sfmatheson

@sfmatheson@fediscience.org

#Biology, Bardolatry, #cycling, #baseball. Writer, editor, #humanist, partner, dad, granddad. #StarWars, #neuroscience, #evolution, #SkyIslands. Previous: PLOS, Cell Reports 🌲🌵 Opinions mine. He/him.
#fedi22 #OpenAccess #ScientificWriting
Searchable at https://tootfinder.ch/.

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cyberlyra, to opensource
@cyberlyra@hachyderm.io avatar

#hci peeps, who's written about the capture of #opensource systems by industry and for-profit companies? Asking for a grant application ...

sfmatheson,

@cyberlyra @ntnsndr @mako @bkeegan @petersuber writes about open science along those lines

sfmatheson, to Neuroscience

This is gold:

"Being scientific is hard for human brains, but as an adversarial collaboration on a massive scale, science is our only method for collectively separating how we want things to be from how they are."

https://www.thetransmitter.org/fmri/breaking-down-the-winners-curse-lessons-from-brain-wide-association-studies/

#fmri
#thetransmitter
#ScienceMastodon
#neuroscience

NicoleCRust, to random
@NicoleCRust@neuromatch.social avatar

If you were to recalibrate, what would you do?

I always suspected I would do something like study those amazing desert ants that navigate via the earth’s magnetic field. But when thinking through the question “How do you want to spend the next 10 years?” more seriously (pretending there are few constraints), that’s not where I actually point myself.

Acknowledging that it’s a tremendously priveleged (and emotional) thought experiment, What would you do with your next 10 years, assuming that thing needs to be useful enough that it’s reasonably supported (and you would continue to get a paycheck)?

sfmatheson,

@NicoleCRust I was going to write "own and run a bookstore" but that seems unoriginal

sfmatheson,

@NicoleCRust I forgot to mention that it's also a coffee shop and maybe sandwiches

sfmatheson,

@NicoleCRust Uh.... I guess that will be up to my business partner :)

MCDuncanLab, to random
@MCDuncanLab@mstdn.social avatar

#Monsterdon Bingo!!!

sfmatheson,

@MCDuncanLab @jonny SOP in economics journals I hear

NicoleCRust, to random
@NicoleCRust@neuromatch.social avatar

Do psychologists "measure"?

Weird question, right?

"Measurements of attributes such as emotions, well-being, or intelligence are widely used for various purposes in society, but it remains a matter of discussion whether psychological measurement is analogous to measurement in the natural sciences, and to what extent it qualifies as measurement at all.'
https://doi.org/10.1080/09515089.2023.2300693
Edit: author is here! @mieronen

My initial take: what?! This seems silly. But I'm starting to warm up to it. It's about causality. Consider: "insomnia causes fatigue"; no one disputes it. But there's not a physical thing in the world called insomnia that causes a physical thing in the world, fatigue billiard-ball-style. Rather, the physical causal chain happens by way of a lack of sleep causing the brain state that leads to the mind state of fatigue (in other words, that word "cause" is doing some heavy lifting in that phrase). The question is: can you meaningfully talk about causality when you have abstracted away from physical interactions?

On one hand, of course - you can develop causal models formulated entirely at the psychological level (rewards, punishments, surprises, mood) that make falsifiable predictions and you can both perturb and measure these things to test those models.

On the other hand, we probably do need to take some care that we aren't confusing ourselves as we throw around that word "cause" interchangeably for things that physically interact and abstractions of those things.

Thoughts? I'm particularly curious about cases in which this type of abstraction has led researchers astray.

sfmatheson,

@NicoleCRust @mieronen I guess I'm not ready to grant the leap from "measurement" to "causation." (I'm just conversing here, haven't read the cited paper.) If "measurement" means something like "quantify" in the context of good experimental practice (blinding, controls), then I'm naturally inclined (PS that's a quantifiable thing that we can measure, heh) to resist claims that the quantification or measurement has anything to do with causation.
1/2

sfmatheson,

@NicoleCRust @mieronen Naively perhaps, I'm thinking of the early days of RNAi when we could harness it and measure its effects and even titrate them, without knowing how on earth the expression of dsRNA in a cell would/could lead to suppression of endogenous expression. I remember thinking about this a lot and found it very interesting.

Is that different from "thought" or "feeling"? I guess, but not (to me) because of any relationship between "measure" and "cause".

2/2

ninokadic, to academia
@ninokadic@mastodon.social avatar

Come up with an acronym for PHD! 📚

I'll start:

Pretty
Hectic
Days

@academicchatter #academicchatter #academia #phdlife #phdchat #phd

sfmatheson,

@ninokadic @academicchatter Pedant Has Dessert

maartjeoostdijk, to academicchatter
@maartjeoostdijk@mstdn.social avatar

How to respond to a reviewer who thinks using 'we' consistently throughout a manuscript (in methods and a little in discussion 'we found' etc) sounds unscientific? @academicchatter

sfmatheson,

@maartjeoostdijk @academicchatter Hi there, I would echo support for your choice (to use active voice) and would go as far as to say that in this century, it is the overuse of passive voice that can sound "unscientific." At most journals (and all journals I know well, at PLOS and Cell Press), this "advice" from the reviewer could and should be simply ignored, both because it's not the reviewer's call and because editors should agree with you.

sfmatheson,

@jsdodge @maartjeoostdijk @academicchatter Amen to the intentional use of passive voice! Methods section is most obvious place for it but there are others, and I'd emphasize "intentional use."

I mean, every time we write "...but the role of X is unknown" we are using the passive voice. Can you imagine the LOLs if someone wrote "but I don't know the role of X and neither do you"?

kevinbolding, to Neuroscience

What do we think are “open science” venues for short reviews in neuroscience? #neuroscience

sfmatheson,

@NicoleCRust @kevinbolding @elduvelle_neuro @eLife @nbdt_journal @NeuroSchnell Reviews are typically invited but suggestions are always welcome. @NeuroSchnell is the right contact at @PLOSBiology and I would be glad to make introductions at Comp Bio if you are interested. Thanks @NicoleCRust for tagging!

NicoleCRust, to Neuroscience
@NicoleCRust@neuromatch.social avatar

Looking for paper leads on: a genetic network w/ attractor states linked to brains

I'm fond of the approaches in this paper:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2571012/

The gist here is to model a genetic network as a dynamical system with two attractor states (in this case, it's leukemia and the states are apoptosis on-versus-off).

I'm looking for leads to papers that apply this type of approach to model genetic networks (not neural circuits) that have something a bit more to do with the brain; ideally not cancer.
(This is not my field). Huntington's? Fragile X? Anything neuron related?

Thanks in advance!

#complexity #neuroscience #genetics #systemsbiology

sfmatheson,

@NicoleCRust Even if you don't find what you're looking for (cue U2), a browse through Hana El-Samad's work is likely to inspire 🙂

meg, to random

Two things are blowing my mind tonight. The new Beatles' song with George Harrison's ghostly guitar riffs (the darkhorse was always my favorite). And new research suggesting starfish are just a head without a body. Convince me these cool things are unrelated.

sfmatheson,

@meg Those two things are OBVIOUSLY related

Thanks for pointing it out :)

sfmatheson, to TwitterMigration

I was over at the Toxic Bird Site (no judging) and saw the rage at Mike Eisen for his brainless retweeting of a post from the Onion. I was reading Inna Slutsky's resignation from the @eLife board and... I'm not sure but I think I saw the moment (14 Oct, 1750 Pacific Time) that Eisen deleted his Twitter account.

Check me on this?


sfmatheson,

@elduvelle @MarkHanson Hi all, yes the context is easy to find on Xwitter, by looking at eLife statement about "investigating" re breaches of code of conduct, and responses to that statement. Thanks @MarkHanson for finding the relevant tweet.

sfmatheson, to random

@pluralistic:

"All this raises the question of what can or should be done about Twitter. One possible regulatory response would be to impose an "End-To-End" rule on the service, requiring that Twitter deliver posts from willing senders to willing receivers without interfering in them. End-To-end is the bedrock of the internet (one of its incarnations is Net Neutrality) and it's a proven counterenshittificatory force..."

1/2

petersuber, (edited ) to academia

Thank you to the #NobelFoundation for taking the nomination of #KatalinKarikó seriously. She was forced out of a high-prestige university, didn't win high-prestige grants, and didn't publish in high-prestige journals.

Readers: Does your institution squeeze out faculty with the second two properties? Think carefully before answering. If so, then the problem is systemic and not limited to #UPenn (except for Penn's claim of undue credit).

#Academia #Medicine #Nobel
@academicchatter

🧵

sfmatheson,

@petersuber @academicchatter it's not PennState

sfmatheson,

@petersuber @academicchatter Nice!

sfmatheson, to random

Opinion piece at #PLOS Global #PublicHealth

by Chiamaka P. Ojiako, Lazenya Weekes-Richemond, Vuyiseka Dubula-Majola, and Marie-Claire Wangari

Who is a public health expert?

-Expertise is not limited to medical or health professionals
-Expertise is not limited to academia or high-income nations

"The current understanding of global health expertise is reflective of embedded elements of residual colonialism that considered white individuals as the only experts."

https://journals.plos.org/globalpublichealth/article?id=10.1371/journal.pgph.0002269

1/2

sfmatheson, to random

Post a meme that lets us get to know you better (H/T @SpeciationLab )

sfmatheson, to random

How big is the #unknome? In other words, how many of the 20,000 or so genes in the human genome are unknown (in function)? Is there a gradient of unknown-ness? A new paper in @PLOSBiology by Rocha and colleagues introduces us to the unknome and then adds some good stuff, which is the least the authors can do after telling us how little we know about human gene function.

#Blaugust2023
#genome
#omics

https://sfmatheson.blogspot.com/2023/08/the-known-unknowns-of-biology-welcome.html

sfmatheson, to random

The word '' was born in the 1920s when someone blended 'gene' with 'chromosome'. (The -some in 'chromosome' is from a root that means 'body' as in 'somatic' or 'psychosomatic'.)

Then science started adding -omes. Proteome, transcriptome, phenome, even spliceome. But the best by far is the : the set of all genes of unknown function.

New paper in @PLOSBiology about the unknome does a screen for basic function of these "mystery proteins"



1/2

sfmatheson,

@PLOSBiology Also article in Wired: https://www.wired.com/story/unknome-proteins-human-genome/

https://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002222

And their database is here:
https://unknome.mrc-lmb.cam.ac.uk/

sfmatheson, to Tucson

I'm inspired by the of southern Arizona and northern Sonora. They're literally islands, and a giant laboratory for the study of evolution. The hashtag is in my profile so it's about time I wrote about them! Looking forward to more, and hoping to get directly involved in research somehow. Maybe I can be a volunteer bug collector?






https://sfmatheson.blogspot.com/2023/08/sky-islands-one-of-earths-great.html

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