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,








I’ve been thinking about that Facebook study that got everyone up in arms about ethical breaches and whether or not manipulating people’s emotions is OK to do if they aren’t informed.

Of course, we all signed our whole lives away to whatever online company we have an account with (yes, even the services you pay for, that’s true,  just maybe a little less so). Living in the 21st century, by definition, by being connected almost means you’ll be giving up info. It’s like living in a small town; everyone knows everyone else’s business (whether they talk about it openly or not). So be as open or not as you like, just know that basically none of us will every be elected to public office or be employed ever again.

Well, maybe it’s not that dire. Our lives are complicated and messy and it’s a bit culturally unacceptable to show that to other people (I do have my levels of stories I’m willing to share and those things I keep to myself or only share with close friends who’ve earned the right to hear those stories).

What I want to talk about is some of the apparent discussion that the negatively manipulated people int the study were more negative and could have slid into depression or gotten even more depressed. I don’t think it quite works that way, and the data in the study was apparently quite a subtle effect, which makes sense…it is kinda not OK to not tell people you’re intentionally manipulating them, but absolutely not OK to radically manipulate someone so they harm themselves or others.

There’s a narrative that on social media, the only things we share are the best parts of ourselves, the awesome things we’re doing, our kids doing those kid things, cats, etc. However, it’s simply not true; people share all kinds of stuff on social media, some serious, some light-hearted, some dark, etc. Look at my Facebook or Twitter feed and it’s filled with rather depressive content (I still hate the thought that I may have contributed to someone’s negative mood because of it– one reason depression is hard to talk about is that most depressives I have known do not want to bring anyone else down, including professionials, not just friends…and so they (me!) keep to themselves, keep it inside).

In terms of this study, however, the thing that doesn’t resonate with me is the fact that the positively manipulated people showed an uptick in their positivity in things they said/shared. That may well be the case for a non-depressive. However, when I was most depressed, positive posts from friends and others actually made me feel worse. Even still, the positive aspects of social media really do have a negative impact. I see all my friends and things I’m interested in grow, change, do interesting things while I was (and still feel I am in some ways) stuck in the same plaec, same things day in, day out, incapable of those things being expressed to me in my friends’ experiences: love, laughing, enjoying life, all that. I’m genuinely happy for them being out experiencing the world, I just wish I could do that too; that I don’t feel such a prevalent feeling of being removed from the world even if I’m right there doing something myself. Maybe I’m experiencing things more now, but a lot of life still feels flat to me; I’m not pushing myself enough outside my comfort zone? Maybe I just need to leap more, analyze less.

So while yes, there’s a discussion to be had about boundaries and privacy and sharing in this information age, it’s not as if any of us (especially us ‘knowledge workers’) will get away with not using these online services to do our work (in this way, we’re having to become more like entertainers; people in the public eye, maybe there are things we can learn from them). The only solace I take right now is that algorithms are comically bad at getting ‘me’; if I buy a gift on Amazon– for someone else! I still get emails advertising that very product to me…hey Amazon, it was a gift I tried to be thoughtful about for another human who’s not me…not interested!…or even worse, I bought something and suddenly there’s an email advertising that thing to me…hey Amazon, I bought the thing you should know that, I don’t need 2 of it!.







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.