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365 Days of Academia – Year two

And nothing was wrong with me…

Last summer I had some sort of autoimmune thing kick up. Frankly I’m not sure it was autoimmune or what the hell it was, but it hurt, left me feeling exhausted, and caused my hands, face, and elbows to form raised red spots that later peeled off (here). It was incredibly painful, made me question the minor breakouts of whatever it was that had been going on for a good ten years or so prior, and was a red flag that I was not okay. But the pandemic has been ongoing so getting attention from the VA, which is notoriously awful, had been difficult. Had been, I finally got the chance to see someone.

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Depression, a tale of hunger

Let’s pretend you have a pet that is constantly hungry. You can’t leave the house, you can’t sleep, you can’t even take a shower because anytime you want to do something for yourself this monster of a pet just won’t allow it to happen. It’s hungry. It wants to be fed and it wants to be fed NOW. Oh you’re exhausted, feed it. You want to do something for yourself? Too bad, feed it. It’s all consuming, it never sleeps, it never is satisfied, and you cannot get rid of it. Chronic depression is the pet you never asked for that demands your attention all day, every day.

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On designing experiments

After meeting with my Co-PI and discussing the super cool experiment he wants me to do (here) it sounds like I’m in control here. Scary thought, right? This is that whole working WITH my Co-PI and not FOR my Co-PI, he trusts me to make good choices. I mean either way he’s going to need to sign off on it when I finish the design, but it’s kind of interesting to be the one who gets the say in how we do this.

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Surprise teaching, seriously.

Well this is awkward. My main-PI just asked me to teach a course on MATLAB to our new summer interns. Most of them have never used MATLAB before and those that have probably know very little about it. To fix this my main-PI told me that I was going to teach a course on it. At first I thought it was one, but it turns out he want’s four classes (two hours long each) on it. I was trying to have a light summer, but that doesn’t look like it will happen.

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Journal papers update!

Not a typo, journal papers as in multiple. This year I’m planning on submitting three different journal papers. I’ve already submitted two and got feedback on them, so technically resubmit those. The third is still a work in progress and to be honest, there could be a fourth that I submit this year as well. Basically there’s a lot going on and it’s all pretty mindboggling that I can’t seem to get any of this off my plate. It’s a process for sure, but even though I’m still hard at work, there’s been some progress.

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The importance of boundaries

Often times I hear stories about people who feel powerless doing a PhD and I can understand why. You’re given a position with some freedom, certainly more than you had as an undergraduate, but at the same time you have no real power. You’re an adult who is starting a career, but you have very little say in that career. The system is designed in such a way that you need to trust that your PI will take your feelings into consideration, but that doesn’t mean that they have to, are incentivized to, or frankly that they even will.

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Surgical shadow update!

Well I finished my surgical shadow today. Frankly I’m exhausted, maybe I was just too excited, but I got roughly zero sleep last night. That said, it went better than the last shadow where I had just gotten my second dose of vaccine the day before. Now that was not my idea of a fun time! So per the usual I cannot go into the details, but I can talk vaguely about what happened and what’s next.

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On finishing a story

I am an avid reader. I absolutely love books and if I had more time I would probably read even more than I do. Despite being incredibly busy, I read daily and the amount I read varies wildly depending on how much time I have. Still, I manage to read an hour or so a day depending on how I’m feeling. So far this year I’ve read 19 books with a goal of hitting 30 by the end of the year. I would’ve gone for the whole book a week thing, but that felt like too much pressure for something I enjoy doing as a hobby. The problem with all that reading is inevitably stories end.

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Another surgical shadow

Just FYI, I didn’t take this and I’m pretty sure it’s just a stock photo, but it works for the post. I wouldn’t want to cause any privacy issues.

Well it’s officially on the books! Monday (super early) morning I will be shadowing my second surgery. For those new around here this was the first. It was an awesome experience and I’m excited to do it again. Today we’ll talk about why I, as someone who does non-invasive research, is even attending surgeries and what I get out of them. There is an actual practical reason to attend, but it’s also just super interesting!

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The best laid plans…

The full quote is “the best laid plans of mice and men often go awry” and is from a poem, but also inspired the book title, “Of mice and men”

Well this week has been a serious rollercoaster of emotion. There have been incredibly high highs and extremely low lows. It’s so bad I’m not even sure what’s going on at the moment and it’s throwing my entire life into chaos. I wish I were exaggerating, but unfortunately I am not. So what has me so out of sorts? My academic plans are entirely up in the air now. For the next few months (up to 6 months) I will have to sit and wait to figure out what I can do about it. Let’s just start at the beginning.

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Intro to ICA

Independent component analysis, probably not something you hear about all that often unless you’re in a field that uses it. If you’ve found this via google or the such, then you’re probably looking for an explanation on what the heck ICA is and how to use it. Fear not, today we’re going over the why of ICA, why it works, why we use it, and why it isn’t the perfect tool we wish it was. Hint, the reason it isn’t perfect is because of math, stupid math. Quick note, I’ll be focusing on EEG uses for ICA, but there are tons of other applications and this knowledge will still apply to them as well.

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First class of the summer

I’m teaching again! Okay, I didn’t exactly stop, I mentor and do other things, but tomorrow is the first class of the summer that I’m teaching. Which means today I need to finish the slides I’m using, review the materials, and get everything ready so everything will go smoothly. There’s a lot of moving parts that have to happen and while I’m not particularly new to this, it will be the first time teaching the topic. What topic is that? Well…

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Journal problems

I feel like I’m playing the how many journal papers can I have in review at once game and I hate it. Since there’s so much going on I think it would be a good idea to discuss a little bit on what I have up in the air at the moment, why I’m so freaking annoyed about the situation, and what comes next. Most of this is just me being frustrated and venting about the process, but what the hell, sometimes it’s okay to complain. I think that’s pretty much what grad school is anyway, getting better at complaining.

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On Memorial day

I come from a somewhat long line of military service. When my grandfather immigrated to the US he served in the Navy and fought in the Korean war to become a citizen. My father served in the Army and enlisted specifically to fight in Vietnam. Then I went off to the Marine Corps shortly after 9/11 and subsequently Iraq. War is hell, but then again so are people. It’s Memorial day, which means today is my time honored tradition to tell you all to just stop.

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On birth and family

Sometimes a topic just rattles around in my head until I get it out. Today is one of those days. A friend recently decided to cut ties with some toxic family and it was probably well overdue. I’m happy for them and I think they are making the right choice, but I know not everyone would see it that way. Sometimes people confuse the idea of family and romanticize it, but the truth of the matter is family isn’t the people who gave birth to you, it’s the people you choose.

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The hunt for funding

Funding, a running theme around here. When I started my PhD it was clunky, I had no clue what I was doing, but I new that I needed to have some money because the first rule of doing a PhD is that you DO NOT pay for your PhD. That much I knew from my Masters (which I was lucky enough to not have to pay for because my PI at the time was just starting out and had funding for me). The rest was up in the air and has been up in the air for a little bit now, so today I’ll be talking about my funding history and where I’m at now. It’s all a little up in the air at the moment, but I’m optimistic.

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Surprise summer project!

I’m super excited! My Co-PI sent me an email late yesterday asking me if I had time to help with an experiment. I absolutely love my Co-PI’s lab and all the stuff they do (throw back to this post), so of course I wanted a project! Well I read over the proposal and what he wanted me to do and let’s just say that I am in for a fun summer. I cannot wait to get started, since I can’t go over the details about what I’ll be doing, I think I’ll talk about the consequences.

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On having two PI’s

My two PI’s, a comedy/drama TV show I want to make one day which just happens to be based on my life. Yep, for those who are unaware I have a dual appointment in a hospital where I do a lot of my research. It’s amazing and it really makes me excited to focus more on the clinical side of things, but it means that I have not just one, but two PI’s and that isn’t a bad thing! It’s just a bit of work and can feel like being caught in the middle.

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How to find the right lab for your PhD

Going into a PhD program is a confusing whirlwind of stress, new experiences, and the general feeling of being lost. You do belong there… right? You know what’s harder than making the choice to get your PhD? Finding the lab you want to call home for the next five or more years. Inspired by advice I gave to one of the undergrads I’m mentoring, today we’re going to talk about how you should hunt down a lab you want to be a part of. It’s that time of the year again, but don’t worry, finding the right lab for you doesn’t need to be scary.

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The start of summer teaching

Today is the start of our labs summer classes. This marks the beginning of roughly 12 weeks worth of lectures on the stuff we do in the lab for our undergrad and high school students. It will be a chance to teach them how to use some of the techniques they will be working with during their summer with us and it will also be a good refresher for everyone in the lab, because we tend to focus on very specific analysis when we do our research it helps teaching each other some of the things we do well.

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Path planning

I’m an anxious person, I acknowledge this. PTSD, anxiety, depression, just a few of the things I live with and try to manage daily. To help keep me sane(ish), I have certain things I do. I like making to-do lists, having a well organized calendar, and I like to keep track of where I’ve been and where I’m going. That last one, that’s the topic for the day. With summer here things have changed. I am done with classes, I’m going to be teaching (here), I set my “lazy goals” (here), and it’s the time where I review my progress and plan for the next year. I figure others may benefit from doing something similar, so let’s go over how I do this.

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A data detective

You did a cool experiment, you have some interesting data, and you found something unexpected! Great, but what does it mean? Sometimes the answer isn’t as straightforward as you may hope. That’s the problem for the day, I found something in my data that makes no sense and the worst part is I have no idea what it means. It’s definitely something, so now I need to go through the steps of making sense of it. That’s the problem with doing something new, you have no frame of reference for the result.

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Summer teaching

It’s that time of the year again! We’re taking on undergrad and high school students for the summer research program! An exciting chance for people to get their hands dirty and learn what it’s like to work in a lab. The best part is that most of the people attending are paid! That’s right, undergrads are paid to be there. That also means I get to put on my teacher hat, which I absolutely love. Today we’re going to talk about what I’m teaching and I’ll probably spend a bit of time talking about how much I enjoy teaching, let’s go!

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The last day of the conference

Today’s the day! The last day that is, the final day of the conference I’m attending. The past few days I’ve talked about different aspects of conferences in general and I’ve touched on why virtual conferences are important, needed, and should be the norm. I’ve also talked about the difficulties presenting at a live conference when you have disabilities that make public speaking a challenge. Today I figure we can round out the topic by covering some of the good things about conferences and why you want to attend when you can.

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Presentation anxiety

Today is day two (of three) for the first conference of the year for me (more here). Presenting live is always a challenge and the difference between a good presentation and an okay presentation (any attempt is at least an okay attempt in my opinion) is a combination of planning, practicing, and luck. Of course there are things that can make this particularly difficult, for example one of the issues I have is aphasia, so while I can write normally (mostly), speaking can be a challenge. This is particularly apparent when I’m stressed, so presentations are a challenge.

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The first conference of the year

Today marks the start of the first conference of the year for me. This was the one that was unfortunately named far too similarly to the other conference I was awarded a slot to speak at (here). It’s three days long and is completely virtual (thankfully!) so I won’t be traveling just yet even though things are relaxing (far too early in my opinion). I figure today since I’ll be doing that we can discuss why I’m happy that we made the switch to virtual and why I am angry that it’s going to change soon.

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On saying “thank you”

The day to day pleasantries, I’m sure we go through the motions on a regular basis, please, thank you, it’s pretty engrained into most of us. At least I would hope, broad statements like that always have exceptions, but more often than not I would like to believe that the majority of people are decent enough to say thank you to someone who is doing something for them, even if it’s just their job. Sometimes simply saying thank you can have a huge impact to a person, even if you don’t expect it to.

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Half done, or half left?

With the end of the term, I’m dealing with a lot of complex emotions. Maybe it’s the fact that my funding is running out soon and I need to come up with options before I take (at best) a significant pay cut. It could be the fact that my research, the stuff I REALLY want to do seems to keep slipping further away from me. It may even be because I’m still, STILL trying to get my papers published and it’s just disheartening. Whatever the reason, I’m at the halfway point and I’m just not sure what I’m feeling exactly.

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Return of the lazy goals

It’s the end of the term and that means two things. The first is that I no longer have to worry about classes. Actually that’s going to be a permanent shift now that I’m done with the required classes for my degree (aww yeah!), so that’s handy. The second is, of course, taking extra time to focus on my mental health. Hence what I like to call my lazy goals, because let’s face it, goal setting just feels like the adult way to make sure you’re relaxing the way you really want to.

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The CDC guidelines and you

The CDC announced that YOU NO LONGER NEED TO WEAR A MASK… if vaccinated. Yep they put the important part in nice tiny font and after a year of people actively putting others at risk because they would rather throw a fit about wearing a mask than help stop the spread. Roughly just over a third (~36% as of this writing) of the population has been vaccinated. What’s troubling is the large number of epidemiologists and scientists in general were shocked by the CDC announcement. So what now?

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The first in-person meeting

Well today we met as a lab for the first time since the pandemic hit in person. I wasn’t a fan, still am not a fan, but didn’t get a choice in the matter so I went. Thankfully everyone was masked and agreed that it was probably for the best since in my case specifically, I work with a very vulnerable population. It was nice to see everyone, but it was mostly a waste of time, mostly.

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Meetings and more meetings

Today was going to be about my meeting yesterday with my Co-PI, buuuut it turns out that I have even more news than that! How did that happen? Well I got an email from my main-PI asking me about my plans for the summer, when I wanted to finish the long, horrible, project I’ve been trying to work through, and more importantly, my funding situation. After some emailing back and forth things are looking dare I say good?

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So I shot myself in the foot

Ever say something dumb and immediately regret it? Yeah I made a huge mistake and ended up giving myself a ton of work for no reason. Well there was a reason, it just wasn’t needed. I don’t know why I do this to myself, but the good news is I got the work done. Okay, fine I’ll explain, it’s not a long story, but it is a funny one (at least now that the work is finished). It’s also a good reminder to never do that one again.

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The transition to summer

Well it’s official, my grades are in. Okay not “official” exactly, but they posted to the class website and I passed, obviously. In hindsight it’s funny because I was constantly worried about how well I would do in the class, especially with this project being worth so much, but I managed to get 100% in the class, so there’s that. Now I am statistics and it bends to my will! That would be a super power for sure, even though the class was a pain, I’m glad I took it. Now I make the slow transition to summer. It’s slow because it doesn’t happen all at once, but I’m excited.

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Data mysteries

Data processing, it’s mind numbing sometimes. I guess it depends on the dataset you’re working on, but in this case it’s just a formatting thing. Literally copy, paste, rearrange, things like that. The issue is the volume of data you’re working with. The whole thing can take hours just to get done properly, but with any luck you’ll only have to do it the once. Most of the time I’m not that lucky, the last dataset I worked with for my Co-PI I reformatted five or six different times. While that isn’t the topic of the day, it’s a good way to start the conversation of the day.

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Journal paper update

With all the things going on I never got the chance to talk about some non-class news. The downside is it’s not good news, but on the scale of horrible things to happen recently it’s not that bad. Back in February I submitted a paper for journal publication and we got rejected. Not great news, but the reviewers were not super critical and with some minor changes we should be able to resubmit it. I figure today we can go over the stuff that needs to happen now since I’m the first author.

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The end of the term

Time to catch up on my reading… eventually.

It looks like I survived. Another term down and one step closer to the finish line. It’s not quite the clean victory I was hoping for, but after yesterday I now no longer have any class requirements for my PhD. The only requirements I have now are with my dissertation, so now I can focus on that work exclusively. I’m not going to lie it feels pretty good. Since the end of the term isn’t as clean cut as I was hoping for. I figured today we can look at the leftovers from the past week of panic. We might as well after the week I had!

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Major milestone 3 (of 3)

I’m exhausted. Let’s just get that out of the way. I don’t think I’ve ever had so much work to get done in my life. No, scratch that I know I’ve never had this much work to do in such little time in my life. My eyes feel like they are about to bleed and I’m afraid if I turn my head to the side my brain will leak out my ears. The end of the term is usually an academic marathon, but this is ridiculous. It’s just been deadlines left and right. Anyway today is the end of the next set of major milestones, it’s not the victory I was hoping for, but I’m hoping rest will not be too far behind.

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Time for the big finish

Well call me a wizard because not only did I somehow manage to get everything done yesterday that NEEDED to happen, I also somehow managed to make more work for myself. Yeah, the universe hates it when I’m productive apparently. I’m tipping the balance and that’s never a good thing. But seriously, I now have more work to do and a lot of it is due tomorrow. Don’t worry, I’ll explain. Later I’ll probably cry about it too. (not serious) (super serious)

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Major milestone 2 (of 3)

Can’t stop now. We’re at what I’m calling major milestone 2 of 3. Yep, yet another batch of stuff is due today. I’m not super thrilled with all this and I still have so much to do before Friday I want to scream. As with major milestone 1 (here), we’re going over what I have done (spoiler not enough), what I need to do (a whole lot), and the plan to get it finished (cry for a few hours). Let’s just dive into it since there isn’t a whole lot of time (for me anyway).

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One major milestone down

Yesterday was sort of a cliffhanger. Everything was due, not a lot was fully complete and I had not one, but two things that my main-PI needed to urgently respond to and he was MIA. I swear you couldn’t write something with more drama if you tried (at least for a PhD candidate). Never fear today I’m taking a brief respite from the work I need to get done today to share what happened yesterday. As the usual this week, it was a wild ride all the way to the end.

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Major milestone 1 (of 3)

The good news, like it or not today I will have less work to do! The bad news is that I’m sort of up against the wire here. As promised, it’s all deadlines all the time for the next week. While this may not be the most useful or exciting read, it certainly is going to be a dramatic finish (see: train wreak). Today for simplicity since there’s so much to do and literally only days to do it, let’s go over what I have to do today and exactly where I am in all of that work. Spoiler, it’s not looking pretty.

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The first major deadline

Well tomorrow is the deadline for several of the things I’m working on, including but not limited to things I still need to get done today! Fun times for sure (not really). As promised yesterday we’re pretty much just watching the super slow train wreck that is occurring. To be fair it’s either going to be an extremely close call or a complete disaster, but that’s just how these things go sometimes. Let’s dive into what’s due tomorrow and where I am exactly in the process.

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On the importance of milestones

We’re counting down the days and there’s still so much to do. It’s probably going to be updates from here to the finish line because let’s face it, there’s not much time for anything else! Since yesterday I talked about the importance of planning and why it’s good to lay things out, I figure today I’ll talk about the importance of milestones since I have about a dozen or so I need to hit! For the sake of time, let’s just dive right in.

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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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The thing about deadlines

Man pressed against glass in office. The entire office is full of papers pressing against him. He's drowning in work.

It’s no secret I’m running around trying to finish everything I need to do lately. Deadlines for just about everything all fall within a few days of each other. I literally have a about a dozen things all due next week plus or minus two days. I’ve been trying to remain calm and remind myself that I’ve been in this situation before and it always works out in the end. That doesn’t stop me from stressing out and yesterday I got an email that could derail a lot of the planning I’ve been doing to make certain that all the work gets taken care of. Yep, I got another job to do.

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Learning can be painful

Well today was the final lab meeting of the term. While the weekly meetings will (probably) be continuing, it’s still a big deal and could (hopefully) mean the end of my six weeks or so of torment. Normally I give it a few days before I talk about just how badly the meeting went, but this time was different and I’m thankful for it. The difference? My main-PI was out for medical reasons, so we got to talk about the project a little more freely.

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An end in sight

Hourglass on laptop counting down
Hourglass on laptop counting down

Well I had an awkward conversation with my main-PI yesterday about some of the progress I had made and while he seemed generally supportive, it unfortunately wasn’t particularly helpful. All that work I had hoped to finish over the weekend? Still going, but there’s other things going on too so we’re counting down to the end of the term now and there’s an end to a lot of this, but it’s going to be (as always) a race to finish.

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Flexible coding for data visualization

My main-PI has an odd habit of wanting us to edit things as we’re presenting them. I’ve watched this happen and had to do it myself. Suddenly you find yourself editing a paper/grant/etc. and forgetting how to spell your name because you’re so flustered. It isn’t just papers though, it’s our visualizations that we make. He will ask us to go in and change things as they are being shown. This has happened to me several times already and more often than not I’m ready for it. So today I figured I would go over some of the things I do to make sure that I don’t spend the entire time sweating over edits to my code.

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Apparently I’m close?!

We’re talking about it again, the fact that every week for the past 5 weeks now I’ve been given tasks to do and then presenting on them the following week. It’s been… hard. However, my main-PI gave me hope that the end of all this is close, at least that’s the hope. He said I was close, so today we’re going to talk (as usual vaguely) about what I have left to do before this weeks meeting and why I cannot wait to be done with this.

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