@biogeo@mathstodon.xyz avatar

biogeo

@biogeo@mathstodon.xyz

I'm a neurophysiologist interested in computational approaches to modeling and data analysis. I work at West Virginia University's Rockefeller Neuroscience Institute, but all opinions are my own, and probably confused.

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biogeo, to Neuroscience
@biogeo@mathstodon.xyz avatar

Neuroscientists and electrophysiologists of Mastodon, what would your top choice analysis tool be for a novice getting started with working with ECoG data? I have a graduate student I will be co-mentoring starting this Fall who is very bright but has no programming experience, and I'd like to help her get up and running as quickly as possible. I've generally been a roll-my-own-analyses type of electrophysiologist so I don't have a favorite framework to get her started with. I know EEGLAB is popular, but my main experience with it has been helping other people get their Matlab path working properly again after something in EEGLAB clobbers it. I've played with MNE in Python but it doesn't seem to be as purely-GUI as EEGLAB and I don't want her to get bogged down in learning Python before she can do any analyses at all.

So, what's your favorite tool for ECoG analysis? What would you recommend a student who's starting from zero background in electrophysiology or programming begin to learn in 2024?

Boosts for reach appreciated. I also just like hearing folks' opinionated takes on their research tools.

#neuroscience #electrophysiology #ECoG #mentoring #EEG #LFP

jonny, to random
@jonny@neuromatch.social avatar

There are lots of pop science type "neuromyths" like the Mozart effect, and there are lots of stories about how what we would call "consciousness" works that arent based in contemporary western neuroscience, but I want to find more mythology about the brain the organ - like how its a big antenna or where a bunch of little ant monsters have dug tunnels and whatnot. Bodily mythology that tries to explain what the heck we are made of

biogeo,
@biogeo@mathstodon.xyz avatar

@jonny Not sure if this is quite what you're looking for, but the myth of the "triune brain", that our brains are composed of distinct "reptilian brain", "paleo-mammalian brain", and "neo-mammalian brain" components, has been frustratingly persistent. It's based on bad neuroanatomy and bad evolutionary theory and has been known to be completely wrong since at least the 1980s, but is still sometimes found in psychology textbooks or taught to medical students. I've even seen well-respected late-career neuroscientists reference this idea as though it had any kind of scientific validity.

biogeo, to Neuroscience
@biogeo@mathstodon.xyz avatar

One of my favorite things in is the number of structures with names like "nucleus ambiguus" (ambiguous nucleus), "substantia innominata" (unnamed stuff), and "zona incerta" (uncertain zone).

If I were making a neuroanatomical atlas in the 19th century, I definitely would have called something "locus draconum," as in the old navigational charts' "here be dragons".

biogeo, to random
@biogeo@mathstodon.xyz avatar

Rest in peace Louis Kokonis, my high school calculus teacher. He just passed away at 91 years old, still teaching calculus to high schoolers. We all used to joke that he was impossibly ancient to still be teaching, and that was more than 20 years ago. His dedication to teaching mathematics is really humbling. He had a quiet voice and was slow to anger with sometimes rowdy high schoolers, but even as a dumb 17-year-old you could tell all he really wanted was for you to understand how cool what he was teaching you was. I remember his shy but sweet smile when kids who weren't necessarily the best students but were still showing up and doing the work would get jokey and tease him a bit. He seemed to genuinely enjoy his connection with every student no matter their level. For myself, he gave me the foundational tools to study physics and ultimately pursue a career in neuroscience. He was a really good man who improved a lot of young people's lives during his 60 year teaching career, and he'll be missed.

https://patch.com/virginia/delray/louis-kokonis-longest-serving-alexandria-public-schools-teacher-dies

biogeo, to random
@biogeo@mathstodon.xyz avatar

Greatly enjoying Kaue Costa's minisymposium talk at , started by rooting the model based/free distinction to the traditions of thought coming from Tolman versus Thorndike. Nice bit of history.

NicoleCRust, to random
@NicoleCRust@neuromatch.social avatar

A wow prescient quote from 1865 that will resonate with my anti-reductionist friends

“Physiologist and physicians must never forget that a living being is an organism with its own individuality. Since physicists and chemists cannot take their stand outside the universe, they study bodies and phenomena in themselves and separately, without necessarily having to connect them with nature as whole. But physiologists, finding themselves, on the contrary, outside the animal organism which they see as a whole, must take account of the harmony of the whole, even while trying to get inside, so as to understand the mechanism of its every part. The result is that physicists and chemists can reject all idea of the final causes for the facts that they observe; while physiologists are inclined to acknowledge a harmonious and pre-established unity in an organized body, all of whose partial actions are interdependent and mutually generative. We really must learn, then, that if we break up a living organism by isolating its different parts, it is only for the sake of ease in experimental analysis, and by no means in order to conceive them separately. Indeed, when we wish to ascribe to a physiological quality its value and true significance, we must always refer to this whole, and draw conclusions only to its effects in the whole.”

Claude Bernard, 1865

Stumbled upon via this excellent take about homestasis (and how it's anti-reductionistic)
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7076167/pdf/fphys-11-00200.pdf

biogeo,
@biogeo@mathstodon.xyz avatar

@NicoleCRust That's a very cool quote from a very interesting time!

You may know "final cause" is technical jargon in Aristotelian philosophy meaning purpose or teleology. The idea was much under attack in 19th century science. Some of Darwin's followers (I think Huxley specifically?) felt that natural selection basically "rescued" the idea (I tend to agree). This sounds like Bernard was joining that argument in favor of the importance of function and purpose in the study of biology.

Amazing how we sometimes keep circling around the same arguments over decades or even centuries in science!

biogeo, to science
@biogeo@mathstodon.xyz avatar

Senior scientists who sit on NIH study sections, apropos of nothing in particular: when you evaluate an application for funding, how much consideration do you give to the broader research and intellectual environment of the applicants' institution?

If an established R1 institution does something like, say, eliminate its mathematics graduate program, does this impact your assessment of the institution's ability to successfully host the proposed research? If you saw an application for neuroscience research project with a computational component to the project, would the school's loss of mathematics PhD students impact your opinion of the relevant intellectual environment sufficient to affect your scoring of this portion of the application, even if none of the named investigators are directly associated with the math department?

This question is genuine, not simply rhetorical.

#science #academia #neuroscience #mathematics #wvu

jonny, to random
@jonny@neuromatch.social avatar

in defense of the utils directory - in this essay I détourne the hell out of all my haters, tracing the imperialist ideologies that drive classificatory systems of order that exclude the unnamable and unsortable. through a liberatory-programmistic praxis it is evident that we are always already in the "junk drawer," and utils is but a....

biogeo,
@biogeo@mathstodon.xyz avatar

@jonny
utils/those_belonging_to_the_emperor
utils/suckling_pigs
utils/mermaids
utils/./*
utils/etc

(Reference: https://en.m.wikipedia.org/wiki/Celestial_Emporium_of_Benevolent_Knowledge)

jonny, to random
@jonny@neuromatch.social avatar

I'm sort of afraid to ask but amidst all the ai blog spam I can't find good information. what's da deal with yno the different #database lib? I understand the difference between dbs with fundamentally different architectures like mongodb and couchdb, but like what's the deal with postgres vs MySQL vs mariadb and whatnot, and how come ppl seem to love to hate postgres?

biogeo,
@biogeo@mathstodon.xyz avatar

@jonny I'm no expert really, but during my PhD after the 10th time rewriting my Matlab analysis code to rearrange my data in a slightly different way for a new analysis question, I made the slightly peculiar choice to spin up a MySQL database (might have been MariaDB actually, this was not too long after it forked off of MySQL) to solve my data management problem once and for all. It was using a sledgehammer to drive a nail, but by golly that nail got driven. In retrospect I could and should have solved my problem much more simply using SQLite, which doesn't require a centralized database server and lets you easily pass around your dataset in one (potentially massive) file, which is better for scientific data sharing. So I don't know about the differences between major RDBMS software, but my experience taught me that relational databases (whether implemented with RDBMS or more ad hoc methods) are amazing and seriously underused in science, and SQLite is a great tool in particular.

NicoleCRust, (edited ) to random
@NicoleCRust@neuromatch.social avatar

POLL: Are you on board with mind/brain reductionism (to genetic expression)?

In 1998, Eric Kandel proposed a new intellectual framework for psychiatry in which brain function and dysfunction can ultimately be reduced to genetic expression but one in which environmental effects (including psychotherapy) play a role (by modulating genetic expression which changes neural circuits and neuron function).

Paper here: https://pubmed.ncbi.nlm.nih.gov/9545989/

Summarized here: https://neuromatch.social/@NicoleCRust/110819846084871415

If you're not on board, why not?

biogeo,
@biogeo@mathstodon.xyz avatar

@NicoleCRust I think this sort of gene expression reductionism is methodologically useful and should be pursued as a practical matter, but I'm not fully on board with it for (at least) two reasons.

First, even accepting a strictly reductionist approach to scientific explanation, I don't think gene expression patterns compose a complete description of nervous system in any meaningful sense. "Connectionists" also propose a fully reductive explanation of the nervous system on the basis of its wiring diagram, for example. I think neither of those contain enough information to recapitulate the other, and both are probably necessary for a full reductionist explanation of the nervous system. I like some of Eve Marder and colleagues' work in the crustacean pyloric rhythm to illustrate how both of these are necessary. I also think that there are other reductive variables necessary for a complete explanation, so those two together are still not sufficient for a reductionist program to succeed.

Second, I don't believe that a reductionist approach provides the best scientific explanations for many questions we have about the nervous system. I'm not in the camp that the mind is "irreducible," but as a matter of what constitutes a satisfying scientific explanation I don't think reductionism always does it. A table is "nothing more" than a bunch of wood in a particular arrangement, but a good explanation of tables may focus more on the structural stability of their shape rather than the mechanical properties of the wood, or on the cultural context of how they are used in dining rituals ("round table" vs "head of the table") etc.

biogeo, to menopause
@biogeo@mathstodon.xyz avatar

My friend Lauren Brent and her colleagues have published a paper on the of and maternal investment in , in the latest issue of . I'm really excited to read this research! They're addressing an important and long-standing question in . And it's .

https://www.cell.com/current-biology/fulltext/S0960-9822(23)00824-2#%20

ColinTheMathmo, to random
@ColinTheMathmo@mathstodon.xyz avatar

Just read an article on the BBC website where someone was ...

"... fatally killed ..."

I've not seen that before ... does it sound as daft to you as it does to me?

biogeo,
@biogeo@mathstodon.xyz avatar

@ColinTheMathmo @paul Sometimes I kill a process in my computer, but because I forgot to sudo, it's non-fatal.

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