We're a little crazy, about science!

Author Archive

War and (hunger) games

The first time someone asked me if I killed anyone I was taken by surprise. It’s a deeply intimate question, but a question that some people seem to ask so flippantly. It’s a taboo, even in my small military circle of friends. One that I don’t talk about and one that we will certainly not be talking about today. I’m reading, or rather rereading, the Hunger Games trilogy and it made me think about the first time I read it.

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More on mentorship

It’s dangerous to go alone!

One of the more enjoyable aspects (see: favorite thing ever) of being a PhD candidate and about half way done with my degree (… WAIT. HOW THE HECK DID THAT HAPPEN?!) is that I get to be a mentor. To be fair, I’ve been mentoring since my senior year of undergrad, but my style has developed and I don’t… flail as much as I used to when I first started mentoring students.

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Dataset mining

We use heavy equipment to mine our data around these parts…

I did an experiment! That’s old(ish) news, but now I have some data to play with… lots of data. So now I get to do something somewhat enjoyable and that’s try to get cool and interesting stuff to fall out of it. All you have to do is shake it really hard and hope for the best.

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A breakthrough

Oh yeah!

Well… where the hell do I even start? Yesterday was actually a semi-okay day. I mean the world is still on fire, the pandemic is still killing far too many people( but somehow not enough for the people in charge to care), and I mean let’s face it, it feels like the human race is in the death throes. HOWEVER, all that aside, my microscopic insignificant day wasn’t bad… now I’m worried.

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Distractions, distractions

Comic by theAwkwardYeti

Why people think that we could be MORE productive in a pandemic is beyond me. I can barely get myself out of bed most mornings when there ISN’T a pandemic killing ~1200 people a day. I mean how high does that number need to be before you too are less productive my fellow compassionate human?

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The Nyquist frequency

Parts to a wave (top left) a example wave (bottom left) and different examples of how waves change based on frequency (top right) and amplitude (bottom right)

A few days ago I realized I had never bothered to explain the nyquist frequency. Considering it’s been over a year now since I explained some of the frequency domain things that I do in my lab, I’m actually surprised I missed something so important. Well, better late than never today we’re going to explain the nyquist frequency and why it matters… to my work at least.

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Health in a pandemic

I don’t want to be another link in the chain. I’m selfish, I don’t want to get COVID, I don’t want to deal with the after effects (if I live to tell the story), and I certainly don’t want to get others sick. My travel is limited to places I absolutely need to go. Unfortunately, that means I’m stuck doing research in a hospital setting, but I mask, wash my hands, and do everything I can to keep safe.

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Thalidomide: A forgotten history

Distaval was the brand name for Thalidomide

The COVID-19 vaccine is coming… eventually. There is a push by Trump to get it out to the general public prior to the election no matter the cost… gee I wonder why? However, we have testing standards in place for a very good reason and while it can be medically necessary to provide promising medicine in a few select cases, this is not one of them. A history lesson is in order and like all history, we may be doomed to repeat it if we don’t learn from it.

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On being exceptional

If you’ve read my blog for any length of time then you know I’ve had a hard life. A very, very, hard life. The thing that keeps me going isn’t money, it’s not the chance for fame, or for people to remember me when I’m gone. The thing that keeps me from very literally killing myself is the chance to help people. That’s a selfish goal, but everything that drives us at its core is a selfish thing.

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Neuralink: Beyond the hype

The sewing machine like robot that is the linchpin for neuralink.
The sewing machine like robot that is the linchpin for neuralink.

Brain machine interfacing, as someone who does research in the field and is getting a PhD in a brain machine interface lab, I think I’m qualified to comment on the progress neuralink. There’s a lot of hype out there, curing disease, ending paralysis, a world where we are part of the machine and the machine is part of us. Is it science fiction, or is there more to it?

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Fact or artifact

Does it belong in a museum though?

A new turn in the saga of my data processing. There has been some concern that the artifact from the stimulation is causing the thing I am seeing in my data. There are arguments to be made for both sides, but let’s go over what that could mean for me.

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Path planning

One would think that the pandemic would put a lot of things on hold. Unfortunately (here in the US anyway) that isn’t the case, it just makes things harder to do because everyone expects you to perform at a higher rate now that you’re not commuting to school… how the hell that works is beyond me.

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So much data

This has basically been my progression in this project.

Well I’ve processed (poorly) about half of my data. Now, when I say poorly I just mean the visuals for it are garbage and I need to tweek the sizes and things to make it look nicer, but the idea is that I’m more interested in finding something than I am in making it look pretty. I’ve processed two of four of my subjects and well I’m excited!

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The after

I’m trying to remain calm. I am an objective observer in the world of science and whatever the result, I will NOT let it cloud my emotions. I am neutral and I will remain that way… oh who am I kidding, I DID IT! Two years of planning and convincing people this would work. Then last night I had my first result, and it was a relief. It was a small step, but one I was afraid the data wouldn’t let me make.

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Into the unknown

Time to cross that bridge…

Today is going to be a somewhat anxious day for me. It’s the day I get to crack open my data and see what spills out. There was a process to get to this point of course, it took me about a week, but today with just a few clicks I’m going to see if I have something or if my idea was never meant to be.

Read more… if you dare!

How to 3D print… yourself!

It’s hip to be 3D…?

Ever have an MRI or a CT done and thought, “I really wish I could do something with that.” Well you’re in luck! Today we’re going to do a quick rundown on how to take a medical scan and convert it to a workable 3D model. Something you could 3D print for example! As with everything else I do around here, this is done with free software so the only limitation is your access to medical scans, but we can get into a work around.

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3D Print… yourself!

It’s hard to tell the scale from this image, but you’re looking at a full sized copy of my spine. Yes, full sized as in big, really big!

You know what’s boring? Going to the doctors office and getting an MRI. You sit there forever! Of course a CT scan is faster, but there’s still a lot of waiting involved and in the end, you get to see a quick glance of the images captured if you’re lucky. Where’s the fun in that? Well I’m here to help you do something with that information. Useful? Maybe. Fun? Definitely!

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School is coming…

3D printed spinal column still in parts getting ready for cleaning and assembly.
Did I mention I 3D printed my spinal column (as in a copy of MY spinal column)? Because I did. I’ll post up an explainer how later, but here it is in pieces waiting for me to have a few free moments to clean and assemble it. In the meantime, this is the teaser image for it.

With classes about to kick off I’m left wondering what will be different for me. This term I’m doing the safe thing and taking a single online course. The rest of my time will be focused on my research and doing what I need to do to be ready for my PhD proposal defense (the step I want to take this fall term. So what am I doing to get ready?

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School and COVID-19

School being cleaned in preparation for students return. This is security theater, it spreads from student to student more readily than from desk to student.
This is security theater, like taking your shoes off at the airport, it does nothing to keep you safe. Instead it makes people feel better, in this case the school for letting your children spread this virus without a care.

School, I would like to consider myself a lifelong student, but formal instruction is a little different than learning on the job or via the web. With classes starting, my stress seems to be slowly ratcheting up. Oh I’ll be fine, I’m taking an online course this term, I’m worried about everyone else.

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A busy day!

Yep I use this image a lot, but it’s such a great representation of our labs work!

Well I didn’t plan for it, but today is a busy day! I’ve got a lot going on at the moment so not a lot of time to write. Let’s just talk about what I’ve done and have left to do so I can get back to it.

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Process the data!

This is what raw EEG data looks like. Seriously, it’s a bunch of squiggles. However, we can make sense of it and we can even write some code to make sense of it in real-time so you can control things with your brain!!! <EVIL LAUGH>

It’s a process… that’s for sure. So you’re a scientist and you collect a ton of data, well now what? We’re talking about me of course. I did it, I collected a ton of data and now I need to do something useful with it. This is the part I wish I could skip over and get to the part where I get all the cool results, but I guess we’ve all got to start somewhere.

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A new chapter and a look back

We’re looking forward today… while looking back too. I did a big thing! I finished my 365 days of academia goal, it felt too big to do, but here we are. So what’s next? Well we’re going to talk about where we are, where we were, and what’s coming, so let’s get to it!

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The end

I fully and completely wanted to die. I like starting stories of my life off that way so you set your expectations low and your pity high. I wanted to die and I tried to kill myself the best way I could think of, obviously it didn’t take. Today is the end of my 365 days of academia project and I feel like looking back, way back. If you feel like reading a super depressing tale, then this is for you!

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Day 364: The lazy goals

An old photo, but one that I think came out nice.

Awhile back I made some goals for myself. They weren’t your normal everyday kind of go get em’ goals, they were what I call lazy goals. That’s right as a full grown adult I reserve the right to have lazy goals. I even check them off on a list, seriously. You should too, it really does help remind you to take a break.

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Day 363: Solid Modeling – Week 10

Dancing tree

This has nothing to do with today’s post, it’s just the most cursed thing I’ve created in SolidWorks.

All good things come to an end. It’s week ten and officially our last post in this quick run through. As always we use FREE SOFTWARE to do this, so if you’re just joining in you can find the  full course in the Solid Modeling for Beginners category and you don’t need to spend money to learn. Since this is our last post I wanted to do something a little different today, let’s get started!

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Day 362: Experiment two

Just a giant case full of the equipment I borrowed from my university for experiments. Pretty sure the school’s office staff thing I was robbing the place though.

Well today is going to be a quick recap of my experiment yesterday. This will be just as much for me as it is for all of you. While I can’t go into the experiment details (since I’m working to publish this) I can give a pretty good overview like I did the last time around.

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Day 361: Accidental history

Impostor syndrome
Art by: xkcd

Ever wake up one morning and realize you’re exactly where you wanted to be. That you’re in a place you never even dared to dream you could reach because, well it was silly to think you could accomplish something like that. Dreams that big weren’t meant for people like you, so you didn’t even bother to think you could get there. Yet… here we are.

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Day 360: Second experiment

Computer

The computer I use to process all my data, even with this it takes FOREVER to finish processing.

Well tomorrow is my second experiment. To be clear, it’s technically the same experiment, just a second person, so maybe it would be better to call it trial two? In any case, while the last one went (mostly) well, there are a few things I’m changing to make this next one even better. Sometimes when you prep for an experiment, you don’t realize what you’re forgetting until you can’t do it, so we’re correcting that this time.

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Day 359: Car problems

Engine

Thought it was the PCV valve, but nope…

Well if things weren’t bad enough as it is with my own little world, we get to add car troubles to the list. Dealing with issues like this during normal times isn’t so bad, besides the bill that is, but this isn’t normal times. Nope, we’re dealing with a pandemic, school is about to start, and to top it off, I firmly do not have the money to fix the damn car, what’s a guy to do?

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Day 358: One small step

Dream big

Sometimes are points in life that you can clearly define as the before and the after. As a child sometimes those points are simple milestones growing up, starting a new school for example or moving to a new town. There is the before and the after. As you get older those points become few and far between. For example, you started a new job. Unless it’s your dream job, you don’t really think of it as one of these points and everything just blurs together. Thus the bar seems to get higher and higher as we age. Today I had one of those points.

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Day 357: Thoughts from the lab

Case

My giant very suspicious case full of equipment from my school lab.

Well today is a busy day! I’ve got a lot going on so hopefully by the time you read this I’ll have all the setup taken care of. Working in two labs seems like a fun and interesting way to do experiments and it is! It’s also a huge pain.

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Day 356: Solid Modeling – Week 9

Lamp render

This week we’re giving our lamp the finishing touches, including the plug! I decided mine needed a table top to sit on this week, but you don’t need to do that if you’re not feeling it.

It’s week nine! Welcome, to my little solid modeling course. As usual, we’re using FREE SOFTWARE¬†to do this, I feel that everyone should be able to learn if they want and this was the easiest way to do that. If you’re just finding my little series, you can find the full course in the Solid Modeling for Beginners category. For everyone else, we’re finishing our lamp today (for real this time!) and next week is the last week in the course! Let’s do this!

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Day 355: Nostalgia for the unsentimental

Memories

One of the oldest photos I still have, it seemed appropriate for the post today.

To say I had a whirlwind of a life would be an understatement. Until my mid-twenties I moved at minimum once every two years. Not just moved across town, as in moved states. To be fair, as a kid it was bouncing between a few states. It wasn’t until adulthood that I started moving further away. Oddly enough, it wasn’t by choice, life just seemed to get in the way of staying in one place long enough to settle in.

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Day 354: Even more paper edits…

bad writer

These feels brought to you by: phdcomics

Whhhhhyyyy!!! Okay it’s not that bad, or maybe it is. I have yet more paper edits to do. It’s frustrating I just really want to be done with this paper and it doesn’t seem to want to end. I’m trying to keep my eye on the prize and do this right, it’s just soooo freaking difficult. I just want this done.

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Day 353: Experimental prep

Matlab

Sometimes a parfor loop in just doesn’t cut it because the things you want to do in that loop aren’t allowed (like save or load data a certain way). In those cases (see above) I can run multiple instances of MATLAB and process my data much more efficiently than if I did it one at a time. In this case I had 8 subjects that needed a rather long mathematical operation performed, so I did it all at the same time. It’s a little silly, but it worked! If you didn’t know you could do that, now you do!

Yesterday I told the story of how we got to this point, a long two year journey and next week I finally get to take the next step. It’s exciting, but it also means because of my flare-up, I’m behind on what I need to do to be ready. Not to worry though, I’m taking it slow so I don’t make whatever I have worse. What goes into an experiment like this? I’m glad you asked!

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Day 352: My experiment is coming!!

EEG Cap

I just really like how this photo came out. Here’s one of my lab mates gelling the electrodes for a pseudo-experiment. The scary looking syringe has a blunt tipped needle, we don’t break the skin in our lab so no pain, just a bit of gel to wash out of the hair once completed.

Okay I’ve got an experiment update today and I’m really excited to share because it feels real finally. I know I already wrote about some of this, but when I reread my previous post, it felt disjointed so let’s go over how we got here and what’s coming. I’m excited, are you excited? I’m excited!

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Day 351: Digital color

Online persona

Anger, after thinking about it, it was anger I felt. Not at anyone in particular, but I was angry and hurt and a lot of other similar emotions, but I was angry most of all. People kept letting me down and it took a chance twitter conversation for me to realize why I was yet again left feeling so fucking angry.

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Day 350: In construction…

extruder

I redesigned my extruder to make it beefier, this has nothing to do with the post, but I’m really proud of it and wanted to share. Haha

Well today despite feeling like refried dog poop I have to go do experiments. It’s part of the job and to be honest I want to do it even though I feel like dried monkey vomit. I could go on, but you get the picture. I do have some more good news not related to yesterday’s news. So that is the conversation for the day.

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Day 349: A story in three emails

Drowning

I was awarded something, we’ll get to the what shortly. I was awarded something and I was excited because it felt like validation of my work. It felt good to have people take notice of my accomplishments. There are precious few times in my life where I’ve got to feel like someone selected me out of a group as exceptional. Here I was being nominated for something! I was walking in the clouds. I could do anything, be ANYTHING.

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Day 348: Solid Modeling – Week 8

Finished Lamp

Left my lamp on in case you needed some light. While we didn’t finish the lamp today (boo) we got pretty far. We’ll finish it next week, but I don’t feel well so I needed to stop, sorry!

Welcome back or maybe welcome aboard! This is week eight of my online solid modeling course. As always we use FREE SOFTWARE for this class so no matter who you are, if you have internet access you can do this (seriously, it’s all cloud based so you don’t even need a fast computer!). If you’re just finding my little corner of the internet, never fear you can find all the courses in the super useful Solid Modeling for Beginners category. They get listed in reverse order, so work your way up from the bottom. Now that we’ve finished the intro let’s dive in!

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Day 347: The precipice of … something

precipice

Today is a mash of things, because frankly I still am not feeling good. My the scaly bits on my hands, face, and apparently elbows (missed that one until last night) haven’t gotten worse (yay), but they haven’t gotten better either (boo). On one hand it’s a realization that whatever is wrong with me was worse than I had thought, on the other, the world still moves forward and unfortunately I have work to do, so what’s a guy to do?

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Day 346: What is going on with me?

exhaustion

It’s going to sound like depression. I realize that as we dive into today. I don’t normally do this, but I’m rewriting this intro because I know what it sounds like. It’s not that, this is something else and it worries me. I know depression, I’m good friends with depression, this is something different so don’t tell me it’s depression, it’s not I promise. It just happens to be worse than I can ever remember right as I’m dealing with the worst flare up [of whatever I have going on] in my entire life, so it couldn’t be a coincidence … could it?

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Day 345: Undergrad research presentations

Virtual classroom

Well today is day one of three for wrapping up our undergrad/high school research experience. We had a group of about 50 I think, just in our lab and a good portion of them were high school students. Because we’re living in a pandemic, this was all done virtually! Today we get the first glimpse into how we did as mentors.

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Day 344: In which we are reminded I’m not that smart

Depression

It will pass, it always does, but for now I feel like I’ve been punched in the gut. I don’t enjoy the feeling of being average, or more than likely below average. It means I have to do twice the work for half the result. I see genuine greatness and know that no matter how hard I try, that will always be out of reach for me. What do you do when you want something so bad you would die to get it and you know you will never reach your goal?

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Day 343: On lab equipment

BrokenLaser1

Luckily this wasn’t my fault, but it does make for a good story now.

It was bound to happen eventually. We all knew it would, but we didn’t expect it to fail in such a spectacular manner. That is to say, all at once. One of the people I’m mentoring checked out some lab equipment since we had come up with a way to do experiments from the comfort (see: safety) of her home. That was the plan anyway…

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Day 342: When stress hurts

Drawing of a man with cracks forming at the back of the neck. He looks sad, looking down.

Drawing of a man with cracks forming at the back of the neck. He looks sad, looking down.

I have a lot of disabilities. Some are more debilitating than others for sure, most are just annoyances or give me weird quirks that people sometimes are frustrated with, other times get a laugh from. For the past few days I’ve been dealing with a flare up so bad I’ve never experienced anything like it in my life. It was a painful reminder that I was in fact stressed.

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Day 341: Solid Modeling – Week 7

Lamp Render

If you’re following along you’ve made it to week seven! This course is taught using FREE SOFTWARE so if you ever wanted to learn how to solid model, this course is the one for you. If you’re just joining then you can find all of our classes listed here in our Solid Modeling for Beginners category. They are in reverse order, so start at the bottom. Today we are setting aside our lightbulb for a moment to create something to put it in. I’ve given up keeping what we’re doing a secret (since I always put the final product in the header image anyway). So with that let’s get to it!

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Day 340: Writing… a lot.

once upon

This is how I start all my technical writing.

Another day, another set of problems. So what better way to put off my writing for the day than to write about not wanting to write. I feel like I’m living in a meme all of a sudden. Today I’ve got about 4353453421 things to write, give or take 4. Is it odd that I would rather be writing this than any of the stuff that matters?

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Day 339: What will school look like?

School

Here in the US we paused, it was only for a moment, it wasn’t long enough, and not everyone did it, but we paused. Then just as quickly as we tried to adapt to the changing times we went back to pretending everything was normal. Beaches opened, restaurants opened, bars opened, we saw celebrations and parties and we ignored a single digit daily death count, which turned into a double digit, then triple digit, now we’re hovering in at roughly 1000 deaths a day from the pandemic.

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Day 338: Feeling stuck, again

feeling stuck

I’ve probably mentioned this before, but I feel stuck. With the pandemic going on and the protests (Which are still happening!) I don’t feel like there has been any forward movement in anything I’ve been involved with. I hate feeling like this, it’s so frustrating especially when I feel like I’m drowning in work to be done.

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