In the original Foundation books, Gaal Dornick was a freshly minted PhD starting their postdoc with Hari Seldon. The TV series alters this backstory, in some ways for the better, but I kind of wish the postdoc detail had been kept. It would have been the first time I can think of that a postdoc appeared in a major work of popular culture!
I want to get one of those old timey "awooga" horns for my ebike but every time I try I am overtaken by the powerful urge to make one, and that is the perfect encapsulation of the two wolves inside me "getting in way over my head DIY" and "love old and preferably busted things"
@jonny My friend got a horn for a truck from a salvage yard in Oakland and put it on his bike, kind of as a joke. One day he sounded it and it scared the shit out of the van driver in front of him, because that van didn't see any trucks around that could have caused the sound, so he slammed on the brakes. And my friend couldn't stop his bike fast enough and went through the back window of that van and earned some truly incredible scars on his face. Healed up with time though. Be careful out there!
Is there like a standard process for like "hey I noticed you made exactly the same argument as me using the same primary refs without citing me after we talked about this a bunch of times, would you mind adding a citation"
I dont like to think I "own" any ideas, and obviously it could be coincidence from working in the same space, but it does get tiring because it happens to me all the time, I think partially bc I self publish and institutionally brainwashed ppl dont think that "counts," and it would be nice to feel respected by people I respect.
@jonny Sorry that happened to you, that's always a bad feeling to have. :( What I usually do is contact the person, talk about how much I was interested in the work (true), and then say "just in case you're interested, check out something similar I've done". And then it's up to them.
I try to assume the best of intentions. We're like chocolate chips in a dough of shared ideas, sometimes people forget where they got inspired, sometimes people get inspired at the same time by the same things. Of course, some times people also just rip off - that happens too.
@jonny my least favorite is the one that renders the "waiting" experience as a coffee cup slowly filling. It's some terrible journal website, I forget which one. They've taken something I love (coffee) and used it against me!
One thing that sucks about #PeerReview being so broken and a vector of domination rather that cooperation is that, in the best case, they can be skillshares as much as anything else. In some code reviews I have given and received, I have taught and learned how to do things that I or the other person wished they knew how to do, but didnt.
That literally cant happen in the traditional model of review, where reviews are strict, terse, and noninteractive. Traditional review also happens way too late, when all the projected work is done. Collaborative, open, early review literally inverts the dreaded "damn reviewers want us to do infinity more experiments" dynamic. Instead, wouldnt it be lovely if during or even before you do an experiment, having a designated person to be like "hey have you thought about doing it this way? If not i can show you how"
The adversarial system forces you into a position where you have to defend your approach as The Correct One and any change in your Genius Tier experimental design must be only to validate the basic findings of the original design. Reviewers cannot be considered as collaborators, and thus have little incentive to review with any other spirit than "gatekeeper of science."
If instead we adopted some lessons from open source and thought of some parts of reviews as "pull requests" - where fixing a bug is somewhat the responsibility of the person who thinks it should be done differently, but then they also get credit for that work in the same way that the original authors do, we could
a) share techniques and knowledge between labs in a more systematic way,
b) have better outcomes from moving beyond the sole genius model of science,
c) avoid a ton of experimental waste from either unnecessary extra experiments or improperly done original experiments,
d) build a system of reviewing that actually rewards reviewers for being collegial and cooperative
edit: to be super clear here i know i am not saying anything new, just reflecting on it as i am doing an open review
@jonny Ha, full disclosure, that issue was posted by Rowan in my lab. You are getting acts of care from multiple sources! 😂
I remember someone posting a long time ago a vision of peer review in which, during the first round, the reviewers would just ask questions. No assertions or statements, just ask questions, to start the process of reconciliation
@jonny Lately I have been starting to think that, given the existence of preprints, publishing papers might essentially be a selfish act. The info is already available in the preprint for anyone to read. The cost of publishing could probably be spent better on someone's salary. The only benefit from the pub accrues to the authors' CVs.
Peer review can provide some value, but this is unpaid labor from the reviewers, not the authors' contribution (and certainly not the journal's).
Another "externality" associated with publishing is just continually inflating the scientific literature, which is already way larger than anyone can read. We all spend so much time cranking out pubs that we have no time to actually read anyone else's work - who is even reading most of these things?
Like other self-advancing acts (eg carbon emissions), publishing could sometimes still be justifiable, it should just be done in moderation and in acknowledgement of its negative effects. Concretely .. I would like to see us all collectively take a deep breath, and publish fewer, more thoughtful papers.
Ok, enough said, now I really have to get back to pumping out some papers to make sure I get my grants and can pay my staff!
Excited to speak at the auditory symposium EARS next week alongside Dr Laura Gwilliams! Stop by if you want to hear about our latest work! Free and online https://www.med.upenn.edu/pennhearing/ears.html
Two #Coding questions, from restarting #Python after doing mostly Matlab for a while.
I really liked Tables in Matlab - what’s the best (fastest, simplest) equivalent of it in Python nowadays? #Pandas?
with Matlab you can use ‘webread’ to one-line load the contents of a public google spreadsheet, as a table - very cool! What’s the simplest equivalent in Python?
@elduvelle For 1, definitely pandas. In fact, I would guess that the Matlab Table functionality was cribbed from pandas.DataFrame, which in turn mostly copied it from R's DataFrame. Agree that this functionality is great ... when I started programming we still had to use constants to label each column number!
For 2, I have used something like:
import pandas
import requests
from io import StringIO
r = requests.get(url)
data = pandas.read_csv(StringIO(r.content.decode('utf-8'))
You need to get the "csv export" version of the google sheet link and put that in the variable url.
I meet with a lot of undergrad students who can't decide between a biomedical PhD and MD. Superficially the paths are similar -- both: require years of prep to be accepted; require years of hard work to complete; and lead to white-collar/professional jobs in the biology space. YET -- and this is the strange part -- one requires taking on $100Ks of debt (MD) and the other will actually modestly pay you to do it (PhD).
Serious question - What are the economic/cultural forces at play that lead to such a drastic difference here? Why are people willing to pay SO MUCH for one of these options, and in fact they often view this as a finely balanced choice?
From what I can tell, folks that are successfully using #Neuropixels for either acute or chronic recordings are using the metal cap to attach to a dovetail holder. My question for #neuroscience : is there ever a reason to use the version without the metal cap?
@seeingwithsound@kevinbolding Can I slightly derail this question and ask who is doing freely moving NP in mice? The only paper I have found is Keshavarzi 2022. My impression from talking to people is that NP is too heavy for freely moving mice (except possibly if you select only males and put them through a neck-strengthening exercise routine)
At a union meeting, talking with someone from a different department. IT revoked superuser privileges from all their work computers so they have to submit a ticket EVERY TIME they want to sudo. They said they have an outstanding ticket to install adobe reader, and in the meantime they CAN'T OPEN PDFs.
usually when I try to talk about how digital #infrastructure impacts every part of our working conditions I'm talking about larger problems like how the deinfrastructuring of our communication systems makes it so publishers become the only venue for our work, which structures our incentive systems and patterns of work from top to bottom. This is way beyond that tho, the very basic ability for information workers to interact with information at all.
@jonny@elduvelle I know a uni where it's even worse, you have to file a ticket to get 30 minutes of admin access to your computer, during which time all of your activities are recorded. Which means they actually have the ability to record your activities at all times
has anyone used SLEAP to pick out the geometry of the arena (walls, levers, whatever) as well as the pose of the animal? If so would that be a "second animal" or a part of the same skeleton somehow?
potential sunday activity for anyone who likes pink floyd and/or wizard of oz: watch "dark side of the rainbow" on youtube. https://www.nytimes.com/interactive/2023/06/23/briefing/the-weekender.html#card2
I had no idea the "cosmic coincidence" was discovered in the mid-90s, I always assumed it had been passed down from the 70s by word of mouth through the decades
if I have been invited to review something that I think has an under-considered ethical foundation and potential for unethical use that perhaps the authors haven't considered, do I review that thing and make that part of the review, or decline to review?
@jonny Yeah I would echo this. When thoughtful people don't participate in problematic processes, then it creates a vacuum where only non-thoughtful people participate. On the other hand, you're not personally responsible for fixing everything that is wrong, or for what happens if you don't participate. I also feel that, if you decide to accept, you need to be prepared for the possibility that you do raise these issues and you are overruled. It benefits the rest of us if you participate, but you pay the individual price for getting involved, so ultimately it's a choice only you can make. 💜
Question for neurophysiologists. Anyone who uses the Intan recording system. How do you sync up other signals (like video recordings) with Intan's neurophys? We have a hacked together system that works but I'd really like to clean it up. What do others do?
@adredish I have my behavior control software flicker the houselight briefly on each trial and then record that control signal as an analog input on my recording system (OpenEpyhs, so Intan-like). It’s easy to pick up the house light flicker in the video to synchronize. I actually wrote up some methods for the sync procedure here: https://www.nature.com/articles/s41597-022-01728-1
Are there better preprint servers than #bioRxiv? Every time I try to post something to #bioRxiv, I have to fight with them that a paper doing new analyses on real data is a "real paper" just because we also do a good job of placing our results in the literature.
Moreover, #bioRxiv has an explicit policy that new theoretical insights are "not suitable for posting" (meaning they don't think theory is a real contribution to the literature), which is bad for science. What are the better other options?
It's almost (almost) as bad as fighting with editorial desk-rejections at a real journal.
the authors suggest that whisker movements are analogous in rodents. I like the comparative approach, but would suggest that gaze positioning might also be very important for rodents too! (this is what our group is looking at, but for hearing)
