The answer to life, the universe, and everything (not really).

I’ve been quiet here lately. But I’ve had things going on. Go check out my other blog The Quiet Branches where I write about plant science each week– it’s been a fun project. Then it has also been a crazy few months in the lab trying to meet several deadlines. And I’ve been taking more online classes. One in learning R and statistics…it’s only going OK on that front. The time it takes to concentrate and truly internalize everything is probably more than I actually have, but I think I am picking up a few things at least. 

I need a career and to feel like I have a life. It’s been really hard to sense that I do have a life even though I know the mere passage of time that I am aware of is life.

I realize I’m not entitled to anything. I am grateful for what I have. This is a call for more humanity out there. It may be there. I just can’t detect it because of where I am or maybe I have faulty sensors. I find it sometimes though.

I’ve been thinking a lot about work and how I really want to carve out a space to not make it all of who I am anymore. In fact, it cannot be all that I am anymore. That will kill me. I am more than my work.

Setting that boundary is difficult and doesn’t seem all that acceptable in the world of work today. Companies/employers are not your friend. And will basically take whatever they can get from you of value. And they don’t care what your life is outside of work so long as it doesn’t interfere with your work.

I’m sure I’m not the first to notice the blurred lines of work and life in modern times. And it seems like there is little slack for life events these days as a lot of us try to do as much as possible to prove our worth. At Tenure She Wrote, @SciTriGrrl wrote a post a few weeks ago about time management and carving out time for people that priorities at work that are truly important.

Prioritize until it hurts is something I’ve heard entrepreneurs say.


Everything will be OK…unless something goes wrong.

Perhaps it’s possible to work through that fever.

The science must go on.

In the entertainment/creative/pro-sports industries, they work sick all the time I hear. Unless you really can’t get out of bed, your’e at work. At least in those industries, they have brief periods of intensity and then they’re off for a time until the next job comes along and it’s intense again for a period of time. I’m not sure science is quite like that.


If you can’t get out of bed due to illness for a day or two…maybe you’re not cut out for being in that industry.

Now let’s say it’s not the flu, but depression or other mental illness that you’re working to manage. Or imagine a sick kiddo and need to stay home with them. I fear the mantra of “you only have value if you work” is the only acceptable way to have value in today’s world (at least in the US). It’s OK until some challenging thing happens and knocks you out of the game, no matter how resilient a person you are.

It’s like species being able to adapt to climate change. Some species undoubtedly will be fine and adapt quickly enough to the rate of change.

Others. Not so much.

Internal value doesn’t matter. The fact that I am enriching myself by reading ,writing, learning stats/R/coding at some level despite the fact that I’ll never likely be a master of any of it, trying to socialize more, being a decent person, helping friends do things. I hope these things are valuable. But fear they’re not. In and of themselves, they don’t produce money and therefore are not valuable.

I am exploring career options beyond academia and it’s really jarring to deal with the fact I feel like I’m basically killing all the training I have and starting completely over again. I know I’ll bring something of what I’ve learned to whatever I go on to do, but worry it’s not enough, never will be, and that basically ,I am useless. I really try not to think that way because obviously it leads nowhere good. At the least, it makes me beat myself up. At worst…

It is a hard mental habit to break.

I have to find evidence to reject the null hypothesis that I am not lifeless.

If the goal is to prove your’e so valuable and in demand that you never have to worry about anything ever, do you get to take breaks? Ask for help? Or is asking for help saying you can’t do things on your own, acknowledging humanity, and there’s just not room for that in the world. Humanity is not valuable.

Except that it is, of course. Why are we working except to keep humanity going. Even for-profit industry has a component of providing a service to the world.

Look like your’e interested, but not too interested, you don’t want to seem desperate, but also not completely aloof either. Where’s the right line? When do you cross it?

All the above thoughts indicates that I probably need to socialize more with close friends. Vacation. Something restorative I haven’t had in quite awhile. Being human in front of another human, not a robot.

I want a pub trivia team to go out with and have fun. And I haven’t been able to build one so far. But it will be a part of my life some how. Until then, I have Good Job, Brain at least.

What is it I do that no one else can? I freely admit my struggles on the internet…that I’m human. I don’t think I’m alone or remarkable for that. I hope I’m not alone in my thoughts. I have learned to manage my depression, which is not nothing, but again, I don’t think anyone actually cares about that.

I can write a lot of words.

I can listen. I can synthesize ideas, edit writing, and think about the bigger picture as well as sweat details. Perhaps sweating details way too much. I think things through and am deliberate (which I honestly do not feel is of any value in the fast-paced world of today).

I can take a lot of punishment and push myself hard when needed, but certainly need recovery time too. I’m human. I’m sorry if that’s an inconvenience for the world.

Just where do I fit? What exactly do I need to get there?

I’m in the science-verse (but note, not at the center):

The science verse is big. I hear there is something beyond it, but it's a horizon that doesn't feel open to me right now. Is there an invisible black hole holding me in the science-verse? So much within it I haven't explored either.
The science verse is big. I hear there is something beyond it, but it’s a horizon that doesn’t feel open to me right now. Is there an invisible black hole holding me in the science-verse? So much within it I haven’t explored either.

What is beyond? I am trying to see and navigate that way. I just hope I can land there, realize there’s some slack in the line where I can work hard, but have a life outside too (my cat demands it…and having time to do taxes is important too). Heck, even staying somewhere in the vast science-verse would be OK with me. I just feel my value lies not at the bench, but in helping others do great work.







The Imitation Game

I review the new movie ‘The Imitation Game’ below. It’s about Alan Turing and the breaking of the Enigma code. If you care about spoilers, they’re here so stop reading now. However, this is a pretty well known story I think these days.

The quote of the movie is

Sometimes it is the people no one imagines anything of who do the things that no one can imagine.

Alan Turing was certainly different. As was Joan Clarke, the sole female code cracker portrayed (again, no idea if this is accurate to Bletchley Park, but the recruiting strategy of using Crosswords in Newspapers is a clever one). And of course the rest of the Enigma code breaking team were likely different in their own ways as well in being quite intelligent at puzzles, games, and other logical work. Basically, this was an era when different minds were not as celebrated as they are today (and in many cases still aren’t and it’s movies like this that really do make the case for inclusion).

Still, it was a whole team (men & women) that broke Enigma with government (military) funding that was fickle, at least according to the movie. I don’t know how true that was, but certainly the approach Turing took; building ‘Christopher’ to crack the code, eventually based on a German weather report (truly, the down fall of all codes is the humans using them and making some mistakes or repetitions) was difficult, expensive and took time to pan out. An understandably impatient British Government needed the code broken to save Britain.

Two of the big stories from Britain that were the keys to World War II were technological or information based. The first is radar that was key to winning the battle of Britain. And the second is the Bletchley Park story of cracking Enigma and keeping the fact that they’d broken the code secret from nearly everyone. The sustained resources put into it and being insistent and putting the pressure on probably didn’t help get the problem solved faster. The stakes were quite clear; The Imitiation Game shows some of the blitz of London and people huddled in underground station tunnels to seek shelter from the bombs. They also show British citizens trying to get on as normally as possible; there’s a scene of an old lady sitting on a pile of rubble with a tea cup sitting next to her.

It demonstrates that solving problems that have never been solved before takes time and different thinking that hasn’t existed before. Even when the stakes are high, rushing out a flawed solution (i.e. solving the Enigma code on one day before it changed encryption the next) isn’t ultimately all that helpful as is made plain when the British realize they have to be very cautious to not signal to the Germans that they’d broken Enigma and let some planned attacks happen anyway based on some statistical models that Turing helped develop and put into practice. It can’t have been easy figuring out the protocols for what German operations would go forward and which The British could counter.

Turing was a mathematical/logical titan whose ideas live on today (as the movie somewhat patronizingly points out at the end we call ‘Turing machines’ ‘computers’ now…). He compares himself unfavorably to Einstein and Newton early on in the movie, but clearly, he had a talent for cryptography. This is also another movie that portrays a scientist like Sheldon Cooper on The Big Bang Theory. I don’t know how Alan Turing was to work with, but certainly it’s the scientist type we see over and over again (obviously, there really are scientists like Sheldon out there, but that isn’t all of us…unfortunately, I tend to be like Sheldon :-/). Certainly, Turing was an important figure in the history of science/math as was Joan Clarke and the rest of the team (I’d actually like to know more about her, but perhaps that’s another movie waiting to happen).

Knowledge work takes time. It often doesn’t deliver an answer on a schedule and is an ongoing process. It’s why governments fund basic science and not companies. The payoffs are too far down the road for most businesses. Turing and his work are part of a long chain of scientists that have contributed to our digital age, and of course, we shouldn’t underestimate those that didn’t develop the tools, but developed the protocols and governance to implement and manage the cracked Enigma code. Without them, likely it would not have been as effective an operation. It truly is remarkable that The British pulled this off and kept it secret for 50 some years.

I’ll takes all types. And determining where each of us fits best with out talents is a good problem to be a part of and solve. I am still largely trying to find where I fit in. In fact, one of the keys in the movie comes from Helen, one of the British women that recorded German transmissions when she says that she has a relationship with the German communication officer that transmits the code since each British recorder is assigned a specific radio tower to record from. Basically, Turing suddenly realizes ‘Oh, people talk to each other and leave traces of themselves in their speech and communication, including identity clues’.

The Imitation Game can partly be seen as a meditation on how we do science now under tight budgets and minds not being free to pursue the big ideas, the out-of-the-box ideas. I suppose a few fortunate researchers get to do that (the few winners in what is becoming a winner take all system in the science world. Because it is a golden age of science. Just not for most scientists. How to best foster creativity and knowledge generation to solve problems has become ever more important in the 21st century and I’m not sure our current systems are doing the best at fostering that kind of thinking.

As the quote from the movie above suggests, people may have been skeptical of Alan Turing and many on the Enigma cracking team because they were different, not ‘normal’ minds, but that’s who it took to break the code. And in fact, Turing was really punished and committed suicide because he was a homosexual, a crime in the UK at the time that he (and I hope the other 49,000 prosecuted under that law) was pardoned for in 2013. In the movie, the investigating police officer is portrayed as being sympathetic (he thought he was busting a spy!), but am not sure that that’s historically accurate either.

I’m not as smart as Alan Turing. But am trying to cobble out my place and certainly, at least in some respects have never felt like I fit in most places I’ve been. I usually am quick to blame myself for this; but perhaps I can learn to celebrate that fact that I don’t fit in as well in many situations and celebrate others that have been excluded, many for systemic reasons that I am fortunate enough to not have had to deal with.

I’d recommend The Imitation Game. The gimmick of jumping in time between periods of Turing’s life (during the war at Bletchley, in the 1950’s, and when he was a prep school student) is a good one, almost making the movie a puzzle to solve. The performances are good and it’s a hell of a story from history.

do you have thoughts on the movie and what it says about the nature of Knowledge work?





Update: For a better take on the history of Bletchley Park and Alan Turing, see this from the New York Review of Books. And this episode of Tech Stuff from How Stuff works. The Imitation Game is certainly a Hollywood version of the Turing story, with historical inaccuracies and all.


Meditating on 2014.

This was my year to do things. And I kind of did. I’ll outline it below in roughly chronological order. And I’m grateful for all the people that helped get it all done.

Content Creation

I did some things/created online content for a startup called HappiLabs, go check them out; they offer a virtual lab manager and auditing of your lab supply costs. Both are good things for any lab. It was a good close look at the entrepreneurial spirit. I may not have it in me to do just yet, but then perhaps I just lack an idea I’m passionate enough about and a market where that idea would be valued.

Regardless, it’s a world I like being in/around and hopefully I can contribute in bigger ways going forward.

I took on an online course in content creation for thought leaders created by a great blogger & doer of things, Sarah K. Peck. I learned a lot about content creation and that lead to my guest post on the ASPB blog “Communicating Plant Science in The Digital Age” that I am pretty proud of even though I know it’s not perfect (trying to list twitter accounts by numbers of followers as a proxy for scope/influence is a bit futile; though my point was valid that I couldn’t find a single plant scientist/organization with over 50k followers compared to other fields).

That also lead to me doing some blog coverage and twitter coverage of the ASPB annual meeting and espousing the great uses of social media for scientists. While being far from an internet celebrity myself, I’d like to think I see it’s value, and I know I’m far from alone as it seemed everywhere I turned this year articles were being written about scientists doing online stuff and winning all the awards and things or something like that. Though that may be confirmation bias at work. Regardless, it’s a world I like being in/around and hopefully I can contribute in bigger ways going forward.

Mental health & self-awareness

I got to talk about my struggles with depression to fantastic science writer Carrie Arnold and what some of my solutions were/are to dealing with it and I still would love to have a job where I got to help academics/scientists improve their mental health as well as improve the system that can impinge upon it. Because I can’t change the system (or at least don’t quite know how/not currently in a position to affect change), I focused on what I can do myself while recognizing it is not fully sufficient to address the systemic pressures that academic scientists face these days (Nature ran a series called ‘ending the doom and gloom’ that I thought was interesting, and tried to at least offer a different narrative even if it’s one I don’t fully agree with). I got to talk about it in a webinar for Bitesize Bio, which was a great experience, though I don’t know if I did the best job addressing what the audience wanted. And I think I may have ignored the webinar software chat box if anyone was trying to get a hold of me during it…oops. I am still quick to criticize myself and note things I need to work on, perhaps hypercritically.

Another thing I learned a lot about this year is privilege (I am still learning); I know I am fortunate in many, many ways and benefit from being white and male in ways I don’t see most of the time. Depression, however, is something that can fully stop anyone and is a factor in ending too many promising careers and lives– Stefan Grimm being a recent example in the STEM world (I wondered here if my experiences with depression informs reasins why I am a feminist). Even one is too many. So tragic and it always drives me to tears whenever I hear a story where a person takes their own life. And though it hasn’t happened so far as I know, I still worry that being open about depression will negatively affect my career.

Learning, trials, and errors

I worked on a sequel to my first ASPB essay (linked above) that I can’t seem to get down on paper well; it’s about how we need diverse voices and communicators in STEM fields (that is an obvious statement it seems to me). And somehow linking that to teaching, writing, and mentoring— the marginalized skills academics need to have but aren’t really counted need to be valued more. If not for the writers, teachers, communicators, we wouldn’t all have the knowledge we have today. It would remain locked up in the Ivory tower, and even worse within each sub-discipline in those towers (cross pollination of ideas is a good thing, in fact it’s often where innovation seems to come from: take an idea from one domain and apply it in another). It may not be as dire as that, certainly, but that’s the fear, that without a network of dedicated communicators that knowledge, science, and ideas, will just not get out into the world. Speaking as a scientist that is working on bettering my communication skills, it can’t be left up to pure researchers all the time. Different people have different skill sets and even interests that certainly can overlap (i.e. scientist and communicator of that science). Maybe I’ll keep working on it.

…somehow linking that to teaching, writing, and mentoring— the marginalized skills academics need to have but aren’t really counted need to be valued more. If not for the writers, teachers, communicators, we wouldn’t all have the knowledge we have today. It would remain locked up in the Ivory tower, and even worse within each sub-discipline in those towers.

In the domain of wanting to upgrade my skills, I attended WiNGS (Workshop in Next Generation Sequencing) at UNC-Charlotte which was good as far as it went, but too short to really get any mastery over the software and techniques involved in next-generation sequence analyses (but several fantastic talks). I also took a MOOC in social network analysis that was interesting, but still feels a bit beyond me at this point. I am still trying to ‘get’ software that is now standard use in academia.

All of this feels like movement though it feels uncertain that it really is. I am gradually learning new things, or at least exposing myself to some new horizons. I even bought into the Adobe Creative Cloud and been using that for various projects both work and non-work related. Mostly teaching myself how to use a few of the software packages; they’re probably do far more powerful things than I will likely ever use them for, but getting into some photoshop/graphic design is fun for me, even if I’m not great at it (yet). More learning.

I also participated in a lot of the Finch and Pea (specifically Josh Witten’s) twitter hash tag games putting science into popular culture. I mention this because it’s just one of the most fun things I have contributed to. And I suppose I can claim it was practice in honing my wit. Though other people are amazingly witty.

What’s next?

That brings me to where I am now. Working on my science in the lab still, though science is not something I see myself doing in the long term or even being a full time academic. However, the skills required of an academic are still the ones I naturally gravitate toward liking/using. I like to teach (though I haven’t had opportunity to do it lately), to communicate— via keyboard mostly, but have gotten a lot better in person. Hopefully my writing has improved and my point gets across better than in the past.

Just where do I go from here? I am still not sure. Am I even ‘enough’ to do anything in this world? And what projects will be both help me grow? These are still questions and I still need to explore.

My new mission is to start a blog to talk about the science more than the culture of science (who knows if that new project will go anywhere). I’ll likely never fully abandon speaking about the people that do science and how we can improve the enterprise of doing science.

And of course, I’ve maintained this blog throughout the year and that’s still a fun activity for me even though I worry about sharing my thoughts with the world sometimes. Two of my favorite posts this year are the tour of NEB I got to take (fantastic place and people there— seriously consider using their products) and reviewing a book on the academia-industry transition.

I know I get things wrong. I am not so sure that my voice is even needed in the world. Other people say similar things to bigger audiences than I do. And for all the connecting I’ve done this year, I still feel disconnected. Like I don’t know how the world works. I still feel like I’m on an island, not deeply connected. Just where do I go from here? I am still not sure. Am I even ‘enough’ to do anything in this world? And what projects will be both help me grow? These are still questions and I still need to explore.

Final Meditations

I had the pleasure of seeing John Hodgman perform live. The last few years, he’s had a theme of post apocalypse existence and meditating on just what existence means, why we’re here anyway and just who we are and what our value is as humans. First, he was very entertaining and fun. And it made me think about my value, just what’s important to me and how I can best do it as we all have limited time to do things and accomplish them. Other than what’s cited above, I’m not sure I have a good answer and still struggle to define what value I bring to the world. While I don’t feel embarrassed to exist anymore (as I really did when I was deeply depressed), I also haven’t gotten to a point where I can confidently say ‘I am a valuable person and here’s what I am about, here’s my contribution that I am making’. Ideally that contribution is some sort of work I can get paid to do (whether a passion of mine or not, but something that I am engaged with).

Getting moving again was important. Getting exploring was important. Starting to use the resources available to me was important— much more of the same needs to happen. Perhaps I’ve started a spark that can grow into a small fire.

The You are no so smart podcast (YANSS) reminded me about the Dunning Kruger effect that says the skills to evaluate how your doing at something are the same ones that make you an expert at something. So we’re not all that good at evaluating ourselves, basically. So that means seeking useful external feedback that I have tried to do more, but probably not enough. It’s part of networking; put ideas out there and see what comes back or better, ask specifically for what you’d like to get feedback on. Most often, if I ask for feedback, I get no response, which I still take to mean ‘nothing about what you wrote makes sense’.

Even when I do get feedback, I worry that people are just being friendly/nice…I want to get better, but do understand that feedback can be hard to give. It’s a part of the growth mindset I have been trying to adopt. It’s hard to put my work out into the world when I grew up (far into adulthood too) with a perfectionist/fixed mindset that stops you from doing anything until perfection happens. I am trying to say “Done is better than perfect” more now. From where I am, I feel like I have years of negative feedback ahead before someone might genuinely say ‘this is OK’. Partly, it’s being smart enough to know when to be confident and when being humble is appropriate– probably the latter occurs more often than the former (this according to Dr. Dunning on YANSS).

I did a lot this year (not all of it is in this post). I’m not sure how much was meaningful or productive (again, I fear confirmation bias, I should look into my blog analytics perhaps). Or how much of what I have done is genuinely moving me forward. Getting moving again was important. Getting exploring was important. Starting to use the resources available to me was important— much more of the same needs to happen. Perhaps I’ve started a spark that can grow into a small fire.

Cat yoga, Millenium Falcon pose.
Cat yoga, Millenium Falcon pose.

I adopted a cat (see photo). He’s 10. And friendly. And has no front teeth. And he’s a cat. He serves no real function other than being a cat. He and I share that we are both, on the surface, probably not that useful (at least that’s my feeling about myself too often). But I have opened up more with people because of my cat, if only to find someone to take care of him when I travel and that has made me more willing to ask for things in other areas of my life too.

There are still things on my list that are really important to accomplish. Getting more on top of my organization schemes, getting rid of old things, deciding faster, finding a job, publishing my work some how, learning more and better data analysis techniques (writing scripts, using R to analyze data, making figures within R, maybe even getting to gene expression analyses from published data sets). And of course, measuring my goals better than I do currently and going in with an idea for what I might get out of an experience. At some point, though, the ‘always be improving’ mantra is exhausting and I need to feel like ‘enough’ where I am now.

And of course, I need to be wary about my depression and hope it truly is mostly in the past. I had a scary few days last month where I was back in a horribly depressive mood, but I have since come out of it and that’s a good sign that it was a temporary state. Before, it wasn’t or didn’t seem to be. Some of this is a feeling of burn out from pushing myself this year and still lacking enough restorative activities in life. Building resilience is really important too and some of that begins with what I’ve been doing the last few years— getting to know myself a lot better.

I am working on it, on my voice, actions, and making them good ones

Here’s to an even better 2015. Not just for me, but for all of you readers too (this blog may not be far reaching, but I am grateful for anyone that does read/stop by). I look around and see the many amazing things everyone else is engaged in doing (Some of that can be seen in the links above), and as much as I celebrate other’s accomplishments or even sometimes support them directly (e.g. investing via crowd funding of science like Paige Brown’s analysis of science bloggers or Jaquelyn Gill’s student’s project on The Falkland Islands), I still long to be that generator myself, making something someone else finds useful. Success tends to build on itself and I hope I am connected enough to keep building.

I am working on it, on my voice, actions, and making them good ones,







Statistics, computer biology and the future. R!

I have been attempting to learn R. And biostatistics and how to analyze large datasets…not having been traditionally trained in these things (at least not in a super formal way).

It’s going slowly in fits and starts. @ALoraine205 suggested I document what I’ve been tryign to learn. That won’t be pretty as I haven’t been able to devote my full attention to it, so it’s easy to forget what I’ve already learned.

So, why do I want to learn to do all of this? Because I want to push myself, but also prepare for the future when statisitics, computers and large datasets are all that will exist in biology in terms of data.

So here’s the inaugural post of an Idi  Ian learning R.

What do I know now?

1. I can load my data into R and am familiar with R studio and some packages.

2. I can do basic arithmetic, and t-tests as well as make very basic plots.

3. I know how to do some very, very simple manipulations of data to format it properly.

4. I know what packages are, but still am very unclear on what most of them actually do in any detail.

What are my stumbling blocks? 

Too numerous to count. Main = Main?! Yes, but in R Main = Main…the mains are different, some how? huh?! Still don’t fully grasp that one. And the help files for the various functions are gibberish to me. It’s English (my native language), but make no sense words do in help file. Googling things isn’t much more helpful.

Some of this blind spot is lack of education in statistics and in handling large datasets; but maybe I’m getting there. I know at least most of the software tools that people use to analyze these large datasets, but still have trouble running them myself nad am not sure how they all fit together with one another.

I am also not a computer programmer, so the command line thing is a little challenging too.

What are my goals?

1. Biggest one is that I want to do all of my statistics and data analysis in R, if possible; I think that’s possible. Most of what I have are continuous data measurements, qRTPCR data and other things like that that R should breeze through. And I would love to be able to better mine published large data sets (microarrays, RNAseq, etc.) as well as design and analyze my own.

Anyway, I hope someone finds my path to learning enlightening some how or can help me along the way; for years, I was terrified of saying I didn’t know something or how to do something (oh, then I’ll just pass this off to someone who does– since taking time to learn something new isn’t something anyone has time for any more…at least that’s how I sense the culture around me). And it’s showing vulnerability- possibly weakness at some level. Hopefully this will help me learn, help teachers figure out where student’s stumbling blocks are (if they’re not aware already) and hopefully we’ll have some fun too. This should become a regular feature on the blog. Let me know if it doesn’t.