Yea, idk. I was thinking of the quotes where you explicitly mentioned Van der Waals forces. Tbc, my preference would be to not be forced to pick a single force
Hi, computational protein engineer and person who-thinks-biology-can-do-amazing-stuff here.
Just wanted to report that while "Proteins are like Folded Spaghetti Held Together By Static Cling" is obviously incorrect as a matter of fact, I immediately thought it was a pretty good analogy for capturing some critical and often under-appreciated aspects of the functionally important character of proteins. When I read the sentences you've quoted him saying about proteins held together by covalent bonds, I (think) I understood what he was pointing at with this and roughly agree. I absolutely did not think he was saying proteins did not contain covalent bonds, but rather that you could imagine an alternative protein-like molecular structure which had all of its key structural and functional characteristics determined by covalent bonds. I believe such a "protein" would, among other things, be predicted to function at a much wider range of temperatures than extant proteins, maintain its structure and function in many different solvents (and probably gas phase?) etc etc.
This analogy is also definitely failing to capture other important characteristics of proteins, some of which the OP mentioned and I agree with.
By the way, if I was forced to say one thing which "held together" proteins (in the sense of "is most responsible for determining the functional characteristics of a polypeptide chain) it would be tough but I might pick something I don't think anyone has mentioned: hydrophobicity/ hydrophilicity.
One impression I could imagine having after reading this post for the first time is something like: "eca would prefer fewer connections to people and doesn't value that output of community building work" or even more scandalously, "eca thinks community builders are wasting their time".
Community building is mission critical. It's also complicated, and not something I expect to have good opinions about currently, overall, because of lack of context and careful thought, among other things.
I have personally found these types of introductions enormously valuable, especially in other phases of my career, and it would make me very sad if people turned them off!
Even if I didn't find them personally valuable, I'd guess that they were still very valuable overall because I expect this to be person and context dependent, and I see others get value.
Even if more should be invested in work connections overall, its not clear that the folks sending me intros (THANK YOU!! PLEASE DON'T STOP!) should be the ones doing the collaboration themselves ("Have you worked with [Someone] on anything? Or do you know anyone who has?"). Gains from specialization could imply that the folks making intro connections should focus on that, and others should do more deliberate working on stuff.
Rather, my nebulous aim is some combo of A) sharing what my intuitions (narrowly trained) say the marginal effect of trading intros for work experience would be, for me, B) gesturing at an opportunity for even more value to be produced by community builders, if my experience generalizes and C) hoping selfishly that someone will help me understand whats going on here, so I quite complaining about it to my dinner companions before impulsively writing a forum post.
Not sure how much of this is in my head, but thats a thing.
Meta note: this was an experiment in jotting something down. I've had a lot of writers block on forum posts before and thought it would be good to try erring on the side of not worrying about the details.
As I'm rereading what I wrote late last night I'm seeing things I wish I could change. If I have time, I'll try writing these changes as comments rather than editing the post (except for minor errors).
(Curious for ideas/approaches/ recommendations for handling this!)
This seems like a great idea- I actually woke up this morning realizing I forgot it from my list!
One part of my perspective which is possibly worth reemphasizing: IMO, what you choose to work together does not need to be highly optimized or particularly EA. At least to make initial progress in this direction, it seems plausible that you should be happy with anything challenging/ without an existing playbook, collaborative, and “real” in the sense of requiring you to act like you would if you were solving a real problem instead of playing a toy game.
So in this case, while “EA should host hackathons” seems reasonable and exciting to me, especially as a downstream goal if working together turns out o be really useful, it doesn’t need to block easier stuff. I dont think a shortage of good hackathon prompts or organizers should stop groups of EAs from voting on the most interesting local hackathon run by someone else, going together as a group, and teaming up to work on something (with an EA lens if you want). Thats just extremely low cost to try out.
(Im also noticing that “Host an awesome EA hackathon” seems like type of collaborative, challenging project a person could team up on!)
thanks for the kind words! I agree that we didn't have much good stuff for ppl to do 4 yrs ago when i started in bio but don't feel like my model matches yours regarding why.
But I'm also wanting to confirm I've understood what you are looking for before I ramble.
How much would you agree with this description of what I could imagine filling in from what you said re 'why it took so long':
"well I looked at this list of projects, and it didn't seem all that non-obvious to me, and so the default explanation of 'it just took a long time to work out these projects' doesn't seem to answer the question"
(TBC, I think this would be a very reasonable read of the piece, and I'm not interpreting your question to be critical tho also obviously fine if it is hahah)
meta note- its super cool to see all this activity! but the volume is makin me a bit stressed and i probably won't be trying to respond to lots even if i do one sporadically. does not mean i am ignoring you!
Are you looking for shovel ready bounties (eg write them up and you are good to go) or things which might need development time (eg figuring out exactly what to reward, working out the strategy of why the bounty might be good etc)?
Yea, idk. I was thinking of the quotes where you explicitly mentioned Van der Waals forces. Tbc, my preference would be to not be forced to pick a single force
Hi, computational protein engineer and person who-thinks-biology-can-do-amazing-stuff here.
Just wanted to report that while "Proteins are like Folded Spaghetti Held Together By Static Cling" is obviously incorrect as a matter of fact, I immediately thought it was a pretty good analogy for capturing some critical and often under-appreciated aspects of the functionally important character of proteins. When I read the sentences you've quoted him saying about proteins held together by covalent bonds, I (think) I understood what he was pointing at with this and roughly agree. I absolutely did not think he was saying proteins did not contain covalent bonds, but rather that you could imagine an alternative protein-like molecular structure which had all of its key structural and functional characteristics determined by covalent bonds. I believe such a "protein" would, among other things, be predicted to function at a much wider range of temperatures than extant proteins, maintain its structure and function in many different solvents (and probably gas phase?) etc etc.
This analogy is also definitely failing to capture other important characteristics of proteins, some of which the OP mentioned and I agree with.
By the way, if I was forced to say one thing which "held together" proteins (in the sense of "is most responsible for determining the functional characteristics of a polypeptide chain) it would be tough but I might pick something I don't think anyone has mentioned: hydrophobicity/ hydrophilicity.
Sorry I'm late to the party- as per the OP's request for short takes with no explanation, mine is that this is probably not worth doing, fwiw.
One impression I could imagine having after reading this post for the first time is something like: "eca would prefer fewer connections to people and doesn't value that output of community building work" or even more scandalously, "eca thinks community builders are wasting their time".
I don't believe that, and would have edited the draft to make that more clear if I had taken a different approach to writing it.
A quick amendment to that vibe.
Not sure how much of this is in my head, but thats a thing.
Meta note: this was an experiment in jotting something down. I've had a lot of writers block on forum posts before and thought it would be good to try erring on the side of not worrying about the details.
As I'm rereading what I wrote late last night I'm seeing things I wish I could change. If I have time, I'll try writing these changes as comments rather than editing the post (except for minor errors).
(Curious for ideas/approaches/ recommendations for handling this!)
This seems like a great idea- I actually woke up this morning realizing I forgot it from my list!
One part of my perspective which is possibly worth reemphasizing: IMO, what you choose to work together does not need to be highly optimized or particularly EA. At least to make initial progress in this direction, it seems plausible that you should be happy with anything challenging/ without an existing playbook, collaborative, and “real” in the sense of requiring you to act like you would if you were solving a real problem instead of playing a toy game.
So in this case, while “EA should host hackathons” seems reasonable and exciting to me, especially as a downstream goal if working together turns out o be really useful, it doesn’t need to block easier stuff. I dont think a shortage of good hackathon prompts or organizers should stop groups of EAs from voting on the most interesting local hackathon run by someone else, going together as a group, and teaming up to work on something (with an EA lens if you want). Thats just extremely low cost to try out.
(Im also noticing that “Host an awesome EA hackathon” seems like type of collaborative, challenging project a person could team up on!)
thanks for the kind words! I agree that we didn't have much good stuff for ppl to do 4 yrs ago when i started in bio but don't feel like my model matches yours regarding why.
But I'm also wanting to confirm I've understood what you are looking for before I ramble.
How much would you agree with this description of what I could imagine filling in from what you said re 'why it took so long':
"well I looked at this list of projects, and it didn't seem all that non-obvious to me, and so the default explanation of 'it just took a long time to work out these projects' doesn't seem to answer the question"
(TBC, I think this would be a very reasonable read of the piece, and I'm not interpreting your question to be critical tho also obviously fine if it is hahah)
meta note- its super cool to see all this activity! but the volume is makin me a bit stressed and i probably won't be trying to respond to lots even if i do one sporadically. does not mean i am ignoring you!
Well I hope it works out for ya! Thanks haha
In case you are looking for content and have interests similar to me I like the following for audio:
And i find that searching for random academics names is more likely to turn up lectures/ convos than podcasts
Are you looking for shovel ready bounties (eg write them up and you are good to go) or things which might need development time (eg figuring out exactly what to reward, working out the strategy of why the bounty might be good etc)?