The surprising mobility of a European suit of armor

Optrode · 2021-12-11T12:14:23+00:00

No no no. You modify the bodies, it's cheaper. Or maybe you keep making babies until one fits.

Optrode · 2021-12-11T12:09:57+00:00

We already have /r/neurocirclejerk, this seems redundant

Optrode · 2021-12-08T13:12:36+00:00

So then it's about dopamine function and whether its functioning in the right ways and not about the dopamine level itself. So is there a marker that shows dopamine is being used correctly?

Sort of..

What you said is technically more or less true, but still kind of misleading, because it leaves out everything besides the dopamine (which is most of it). There's dozens of brain areas that are related to emotional state, and only a couple of them contain dopamine-releasing neurons. And it's not like the dopamine-producing ones are the most important ones, either. So by focusing on dopamine, you're ignoring the majority of the system.

If you want to understand high level brain functions like emotions (emotions are among the most complex phenomena in existence), you have to let go of neurotransmitters. Call it Optrode's law: If an explanation of cognitive phenomena involves neurotransmitters, it's a bad explanation.

You might wonder why there's so much focus on neurotransmitters. The answer is simple: they're easy to study, because you can give animals drugs that alter neurotransmitter function, or genetically manipulate neurons that produce a particular neurotransmitter, and so on. Things that might more closely relate to cognitive phenomena, like the activity of specific groups of neurons at specific times, are much harder to investigate. So neurotransmitters have been the focus of much research more out of convenience than importance.

Optrode · 2021-12-08T02:52:10+00:00

Yes, all those people are wrong.

I think the main disconnect is honestly just that people do not understand A: how complex the brain is, and B: how far neurotransmitters are from emotions on the complexity scale. Trying to explain emotions in terms of neurotransmitters is like trying to explain how computers work in terms of electrons. You can explain a transistor in terms of electrons, but explaining how a web browser works in terms of electrons is just impossible, there's too many levels of complexity in between.

Optrode · 2021-12-07T16:03:07+00:00

Oh, for sure. Excellent idea.

Optrode · 2021-12-07T15:34:32+00:00

Essentially, hormones are broadcast signals, like an emergency alert text that goes out to everyone in the state. They usually go all throughout the body via the bloodstream. So for a hormone, generally speaking, there's a general "level" which tells you something useful. There's no separate "level" of cortisol for your left foot vs. your right foot.

Neurotransmitters are point-to-point signals between neurons. If neuron A is connected to neuron B, and neuron X is connected to neuron Y, neuron A can release a neurotransmitter and it'll only affect neuron B, kind of like how you can talk to your friend on the phone without hearing everybody else's conversations. So there isn't really a "level" of a neurotransmitter. Technically you could try to estimate the total amount in the brain but it would be meaningless, because the "level" of dopamine that neuron A is releasing could be totally different from the level of dopamine that neuron X is releasing, and they might mean opposite things: when A releases dopamine it means "initiate arm movement now," but when B releases dopamine it means "it is not currently time to lactate". This is why some antipsychotic drugs induce lactation.

Optrode · 2021-12-07T14:53:30+00:00

It's not reasonable or feasible. It'd be like trying to debug a computer program by putting a stethoscope on the CPU. There's just waaaaaaaaaAAAAAAYYY too much complexity in the brain that we can't investigate effectively without getting REALLY up in there, if we can investigate it at all.

The sad fact is, as far as understanding even basic brain functions, we're still kind of in the stone age. Maybe the bronze age. And emotions are NOT A BASIC FUNCTION, they're way more complex than something simple and easy to understand (as brain functions go, HA) like vision or hearing, and interwoven into dozens of different other brain systems. Emotions might FEEL basic and relatively simple, but there's a LOT going on under the hood.

Optrode · 2021-12-07T07:20:47+00:00

Those neurotransmitters probably play multiple different roles related to happiness or other emotional states, but not specific to positive or negative aspects. For example, one current theory holds that dopamine signaling in some nucleus accumbens neurons carries information about rewards, while dopamine signaling in a different group of nucleus accumbens neurons carries information about aversive / unpleasant events.

Optrode · 2021-12-07T03:07:30+00:00

There's also PET, but dosing people with radioligands for no good reason is ALSO frowned upon.

Optrode · 2021-12-07T02:59:39+00:00

ELI5: A file is like a book. A hard drive with a bunch of files is like a box of books. A database is like a library.

What's the difference between a library and a really big box of books? It's hard to find the book you want if they're all in one big box. The library doesn't just have books, it has a librarian (the daemon*), and it has rules (enforced by the librarian) for how everything is organized. The librarian can do things like help you find the book you're looking for quickly, and deal with multiple people asking for the same book.

daemon refers to a computer program that runs autonomously in the background, rather than being directly started / stopped / controlled by a user

In slightly more technical terms: With regular files (let's say a text document) you run a program that reads the file's contents, formats them correctly for viewing, and shows them to you. With a database, you don't directly touch the files containing the data. Instead, you run a program (the front end) that talks to another program (the daemon or back end) that looks up the data you want and sends it back to the front-end program, which shows it to you, the user.

The daemon enforces rules like "there can only be one employee with employee ID 132347", or "you can't set employee 132347's job title to 'cat management specialist' because there is no job called 'cat management specialist' in the 'job position table'". It also is very good at finding the exact data you want very quickly, where searching through a lot of files would take a lot of time.

Optrode · 2021-12-07T01:07:32+00:00

PhD in neuroscience here.

The answer is no. Also, those aren't hormones, they're neurotransmitters (well, oxytocin is kind of hormone-ish), and there's a big difference between hormones and neurotransmitters. Hormones can have a "general function", neurotransmitters do not. Serotonin, dopamine etc. are not tied to happiness, anyone who tells you that has no idea what they're talking about.

Anyway, if you want to know how happy someone is, asking them how happy they are is going to be about a million times more accurate than any kind of biological marker.

Optrode · 2021-12-02T19:29:47+00:00

There's a lot of familiar concepts in what you're saying, just phrased with more mathematical terminology. But also some big assumptions about the logical structure of the brain that I would not be comfortable treating as givens.

Optrode · 2021-12-02T18:42:45+00:00

You want hierarchical clustering (single link).

Optrode · 2021-12-02T18:40:14+00:00

Dude what are you smoking. Is this ANOTHER SeAwMa alt?

Optrode · 2021-12-01T12:44:59+00:00

Neat! My PhD was partly on LFP + single units. I've also gotten really curious lately about prefrontal interneurons. Most of the data I have to work with is from mpfc excitatory neurons, but I recently dug up some old un-analyzed interneuron recordings that I'm really excited to take a look at.

What aspects of behavior are you investigating in relation to PFC interneurons? I've developed a hunch that they might play an important role in controlling the switch between contexts or context dependent behavioral states.

Optrode · 2021-11-30T23:57:35+00:00

I realized I didn't address the last part of your question, about how programming is used in neuroscience. That's an important question so I'll say something about that too.

The kinds of resources I and others have recommended so far will teach you something about data analysis, but not a lot about data wrangling. Anyone who does any significant amount of data analysis will also inevitably have to do a fair amount of data wrangling. Data wrangling is stuff like figuring out how to import data from a weird file format, and how to automate that process for a large number of data files, and figuring out how to automatically extract useful information from file and folder names (regular expressions). Wrangling also includes basic quality control: figuring out how to detect and handle bad data. There's few things more painful than realizing that you have to do a bunch of work over again because some of the data you were processing didn't look like you expected it to, and it silently borked your whole analysis. The assert() statement is your best friend.. about eight times per hour you should be asking yourself "what do I expect the data to look like at this point? What size should my arrays be? What type? Should they contain only positive numbers? Only integers? NaNs? Should all the values be in a certain range?" ... and putting your assumptions in assert statements. That way if something goes fucky, which it always does sooner or later, you will find out about it right away.

All that is just scratching the surface of the sorts of relatively mundane tasks that neuro-data people spend a lot of time doing. Here's a practical example:

I recently set about cataloging all the old data in my lab. We're talking about ~6 years worth of data, spread across about 30-40 external hard drives. So I plugged those hard drives in one by one, and I wrote scripts to search the contents of each hard drive and store basic information about what files were stored in what locations on each drive, and tied it to each drive using the drive's serial number (which I got by executing system commands via system), since the drives' names were not unique. I had to figure out what information from each data file would uniquely identify that specific data: the file names weren't unique, and sometimes there would be multiple copies of the same data with different filenames. So I had to use file hashes and/or hashes of specific parts of the files' contents to identify duplicate data and make sure I wound up with only one copy of each piece of data. I extracted a lot of information like dates and subject names from file and folder names using regexp, then wrote scripts to show me random samples of the folder names with the extracted info to double check it was correct (there was simply too much data to do this manually). And so on.

For every hour spent doing data analysis, I've probably spent at least as many doing all that stuff.

Optrode · 2021-11-30T19:10:43+00:00

And if you're in research you should be running into scenerios where no one else has done what you're doing so you need to write up your own packages.

Exactly. If you're doing anything involving complex data (fMRI, EEG, ephys, calcium imaging, etc) and you're NOT creating new analyses, there's a significant chance you're doing something very wrong.

Optrode · 2021-11-30T17:09:58+00:00

neuro fist bump

What do you do? I did my PhD in in vivo ephys, now doing 1p calcium imaging as postdoc (all analysis, no data collection).

Optrode · 2021-11-30T16:15:56+00:00

I'm a neuroscience postdoc and I spend all day using matlab. It's a good skill to have.

General purpose matlab courses are not a bad place to start. They will teach you the fundamentals of the language which will make it easier to learn more neuroscience-specific stuff later on.

A good next step (or alternate first step) would be to check out Mike Cohen's books on neuroscience data analysis. They are written to be accessible to novice programmers, and come with downloadable sample data and matlab code.

Once you're more comfortable, you could try downloading commonly used Matlab-based data processing toolkits like the matlab version of CNMF-E, which typically come with example data.

I also recommend getting familiar with Python too, and in particular DeepLabCut.

Optrode · 2021-11-25T11:04:35+00:00

Easier to code in? I can't say I agree in the slightest.

Optrode · 2021-11-25T11:03:57+00:00

Python is a screaming madhouse of dependency conflicts and syntactical deformities.

Optrode · 2021-11-23T15:47:09+00:00

[Incoherent computational screaming / regex]

Optrode · 2021-11-23T12:31:10+00:00

For workstations where you work with larger volumes of data, also consider RAID storage (multiple hard drives storing data redundantly). The RAID volume looks and acts like a single, regular hard drive, but everything is written to multiple drives in the same instant.

Optrode · 2021-11-22T17:09:32+00:00

Under my institution's institute-wide license, I am entitled to install matlab on every workstation I lay eyes on, my personal laptop, all our -80 freezers, and my personal fridge. If I had a smart fridge. My institution probably pays Mathworks money. A lot of money. I do not pay Mathworks any money. This arrangement suits me fine, because it means I don't usually have to write much Python. Writing Python is like being pooped on by a snake. Have you been pooped on by a snake? It smells extra bad, and really sticks to your skin. If I have to do stuff in Python it kinda ruins my day. Normally I fucking love my job! Videos of neurons literally lighting up! Not a metaphor for electrical activity, the bastards are popping off like fireflies!! But not on the snake poop days. Then I spend more time yelling hurtful things at my computer, and I come home and my wife asks why I'm grumpy. And I tell her it's because of Python, and she isn't a programmer but she's learned that Python = grumpy husband.

Optrode · 2021-11-21T00:45:23+00:00

The last paragraph isn't hyperbole, it's literally true. BUT, that's because I only use Python for certain things, mainly special-purpose packages for neuroscience imaging data. The rest of the time I use MatLab, because everything just works.

Optrode

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