Sunday, February 19, 2017

Taking Stock 2/n How much should I work vs. how much did I work

Six years ago (nearly to the day) I started my lab at the University of Arizona. There have been numerous ups and downs in science and outside of science, but I'm still here. My tenure package was submitted last August (I've gotten good news but nothing official yet), we've just undergone about the third dramatic change in lab personnel, and there's plenty on the plate for the future. I figured it was a good enough time to sit down and begin to reflect on these last 6 years and dream about the next 30 or so. Not sure how many parts this is going to be, hence the /n in the title, but for this second post I'm going to at least provide my own slanted perspective on work/life balance. 1/n here:

Every once in a while the same arguments pop up on the tweets...they go something like this:

followed by
and it escalates after that...
and so on and so forth.... Side note, for a great thread(s) check out what followed this tweet:

 Healthy discussion is great, sharing different viewpoints is great. They are all valid points, and much of the required nuance is trashed by the 140 character limit and difficulty in relaying tone because twitter.

I fall squarely in the camp that every single one of us has different work schedules and different requirements for how much to work in order to be "productive". Terry McGlynn hit the nail on the head exactly when he mentioned that one of the main problems with discussions about work/life balance in academia is that we inherently (ed: often not openly) disagree about what constitutes "success". Some want to win a Nobel prize. Some want to make a difference in the lives of those who have no one else to encourage them. In many ways, these are equally difficult challenges. There are many variations on what "success" is, and they're different for everyone.

One of the greatest challenges I've seen with being a PI is that, in the US system at least, we become used to judging our own worth compared to other people's metrics. Did I get an A in the class? Where do I rank with my GPA? This doesn't ever stop. Did I get into the program I wanted? That person in my cohort just published a paper, why haven't I published a paper? That person works more than me? and so on and so forth. At some point (I'd argue in grad school) we lose the ability to have definitive metrics to compare ourselves against and this is completely unsettling when your career is firmly placed in the context of data gathering. That first day you step into your empty lab space, you try and grab onto any foothold you can to try and gauge whether you are doing *enough*. Ideally, you have great mentors that can guide you along the way and offer advice, and ideally you are getting feedback from those on the tenure committee and during annual reviews, but there's no magical metric to tell you whether you're doing *enough*. Don't even get me started "how many grants and papers you need for tenure" because it's different for different people even in the same department. Allow me an (American) football metaphor for research...some teams try to score a touchdown every single play. Some teams are content to move the ball 3 yards forward every single play. You can be successful using both strategies and mixes of both but both require you to just move the ball forward by the end of the game. I'm not sure where defense plays into this, but I was on a roll so there you go.

There have been weeks when I've worked 80 hours and those that I've worked 0. There have been days when I've worked 24 hours (usually before a grant deadline). There have been many days that I haven't worked because (at least for me), I need to take at least one day fully off every week to stay sane. I tell the people in my lab that my metric for judging whether things are on the right track is that we should set up mutually agreed upon goals and work towards making constant progress towards these goals, and yes, I count failed experiments as constant progress. Aside from having to OK hours on a timesheet, I don't really keep track of how much or how little people work. I figure that everyone has their own rhythms and effective times and encourage them to make the most effective use of their time. I try to set an example through my own actions, but I don't expect them to exactly copy my work habits. Have goals, keep your eye on them, work enough to give yourself a fair chance at accomplishing them. Reevaluate the goals frequently because contexts change. Perhaps the second greatest challenge I've had as a PI is learning to have empathy for other people's working and learning styles. It's not easy, but it's incredibly important. That said, I understand and respect the other side of the argument but it's just not for me. We often have the opportunity to choose what we want in the labs we join, and I think the best we can do is represent how we view work/life balance and *success* so that those that are actively choosing can make an informed decision.

This is getting long, so one last observation about what "work" is. I've learned that I do my best writing and thinking when I'm running or otherwise being active. I've written a lot of my papers while not actually writing. I've written a lot of my papers and grants while not "at work", while in the shower, sometimes in dreams (for real...just kind of wake up sometimes and write stuff down and it's coherent). Does this kind of *work* play by a 9-5 schedule? Is it actually work? I have not clue...but it's what I've done and it's what works for me. I think this was Kern's point above before the nuance was lost to the twitter Gods.

Wednesday, February 15, 2017

Teaching Microbiology in the Era of #Fakenews

Wanted to briefly post about an interesting situation I'm encountering right now in my Microbial Genetics class. We just had a quiz exercise where I effectively asked this True/False question:

True/False During bacterial transcription, RHO-DEPENDENT terminators utilize a hairpin loop

To me, and my understanding of transcriptional termination, the answer is clearly false as far as science knows right now. I went over factor dependent and independent terminators and focused on how factor independent terminators can be identified by hairpin loops in the DNA/RNA sequence (usually followed by something like a run of Poly-Us) and contrasted this with how there was only a sketchy signal for rut sites in terms of rho-dependent termination.

It sucks to be wrong, and especially to make mistakes when lecturing to a class of undergrads, but there is a part of me that loves it when I get challenged by what I've said with actual data. It's a learning opportunity and I enjoy when students go above and beyond to find other sources of info.
My standing agreement with students is that if they can present me with primary literature that demonstrates their argument, I'll give them points regardless of how the quiz was originally marked. I think that's only fair...

However, a couple of times I've run into a situation this semester where students cite non-primary lit sources to demonstrate their point. In the case of the quiz question above, they've cited a couple of YouTube videos about Rho-dependent terminators (here and here) that AFAIK incorrectly state that rho uses hairpins.

I see this as a very small battle in the larger world of #fakenews where we are constantly barraged with other peoples digested opinions and views rather than read the original undigested words. Regardless it's troubling. I'm going to mention this in class example in class today, and point out that "when in doubt find a primary source and look at the original data" is a great go to for deciding what's "real" in these situations.

Friday, January 6, 2017

Taking Stock 1/n

Six years ago (nearly to the day) I started my lab at the University of Arizona. There have been numerous ups and downs in science and outside of science, but I'm still here. My tenure package was submitted last August (I haven't heard back yet but expect to soonish), we've just undergone about the third dramatic change in lab personnel, and there's plenty on the plate for the future. I figured it was a good enough time to sit down and begin to reflect on these last 6 years and dream about the next 30 or so. Not sure how many parts this is going to be, hence the /n in the title, but for this first post I'm going to try and be open about self care needs and the internal struggles that I'm guessing a lot of us face. 

I've always been of the mindset that it's not about how much you work, but whether you make progress towards goals in that time. I've tried to encourage my lab members to take care of themselves mentally, to take breaks when necessary and enjoy the flexibility that comes with working in a research lab. I'm well aware that that line of thinking works for me, but it doesn't work for everyone and so please don't take this as a prescription for what to do but as an example of what's been done. For five years I thought I had everything under control. Sure, research and publishing and funding is always a struggle but it's been a manageable struggle. That all changed seven months ago and I'm still recovering.

My wife's pregnancy had been pretty standard up until early June. At that point she was about 29 weeks pregnant, but was also self employed as an equine vet and still going out to calls. She had been around horses all her life and has cultivated an intuition around these animals that's second to none. Was I worried about her job and my unborn son, deep down yeah. However, I trusted my wife to take all the necessary precautions and be careful, and by all measurements she did and was. I still remember that call in early June because it's one of those moments where time stands still. She had been kicked square in the stomach by a horse, it had thrown her back into a wall and there was a deep cut in her head. Maybe a couple of broken/chipped elbows (never did figure that one out, it was the least of our worries). She was being rushed to the hospital, no clue of how bad anyone's injuries really were. Not going to show you the pic, but there was literally a horse-shoe shaped bruise right on her pregnant stomach.

These are the kinds of situations where your mind tries to prioritize everything into what's essential and what's non-essential. Essential was me getting to the hospital ASAP bc my wife was in and out of consciousness and they didn't know how bad the head trauma was. They didn't know what condition my son was in, there was really no way to know if he had enough oxygen, how badly the internal damage was. It's a unique method of torture, to be a researcher and be incapable of truly assessing how bad the situation was because the tools simply don't exist.

Fast forward and my son was emergency C-sectioned at 29 weeks. Somehow his head was pointing down so that if the horse landed any blow it was a glancing one on his legs. We still don't know if he lost oxygen in the womb at all, but the placenta was damaged. My wife pretty much stayed in the NICU for two months straight (plenty of stories about that for other times), while I watched my three year old daughter at home during that time. It's a testament to the flexibility of our jobs as researchers that it was possible for me to do that. Somehow I managed to get my tenure packet submitted. Somehow I managed to write a couple of papers. Somehow I managed to make the slightest of progress in the lab during that time. Do I remember much of it, not really. I was just focused on getting by day to day one step at a time. There was a lot of stress in directions that I wasn't ready for, but I grew numb to it all for the sake of getting to the next day. It wasn't really easier when Kyle came home from the NICU, but my wife is a superhero and I'll leave it at that.

Why do I mention all of this? Part of it is catharsis. Part of it is that I haven't had the time to properly thank everyone for their help during this time, and so please take these lines as a thank you. All of the support meant so much and made everything easier to cope with. I mean that. I'm also writing this to say that, it has to be OK for us as researchers to be given time to get through difficult situations. Give your people the space they need (within reason). Give your people the help they need whether it be mental or physical. Whether you are an undergrad, grad student, postdoc, can be extremely challenging. I picked this career because of the flexibility and this summer solidified that. Everyone deserves the support that I received regardless of station.

I'm also writing this to describe that I'm not completely back yet. I've tried a couple of times to sit and write grants like I did before, to just pound them out, and I can honestly say that I don't have that gear back (hopefully it comes back...having a 7 month old doesn't help with sleep patterns). I'm getting back to how I felt pre-summer of 2016, but it's happening more slowly than I'd like. I would love to just flip a switch and have everything feel like it did before, but it doesn't work that way. I can't help but think that those months of emotional numbness that it took just to survive have left a bit of an emotional hangover. I've had more science energy lately and I feel better and more energetic every day about my research. I don't know how the story ends, but I do love both my family and my job. Sometimes you don't get to choose how to devote your emotional energy. With help, it's possible to muddle through to a more stable place. I've been way luckier than many and I'm looking forward to what the future has to hold. Still taking things one step at a time though, and that has to be OK too. 

Tuesday, December 13, 2016

mSphere Direct and Peer Review

I guess I've gone through the inevitable "slowdown in blog posts" phase of the blog. To be honest, it's not that I haven't had things to say, it's just been quite hectic as many of you know. More on that later...It's taken some time, but I've found my footing again so it's time to blog some more.

What's drawn me out today is the unveiling of a new take on peer review and publication by one of the societies to which I belong, the American Society for Microbiology (ASM) (see descriptions of mSphere direct here and here). ASM hosts many different journals under its umbrella and I try to publish in ASM journals when appropriate. From my perspective, it's a great society consistently headed by some forward thinking people. Despite some internal disagreements about direction across the membership, the divisions of which are readily apparent if you've ever attended the ASM Microbe conference, I'm going to still be involved and publish there because it's important to support your societies.

A year or so ago ASM started two new journals, mSphere and mSystems. My tl;dr take on mSphere is that it's a useful addition to the cannon which seeks to minimize waiting time to publish manuscripts while filling the niche of a slightly more microbe-centered PLoS ONE. A lot of good papers thus far there, with less emphasis on flashiness of the story and more emphasis on supporting good work. As far as I can tell, mSphere direct will be a new track for publication into mSphere with the goal of relaying "quality" and peer reviewed work as fast as possible.

The mechanism by which mSphere direct is going to minimize waiting times in peer review is that they will now allow you (the author) to seek out and suggest your own reviewers. You will solicit these reviews, and then work with the reviewers to come to agreement on a publication quality manuscript. In some respects this is kind of what we all hopefully do with co-authors anyway (in the perfect theoretical Platonic world where everyone has infinite time to review papers that your name is on with a fine-toothed comb) except that the reviewers will not be co-authors. Instead, the reviewers names will appear along with the paper as a method of accountability. When you submit to mSphere direct, you will submit these reviews and review history and editors at the journal will give you a thumbs up/thumbs down within a few days. No revisions after that, just yes or no. If yes, it's published. Now, this is the natural marriage of two different ideas that ASM/mSphere have implemented in the past: 1) allowing ASM fellows to solicit reviewers along a "fellows track" and 2) mSphere allowing you to include previous reviews from other journals along with your submission to speed the process. I'm guessing that both of these previous ideas have worked reasonably well, to the point of mSphere starting mSphere direct.

I'm guessing that a lot of your own opinions about mSphere direct are going to depend on what you view as main problems with current peer review. There are plenty of problems to choose from, but we all have our own focuses of priority on problems that "really matter" compared to those that are just "burdens" on the system. It's not my place to tell you what to think about this, we all have our own priorities, but I am going to tell you what I think....

mSphere direct's goal is to reduce waiting times to the publication of peer-reviewed manuscripts. Full stop. In my opinion, the advent of preprints have somewhat blunted this problem (obviously depending on how your own scientific discipline has embraced preprints and scientific priority). To me, you post a preprint and so long as the story is scientifically valid that establishes priority. Others might think priority is only established after peer review...that's their prerogative. I'm not a zero-sum worldview person and so I think both can exist at the same time and both work, but given multiple thought lines, this is inevitably going to lead to disagreements that screw over people. I don't know a way around this, suffice it to say that problems of scientific priority have existed even in the "old days"...note how many Nobel Prizes have been awarded to those working in animal systems for phenomena that have been previously described in plants. C'est la vie. I also think that a hybrid system utilizing thorough comments on preprints followed by submission to mSphere direct should also be a valid track and that's up to the editors to decide (I would definitely strongly support such efforts though).

What I and many others that are hesitant about mSphere direct worry about, is that we prioritize faithfulness of the review process over publication times (again, my worldview is heavily biased by being a preep-er and thinking that preprints establish priority). I can also speak to my fears growing up in a scientific world where a similar publication track at PNAS led to <multiple facepalm> levels of crappy papers. I worry that the review process of mSphere direct will enable more crony-ism in science where you pick your buddies as reviewers (or heaven forbid actually offer payments for good reviews) and then submit to mSphere direct. Right now it's on the editors to ensure that the review process is thorough (I'll put my faith in ya'll so long as quality papers come out of this track) as well as firm commitments to avoid reviewer COIs. I can speak as a researcher that avoidance of COIs, while a good first step, will not eliminate crony-ism int the review process. Our best reviewers are those that disagree with us but which we can convince that our story is legit. This type of review process will inevitably soften the review process (for better or worse) because the author will know who the reviewer is and because we all have our scientific friends and enemies. If everyone published with mSphere direct, there would be less worry about "reviewer 3" but...and although it sucks when you get harsh long as the reviews are fair they make the manuscript better. Naming reviewers helps, but it doesn't eliminate the problem.

Overall, I'm cautiously hopeful about mSphere direct but I think they can make one change that will solidify my faith in the journal. Aside from publishing reviewer names, publish the reviews and responses of each paper along side the paper. Let us as critiques see which of certain valid points about the paper were brought up by reviewers and dealt with by authors. Give the reviewers that participate more of an incentive to do a great job reviewing (other than just having their names associated with paper review). I suggest this out of hope, and out of wanting to see my scientific society survive, thrive, and revolutionize.

Thursday, March 31, 2016

Reconciling the Hologenome

There have been a couple of rounds of back and forth in print and online (here, here, here, here, and some shameless self promotion here and here...among multiple other places over the years). There is apparently an mBio special series starting today that teases a "heated discussion" akin to discussion about the neutral theory.

I don't have skin in this game (yet), and have tried to see and understand the points from both "sides". I lean towards the view in the Douglas and Werren paper, but I also see value in ascribing names to concepts. Yes, there are actually valid points on both sides. However, I'm starting to get frustrated by the whole discussion simply because I can't see a reasonable goal to work towards, and to me it seems as though both sides are starting to talk past one another. I won't go too much into it in this post, but I'll try and describe how I see the crux of the disagreement. It makes sense in my own head, but apologies in advance for what I get wrong.

It seems to me that many on the "anti-hologenome" side (for lack of a better word) seem to argue that we have all the models we need right now to get to the heart of interactions between hosts and microbiomes. They point towards GxE, GxGxE, multi-level selection, etc...and cite papers showing that these topics can be dealt with using the tools available. Why invent another term? I feel the frustration that these researchers have because (disclaimer, again this is IMO right now and can change if I'm presented with a great argument or explanation) the holobiont/hologenome concept has some important internal inherent disagreements. To illustrate, I've seen multiple "pro-hologenome" folks say that the utility of the hologenome lies in being able to describe natural selection acting at the level of the host+microbiome. That there is some value added by considering these two entities together. That's all well and good, but if you define the hologenome in terms of selection than there isn't any good way to fit neutral microbes into this worldview (because selection won't affect them). It's an internal inconsistency that Seth Bordenstein has already tried to convince me doesn't exist. All I'm saying, you can't point towards being able to describe selection better as a holobiont (and have this be the main example of why the concept is useful) and then include subsets of the microbiome that are neutral.

To me, the "anti-hologenome" side wants to see the hologenome concept as something that can be a predictive tool for modeling species interactions. The concept is certainly not there yet and I'm not sure if that's really where it's meant to go (see below). The holobiont definition gets a bit fuzzy when you push the limits as many on the "anti" side seem to want to do. Where does it end? What microbes are included? What about non-microbes that are vertically transmitted? The answers may be available, but I haven't seen a clear articulation of this anywhere (sorry Seth). I *think* much of the "anti" side frustration stems from not having clear/crisp enough definitions of the terms involved or the situations where the hologenome concept may apply. Not clear enough for predictive modeling purposes anyway.

Like I said above though, there is value in the hologenome concept writ large! If you squint your eyes and take the 30,000ft view, it's great to have a term that describes natural selection acting at levels greater than single organisms. We can use these terms for public communication of why microbes and microbiomes are important and not to be feared. We can use these terms to capture the imagination of burgeoning scientists or those outside of the fields that we work in. The utility of the holobiont concept is about communication and you don't need to get deep in the details for this to be true. We do actually need another term and another way to explain things like GxGxE and multilevel selection because the older terms aren't cutting it. We don't need a holobiont concept to create new ways to model multi-level selection, but I don't think that's ultimately what it's for.

That's how I see it, and I'm firmly trying to straddle both sides.

Friday, February 26, 2016

Trying to build the cheapest computer that can run an Oxford Nanopore MinION Part I

One of the most difficult things to do in life is to admit that you don't know something. Along those lines, it also very difficult to stumble through learning things (and to make mistakes) in full view of the public. I'm about to do both, but hopefully this process is useful to someone out there. Also, feel free to chime in and tell me where I'm making huge mistakes.

Like many of you I've been following the sequencing developments from Oxford Nanopore pretty closely, and the results have been awesome so far. I'm excited to get a MinION and start playing around with collecting data. However, the first step in the process is finding a computer that actually meets the minimum specs to run a MinION (found here). The most important parts of this (at the moment) are that the machine must run Windows 7 or above, have a solid state hard drive that's big enough to handle the data coming off the machine, have 8Gb of RAM, have an i7 chip, and have a USB 3.0 port. Well, the only windows machine that my family owns is my wife's work computer (it's got the specs but there's no way in hell I'm messing with anything on that machine, out of fear). There are also a bunch of other folks who have reconfigured their other non-Windows machines to run windows, and while I could do that I wanted to take a different tack. So, my goal was to try and build a machine that meets the MinION specs while spending the least amount of money possible. Here goes....

I have hardly ever opened up the case on any of my computers before, and I would equate (at the start) my knowledge of what's inside a computer to "6 year old that is curious about how to make their gameplay better". Luckily, there are a ton of different forums, videos, and websites to guide you through every step of the way. Just know that no matter how much you learn, there are many 8+ year olds out there that can run circles around your computer building skills. I'm cool with that, I just want to build something that can sequence DNA using a USB stick.

First step was to survey the field and figure out what I needed to do. It turns out that Dell and HP build a lot of machines with decent processing power for business purposes that don't really have all the bells and whistles that other computers have. Since (I'm guessing) that these are all bought by businesses and then sold after a few years, it turns out that there are A LOT of these machines that you can buy refurbished. I didn't want to build a computer from scratch (too much of a leap), so I thought it might be good to find a refurbished tower that I could upgrade in other ways to meet the minimum specs. Things I looked for:

1) PCI express slot so that I could add in a USB 3.0 port
2) i7 chip
3) Running Windows 7

Turns out I found a machine that had all of this, and that also has a lot of space for expansion, for 279$ (HP Elite 8200 SFF). There are various flavors of "HP Elite 8200" machines, but I stayed away from the Ultra Slim model just because there wasn't a lot of capability for expansion. Likewise, I stayed away from the regular desktop because it was more $$$.

Here's what the inside looks like:

Next step was to buy a USB 3.0 upgrade, and there are a variety of different versions. If you go with the machine above, you want to be able to fit it in an SFF case, and so you want one that has a bracket for "Low profile" machines. Found one on Newegg for 10$. This comes with the driver you need to load it onto the machine (and which apparently worked the first time), and fits right into the PCIexpress 1x slot. One problem that I didn't anticipate, is that you need to provide power to the USB3.0 ports outside of the PCIexpress slot (on the version I bought this is supplied through a 15 pin SATA connection). There apparently are various ways to wire this, but the refurbished computer already had a splitter going to the DVD drive so that all I needed to buy was a 15 pin Male to 15 pin Female SATA connector (here) for 5$, and Voila! Not sure if this works yet, still waiting for delivery.

Last couple of steps are upgrading RAM and the solid state drive. The RAM is easy, the HP machine I bought has four slots for RAM, and you can buy this on (Crucial will even scan your machine beforehand to make sure the RAM fits). I didn't wan't to go overboard, so I bought 2xGb of RAM from them for 83$. I *think* that RAM works better when it's paired, so that's why I bought 16Gb total, but you might be able to get away with 8Gb if you're going minimum specs. Those basically just snap into the RAM ports on the machine. Easy Cheesy.

Last thing was to buy a solid state drive. Again, I went to and ordered a 500Gb drive (you can supposedly get away with 250Gb with the MinION, but I was advised that bigger is better in this case). Same deal, you can scan your system and make sure you're getting the right part and then order. That drive was 150$ total. When the drive came, I detached the SATA wires from the DVD port and connected them to the drive itself. Then I used this handy step by step guide to clone the original Windows 7 running hard drive to this new solid state drive, then unplugged both hard drives and swapped connections (and took the old hard drive out). Last step was to start the machine up again and, DAMN, it felt good when that machine booted itself up after I swapped hard drives. The SSD doesn't quite fit well in the case, although as long as I don't move it it should be OK for now. Looking for solutions for that in the future.

So there you go, a dedicated machine that can run an Oxford Nanopore MinION (in theory) for about 500$. I'll let you know in the next post whether it passes the basic spec tests before I actually burn in my MinION.

Sunday, February 21, 2016

Coevolution and the Microbiome

Coevolution is defined as cases where two (or more) species RECIPROCALLY affect each other's evolutionary dynamics. Reciprocally is highlighted in every way that I possibly could in the preceding sentence because this aspect really is key. It's a difficult concept to get a grasp on and an even more difficult concept to actually test in nature. I don't want to spend too much space going over the ins and outs of coevolution because numerous people that are smarter than I am have done that in accessible ways...My favorite being Dan Janzen's "When is Coevolution". (For other good lists that are slightly longer and more intense, see Scott Nuismer's or John Thompson's Google Scholar page). I'm missing a bunch of other stuff out there, but it's late so please forgive me and add any other great links in the comments.

I mention this because there is a lot of work being published on microbiomes right now, and I'm sensing a pretty strong tendency across manuscripts and presentations to state that microbiomes and their hosts have "coevolved". In some cases this is certainly true (best examples I can think of off the top of my head are nutritional symbionts in insects, some nodulating Rhizobia in legumes, Plasmodium in humans, and Vibrio-Bobtail Squid). Here's where it gets fuzzy, and I'm largely focusing on human microbiome studies here because they often get all the many cases where researchers claim that microbiomes and hosts have "coevolved" there is absolutely no evidence that this has happened. Sure, there are trends and correlations that make it seem likely that coevolution has taken place. However, read the Janzen piece above again and find me a study where researchers have reciprocally tracked genetic changes in the microbiome and have seen direct evolutionary (read:heritable) changes in human host populations. It's nearly impossible (let alone ethically challenging) to track fitness in human populations over time and cleanly and directly relate those to changes in the microbiome. Codiversification != coevolution, so any story that mentions Helicobacter pylori and humans is pretty much right out (h/t to Jonathan Klassen for that one). Moreover, health != fitness. By definition, obese people are unhealthy yet they can still have kids at a decent clip (note, I'm unaware of studies actually measuring the fitness affects of obesity in humans but would love to hear about them if you know of any). Likewise, much has been made about H. pylori affecting human health negatively through gastritis/gastric cancers and positively through asthma/GERD prevention. I'd love to hear how these things directly affect fitness in human populations, but there's absolutely no data to these points. Proto-humans might well have had gastric problems from H. pylori, but I'm betting that there were many other things that directly impacted their lifespans and fitness with greater magnitude. Please don't get me wrong, I'm not saying that it's impossible that humans and their microbiomes have coevolved, I'm saying that there is no direct evidence that directly addresses the hypothesis of coevolution outside of a handful of pathogens.

All of this is a roundabout way of saying that studying (and demonstrating) coevolution is really really really difficult. You need to actually measure how species 1 directly influences evolution in species 2 AND how species 2 then directly affects evolution of species 1. Reciprocality is key. There are many examples where species 1 influences some trait on species 2, but that doesn't mean that evolutionary dynamics in species 2 will be affected. Likewise, it doesn't mean that species 1 will then be reciprocally affected by this trait change.  Moreover, we don't have good models of host-microbiome coevolution because the math is difficult/complex so we therefore don't have very clear ideas about what parameters matter most to drive coevolutionary dynamics. One of my near to mid term goals in science is to try and change this, so as a first step I'm trying (fingers crossed) to organize a workshop at NimBios (probably in Fall 2016) to bring 35ish smart people from across the globe together to talk about how we begin to frame questions about host-microbiome coevolution. If you're interested please fill out the form at the following link:

I'll be submitting a workshop proposal by March 1st, and will keep you up to date on what's happening. If you're curious about NimBios and workshops, overview can be found here:

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