Exciting development for brain stimulation therapies.
Building on work that teases apart causes in a complex system, predicts which stimulating electrodes will be effective based on resting activity alone.
Amin Nejatbakhsh, Francesco Fumarola, Saleh Esteki, Taro Toyoizumi, Roozbeh Kiani, and Luca Mazzucato
In a complex system, variables are nonlinearly related; consequently, you can play some nifty tricks. This one is called convergent cross-mapping (CCM). More of us should know about it!
Crowd sourcing big data collection efforts in the brain research space
Looking for both details as well as a conceptual parsing of the space. Here's a partial list (and a conceptual parsing,n loosely organized around -omics): https://en.wikipedia.org/wiki/Omics
@NicoleCRust here's some lit on "big data" collaborations :). I tend to be more interested in ppl who study the sociotechnological dynamics of these projects than indexing the projects themselves, so these are mostly useful if u are interested in.
So for maybe the largest current effort i'm aware of, see the NIH's biomedical translator project. @parrhesiastic did a lot of embedded work here but I think the ethnography stuff is mostly unwritten?
one of their papers: https://onlinelibrary.wiley.com/doi/abs/10.1111/cts.12592
(and CoI alert I criticized some of the ideological underpinnings of that kind of effort here: https://jon-e.net/surveillance-graphs/#nih-the-biomedical-translator )
he's also done some other interesting work with david ribes that might be relevant to parsing this question :).
and another that's probably most directly relevant to your question, this short piece on neurodata.io: https://www.nature.com/articles/s41592-018-0181-1
you may notice that the last dataset uploaded there is in 2017, which is a recurring problem in this space - since people build them as self-contained platforms, they build them over and over again. turning towards a federated -> peer to peer model is the main thing i'm working on right now so we can break that pattern.
and this piece from 2020 that i think is an interesting counterpoint to the mainen piece. where they advocate "grassroots" collaboration, this group is more interested in centralized, platformatized infrastructures: https://doi.org/10.1146/annurev-neuro-100119-110036
this piece from Matthew Bietz and colleagues is i think really excellent at concretizing the tensions of these kind of 'big data' projects, from a little more than a decade ago but it's still relevant: https://doi.org/10.1007/978-1-84882-854-4_15
if you've never read it i think Data Feminism is pretty essential contextualization/criticism for thinking about 'big data' projects in general: https://data-feminism.mitpress.mit.edu/
an example of distributed collaboration that doesn't aspire for universality/completeness but radical inclusiveness: http://arxiv.org/abs/2205.00079
that's probably enough (too much) for now, a sort of random sample of a few searches in my zotero library, feel free to ignore them or if you want more on a specific topic lmk <3
How do you feel about the phrase "virtuous cycle"?
The phrase "bench to bedside" in biomedical research implies that big scientific discoveries (at the bench) are transformed into new clinical treatments. The problem is that the "to" implies a uni-directionality of the sort that is very misleading; it just doesn't happen that way very often. More often, the bench and the beside work reciprocally and iteratively (to arrive at treatments and cures). We need an equally vivid phrase that better captures how it actually works, but what?
One phrase that I've heard a few times over the past year is "virtuous cycle". Like this:
"bidirectional interaction between scientific investigation and clinical practice will continue to play a fundamental role, with models and biomarkers informing prognosis and treatment while being informed by clinical insight, engendering a virtuous cycle." https://pubmed.ncbi.nlm.nih.gov/34236622/
More broadly, I'm looking for vivid ways to embrace reciprocal interactions (A <>B) and replace the oversimplification of domino chains (A>B). Things like "reciprocity" = "yuck".
I sometimes like "virtuous cycle". Merriam-Webster tells me that it's "a chain of events in which one desirable occurrence leads to another which further promotes the first occurrence and so on resulting in a continuous process of improvement." But when I search for it, I see it associated with McKinsey & Co. and Bezos and all sorts. :(.
What associations, if any, do you have with the phrase "virtuous cycle"? Do you know of any alternatives/equivalents?
Gene ontology, https://geneontology.org/
Referenced in over 159,000 papers, the goal of the gene ontology resource is an "up-to-date, comprehensive, computational model of biological systems, from the molecular level to larger pathways, cellular and organism-level systems."
The Cognitive Atlas, https://www.cognitiveatlas.org/
A collaborative knowledge building project that aims to develop a knowledge base (or ontology) that characterizes the state of current thought in cognitive science.
(Ontology refers to how we classify and group things as we explain them, aka: what's close to what).
The fact that these are two databases not one illustrates where we are (in brain/mind research). If only we could unite them!
Looking for: drugs developed using systems biology / complex systems (probably cancer).
I'm looking for examples in which the appreciation that a genetic network is configured (not as a domino chain but) as a complex system led to the identification of a therapeutic target and a new drug.
I know that there are examples of that we can point to explaining 1) why existing drugs don't work or 2) are in the clinical pipeline (eg clinical trials). But do you know of any "success stories" that are approved and in use?
Anything in the "brain" space is particularly appreciated but I'm open to anything here (and I'm guessing that the most likely space is cancer).
Despite the fact that y'all are much more interesting than the thing I have to do today, it needs to be done. So if I post, please hold a mirror to this sign: GET TO WORK NICOLE.
Stigmergy is a form of self-organization. It produces complex, seemingly intelligent structures, without need for any planning, control, or even direct communication between the agents. As such it supports efficient collaboration between extremely simple agents, who may lack memory or individual awareness of each other.
Describes how the characteristic shapes of the mounds of different species emerge. "During mound construction, environmental factors such as heat flow and gas exchange affect the building behavior of termites, and the resulting change in mound geometry in turn modifies the response of the internal mound environment to external thermal oscillations."
Gratitude to @deevybee for helping to clean up science! A delightful dive into why and how here, in The Transmitter:
Last year, when Dorothy Bishop wanted to figure out how six suspicious-looking manuscripts had all been accepted for publication in the same psychology journal, she decided to set up a sting operation ...
This is Bishop’s second act — one centered on sleuthing. A hobby she thought she could dabble in during her retirement has expanded to fill most of her days, she says — an unsurprising development to those who know her. Norbury, who describes Bishop as the “quintessential scientist,” says that no matter what issue Bishop tackles, “she just wants to know the truth.”
Books written by anthropologists embedded with scientists?
I'm reading a book about an anthropologist who embedded with psychiatrists for several years to figure out how they are trained an what they think. Here's a great quote:
"Sometimes they talk about mental anguish as if it were cardiac disease: you treat it with medication, rest, and advice about the right way to eat and live. A person who has had a heart attack will never be the same—he will be always a person who has been very seriously ill—but he is not his heart attack. His heart attack is in the body, not the mind. When psychiatrists talk in this manner, psychosis and depression become likewise written on the body ... Sometimes, though, psychiatrists talk about distress as something much more complicated, something that involves the kind of person you are: your intentions, your loves and hates, your messy, complicated past ... From this vantage point, mental illness is in your mind and in your emotional reactions to other people. It is your “you.”
As The Transmitter rolls out, don't hold back those comments!
I just left one thanking @analog_ashley Ashley Juavinett for an excellent article on how to teach the Churchland et al (2012) article “Neural population dynamics during reaching".
It's all there: context; rough bits; options. She even provides a Google Colab notebook. Wow!
“I don’t know scientifically what to do with one neuron anymore because of these challenges we're running in terms of relating it... It’s about looking at populations of neurons and how they relate. This isn’t representational bashing, at all. It’s simply that the data don’t largely get captured by that type of perspective. We see far more neurons doing idiosyncratic things than we see doing the canonical things.”