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Thoughts from the Lab

The final year

Well today kicks off the final year of 365 days of academia, this will be year four of my little project and year five of my PhD. There is a chance we may have to extend slightly, but for now I’m keeping my eye on the prize and until the deadline comes and goes, I am planning to do whatever I can to make sure I graduate on time. It’s going to be a challenging year, but since it’s a new beginning let’s talk about how we got here. Three years is a long time after all!

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On the design of experiments

Okay, well a lot has happened today and I’m not even sure where to start! I guess the main thing I want to write about today, despite being exhausted, is planning. I plan everything, I probably write more about my plans than anything else now that I’m done taking my required classes. It’s no secret, I love planning because having a plan means knowing what to do when that plan goes sideways. It means knowing what to look for before a plan goes sideways. Most importantly, it lets you know you’re on the right track.

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Attack of the code

Here’s the thing, all code is bad code. Some code is just better than others. For every person who writes a program, there’s someone else who would do it a totally different and, to them, less complicated or confusing way. However, as long as the code you write works, it shouldn’t really matter how badly it’s written, right? To me the difference between bad code and worse code is comments. The frustrating thing about taking apart someone else’s code is that there are rarely enough comments to figure out what the hell is going on.

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Fantastic posters and how to make them

From the ever accurate PhD Comics

It’s that time of the year again, time to make a poster! I’ll be doing at least a couple this year to display some of the work I’ve been doing, but the current one I’m in the process of finishing up is for the summer conference the hospital holds. They sent out a template and a example poster from last year’s event, but the example was bad. Like really bad. So maybe we need to talk about what makes a good poster, because apparently people think they need to be books.

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Everything you ever wanted and more

You wake up one morning and get a frantic phone call. A family member lets you know that a person very close to you, someone you miss dearly, maybe even someone you thought was dead, was very much alive. A dream come true, right? If you are like me you would rush out the door and do whatever it takes to find the person. But it gets better, you don’t have to plan a long flight or find money to make the trip. They live close by, very close. It’s a dream come true.

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Time management and a busy day

As usual, it’s a busy day. This one however is particularly busy and there’s not a lot I can do about it except pull out the magical powers of time management, set some goals and limits on how long I can work on things, keep my head down, and hope for the best. The day will end, eventually, but the amount of work I finish is, in part, up to me. How do I manage to be productive? Well a pseudo-structure method helps.

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Self-promotion in science

I admit it. I’m bad at promoting myself. It’s hard and I hate it. I’ve made a concerted effort to do just that though and over the past couple of years I think it’s helped, maybe? The problem is half of the metrics we use to measure success as a researcher come down to popularity. Things like h-index are great measures, but what they are measuring isn’t always how good your research is, more like how many people know your work. Which to be fair are similar, but still different things.

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Living through history

When I was a kid I thought history was something we read about in text books. World wars were from a “less civilized” time, we are a modern people after all. With the fall of the USSR along with the start and end of the gulf war not too long after, I thought, perhaps foolishly, that history was a thing of the past. I never suggested I was the smartest of children. But here we are, living through history. I didn’t realize it could be so painful, then again maybe if I had paid more attention I would’ve known.

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Forgotten inventions, or so you want a patent

Fun fact about me, I enjoy making things. You know, in case that wasn’t obvious. But, once upon a time I thought it would be smart to make sure I protected my ideas so I hold one patent based on something I came up with. Or at least I did have one patent, now once the paperwork is done it will be two. Unlike my in progress papers I can actually freely talk about this, but for the most part I think the journey is the important part of the story.

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Word play

Come on in…

It’s been a day, so I don’t have a whole lot of energy to write or to think for that matter! But my brain works in mysterious ways, even to me. So I thought I would talk about a word that somehow bounced into my head and as any good brain does, it made some very odd connections. Today we’re talking about the word sane. Or rather the word insane, with me so far? Because this is where we get a little crazy.

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The end of a story

I love to read and if you do too you can probably empathize with this. What is it about the end of a story that makes the disconnect so painful? Maybe painful isn’t the right word, jarring perhaps? Abrupt? Whatever the adjective you choose closing one book leaves a world of possibilities for the next, but for me, there is always a bit of a hangover jumping from one universe to the next. Leaving me to wonder if that’s a common phenomenon.

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The mysterious data

I sometimes miss the days when the answers were in the back of the book. At this point I would take even just having answers that are semi related to the questions I’m trying to work out. Being a researcher is a double edged sword. On one side, for a brief moment in history you will know something that no other person in the world knows. On the other, how do you know that it’s correct? Questioning your results is an important part of research and right now, there’s more questions than answers.

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The value of work

Close-up Of Jobs Text On Wooden Blocks Over Keyboard In Office
Close-up Of Jobs Text On Wooden Blocks Over Keyboard In Office

I recently saw a post on Twitter about the lack of postdoc applicants and it made me think about how little we really get paid. While inflation and the general cost of living (e.g., cell phone, transportation, housing, etc.) is increasing at an enormous rate, the amount we get paid as students or even postdocs is so low it’s almost insulting. Which highlights so many problems all at once it’s hard to figure out where to start the discussion.

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A belated thank you

As of yesterday I now know the schedule for the DARPA Risers 2022 conference. Or rather just the conference part itself, the website makes no mention of the Risers program specifically, again adding to the mystery. If the confirmation email I got was any indication, the information will be forthcoming in the next few weeks. So I now know who will be speaking at the event and I’ve discovered the universe isn’t without its own sense of humor.

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Data visualization dilemma

Data visualization is an important topic to think about. How do you best convey what the data are telling you? It’s something I struggle with because I take it so seriously. Most things can be done simply, the old standby the line graph, box plot, or even scatter plot all work well enough, but more often than not, you want to tell a story and sometimes the obvious plot isn’t the best choice.

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Intellectually curious

I don’t recall what sparked the memory, but I was reminded today of an email I got from school-PI complimenting my new job. He said I was intellectually curious and that struck me as a touch odd because I assume we all are in our own ways. It’s not that I’m not appreciative of the complement, because I am, it’s just that I never understood how we can live in a world full of mysteries and not want to at least glimpse behind the curtain.

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Big claims and big evidence

In science, ideally, when you make a large claim, you need a lot of evidence to support it. In theory anyway, in practice with the speed of the internet, claims often get taken as truth no matter how self correcting later. The claim that vaccines cause autism for example has been thoroughly debunked over and over, but the claim still persists despite the piles of evidence to the contrary. Global warming is another good example of how having a lot of evidence doesn’t mean acceptance.

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The value of clean data

Actual EEG data I’ve collected, this is “raw” or untouched data.

In my line of research we have fancy algorithms to remove outside contamination to the data we collect. The problem with collecting electrophysiological data (electrical recordings from a person) is there is so much damned noise everywhere. The problem is magnified when you collect data that have a low signal to noise ratio (meaning lots of noise, not a lot of signal). Signal in this case is the thing we’re interested in measuring and while we have dozens of algorithms to filter (remove) the noise, there’s still no substitute for data that was well collected.

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MK-Ultra, or lies my government told me

Still from video taken in 1955, artist William Millarc takes part in an LSD experiment alleged to have been part of the MK-ULTRA program.

I love a good horror story. Now, personally I prefer fiction, but sometimes truth really is stranger than fiction. As the title of the post suggests, we’re talking MK-Ultra since I love the absolute absurdity of the story and frankly it’s a great illustration of how little the common person knows about what the government does in the dark.

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The invisible self

What drives you? Who would you be if the world around you stripped away all the pretenses of how you should act and who you need to be and just let you be you? If it’s a bit too philosophical or overwhelming to think about, then maybe we should all take the time to ask ourselves if we are the people we want to be. Then again, I don’t have the answers, so maybe I’m just as lost as everyone else.

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The road less traveled

“Two roads diverged in a yellow wood…” and that’s twice in almost a year exactly that I’ve started a post off with that line. The title of the poem isn’t the road less traveled, but I’ve decided that for today, that’s the name of the post. I have not had an easy life, some of that was because of birth, but a lot of it was based on the choices I’ve made. While the poem isn’t really about how hard life can be, when I thought of today’s post Frost’s poem popped into my head. Because the road less traveled, fucking hurts.

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In defense of pain management

Chronic pain is different for everyone, for some it feels like razors, for others even bee stings.

Well this seems to be coming up a lot lately. One of the things about working in a hospital is you get to see a lot of different opinions and cases from doctors from all areas of expertise. It gives everyone a well rounded education and frankly no matter where you are in your career it’s always good to keep up with the state of the art in your field and adjacent fields. I’m in the neurosurgery department so we get to talk a lot about the brain and spinal cord, which means pain is a frequent topic.

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The research struggle

Working in a research hospital is awesome. Things are streamlined that aren’t in academia and this was probably most apparent when I first started doing research in that setting almost three years ago exactly now. There is still a lot of red tape and things that need to be approved, ethical research is important in both academic and clinical research, it’s just handled by others instead of it all being your job. That doesn’t mean clinical research is all sunshine and rainbows though.

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Old student, new tricks

With a little luck, I’m a year away from graduating. It’s been one hell of a journey and I really hope I hit this goal. Still, I keep thinking what’s next and the truth is the future looks a lot like the present. It’s not just because I’m now working at a research hospital, that helps, but what I mean is that the difference between being a student and being a researcher isn’t all that different. You have to learn new skills.

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People are squishy and other science explanations

A recent blog comment reminded me of something I said the other day to surgeon-PI. Keep in mind that surgeon-PI and I have only known each other since he started at the hospital, which isn’t long. While we were doing an experiment in the OR, so under his watch, we discussed some of the challenges with the experiments we were doing and when we tried to change things on the fly he said it was bad science, to which I replied people are squishy. I said what I said damn it!

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Chaos as enjoyment

Well today’s post comes far later than I would’ve liked, but hey it’s been a day. What kind of day? Well surprise, surprise I cannot talk about it! That’s the theme, I get to hint at stuff for a year or so and then surprise everyone with the paper after the fact. But today did inspire something that I can talk about and that’s why today we’re talking about why I love research so much!

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New year, new experiments

We are an alarming number of days away from the new year. Where did this year go? Why did it suck so bad? Why was this possibly the best year we will see in our lifetimes? Why am I asking so many damned questions? Am I having an existential crisis now that the year is coming to an end? That was a legit question and not part of the running gag. I’m a man who likes his plans, so let’s look at what (I hope) is instore for next year.

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The year I met Alice

Not quite that Alice, but I definitely felt mad afterward.

Every year around this time I think of Alice (not her real name). Alice and I have a lot in common. We have the same last name, same initials, and we had no idea the other existed until one day when I randomly checked my email and discovered a serious case of mistaken identity. That was my introduction to Alice, so every year I think about her and wonder how she’s doing. But my dear reader, the story isn’t about the emails. The story is about what happened next.

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Smile for the camera

Today is photo day! What is photo day you may ask? Well it’s the day we take pictures. Okay, probably a little brief, today is the day that we’re meeting with the lab and school public relations team to release a joint statement about our new award. It’s the first award for our new collaborator (surgical-PI, who I still need to find a better pseudonym for) since he just started his new lab at the hospital at the beginning of the year. While it’s not a major award (dollar amount), we tend to celebrate these things anyway, so we’re taking pictures together, surgical-PI is getting a tour of the school lab, and we’re going to get interviewed about the details of the project.

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Why is it always a rush?

Well my latest grant is due at the end of the week, so I am now just a few short days away from the deadline and rushing to meet it. There has been plenty of time between when the proposal for funding went out and now, so why does it always feel like things are last minute? It probably has to do with the iterative approach to writing and the edits that go on forever. Since I need a break from scientific writing I figure now would be a good time to talk about the process and why a far off deadline is never enough.

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Conferences in a pandemic

I’m vaccinated, I got vaccinated back before most of the public could because I work and do research at a hospital. Because I work with a vulnerable population, some of whom cannot be vaccinated, I still take the pandemic very seriously. I wear my mask like I wear any other piece of clothing and the hospital understands this risk because unlike schools and other places in the area, masks are still mandatory. It’s not just a vaccination issue, it’s that vaccines are 100% effective and not everyone can be vaccinated or has access to get vaccinated. So when my favorite conference came around, I was torn about attending… was.

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The game plan

A pirate's treasure map
A pirate's treasure map.

Well I’ve got two days (not counting today) to get so much stuff done I don’t even know where to start. The good news is I’m feeling slightly better about my odds. The bad news is nothing is done so there’s nothing to celebrate just yet. I have a plan though and I feel good about the way I laid out my work, if I’m careful (and lucky) I’ll be able to get it all done. We’ll see, it’s going to be tough, but today let’s cover why I plan my work when I get swamped like this and how you can do it too.

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On the prefrontal cortex and abuse

Adulthood is often thought of as the point where you’re done developing. Most states for example don’t allow anyone under 21 to drink because that was where we drew the line, but we allow people as young as 18 (here in the US) to join the military, vote, etc. You may think that this would be roughly where we stop developing and that would explain the somewhat artificial line we’ve drawn. The truth is much stranger than that and when it comes to the brain you don’t develop evenly.

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A week in review

I figure it’s a good time for the recap of the week. I mean there was a lot going on and while I want to spend some more time on my “in statistics” series, I also really need a break. So instead of spending a lot of time making sure the information I’m presenting is accurate, concise(ish), and (with luck) well thought out, I figure it would be easier to talk about the things I’ve had to do this week and the things I get to look forward to! Joy, welcome to life as a PhD candidate.

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Clinical research in a pandemic

Male and female characters scientists or lab attendants working in science laboratory using microscope, lab glassware, vector flat illustration. Scientific research, experiment, science and education.

One of the more interesting things about the pandemic is that everything at the university level shut down. They still send out emails suggesting that everyone wants to go back to in person classes, but they haven’t followed through with that threat. Human participant research has been halted and even though we’re probably going back to “normal” in the fall, right now nothing is happening. That’s at the university level though, clinical research is a different story.

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Another approaching deadline!

Well it’s going to be down to the wire this week. It’s good to know we’re keeping the theme, if you’ve been following along for awhile you already know it’s always down to the wire. This week is particularly challenging because I have competing interests for the time I have. There’s only 24 hours in a day, so there’s only so much work that can get done. I would prefer to not do it at the last minute, but here we are… again.

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The lonely cultist

Listen closely as I am going to divulge a secret from the universe. It will be so earth shattering that you will forever remember this movement. There will be an irrevocable before and after. It has taken me decades to uncover this secret and as the sole owner and guardian of it, I am trusting part of it to you. You can be a part of something larger than yourself, find secret truths, and if you are ready to receive them, find your own. There are secrets in this life hidden just beyond human sight and they are waiting for you to find them. They are calling out to you in the wind. Do you hear them? Are you ready?

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Great expectations

What did you want to be when you grew up? Sometimes the question ends in hilarity, a dinosaur, a unicorn, or maybe some other type of animal. Sometimes it leads to dreams of a sci-fi future, deep space traveller, Mars colonist, maybe a superhero. Whatever the answer is, they all have something in common. No one dreams of being average, but the average exists because so many people fall into it. Most of us have our dreams die as the reality of our existence becomes clear. I say fuck that, dream big until your last breath, why not?

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Full speed ahead

Neither rain, nor sleat, nor pandemic, nor freezing to death stop us from moving forward. I think that’s how the PhD motto goes anyway. Since the past week we’ve been struggling to simply live, we’ve had the whole city sort of on pause. That pause has come to an end, there is no recovery period here, it’s straight back to work. That’s a feature of capitalism, not a bug and it isn’t limited to getting a PhD, but we’re definitely included in the back to work group.

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On the stories we tell

It’s been a busy week, there was so much to do that I was worried it wasn’t going to all get done, but here we are! Things got done, mental health was prioritized, and I figure it’s a good time to talk about words. Or rather the stories they form, it’s a complex topic and this is really more for me than anything, a friendly reminder that I really enjoy writing. After all, while this blog is meant to help others, it’s also a message in a bottle to my future self, a reminder that I was really here and actually did the work. An ever growing time capsule of my thoughts if you will.

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The road to a PhD program

In hindsight this post should’ve happened a long time ago, like year one and day one of my 365 days of academia project. Things have… evolved in ways I didn’t understand when I started this, originally the project was simply going to be a notebook for my classes, then it turned into my journey as a whole, and even what I do in my spare time. Like anything we create it took on a life of its own and I’m reminded I should touch on the process to getting accepted into a PhD program.

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Scientific figure design

Well I’ve done it… sort of. I edited the grant for the semi-last time. Now we’ve got a working copy that reads the way we want it to read, so it’s off to the scientific writer to read over it and make sure it sounds good. You would think that means my work is done, but no. I need to do arguably the hardest part and create some of the figures we will use in the paper. Writing well takes practice, but making a good figure, well that’s art.

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Not cool Robert Frost!

“Two roads diverged in a yellow wood…” starts Frost in a poem that most people are at least familiar with, but typically is misnamed. The poem is often identified as, “The Road Less Traveled”. This makes sense because the poem talks about the thought process behind why he chose the road less traveled and that it was worth it. That’s not the name of the poem though.

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New year, new grant

It’s all connected somehow… I just know it.

Nope, still on vacation… I tell myself as I make arrangements to meet with my Co-PI. This is important though and unlike some of the other projects it has a firm deadline. That’s right, I’m writing a grant. No this isn’t an update to the last one I wrote, this is a whole new one. How did I end up in this position? Who knows, but I’ve been trying to figure it out since it happened. Let’s discuss, shall we?

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A look forward

It’s a new year, a new chapter, and it’s time to set some new goals. What kinds of craziness will I accomplish this year? Well I have a few ideas. No pressure or anything, I don’t want to force myself to fit things into the year just because I planned for it. Instead I like to set goals so I can check things off a list (I do love my lists). So even if that list rolls into the next year, it’s not the end of the world. Just a helpful hint for those of us who are chronically anxious!

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A year in review

So long 2020, while the calendar is a human construct, I hope that the significance means something for mankind as a whole. Who knows maybe we will finally take the pandemic seriously, or global warming, maybe even gun violence. Yeah, I don’t think so either, but one can hope. In lieu of stating my hopes for humanity, let’s just take a quick look back at the year I’ve had and what this new year holds. This is my year in review.

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The perils of publishing

So you want to publish some science. I don’t blame you, as a scientist we’re driven by the “publish or perish” mindset. The further along you get the more you’re stuck having weird nightmares about h-index and impact factor. Or maybe that’s just me, who knows? In any case, any publication is a labor of love, one that typically turns into a labor of spite. Because publishing isn’t easy, or maybe that’s just me.

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And finally something good…

I don’t know why my mind went with hidden treasure, but that’s what we’re going with today.

It was bound to happen eventually, some good news for today! I had a meeting with my Co-PI and we went over the latest findings in the dataset I’m processing for my “super secret” technique and I have to say it went much better than was expected! He’s excited, I’m excited, we’re excited. The issue is we don’t know what any of it means, but I think that’s why it’s so exciting!!!!

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The power of indifference an open letter to the scientific community

indifference

Suddenly your absent-minded thoughts are shattered by a loud noise. Quickly you look around, to the left of you, you see it, and a child has been shot, you see them bleeding heavily. People are standing around with their phones, some calling emergency services, some filming, but most looking confused and scared. No one is actively trying to help; you hear that they are afraid that the person, or persons, who shot the child is still around. What do you do next, do you choose indifference, or do you help?

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Trumped: Why the election is a symptom of a bigger problem

Donald trump hands

Donald trump hands

Right now you are probably thinking that I am going to unleash some poorly thought out diatribe about president elect Trump. No, that is not going to happen. It is not going to happen because he is not the problem, you are the problem, I am the problem, and we are the problem. That goes for those of you who are atheists, Catholics, Muslims, conservatives and liberals, or anything in-between.

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