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.

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.

The second happened yesterday (Ian is live tweeting a bunch of talks at BEACON and Maren Freisen (@symbiomics) was talking about her Medicago research)

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.

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:

                                                          Is this "ecological epistasis"?

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:

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.

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.

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