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Posts tagged “science

The next big experiment

Well things are moving fast around here, like I predicted they would this year. Of course, things are currently going better than I had hoped, but that could change. Last week was a busy one and next week will be no different, but next week is a particularly big week, because I’m going to be doing another experiment for a somewhat different project. Yep, another “big idea” experiment is coming.

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The last paper response

Well it’s been a few weeks since I got the response back for “last paper” since I have roughly three weeks left to finalize all the edits they requested, this weekend I plan on tackling most/all of it so that we can get the ball rolling with my collaborators so I can (hopefully) get the response back to the editors before the deadline they set. Because there is a deadline and I do not want to be late, mostly because it will make more work for me if I am.

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The first time is always the hardest

If something can go wrong, it will go wrong. Especially when it’s the first time. I’ve got my first dataset for my PhD dissertation, but it was a battle of wills and the technology made sure to let me know, it’s in charge here. But at the end of the day, I got what I wanted, so it’s a win, even if it’s a bit of a loss too. Frankly, I’m so exhausted right now so forgive me if this post is all over the place, well more than usual.

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When DARPA calls

Fifteen years. It’s been roughly fifteen years since I started this journey and the dream was always the same. We all have stupid dreams as a kid, we want to be astronauts and sports stars, but the odds aren’t in our favor. We’re told to be realistic. Sorry kid, your dreams are too big. You need to shrink yourself to fit into the tiny box we as a society provide you. I was never good at following instructions, so maybe that’s why the past fifteen years have been a special kind of hell, but today, today made it all worth it.

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The first dissertation experiment

One of my favorite photos I took years ago of my labmate gelling a participant for an experiment. The syringe holds a conductive gel, the needle is blunt tip so it doesn’t hurt or puncture the skin. The gel bridges the air gap between the scalp and cap because hair gets in the way.

It had to happen eventually! But not today, this Friday however will mark the first of several experiments I will be undertaking in the (currently) slow march to my PhD. In an effort to help people understand that experiments aren’t just something that happens at the scheduled time, let’s take a look behind the scenes at what I need to do between now and Friday to get ready. It’s going to be a looong week.

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The mental health stigma

You don’t look depressed. Chances are if you struggle with depression you’ve heard that once or twice, or dozens of times on a seemingly never ending loop. If you have a broken bone you can be diagnosed via an x-ray or CT. If you have cancer, there are blood tests or MRI scans that can catch it. If you get sick, rapid tests or PCR will tell you if it’s COVID. But how do you diagnose depression?

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Another deadline rush

Why is it always a rush?! I wish I had answers, maybe as scientists we just like to procrastinate, but whatever the reason, we have a huge deadline just five days away and it feels almost insurmountable. As hospital-PI puts it, I have 12 hour nights I can get it done, he’s kidding… I hope. It’s time to break out the hard stuff, caffeine that is, and get ready for the week ahead.

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The lab brain drain

Today was another proposal defense! No, not mine thankfully, but one of my labmates who’s been in the lab for some time now. As the term is coming to a close, I think a lot of us are in the proposal defense phase, which means things will be changing dramatically in a year or so for the lab. It made me realize that there was a rather large gap between those of us finishing and the new members, which means big changes once we graduate.

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So you want to build a humanoid robot

See, standing on its own!

IT’S ALIVE, ALIVE! Robot paper is live that is and to celebrate this achievement, I’m giving away all my secrets. My poor robot was two long years of work to get right and four years to publish this. But as of this writing, it’s possibly one of the most advanced platforms around, if not the most advanced. That’s a bold claim, so let’s talk about how I did it, why I did it, and what makes it so advanced. This was four years coming, so forgive me in advance for the long post. I’ve REALLY wanted to talk about this.

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The cost of research

I’m not sure why, but lately I’ve been tasked with gathering quotes for new equipment. It’s not even just with the hospital side of things either, the school side has suddenly asked me for quotes as well. I understand the logic of having gather the quotes like this, after all it’s a huge time sink, but I’ve learned a lot over the past month or so from dealing with all this and that is research isn’t cheap.

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3 aims, 2 experiments, 1 year

It’s now official, I have a rough timeline for everything I want to do and I’ve got the greenlight from my committee that the work I propose to do will be enough to earn my PhD. I’ve spent the past day trying to plan out the rough outline of what the next year will look like in context with all the other work I will be doing and it will be busy!

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Weekend outreach

A few of the exoskeletons we have in the lab

It’s been a super busy week, but we’re not done yet. That’s right, my inability to say no to things has come back to haunt me! It’s not that bad though, two 15-minute talks to two different groups and that’s the extent of it. So you know not too bad, but I do enjoy doing some science outreach when I have the chance anyway, so not totally a bad deal.

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The last project

Today was my proposal defense day and I would like to say it went well. I would like to. Kidding, I think things went okay. I’ll leave that to the handful of people who read my blog regularly to judge. My committee members all thought the work was interesting and my plan of attack was good, so now the real work begins. It’s the last project before I get my PhD.

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The main event

Well tomorrow is D-day, proposal defense day that is. Technically there will be one more defense day after that, my actual PhD defense. The difference being, when that’s all done I’ll have a piece of paper to show for my efforts. That won’t come until next year… hopefully. But in the meantime, tomorrow is the (other) big day and I’m getting just a touch nervous! After all, it’s only the next year or so of my life I’m laying out for my committee members, what could go wrong?

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An ounce of preparation

What a week. It’s only Wednesday and it feels like it’s just never going to end. There are three major events coming up this week, meaning I will be working this weekend unfortunately, but at least I made it through the day. Tomorrow will be a major event for me, dare I say bigger than my proposal defense just two days away.

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The return of big idea

I had hoped to discuss robot paper today, but something more exciting has happened so today we’re talking about the “big idea’ I had a while back. It feels like it’s been forever since I had the idea, but things were moving slowly lately so we’ve had to wait. I’m happy to say the wait is finally over! If all goes well, by the end of the week I’ll have the first dataset from big idea and I am very excited!

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The new papers

With three out of four of the papers I was working on published — or at least in the case of robot paper, about to go live any day now — I’ve got a new batch of papers I’m working on. Thankfully I don’t think I’ll have another pileup of work like that again, hopefully. Currently I’m working on two different papers and I already have plans for at least six more, so it will be a busy year for me.

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The OR waltz

It’s back to the OR I go! Which means exhausting times ahead, but also very exciting times. It’s been months since our last OR experiment and things have been shelved, literally, equipment has been packed away because we weren’t using it. So it’s time to once again to shake out the equipment and do our familiar dance with the clinical staff.

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The first practice

My dissertation proposal date is fast approaching and I just barely set it! There’s still some work to be done, but today was the first practice presentation in anticipation of the big day. I’m happy to say it went better than expected, but there are a few things I need to change. Since, as usual, we can’t talk about the details of the proposal itself, I can talk about the changes. As an added bonus that’s a broadly applicable thing to talk about, so it may not just benefit me.

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The proposal defense date

Single business person untangling giant rope

Okay not going to lie I had a minor freakout the past few days. One of my committee members wasn’t responding to my emails so I could not schedule my proposal defense. Last night out of the blue, reality smacked me in the face and it occurred to me that next week was the first week I was trying to schedule and time was running out. People are busy and I didn’t want any of the PI’s to have a conflict. But it all worked out…

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New and old projects

It’s finally my chance to put my own spin on the stuff coming out of the hospital lab and I’m incredibly excited about what is coming. Unfortunately I can’t talk about it! However, I’m hopeful that this year will be an excellent year for me with regards to the research I’m doing. Things are slowly falling into place and while we’re still at the beginning, things are looking bright.

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Slides, robots, and figures. Oh no!

I’m trying to figure out how to incorporate this into robot paper (not serious… semi serious)

Since there’s a mile long list of things I need to get done this weekend, let’s just grab the top three time consuming things and cram them together into one post! When I took on the full-time job while (hopefully) wrapping up my PhD, I didn’t expect for things to be so… busy? Okay, things are always busy, that’s a theme of any PhD journey, but it does feel a bit excessive lately!

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The big rush

A while ago I had an idea, a “big idea,” but the second I had that idea the clock was ticking. Because ideas are not that unique. There is a gap in research and we try to fill that gap when we see it. I noticed a gap and because I noticed it, there’s no reason others won’t notice it as well. Now we’re in an unseen race to publish and there’s still some speed bumps in the way that are causing some issues. I’m hopeful we can get there first, but I wouldn’t be surprised if we had competition.

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The other presentation

With just a few days to work on the project, I was asked to present the data we’ve recently finished collecting at work. The presentation will happen Monday, as in three days away Monday. So between now and then, I need to process the data, make some figures (so many figures), and generally draw some sort of conclusions based on the work.

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The finalized proposal

Well today was kind of a big step, I’ve finalized my proposal, got school-PI’s approval to send it out, and now I’m just waiting for a few people to select their availability so we can schedule the actual defense. I’m just a touch nervous! I still need to modify my slides and of course practice, but we’re now roughly two weeks away from the actual proposal defense!!!

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Figure rush

Always with the figure making! Why do we need to make a figure, damn it I’m an engineer not an artist! Yet I’m in a tight spot for the moment because I need to start creating about half a dozen figures showcasing the stuff that we’re doing at work. Oh and I need to make at least one more for the dissertation proposal, not including any additional figures for my slides. It’s going to be a rush job for sure.

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The proposal edits

We’re just a few short days away from the two week mark to dissertation proposal defense day, maybe, I’m still waiting for responses from three committee members, two of which I speak with on a regular basis, so I’m not too worried about them, one has been ignoring everyone’s emails, so I am slightly anxious to hear back about that one. Since the time is rapidly approaching I need to have both my written proposal and slides figured out, like now.

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Not so smooth sailing

Incredible art by: Nunzio Paci check out the rest of his stuff, he’s super talented!

When we last left our exhausted student/medical professional he was anxiously awaiting the meeting that was scheduled for today. It was a rough ~24 hours, but here we are on the other side of the meeting and now there’s a firm(er) plan in place moving forward. So what does that mean for our haphazard student? Well, it could be worse… probably… maybe?

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Committing to the story

For the past few days I’ve been talking about telling a story with your data. Because at the end of the day as a researcher that’s what we do. We do an experiment and, assuming it goes well, we have a story to tell about the result we found and what it means to the people reading the paper. Ideally any good story will have great visuals to add to the story and to help the reader. Which is where I’m still stuck…

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Characterization of interlimb interaction via transcutaneous spinal stimulation

A graphic hospital-PI put together to share our results. I made the figure on the left under the methods heading, which I’m still very proud of.

I was debating about talking about this because I’m “only” the second author on the paper. Apparently I’ve gotten picky now that I have a handful of first author papers in review/published. I’m joking, but seriously, this paper has a special place in my heart and today I want to talk a bit about the science, but also the story behind the paper, because it is an interesting one!

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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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On the shoulders of giants

Tomorrow I’m doing something for the first time, ever. I got an email yesterday with the good news and while we don’t have all the equipment we need for the project, we can still get some good data and an early look at what the data will look like. I’m so excited I’m shaking, I barely slept last night, and my mind is swimming with the possibilities. This is what it’s like doing research on the edge.

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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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The first one

Ever look up an answer in the back of the book? The problem with research is there’s no back of the book, but typically when you do an experiment you can at least glance at research surrounding your work and make sure you’re not going completely off the rails. Because I like to make my life unbelievably difficult, and because I don’t like taking small steps forward, I’m going to (hopefully) be the first to do a few things this year. But it’s not as glamorous as it sounds.

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A town on fire

Section of Route 61 or graffiti highway, nicknamed such because it’s a highway and there’s a lot of graffiti. Sadly a few years ago they covered it with dirt because a lot of the graffiti was obscene.

My brain works in mysterious ways, but did you know there’s a town that’s burning and will probably be burning for another (roughly) few hundred years? Not a town exactly, but it’s yet another case of truth being stranger than fiction. If you’re not familiar with the story, or just like learning more when you can, let me introduce you to the town of Centralia.

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More on failure

After a rough night of sleep I knew exactly what I wanted to talk about today. Failure. Because like I mentioned yesterday, in my journey to a PhD, there was plenty of it. Part of this was due to the fact that I had no idea what the hell was going on or how to prepare for my PhD, but a big part of this was due to the fact that I held a belief that wasn’t true. I thought, because it’s what we’re told, that when applying to grad school grades aren’t the only thing that matters. And I was lied to.

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The transition to grad school

It’s that time of the year again for anyone who’s applied to grad school. This is roughly the time people get acceptance letters, or if you’re like me a pile of rejection letters, but look at me now MIT! Can you tell I’m bitter? Any sort of life transition is hard, be it high school to college, college to work, or even sleep to awake (or is that just me?), transition can feel downright scary. Well the person I’m mentoring “Kay” is about to take that jump and I can’t lie, I’m super excited for her.

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And then DARPA appeared…

DARPA and I go way back. Right after I got out of the military back to be exact. Not that more than one or two people even know my name (and probably only vaguely), but DARPA is the reason I’m where I am today, even if the people who helped me get here don’t remember me. As much as I love the DARPA origin story, that’s all it’s ever been, that is until today, when school-PI let me know that DARPA was paying attention.

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The IRB and committee and dissertation proposal, oh my!

Well today has been eventful! After a bunch of emails, meetings, and miscellaneous things, I have a clear shot to my dissertation proposal! I don’t want to say it’s been smooth sailing or that things won’t be rough, but I’m feeling optimistic after all the news. Since there’s a lot, I figure we can cram it into a single post as I take the next few steps to the big proposal defense day.

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The PhD dissertation proposal

Spinal column shown through a semi-transparent person
Spinal column shown through a semi-transparent person

Well we’ve finally arrived, for real this time, to my proposal timeframe. There are a lot of things that need to happen between now and when I defend my proposal, but thankfully most of those things are started or almost finished. The one thing that isn’t started… well that would be my actual proposal. Be not afraid! I’m going to have the draft done today, or at least that’s what I’m telling myself.

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A (not so) small celebration of… me

a gold star
a gold star

I can write small novels on the accomplishments of others and praise the work they do, because the work they do is worth praise. I think I come off overly flattering, but I mean every word of it because people deserve to be celebrated. Well sadly, I lack that ability for myself, but I’m pushing through the skin crawling feeling that I should delete this and write something else to celebrate a victory, or at least an acknowledgement of a win. So today we’re talking about my least favorite subject, me.

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Back in the OR!

Well we finally got approval to head back to the OR. We were having some issues with our sample size, as in we hit the max for our protocol, but after a little bit of work we’re going back! The good news is that this doesn’t just affect the project I’m working on, this means I can move forward with the other project I’ve been dying to start.

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On randomness

Pick a number between one and ten. You picked the number seven. Was I right? Doesn’t matter, the point is there’s a slim chance you picked one or ten. The reason is simply because humans are bad at random number generating. Fear not! Computers are bad at it too, but that’s a problem for a world that revolves around cyber security. Randomness is so important to our daily lives, that we don’t even notice it… mostly.

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The final push of “last paper”

Amid all the chaos that the lab visitor we had yesterday caused I wouldn’t blame the causal reader if you thought that the robot project was my only focus. Hospital-PI summed it up best when he said we’re all working on roughly four projects at any given time and I responded with, “you guys are only working on four?” Don’t get me wrong, I like it this way.

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Inter-lab rivalry

Still from Science Kombat, because sometimes Newton just needs a good smackdown.

There’s nothing wrong with a little competition. In the field of research you’re either the first or your a footnote, so we rush to be the first when we know that other labs are on the other labs are not far behind. Our lab knew it was coming, there was already rumblings of something big coming from another lab, but when it finally came, we were both surprised, but not exactly shocked. It’s a pretty impressive paper.

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Another robot appears!

In the middle of the week we’re expecting some visitors that could lead to funding for our lab! Not that we need more projects, we already have over a dozen different projects we’re trying to power through and only three of us (including hospital-PI) to get them all done. Since we have so many projects, we’ve split them in half, literally. I’m taking all the lower limb projects and my labmate is taking upper limb. What does this have to do with the visit? It turns out, a lot.

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Return of the “technique”

splatter color brain
splatter color brain

With all the excitement around here with the progress made towards making “big idea” a reality, you may think that I’ve forgotten about other projects and things I’m working on. That isn’t the case and I have other exciting updates regarding something I’ve been calling my “super secret technique” not the most descriptive name, but that’s sort of the point. It’s not “big idea,” but is sure isn’t a tiny idea either.

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The big pitch

Today was the day we pitched a proposal to two of the doctors that can help make my “big idea” a reality. It did not go anything like I planned, some of what happened was funny, some of it was horrific, but mostly it went how it needed to go. Things never go as you plan them, but this was just completely off the rails.

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A big meeting

Well I’m excited, tired but excited. It’s been a long week and that is partly because I have a meeting tomorrow to discuss a project that will be a big help in my PhD, but also a really cool project in general. We also have a second big meeting next week with some guests coming to see the research side of the hospital, so yeah busy!

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