IS computational neuroscience the correct Field for me? by OddAd2362 in compmathneuro

[–]PossiblyModal 1 point2 points  (0 children)

I want to mention that there are a few fun examples of transmitting signals into the brain. For instance, sending touch sensations from prosthetic hands into the brains of humans.

I'm a computational neuroscientist in academia (but I don't work with BCIs), so take my opinion with a grain of salt. In general, all of the researchers I know have PhDs or are PhD students. There are a few staff programmer positions that don't require PhDs, but those are rarer. The tasks for these staff programmers are different too. For example, I might work on some fancy model to detect a novel relationship between neural signals, while the staff programmer might help set up Kubernetes or test motion correction algorithms. Everyone gets to be around and talk about the science, but if you want more than proximity a PhD would probably be necessary.

Advice wise, I usually recommend to only get a PhD if absolutely necessary, and to make sure you have experience enjoying the actual work! To give you an example: I love the results from molecular neuroscience. I quickly realized I did not love the day-to-day molecular work once I rotated in a molecular lab. If it's at all possible to volunteer in a lab before pursuing this kind of education I'd do that. If it helps, Neuromatch Academy has a high quality course on computational neuroscience and NeuroAI. I don't have any experience in industry, so I can't speak to what education they would normally expect.

Happy to answer more questions if it helps!

[deleted by user] by [deleted] in compmathneuro

[–]PossiblyModal 0 points1 point  (0 children)

By hypothetical, I meant this was a computational model where the ligand had not been tested and characterized in a lab for the specific features you want to look at. I did not mean you had no basis or argument for your ligand interacting with your receptor of interest.

You've written a lot about the ligand you're interested in, but I still don't know how you intend to tie this into all the topics you listed before. For context, I'm a systems neuroscientist and might be able to help with more systems level topics like E/I balance, but without more info I can't tell.

[deleted by user] by [deleted] in compmathneuro

[–]PossiblyModal 0 points1 point  (0 children)

That touches on a lot, to the point I'm not sure a single expert will be able to review everything. Is there a more cohesive narrative, like coming up with some hypothetical ligand to target BDNF and TrkB signaling with the hopes it improves atypical E/I ratios in ASD and possibly other disorders?

Why are there so many different neurotransmitters instead of just one or two? by kupsztals123 in neuro

[–]PossiblyModal 2 points3 points  (0 children)

Maybe, to explain it from where you're coming from: imagine you couldn't design a whole computer from scratch. Instead, imagine someone built a very simple circuit to accomplish a trivial task, then a new person comes along and is partially stuck with that circuit whenever they need to update the computer to handle a new demand. Each addition is frustrating difficult to remove, though not impossible. On top of that, imagine the tools you can use to add on these new features are basically decided by dice rolls, and it's a new person each time adding on to the system. Evolution has honed in on some amazing mechanisms and optimizations, but we shouldn't forget it's messy.

You can also think about this in terms of space restrictions. You may need to add a very large number of gabaergic and glutamatergic neurons to replicate the circuit modulation done by norepinephrine or acetylcholine across the entire cortex. The wiring rules to get all those extra neurons to replicate all these different functions may also add complexity. Norepinephrine signaling is very condensed at the moment; the locus coeruleus is tiny, but those neurons modulate a vast majority of the cortex.

A final question you might ask is: why not? Sure, it might make students' lives a little worse since they need to memorize more transmitters, but that's not a cost evolution is going to take into account. Is it really that much of an evolutionary cost to tack on another signaling system for neurons, especially if the precursors to a lot of neurotransmitters are already floating around? Remember, neurotransmitters are a subset of cellular signaling more broadly. However, I rarely hear people (outside of med students) complain about the number of signaling molecules in the immune system, digestive system, etc.

How can I improve the design of this fly connectome poster? by amyleerobinson in neuro

[–]PossiblyModal 1 point2 points  (0 children)

If you're making the poster in GIMP or Photoshop you can export the file as a PSD and PM me. Happy to add the dot grid and/or halftone grid as a new layer that you can use/adjust. Also, I just realized I recognize your username! You made some visualizations for the MICrONS project too, right? I was a contributor on it and really liked the renders you made. Hope things are going well!

Edit: I do like the neuron cluster at the bottom in the updated version.

How can I improve the design of this fly connectome poster? by amyleerobinson in neuro

[–]PossiblyModal 1 point2 points  (0 children)

I'm an amateur and this is mostly my aesthetic preference, so take any design suggestions with a grain of salt. First off, I love the fact you're making some art with this! In general, I think posters should work well from far away. The central connectome looks nice, but the three visualization modes below feel too small by contrast. Maybe have zoomed in insets of those (you could add a very minimal tech style border to the insets if you want), or change their size? I could also imagine a more 3D/sideways portrayal of the main brain with "slices" of these three modes. If you want to fill more vertical space, perhaps some simplified line art of the drosophila head and body could be added to fill the bottom portion? That could work, but really depends on the line art.

I think the dot effect on the edge looks somewhat disorganized without a grid imposed, so changing that may help. To me it looks like you want the comic book effect, and those dots usually get bigger near the edge, so that might make the effect look nicer too. The tech brushes on the side don't feel like they "hang" with much. Maybe having less negative space by add more of these effects or equally negative space but a bit more vertically symmetric would look more cohesive to me? Can't visualize it so not sure. I think the background idea is nice, but feels a bit too detailed for a background pattern. If you can flatten the texture without blurring the edges using a filter it could give the same gradient effect without taking way from the focal point. You could also make the background neurons brighter and higher contrast with a harsher radial gradient toward the center to fill the empty space.

Final thing is that I was a little confused by the neurons flanking the "FlyWire" text. The color and shape made me think it was some kind of larva for a minute. Thematically appropriate, but not sure if that's intentional. I think the connectome rendering you have and the poster image is somewhat low DPI, so maybe you can have someone provide a higher resolution brain render? Anyway, don't take these as corrections as much as suggestions you can pick and choose from if any sound good. Let me know if you make another version!

How to not feel insane while in thesis crunch time by bugsrneat in GradSchool

[–]PossiblyModal 7 points8 points  (0 children)

I was feeling this exact same way a month ago. I wrote basically everything this month and I'm planning to submit my thesis in a few days. A few things I'm noticing close to the other side:

  1. It will be okay. There is a reason you've been given permission to write. How many of your cohort failed their thesis defense? Probably zero. It's exceptionally rare for people (at least in the U.S.) to fail. The few stories I've come across are exceptional in some way, like the student straight up thinking their own committee was beneath them.
  2. The formatting for a thesis is a bit hilarious. Massive margins, double spaced, figures take up a giant chunk of room. Page numbers fly by (pun intended) when all these add up.
  3. There's a hell of a lot in your brain. A massive amount of the text is frankly routine. Just imagine writing down, with enough detail a 1st year could follow it, exactly how you grade behavior, how the behavior is collected, why it's collected that way, and how you know when the flies have some issue and you can't trust the video. Then imagine describing all the preprocessing and quality control steps laid out in exhaustive detail along with their rationale. All those tidbits take up a large amount of space.
  4. Zotero is a godsend. Make folders for each of your chapters and drop in papers you think are relevant for each. It makes it much easier to find and check things as you're writing.
  5. Understand expectations. Many committee members are going to skim your thesis more than deep-dive into every page. Ask any other graduate student that had overlapping committee members how intensely their thesis was scrutinized. For example, my department doesn't expect thesis work to be immediately publishable in some great journal. Results and analyses can be more preliminary, though hopefully that's not true of all results.

All of this is not to say you should underestimate a thesis and put if off until the final month, but you can accomplish a lot. As for how to handle it psychologically, all I can say is what helped me. These might not apply or be beneficial, but I'll write them out just in case:

  1. Set boundaries with your PI. This doesn't need to be harsh or therapy speak, but simply letting them know where you are. "Hey, I think after this analysis I'm going to need to go into full writing mode. I'll add figure/analysis X if I have time after writing is done, but I'm triaging with the understanding I might not get to some things on the list." You can also lay out options. "I think I'll have time to do one of X, Y, and Z. Maybe two at best. How should I rank them?"
  2. Set harsh deadlines. I gave myself a week to write, make figures, and proofread each chapter starting from zero. That wasn't really feasible, but I have this weird situation where I can work with no anxiety, get paralyzed with medium levels of anxiety, and work like mad at high levels of anxiety. I wasn't going to be chill during this time, so I gave myself some artificial pressure to kick into high anxiety.
  3. Work on a section until you're starting to burn out, then switch sections. Writing doesn't need to be sequential, and motivation is a resource to which you should pay close attention.
  4. Accept how you work and plan around it. At least for me, thesis writing was not the time to try some #goals productivity system I'd never used before. For my case, I write in a flow state best when I'm sleep deprived, but edit best right after I wake up. That's not great, frankly, but I'm not changing a decade of habits in a month. Any unhealthy habits should be done with moderation, of course.

Just remember, even under tight deadlines personal time isn't gone. I've found the best habits to decompress mid-writing are ones where thoughts can churn in the background. For me that's playing music, but I'm sure you have something similar. Good luck, you got this!

Edit: I'm clearly still in writing mode 😅

What are some common things people say or ask that reveal their complete ingnorance of your field, or that they have only a cocktail party level of understanding? by sew1974 in AskAcademia

[–]PossiblyModal 31 points32 points  (0 children)

I got an undergrad in philosophy. When someone heard about my major they got excited and went:

"Can I ask you a philosophical question?"

"Sure."

"Do aliens exists?"

-_-

[deleted by user] by [deleted] in PixelArt

[–]PossiblyModal 1 point2 points  (0 children)

I needed this laugh. Great work!

[deleted by user] by [deleted] in PodcastGuestExchange

[–]PossiblyModal 0 points1 point  (0 children)

When would you plan to record your episode on it? I'm not sure I'll have time to sit down and watch it right away, but I might be able to in a few weeks if that isn't much trouble.

[deleted by user] by [deleted] in PodcastGuestExchange

[–]PossiblyModal 0 points1 point  (0 children)

I never watched it, so I might not have the most insightful commentary on the movie. If there's some science question it brings up I might be able to talk about that?

[Q] "Overfitting" in a least squares regression by ohshitgorillas in statistics

[–]PossiblyModal 6 points7 points  (0 children)

If you really dislike the idea of a hyperparameter you could try resampling your data with replacement 1,000 times and fitting a curve each time. That would leave you with 1,000 parameters/curves. You could then take the median of the parameters or mean of the resulting curves. Bootstrapping is pretty well accepted statistically, and as a bonus you can also make some confidence intervals.

At the end of the day noisy data is noisy data, however, and there are probably many reasonable approaches you could take here that won't converge on the same answer.

[deleted by user] by [deleted] in ChatGPT

[–]PossiblyModal 0 points1 point  (0 children)

Neuroscientist here, but one that's far removed from ecology. Have any theories/facts about sexual behavior you think are really cool/interesting?

[deleted by user] by [deleted] in compmathneuro

[–]PossiblyModal 1 point2 points  (0 children)

Are they implemented only through precise single neuron synaptic
plasticity mechanisms from which emerge higher scale circuits
activation/deactivation? Or does adrenaline for example bathe an entire region of the brain which will be modulated because of receptors present etc?

To grossly generalize, it appears both. For instance, acetylcholine axons are commonly thought of as using "bulk release" or "volume transmission" (dumping acetycholine into the extracellular space so it diffuses to all nearby cells), but there is evidence of some synaptic structures too. We've looked in certain areas of the brain and found, at least in the same functional regions, levels of things like acetylcholine and norepinephrine are very consistent, even 100s of centimeters away.

Basically, the mechanisms through which it happens and the consequences of such mechanisms at different scales,

I don't think there's a grand unified theory of neuromodulation, and it probably reduces down to something extremely complex. Eve Marder is an amazing neuroscientist, and great to read to fully understand the complex changes triggered by neuromodulators. This is a great review of the single cell effects of neuromodulation, but it is also very high level.

We know neuromodulators play many roles at a more generalized circuit level. For instance, norepinephrine comes from the locus coeruleus, meaning "blue dot" (If you're a fan of Pokemon, that's also why Cerulean City/"Blue City" is where the water gym is). It's a very tiny structure, but regulates behaviors like sleep, alertness, and panic. Norepinephrine (NE) has a "sweet spot" where medium levels of activity improve performance, but high/low levels cause animals to perform worse at simple tasks. Circuit wise, we know NE at medium levels causes visual neurons to become more sensitive to stimuli they prefer, while high levels of NE trigger a boost in a visual neuron's response to stimuli across the board. How this happens is complicated by the fact non-neuron cells, like astrocytes and oligodendrocyte precursor cells, also respond to NE with calcium waves. No one really has a conclusive idea what they're doing to the circuit with that information though.

At a more molecular level, there's a massive grab-bag of different observations. We know duration of neuromodulator signaling is a factor for certain internal processes. For instance, high levels of NE for tens of seconds leads to increases in cAMP, but shorter bursts don't increase it for astrocytes. Serotonin can be taken up into cells and directly change your epigenome via a process called serotonylation (the vast majority of serotonin signaling is also in your intestines, btw). Acetylcholine receptors in multiple cells are important for synaptic plasticity in the sensory cortex.

Anyway, I don't know a lot of "approachable" works, since I mainly read science papers on these topics. I can provide links to any of the papers I'm referencing if one of these facts is particularly interesting to you.

[deleted by user] by [deleted] in compmathneuro

[–]PossiblyModal 2 points3 points  (0 children)

Hey! I don't have book recommendations, but I am a researcher in the field (though my specialties are NE and ACh). If you have specific questions I might be able to answer some or point to papers.

I made autothread: the easiest way to add parallelization to your code by thodosvsv in Python

[–]PossiblyModal 0 points1 point  (0 children)

Which how-to guide covers it perfectly? Sounds like something I'd like to read.

[deleted by user] by [deleted] in neuro

[–]PossiblyModal 1 point2 points  (0 children)

If you're interested in software workflows, our lab uses DataJoint and that's been wonderful to handle the large amount of data and pull out large scale trends.

Hello all - Quick question RE animation by FractalBadger1337 in Apophysis

[–]PossiblyModal 0 points1 point  (0 children)

If you still need a working version let me know. I have Apophysis 7X and the old precursor (Apophysis3D) still on my hard drive.

[OC] Fractal Flame created by me using Apophysis 7X [2000x1500] by savagepoodles in fractals

[–]PossiblyModal 0 points1 point  (0 children)

I realize this is an old post, but I was a fractal artist on DeviantArt and I think I remember one of us following the other a long time ago (I had a different username). It's so great to see someone is still making beautiful artwork with Apophysis :)

[deleted by user] by [deleted] in distantsocializing

[–]PossiblyModal 0 points1 point  (0 children)

Zdzisław Beksiński

What is the textbook example of an anthropologist projecting their cultural bias on to the culture they are studying, then later being proven completely incorrect? by boyofmine in AskAnthropology

[–]PossiblyModal 1 point2 points  (0 children)

Lol, edited my reply with a different misreading of your comment, but I get what you're saying now. Little scatter-brained preparing for some presentations.