaseolicola, which basically means that this plant was thought to be highly susceptible to all flavors of this particular pathogen. I had actually found that one strain (Pph 2708) grew 10-fold less than a very closely related strain (Pph 1516) in this cultivar (Fig. 1).
When I did pod inoculations, although the response was somewhat variable, there did seem to be some immune recognition of Pph 2708 compared to other strains (Fig. 2).
You can tell that there is something different in this inoculation because the water soaked halo is smaller for Pph 2708 than other strains, except for the avirulent mutant that lacks a functioning type III secretion system (Pph 1448a hrcC-).
So there it is, I've got two very closely related strains of P. syringae that slightly differ in pathogenicity. I have genome sequences for these (will link when I've stored up the strength to navigate the Genbank submission). There aren't many differences between them, on the order of hundreds of SNPs and tens of gene presence/absence. I had everything set up and ready to go to finish off the story once I got to Tucson and set up shop.
Here's where the problem arises...even though the result is solidly replicated under North Carolina conditions there is no growth difference between Pph 1516 and Pph 2708 in Tucson. A lot of strains I've worked with behave differently here in the desert compared to the land of tobacco and barbecue, and my guess is that it's because there is literally no humidity in the air. Since plant immune responses are linked to abscisic acid I'm guessing that the lack of humidity really annoys them when I take plants out of the growth chamber to perform inoculations. Not necessarily the lack of humidity per se, but the necessary change in humidity that accompanies taking plants out of the growth chamber. Yes, there are ways to Rube-Goldberg my way around this problem, and I have thought about a walk in growth chamber, but truth is other things worked better and I've concentrated on them. On top of that I'm using slightly different soil (what I could get my hands on), it's a different growth chamber, etc...Point is, I have a result that I would not think twice about publishing if only I hadn't tried to replicate this experiment in a different place. This happens a lot.
Some of the chatter has been along the lines of "BUT...REPLICATION IS A PILLAR OF THE SCIENTIFIC METHOD. THERE IS A SERIOUS PROBLEM IF MOST STUDIES CAN'T BE REPLICATED. WASTE OF THE MONEYZ!!! GRUMBLE GRUMBLE..."
At the top of this post I'm hoping to add a slightly more nuanced opinion here, followed by some unpublished results at the bottom to serve as a cautionary tale. I don't really disagree with worries about the state of science. Replication is of the utmost importance for research, and if results aren't robust there must be a way to keep track. Perhaps post pub peer review and comments will fill this particular niche. Experiments now are built on a foundation of experiments and models pioneered over years and decades. If you are interested in getting involved in a new research direction, one of the most important things to do is actually see if you can replicate foundational results in your hands in your own lab. That being said, biology is hard. Replication of single experiments under well controlled conditions can easily be thrown off by Rumsfeldian unknown unknowns. I remember hearing from someone (I want to say it was Paco Moore and that there is a paper somewhere on this which I can't find with quick google searches) that measurement of fitness in the context of Rich Lenski's long term E. coli experiment can be slightly altered by University water quality. In grad school I remember Patrick Phillips describing an experiment with nematodes where the assay would only work for about two weeks a year because the stars and sun and temperature aligned to yield the perfect experimental environment. It turns out that physiology and behavior of living organisms can be extremely sensitive to just about everything if you measure closely enough.
This problem is compounded even more when you are dealing with multiple living organisms, for instance, when your research area is host-pathogen (host-symbiont, same diff) relationships. I can't speak for anyone that works with animal models, but I can definitely attest that plant immune responses are EXTREMELY sensitive to pretty much every stimulus you can think of. Since plant immune responses are dependent on cross-regulation across multiple hormonal pathways, even the slightest change in some environmental factors can completely shift the likelihood of infection. This is exacerbated by having to grow plants for multiple weeks before you can actually do the experiments, all the time worrying that some random lab malfunction (3am growth chamber overheating anyone?) will render batches of host plants unreliable. Different labs will have different water, soil, temperatures, humidity (low humidity in Tucson is the bane of my lab existence sometimes!), etc...When I started working on P. syringae and plants as a postdoc, I would get very frustrated at my inability to replicate other peoples published experiments. The more time I spent in the lab, the more I realized that that's just the way it is sometimes. Don't get me wrong, there are a variety of other reasons that replication may fail, but when you're crying into your lab notebook at 3am keep in mind that it's incredibly hard to control both the host and pathogen growth in the exact way that the published experiments were performed.
I'm guessing that every PI that works with phytopathogens and plants has a story where there was an interesting phenotype which couldn't be replicated when they moved to a different lab/University. As a postdoc I remember screening through 50 or so very closely related isolates of P. syringae pv. phaseolicola to look for subtle differences in virulence on Green (French) bean. The goal here was to minimize random genomic variability between strains, by choosing very closely related strains, so that I could hopefully quickly pin down genotypic differences underlying interesting phenotypic differences simply by looking at the genomes. Basically GWAS for microbes to use a looser term. This was one of the experimental directions I started as a postdoc and was hoping to continue as PI in my own lab. One of the most solid results I had was a subtle difference in growth between two strains on French bean cultivar Canadian wonder. Canadian wonder is the universal susceptible cultivar to P. syringae pv. phaseolicola, which basically means that this plant was thought to be highly susceptible to all flavors of this particular pathogen. I had actually found that one strain (Pph 2708) grew 10-fold less than a very closely related strain (Pph 1516) in this cultivar (Fig. 1).
When I did pod inoculations, although the response was somewhat variable, there did seem to be some immune recognition of Pph 2708 compared to other strains (Fig. 2).
You can tell that there is something different in this inoculation because the water soaked halo is smaller for Pph 2708 than other strains, except for the avirulent mutant that lacks a functioning type III secretion system (Pph 1448a hrcC-).
So there it is, I've got two very closely related strains of P. syringae that slightly differ in pathogenicity. I have genome sequences for these (will link when I've stored up the strength to navigate the Genbank submission). There aren't many differences between them, on the order of hundreds of SNPs and tens of gene presence/absence. I had everything set up and ready to go to finish off the story once I got to Tucson and set up shop.
Here's where the problem arises...even though the result is solidly replicated under North Carolina conditions there is no growth difference between Pph 1516 and Pph 2708 in Tucson. A lot of strains I've worked with behave differently here in the desert compared to the land of tobacco and barbecue, and my guess is that it's because there is literally no humidity in the air. Since plant immune responses are linked to abscisic acid I'm guessing that the lack of humidity really annoys them when I take plants out of the growth chamber to perform inoculations. Not necessarily the lack of humidity per se, but the necessary change in humidity that accompanies taking plants out of the growth chamber. Yes, there are ways to Rube-Goldberg my way around this problem, and I have thought about a walk in growth chamber, but truth is other things worked better and I've concentrated on them. On top of that I'm using slightly different soil (what I could get my hands on), it's a different growth chamber, etc...Point is, I have a result that I would not think twice about publishing if only I hadn't tried to replicate this experiment in a different place. This happens a lot.
Monday, September 2, 2013
Fear and Reviewing in Academia
I've got at least two things going against me. For one, most of human communication is non-verbal. Whatever I say or write in critique of a paper is always more easily misinterpreted than if I were to say the exact same words to the authors in person. Second, it's likely that inherent biases in our brains will always influence how you read and interpret a critique. Malcolm Gladwell sold a lot of books on this premise.
Within the last year I was a reviewer on a paper for a journal where technical aspects of experiments within the manuscript are the most important factor in acceptance. As a reviewer I had absolutely no problem with the technical aspects of the manuscript, but I personally think that the introduction and discussion should be completely rewritten to de-emphasize what ends up being the take home story. I wrote that I didn't think the manuscript should be accepted in this state and suggested a variety of other ways to report and analyze the data which would allow the paper to be received by a larger percentage of the relevant audience. I was essentially arguing over subjective differences between the authors and I, even though the paper was technically OK. Ultimately the paper was published without the changes. This is how the system works, and I'm OK with this outcome (again, the paper is technically OK).
I want to be able to describe the specifics of this experience in a blog post, and maybe even a manuscript because I think it highlights one major downside of the "publish if experiments are technically OK" suite of journals. I want to write a post-publication critique of this article and include my actual review. I'm motivated enough to write a paper highlighting the dangers of crystallizing subjective interpretations in the form of a manuscript that glosses over this subjectivity. All this being said, I am currently an assistant professor on the tenure track. I don't want to make enemies, even though (as anybody who knows me will attest) nothing I say is ever meant as an ad hominem attack. I can be direct and this is off-putting to some, but I do this for the sake of making the story better (It's the New Yorker in me). I think that science advances much further without in-fighting and with colloquiality. I simply want science and research to progress in an efficient way with self-corrections of confusing statements. We can disagree, but let's do this over a beer and shake hands at the end.
Since I'm currently untenured, I'm absolutely terrified at inadvertently pissing the wrong people off and therefore tanking my career (and my family's well being). There are always camps in science which disagree with one another. Some of the best examples are described in Provine's "The origins of Theoretical Population Genetics" and Hull's "Science as a process". Ultimately, I'm OK if I'm lumped into a camp in some way or another but I want this to be for strictly science reasons not personal ones. In order to get tenure in the US, I must have outside letter-writers from peer institutions (some chosen by me, some by the college). These letters will hopefully describe how I make worthwhile contributions and further research in my area of expertise. One bad letter can tank my career. It's possible that someone may read a blog post (or critique of a paper) and simply take it the wrong way. Since I'm reviewing these papers, they are definitely within my realm of expertise, and so the authors have a chance at being selected by my higher ups as letter writers. I worry that critiquing a paper I've reviewed will be looked down upon by the editor, who in many cases is within the ballpark of potential letter writers. If I critique a paper over subjective and controversial interpretations, there are others out there who may hold the same viewpoints (who aren't authors on the manuscript) that could be off put by my critique. Letters are just one aspect of tenure. What if these critiques limit the chances of me being asked to speak about my work at conferences? What if these critiques make it more difficult for me to publish my own papers or get grants due simply to psychology? Is that risk worth it even if post-publication review might make a difference or open up an important discussion?
There are a bunch of folks that describe a utopian world where post-pub review is the norm, reviewers are always named, and reviews made public. I want to live in a world where I can sign my name to reviews and comment and critique papers in blog form or in a comment box next to the article. I want to be able to write papers with an opposing viewpoint. Often times fears of this world are stated hypothetically. I'm aching for a real and open discussion about the topics I raised in my original review, I think this would hugely benefit the field. I'm terrified, at least at this point in my young career, at what happens if I become the dog that catches the car. Maybe anonymity and pseudonyms are best for some things...
I don't know that there is a fix because of the way human brains work.
Update: For some the comment box works, for others not so much. Feel free to email me comments and I'll post (I'm pretty easy to find).
Comment from Rich Lenski (http://telliamedrevisited.wordpress.com):
I think there are three issues here that I’ll try to unpack. Issue #1 is the worry over potential repercussions for your career from the authors of the paper. That’s obviously important, but let’s set it aside and look at the other two issues.
Within the last year I was a reviewer on a paper for a journal where technical aspects of experiments within the manuscript are the most important factor in acceptance. As a reviewer I had absolutely no problem with the technical aspects of the manuscript, but I personally think that the introduction and discussion should be completely rewritten to de-emphasize what ends up being the take home story. I wrote that I didn't think the manuscript should be accepted in this state and suggested a variety of other ways to report and analyze the data which would allow the paper to be received by a larger percentage of the relevant audience. I was essentially arguing over subjective differences between the authors and I, even though the paper was technically OK. Ultimately the paper was published without the changes. This is how the system works, and I'm OK with this outcome (again, the paper is technically OK).
I want to be able to describe the specifics of this experience in a blog post, and maybe even a manuscript because I think it highlights one major downside of the "publish if experiments are technically OK" suite of journals. I want to write a post-publication critique of this article and include my actual review. I'm motivated enough to write a paper highlighting the dangers of crystallizing subjective interpretations in the form of a manuscript that glosses over this subjectivity. All this being said, I am currently an assistant professor on the tenure track. I don't want to make enemies, even though (as anybody who knows me will attest) nothing I say is ever meant as an ad hominem attack. I can be direct and this is off-putting to some, but I do this for the sake of making the story better (It's the New Yorker in me). I think that science advances much further without in-fighting and with colloquiality. I simply want science and research to progress in an efficient way with self-corrections of confusing statements. We can disagree, but let's do this over a beer and shake hands at the end.
Since I'm currently untenured, I'm absolutely terrified at inadvertently pissing the wrong people off and therefore tanking my career (and my family's well being). There are always camps in science which disagree with one another. Some of the best examples are described in Provine's "The origins of Theoretical Population Genetics" and Hull's "Science as a process". Ultimately, I'm OK if I'm lumped into a camp in some way or another but I want this to be for strictly science reasons not personal ones. In order to get tenure in the US, I must have outside letter-writers from peer institutions (some chosen by me, some by the college). These letters will hopefully describe how I make worthwhile contributions and further research in my area of expertise. One bad letter can tank my career. It's possible that someone may read a blog post (or critique of a paper) and simply take it the wrong way. Since I'm reviewing these papers, they are definitely within my realm of expertise, and so the authors have a chance at being selected by my higher ups as letter writers. I worry that critiquing a paper I've reviewed will be looked down upon by the editor, who in many cases is within the ballpark of potential letter writers. If I critique a paper over subjective and controversial interpretations, there are others out there who may hold the same viewpoints (who aren't authors on the manuscript) that could be off put by my critique. Letters are just one aspect of tenure. What if these critiques limit the chances of me being asked to speak about my work at conferences? What if these critiques make it more difficult for me to publish my own papers or get grants due simply to psychology? Is that risk worth it even if post-publication review might make a difference or open up an important discussion?
There are a bunch of folks that describe a utopian world where post-pub review is the norm, reviewers are always named, and reviews made public. I want to live in a world where I can sign my name to reviews and comment and critique papers in blog form or in a comment box next to the article. I want to be able to write papers with an opposing viewpoint. Often times fears of this world are stated hypothetically. I'm aching for a real and open discussion about the topics I raised in my original review, I think this would hugely benefit the field. I'm terrified, at least at this point in my young career, at what happens if I become the dog that catches the car. Maybe anonymity and pseudonyms are best for some things...
I don't know that there is a fix because of the way human brains work.
Update: For some the comment box works, for others not so much. Feel free to email me comments and I'll post (I'm pretty easy to find).
Comment from Rich Lenski (http://telliamedrevisited.wordpress.com):
+++
I think there are three issues here that I’ll try to unpack. Issue #1 is the worry over potential repercussions for your career from the authors of the paper. That’s obviously important, but let’s set it aside and look at the other two issues.
Issue #2 is that the authors of this paper ignored your useful suggestions. Nonetheless, the paper was accepted and published. That’s annoying. But from what you wrote, it seems you don’t think that particular paper is a very important one in the grand scheme of science. So I think you can let it go with respect to #2, and focus on the interesting and important work that you yourself are doing.
Issue #3 is your broader concern that journals that require only technical correctness may be weakening or diluting the scientific literature. In that case, if you feel strongly about it, then I suggest you look for an outlet where you could write a short editorial or perspective on this issue. You could mention that you were involved in such a situation, but there's no need to name authors or even the journal (or you might mention several journals where this is the policy). To illustrate what you’re talking about, you could construct a strictly hypothetical case where: a paper is technically correct but ignores some issue; a reviewer asks that issue to be explicitly noted; the authors ignore the advice; and, because the paper is technically correct, the editor gives the go-ahead and it’s published. Given all the subtleties and complexities of real science, it will probably be easier for you to construct and explain a hypothetical case than to explain the actual case that bothers you. Plus, notice that issue #1 has gone away!
+++
Tuesday, August 27, 2013
So you want to be a postdoc
As with many of these posts so far, I was slightly involved in a twitter conversation last week that touched on a topic I've been meaning to write about. What makes for a good postdoc experience? Keep in mind that I completely understand that everyone is different, and so the following certainly doesn't apply universally. In the very least this should provide some insight into how I run my lab and what I expect from people within the lab (including PDs), so if you're considering working with me in the future take these words as a brief intro into my style.
1) Be able to say "No" to your PI
As a PI, it's very easy to come up with ideas when reading papers and seeing talks. There are all sorts of new projects in every direction and this can be kind of overwhelming. Keep in mind that the goal as a PD is to write grants, papers, and generally be productive by seeing experiments through tho the end. It is very easy for your PI to say "why don't you try this" or "maybe this is something we should think about" without having to actually do the experiments. One of the most important skills as a postdoc is to be able to say no to your PI. If you can't say this simple two letter word without anxiety, you will simply run out of time in the lab and be swamped. Extra bonus, this skill often comes in handy later after you've landed that tenure track job and you're asked to be on every committee possible.
2) Don't take everything your PI says as gospel
Your PI is a researcher just like you...the difference is that they're more experienced at the job. They've likely interpreted more data sets, read more papers, dealt with more rejection, etc... Simply stated, your PI has had more practice than you at your job. However, within this context, realize that PIs are wrong all the time. If we mention/cite a paper we may be misremembering it. There may be some new and better paper (which we haven't read because, trust me, it's hard to keep completely up on the literature in real time) that has disproved the first. There's a very real chance that the data we remember is more nuanced than we think it is. Always read the primary literature and interpret the data for yourself.
3) It's OK if your PI disagrees with you, but know when their evidence is overwhelmingly good
That being said, your PI isn't wrong all the time. There will be times when you want to argue over interpretation, and that's OK, but learn to know when you've lost the argument. Trust me, this will save you much time and effort in the end.
4) Help your PI be a better mentor
I am very good at being me as a researcher. I understand my own body rhythms and know when my most efficient working hours are. I know exactly what type of mentorship and interactions I needed to succeed. I understand myself reasonably well, but everyone is different. One of the most difficult parts of mentorship at any level is understanding what the other person needs from you in terms of opinions, information, and interaction. How do you motivate someone else? You will have a much more successful PD (I think) if you can discuss with your PI exactly what kinds of feedback and interaction you need and expect. Think about what kinds of feedback you require in order to succeed. Have an open discussion, in the end this is the best possible situation for both of you.
5) Don't be afraid to start small pilot side projects
Never be scared to start small projects on the side (for me small projects require less than about 100$ of new supplies). If money's an issue your PI will let you know. If you read about a new technique, try it and see what happens. Screen a bunch of isolates for presence of a PCR product. Mix two strains together to see who wins. This will give you added experience designing experiments and interpreting data in a new framework. In the very least you will learn the hugely important skill of cutting bait when things aren't working. In the best case scenario you will develop projects that you can take with you to your new lab.
6) Have continuing and open discussions with your PI about which projects you can take
Data sets change. Some experiments work and others don't. The most tension I've seen between PIs and their PD always seems to be over ownership of projects. Be clear with your PI about what you want to take with you even before you start applying for jobs. If you've had some small side projects work, tell your PI and have the discussion about who "owns" what. The more open you are the clearer limits will be when you are starting your own lab.
7) Don't be afraid to apply for independent fellowships
I've seen some cases where PIs don't want their PDs applying for fellowships because the time invested could be better spent on experiments, I strongly disagree. If you land a tenure track job, you will have to write grants for a living and the more practice the better. Even if you have a paycheck through your PI's grants, independently earned fellowships are a huge CV boost that can help you land a job. It's worth the effort, just make sure you don't drop the ball on your experiments.
8) You are not hired as a technician
You aren't there to have your PI feed you experiments to do, you're hired as a PD to be an independent thinker. To design new experiments, to read papers, to try and figure out new directions for the project to go. It's a bad situation if your PI is hawking over you and giving you precise direction at every step. You will not develop the skills needed as a tenure track researcher and your PI missed a golden opportunity to push their research program forward.
9) Take every opportunity to speak, teach, and mentor
It's very likely that you will have to do these things when you are a PI, and (as I've said a bunch of times above) the more practice you have the better. If you have the chance to give guest lectures or teach a course (so long as your PI is OK with this) go for it. You will never understand a topic better than when you have to explain it to someone from first principles. You may even see the problem in a new light or make new connections. Practice can only help you out later when your doing these things continuously.
10) Enjoy your life as a postdoc
Your postdoc is likely the last time, for a while, that you will get to decide where you want to live. The job of being a PD is about performing experiments and writing papers, but you are a person outside of the lab too. A researcher's life is stressful, so use the time outside the lab to enjoy the world around you. Feel free to go to a lab X to work on an awesome project, and completely disregard the outside world, but I'm just saying that there is more to life. I often find that some of my best thinking gets done while I'm out running...There might not be as awesome a project in lab Y, but if the quality of life is better you may end up with a more fruitful and fulfilling postdoc experience.
1) Be able to say "No" to your PI
As a PI, it's very easy to come up with ideas when reading papers and seeing talks. There are all sorts of new projects in every direction and this can be kind of overwhelming. Keep in mind that the goal as a PD is to write grants, papers, and generally be productive by seeing experiments through tho the end. It is very easy for your PI to say "why don't you try this" or "maybe this is something we should think about" without having to actually do the experiments. One of the most important skills as a postdoc is to be able to say no to your PI. If you can't say this simple two letter word without anxiety, you will simply run out of time in the lab and be swamped. Extra bonus, this skill often comes in handy later after you've landed that tenure track job and you're asked to be on every committee possible.
2) Don't take everything your PI says as gospel
Your PI is a researcher just like you...the difference is that they're more experienced at the job. They've likely interpreted more data sets, read more papers, dealt with more rejection, etc... Simply stated, your PI has had more practice than you at your job. However, within this context, realize that PIs are wrong all the time. If we mention/cite a paper we may be misremembering it. There may be some new and better paper (which we haven't read because, trust me, it's hard to keep completely up on the literature in real time) that has disproved the first. There's a very real chance that the data we remember is more nuanced than we think it is. Always read the primary literature and interpret the data for yourself.
3) It's OK if your PI disagrees with you, but know when their evidence is overwhelmingly good
That being said, your PI isn't wrong all the time. There will be times when you want to argue over interpretation, and that's OK, but learn to know when you've lost the argument. Trust me, this will save you much time and effort in the end.
4) Help your PI be a better mentor
I am very good at being me as a researcher. I understand my own body rhythms and know when my most efficient working hours are. I know exactly what type of mentorship and interactions I needed to succeed. I understand myself reasonably well, but everyone is different. One of the most difficult parts of mentorship at any level is understanding what the other person needs from you in terms of opinions, information, and interaction. How do you motivate someone else? You will have a much more successful PD (I think) if you can discuss with your PI exactly what kinds of feedback and interaction you need and expect. Think about what kinds of feedback you require in order to succeed. Have an open discussion, in the end this is the best possible situation for both of you.
5) Don't be afraid to start small pilot side projects
Never be scared to start small projects on the side (for me small projects require less than about 100$ of new supplies). If money's an issue your PI will let you know. If you read about a new technique, try it and see what happens. Screen a bunch of isolates for presence of a PCR product. Mix two strains together to see who wins. This will give you added experience designing experiments and interpreting data in a new framework. In the very least you will learn the hugely important skill of cutting bait when things aren't working. In the best case scenario you will develop projects that you can take with you to your new lab.
6) Have continuing and open discussions with your PI about which projects you can take
Data sets change. Some experiments work and others don't. The most tension I've seen between PIs and their PD always seems to be over ownership of projects. Be clear with your PI about what you want to take with you even before you start applying for jobs. If you've had some small side projects work, tell your PI and have the discussion about who "owns" what. The more open you are the clearer limits will be when you are starting your own lab.
7) Don't be afraid to apply for independent fellowships
I've seen some cases where PIs don't want their PDs applying for fellowships because the time invested could be better spent on experiments, I strongly disagree. If you land a tenure track job, you will have to write grants for a living and the more practice the better. Even if you have a paycheck through your PI's grants, independently earned fellowships are a huge CV boost that can help you land a job. It's worth the effort, just make sure you don't drop the ball on your experiments.
8) You are not hired as a technician
You aren't there to have your PI feed you experiments to do, you're hired as a PD to be an independent thinker. To design new experiments, to read papers, to try and figure out new directions for the project to go. It's a bad situation if your PI is hawking over you and giving you precise direction at every step. You will not develop the skills needed as a tenure track researcher and your PI missed a golden opportunity to push their research program forward.
9) Take every opportunity to speak, teach, and mentor
It's very likely that you will have to do these things when you are a PI, and (as I've said a bunch of times above) the more practice you have the better. If you have the chance to give guest lectures or teach a course (so long as your PI is OK with this) go for it. You will never understand a topic better than when you have to explain it to someone from first principles. You may even see the problem in a new light or make new connections. Practice can only help you out later when your doing these things continuously.
10) Enjoy your life as a postdoc
Your postdoc is likely the last time, for a while, that you will get to decide where you want to live. The job of being a PD is about performing experiments and writing papers, but you are a person outside of the lab too. A researcher's life is stressful, so use the time outside the lab to enjoy the world around you. Feel free to go to a lab X to work on an awesome project, and completely disregard the outside world, but I'm just saying that there is more to life. I often find that some of my best thinking gets done while I'm out running...There might not be as awesome a project in lab Y, but if the quality of life is better you may end up with a more fruitful and fulfilling postdoc experience.
Thursday, August 15, 2013
Is "Ecological Epistasis" a Good Term?
I've been inspired by a couple of recent twitter conversations I've had to write a post and basically lay out why using the phrase "ecological epistasis" triggers my population genetics spidey-sense.
The first conversation happened about a month ago while I was sitting through previews for the completely satisfying movie Pacific Rim.
Epistasis between the nuclear genome and #microbiome underscores the #hologenome Not a far fetched idea and soon to be non-controversial.The second happened yesterday (Ian is live tweeting a bunch of talks at BEACON and Maren Freisen (@symbiomics) was talking about her Medicago research)
— Seth Bordenstein (@Symbionticism) July 14, 2013
Friesen: Although she phrased it as ecological epistasis. #2013beacon.I'm using this space as a way to crystallize my thoughts and to try and solicit other opinions. I'm also going to try and be involved in Seth Bordenstein's G+ chat on the hologenome in a couple of weeks, so consider this a bit of a warmup.
— Ian Dworkin (@IanDworkin) August 14, 2013
Epistasis is a tricky word. Problems arise when different (yet highly related and somewhat overlapping) groups start to use the same word yet mean different things. One of the people responsible for making me the scientist I am today has written on this topic (here and here), so I won't go too much into it. To summarize though, you can define epistasis in the quantitative genetics sense (multiple loci interacting in a non-additive way), in the small genetic sense (two proteins actually interact or function in the same pathway as would be found by genetic screen) or you can define it in the larger genetic sense (interactions between multiple genes). Neither is wrong per se, but use of the same term can get confusing depending on your audience. I don't have a problem with any of these definitions, but I just think that making headway in biology always becomes more difficult when you have to start referencing quotes from Justice Potter Stewart.
So here's a couple of my problems with "ecological epistasis". This uses the latter definition of the term that I mention above, gene interactions writ large. If you have two co-evolving organisms, genes from one organism interact with genes from the other organism in the population genetics sense, fitness of one organism is dependent on the other organism, all well and good (if I'm misinterpreting, please let me know). We already have language to describe these circumstances though, in terms of Gene by Environment (GxE) interactions without the need to invoke the "e" word. In this case each organism is the co-evolving organisms environment variable. Why not modify this term a little bit and call it GxEG (environment/genetic) interactions? There is nuance in this specificity that isn't captured by using the term epistasis. This isn't really my area of expertise, but I'm guessing that dynamics that apply to interactions between genes residing in different genomes may be inherently different than those in linked together and vertically inherited.
The second idea that needs clarifying IMHO is what the limits on interactions between organisms are when speaking in population genetic terms. When I've seen the phrase "ecological epistasis" used, it's in reference to interactions between intimately co-evolving organisms. However, if you are going to define the term as interactions between genes in different organisms without specificity, you could extend the definition in absurdum. Much of my work focuses on plant pathogenic bacteria, and genomes of both the host and pathogen encode for proteins that mediate interactions between the two. Is this "ecological epistasis"? Stepping further back, this morning I killed a cricket that tormented my household last night (keeping my 8 month pregnant wife awake more than usual...I have no regrets about my actions). In result this is no different than a pathogen killing a host, just that co-evolutionary interactions are weaker between me and the cricket population at large than in typical pathogen/host dynamics. My foe and I both have genomes that encode for proteins that ultimately mediated our interactions this morning. Is this "ecological epistasis"? Ian Ziering managed to fight off a shark with a chainsaw:
I'll save my hologenome critiques (great term, needs limits on the definition) for a future blog/G+ chat. My point is simply that if you start defining interactions between organisms, that these interactions can take a wide variety of forms that you may not inherently consider. Specific wording could avoid me having to make sharknado references.
It's not that I think that using "epistasis" in the context of interacting organisms is improper. I think that the term is muddled enough as is that it doesn't make sense to use it for the sake of linking onto an already established (and muddled) term. Using "ecological epistasis" doesn't clarify things in the way that a more nuanced term could, at least to me, but maybe I'm just missing something?
Update: Maren Friesen has clarified what she was referencing in her talk:
ecological epistasis!=GxE; it's non-additive effects of spp on ecosystem @Symbionticism @surt_lab @IanDworkin @Graham_Coop @liveinsymbiosis
— ML Friesen (@symbiomics) August 16, 2013
So...4) non-additive interactions between species (not genes)
Update 2: Great response by Maren Friesen
Monday, August 12, 2013
What if Diet Soda Wasn't Diet?
Ideas are cheap, actually pulling off the experiments is the difficult part. Sometimes these experiments aren't even possible to do at the present time. I'm probably not the only one who has a running list of experiment ideas in a text document, many of which will never see the light of day. I'm going to start something new around here by posting about research/experiment ideas that I think would be interesting and informative, but which I have absolutely no time to carry out right now (however, if you're up for collaborating definitely shoot me an email!). I'm naturally curious, so it would give me great pleasure to see SOMEONE figure out the answers to these observations or actually carry out experiments. Hell, someone might have even already done the experiments (if so, please send me a link in the comments!). Use these posts for inspiration or even just to get a feel for how I think about science, especially if you're keen on being my grad student or postdoc in the future. Point is that ideas are cheap but my mind keeps grinding. So without further delay here's where it goes sometimes...
Since my undergraduate days I've had a thing for "diet" drinks. Soda, fruit juice, etc...I always go for the "light" version. First it was the deliciously aspartame-filled Diet Coke (I definitely don't have phenylketonuria) and I've since transitioned into deliciously sucralose-filled products. Supposedly, drinking diet products can help you shed weight (see here but also here). Diet soda et al. have no calories because they contain artificial sweeteners that can't be metabolized by your body. I've always believed this, I could be completely wrong but this seems right. Relevant to this story, it does seem as though drinking diet soda can actually make you gain weight and can increase the incidence of type II diabetes (Hmmmm...)
Here's the thing. Your body is also teeming with microbes, especially in your digestive tract, billions of them. Some of these can even aid digestion by breaking down products. If there is one thing I know that microbes are good at, it's adapting to use novel resources. Unexploited potential energy sources are just another niche that microbes can thrive in. I don't see why microbes can't break down, or easily evolve to break down, aspartame, sucralose, and Truvia.
So here's a couple of potential experiments. I'd like to take some gnotobiotic mice, as gut flora may influence their weight. In the lab I'd adapt a suite of common gut microbes to growing on one of the artificial sweeteners. Then I'd transplant these bacteria back into the gnotobiotic mice in one group, and "ancestral" bacteria that can't break down the sweetener into another group. Next I'd feed different groups of mice a diet supplemented with one of the three sweeteners (as well as a regular control diet). The null hypothesis in this case would be that there will be no different in weight gain attributable to evolved vs. un-evolved microbes. A second experiment is really just a converse of the first. Basically I'd feed mice with "normal" gut flora a diet supplemented with one of the three sweeteners or the control diet with none. Then I'd measure if the ability of gut microbes to digest the artificial sweeteners changes over time. Null hypothesis here is that there would be no change in the microbe's abilities to break down artificial sweeteners over time.
So that's the outline. Thoughts? Has this been done? If someone does this will the artificial sweetener industry put a hit out on them?
UPDATE: Thanks for the input folks! Definitely understand now that there is much less artificial sweetener in diet soda than regular. Maybe not the best example, but, doesn't change the thought experiment. I know people who replace regular sugar with sucralose or Truvia in coffee and baking. They use the exact same amounts so, plus or minus differences in the molecular formulas, there's roughly the same potential mass going in.
Since my undergraduate days I've had a thing for "diet" drinks. Soda, fruit juice, etc...I always go for the "light" version. First it was the deliciously aspartame-filled Diet Coke (I definitely don't have phenylketonuria) and I've since transitioned into deliciously sucralose-filled products. Supposedly, drinking diet products can help you shed weight (see here but also here). Diet soda et al. have no calories because they contain artificial sweeteners that can't be metabolized by your body. I've always believed this, I could be completely wrong but this seems right. Relevant to this story, it does seem as though drinking diet soda can actually make you gain weight and can increase the incidence of type II diabetes (Hmmmm...)
Here's the thing. Your body is also teeming with microbes, especially in your digestive tract, billions of them. Some of these can even aid digestion by breaking down products. If there is one thing I know that microbes are good at, it's adapting to use novel resources. Unexploited potential energy sources are just another niche that microbes can thrive in. I don't see why microbes can't break down, or easily evolve to break down, aspartame, sucralose, and Truvia.
So here's a couple of potential experiments. I'd like to take some gnotobiotic mice, as gut flora may influence their weight. In the lab I'd adapt a suite of common gut microbes to growing on one of the artificial sweeteners. Then I'd transplant these bacteria back into the gnotobiotic mice in one group, and "ancestral" bacteria that can't break down the sweetener into another group. Next I'd feed different groups of mice a diet supplemented with one of the three sweeteners (as well as a regular control diet). The null hypothesis in this case would be that there will be no different in weight gain attributable to evolved vs. un-evolved microbes. A second experiment is really just a converse of the first. Basically I'd feed mice with "normal" gut flora a diet supplemented with one of the three sweeteners or the control diet with none. Then I'd measure if the ability of gut microbes to digest the artificial sweeteners changes over time. Null hypothesis here is that there would be no change in the microbe's abilities to break down artificial sweeteners over time.
So that's the outline. Thoughts? Has this been done? If someone does this will the artificial sweetener industry put a hit out on them?
UPDATE: Thanks for the input folks! Definitely understand now that there is much less artificial sweetener in diet soda than regular. Maybe not the best example, but, doesn't change the thought experiment. I know people who replace regular sugar with sucralose or Truvia in coffee and baking. They use the exact same amounts so, plus or minus differences in the molecular formulas, there's roughly the same potential mass going in.
Monday, August 5, 2013
Yes Mom, I do study GMOs
Reading Amy Harmon's great piece on GMOs and citrus greening inspired me to write this post. What follows is a slightly fictionalized account of a conversation I had with my mom. Don't worry, these conversations actually happened pretty much how I describe. I recently stopped home for a couple of days (my favorite conference to attend is but 2 hours away from my parent's house in VT) and eventually found myself arguing with her about the benefits of genetically modified organisms (GMOs). Her main comment was something along the lines of "How do you know what happens when you stick a lemon gene into corn. There could be horrible side effects". I found myself making the case that substantial scientific evidence exists concerning on the safety of GMOs and human health as well as describing how corn was completely different from it's non-domesticated (and hence non-genetically modified) ancestor teosinte. Standard stuff really, and the conversation ended in rhetorical standstill as is par for the course when I disagree with my parents.
A few hours later my mom asked me about my own research program. I started to tell her about horizontal gene transfer (HGT) in microbes, how the transfer of such genes is a driving force for microbial evolution, and finished by describing how we know very little about the side effects of HGT. Then it hit me, my research links up perfectly with the discussion about the side effects of GMOs. HGT is a natural process that is effectively indistinguishable from the creation of GMOs. At a forest through the trees level specific genes start out in species A and are transferred to species B. In the case of HGT, the vector for transfer can be a plasmid/phage/transposon/etc whereas for GMOs the vector can be a plasmid/phage/transposon/etc. In the former, random chance (and many other factors such as environmental proximity) determine which HGT events occur, whereas in the latter it's humans that determine which occur. The only (arguably subtle) difference between HGT and GMOs is what structures selection pressures. In the case of HGT, natural selection culls out unproductive combinations of genes and backgrounds whereas with GMOs humans directly select and screen for the most "productive" combinations. You could even argue, thinking about the selection pressures on the movement of antibiotic resistance genes in microbial pathogens, that there is substantial overlap even in selection pressures. If you just focus on the movement of genes and don't worry about the how, the natural process of HGT and artificial process of GMO creation are exactly the same. What we learn about the side effects of HGT will be directly applicable to understanding the side effects of GMOs, i.e. for figuring out how badly a single lemon gene would screw up your tasty corn. My research can actually be able to address my mom's original question.
"Ahh...but Dave", you might say, "microbes are different than corn". Well, it turns out that HGT occurs much more frequently in multicellular eukaryotes (like corn) than we previously thought. Aphids come in different colors because they have acquired carotenoids from fungus. A substantial portion of the genome that codes for your steak is potentially derived from snakes (arguing about the precise percentage can get a little hand-wavy since this may only be one HGT event). Michael Douglas may have gotten oral cancer because of viral HGT. Perhaps most relevant to this discussion, there is a gene in sorghum and rice that is has been acquired from a parasitic plant. The list goes on and on and will only grow as more genomes are sequenced. Yes mom, even though I study the transfer of microbial genes, I'm still studying nature's GMOs.
A few hours later my mom asked me about my own research program. I started to tell her about horizontal gene transfer (HGT) in microbes, how the transfer of such genes is a driving force for microbial evolution, and finished by describing how we know very little about the side effects of HGT. Then it hit me, my research links up perfectly with the discussion about the side effects of GMOs. HGT is a natural process that is effectively indistinguishable from the creation of GMOs. At a forest through the trees level specific genes start out in species A and are transferred to species B. In the case of HGT, the vector for transfer can be a plasmid/phage/transposon/etc whereas for GMOs the vector can be a plasmid/phage/transposon/etc. In the former, random chance (and many other factors such as environmental proximity) determine which HGT events occur, whereas in the latter it's humans that determine which occur. The only (arguably subtle) difference between HGT and GMOs is what structures selection pressures. In the case of HGT, natural selection culls out unproductive combinations of genes and backgrounds whereas with GMOs humans directly select and screen for the most "productive" combinations. You could even argue, thinking about the selection pressures on the movement of antibiotic resistance genes in microbial pathogens, that there is substantial overlap even in selection pressures. If you just focus on the movement of genes and don't worry about the how, the natural process of HGT and artificial process of GMO creation are exactly the same. What we learn about the side effects of HGT will be directly applicable to understanding the side effects of GMOs, i.e. for figuring out how badly a single lemon gene would screw up your tasty corn. My research can actually be able to address my mom's original question.
"Ahh...but Dave", you might say, "microbes are different than corn". Well, it turns out that HGT occurs much more frequently in multicellular eukaryotes (like corn) than we previously thought. Aphids come in different colors because they have acquired carotenoids from fungus. A substantial portion of the genome that codes for your steak is potentially derived from snakes (arguing about the precise percentage can get a little hand-wavy since this may only be one HGT event). Michael Douglas may have gotten oral cancer because of viral HGT. Perhaps most relevant to this discussion, there is a gene in sorghum and rice that is has been acquired from a parasitic plant. The list goes on and on and will only grow as more genomes are sequenced. Yes mom, even though I study the transfer of microbial genes, I'm still studying nature's GMOs.
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