Just a heads up - the discussion phase UI is not nearly as slick as the single-person UI. I'm seeing a really crowded document where it's hard to connect the notes on the right to the content on the left.

Yes, I agree — it looks a little cluttered and crazy. With regard to connecting notes and content — you did click them right? Did you mean it's hard to see which text a comment refers to? We could try removing all other highlights when a comment is selected. That should look nice.

I did not realize that I could right click them. This is helpful to know. Removing other highlights would help to clarify more, but knowing about the right click bit is a huge help already.

Can you start with: What would the funding process be like with thinklab? Paint a picture of the world for me. What's better in it?

Would it be helpful to specify these as things that thinklab lets you create: a Thinklab Notebook and a Thinklab Proposal. The notebook provides the tools to perform open and collaborative science, while the proposal provides you with the tools to get broad feedback on a grant.
I always find "facilitates" less concrete than the outputs.

This is not discussed in the proposal below. If you're not going to talk about it, I'd suggest removing it.

Why?

who is convinced? thinklab or the open science community as a whole?

Thinklab is convinced :) I take it this wasn't clear?

How valid is this concern? How valid is it if they are already doing rigorous and reproducible research?

Hm, I'm not really sure what you're getting at here?

Is it valid for scientists to feel that openness is not in their interest, or do they feel this as a reaction to the state right now? Is there some downside to openness that even the right incentive structure can't fix? Is that concerned lessened if they are currently using best practices for reproducibility and rigor?

argh.. I still don't get what you're saying :( Are you suggesting that many scientists feel it is not in their personal interests, but in reality it is? (Because they don't fully appreciate the benefits?) Anyway, the point here is to lead into a statement that Thinklab's goal is to create incentives for scientists so they do feel it is in their interests.

Sorry - I'm not doing a good job of this. Inherently in science is there some value at some time to a system that doesn't require everything to be open. Does it help people take risks/etc that they wouldn't take in an open system?

An alternative is that most people are closed right now because things are hyper-competitive or that this is the way things have always been.

If the second case is true, then I'm going to look for solutions that maximize openness because they're good for science in the long run. If the former is true, I'm going to look for things that promote openness but don't necessarily require it in all cases.

I don't have an answer. This question just came to mind when reading this part.

Okay I get it! You mean scientists have reasons for not be open that are valid in the sense that forcing them to be open would be bad for science as a whole. There may be. Although I suspect those benefits are far outweighed by the benefits of being open in most cases. It's something to keep in mind

This could be resolved by using "by default" as a qualifier for the entire process being open. There are numerous conditions under which openness isn't an option even if the scientists would want it (think patient privacy, locations of near-extinct species or archeological sites in danger of being looted).

Enable? Do tools that do everything required already exist + you're making better, or do they not exist outside of your platform?

They exist, but they need to be coupled with a) a points and/or monetary system that rewards participation and b) a system that directs researcher attention to discussion that is relevant to them. I assume you're raising a concern and creating tools that already exist.

Well, I'm trying to get towards whether or not you're doing a bit more than facilitating. The overall structure of this grant doesn't entirely work for me. It feels like lots of detail about thinklab up front. I want to see up front how the world will be different with thinklab in regular use.

I think you should lead with this section. Why first.

Each of these points is somewhat long. Instead, can you flip this to describing what the workflow of open grant applications is like. You could then work in the benefits there. You don't even need to mention thinklab specifically. That could come up later. This same point applies to 1-4 here.

Is there data on how long project's usually take? Ron Vale found, for example, that it now takes UCSF graduate students on average 6 years to publish their first paper [1].

Any examples where early feedback was beneficial or where a lack of feedback was harmful?

One could easily argue that such specific input could as well be given only after funding has been obtained.

Any examples? Open source software could be a relevant example for 2 and 3.

Q&A sites like SEQanswers and Biostars could be other suitable examples.

This is a strong point, but more for the general concept of open notebook science than specifically for what this proposal is about.

Hm, I was thinking the ideal time to form collaborations would be when ideas are still forming. I'll rephrase this a bit to be clear what it's referring to.

That would be an excellent time indeed. It is just a problem of too generic phrasing.

Collaboration can form at any point in principle. Laying out the research process in detail renders more of those points discoverable by potential collaborators.

I understand that you want to give credit, but this is not the place to do so. You want to end on a punchline. Now you have a punchline, followed by "oh this is actually not really our idea".

I take your point. Any suggestion on where I could move this? Maybe to the beginning of this section? It shouldn't come off like we are just taking his ideas. These are all ideas derived from first principles analysis. But it seems only right to link to Daniel's work because he has been out there promoting open proposals the most.

In my opinion you could drop the sentence entirely and just cite reference 1 somewhere (I lack the overview to tell where).

No need to mention my name. A good place to reference such related efforts might be right after "Thinklab is intended for broad use across all of science, including biomedical research." above.

His name is spelled Daniel Mietchen

Crap. Embarrassing. I thought that was fixed. Sorry Daniel!

Versioning would be useful for such cases, and a mechanism for removing comments that do not apply to later versions any more.

There actually can be versions — and in the new version your name will be corrected :) All of these inline review comments are tied to this particular version.

Could you slightly rephrase this to: Why should/will scientists participate? With the current phrase you need to make an iron clad case that people actually will do it. I don't think you have the evidence for this yet. With the re-framing, it just needs to be clear that it will be advantageous for scientists to participate.

Agreed.

I'd re-write this bit also as above. What does the world look like when researchers are using thinklab? Highlight the points where it's better for the scientist.

See above: why is the world better for funders - paint me a vivid picture.

Strange backwards phrasing that initially makes it sound as if you doubt your own goal. "We believe science funders are in the best position to ..." would be a much stronger opening.

A critical reviewer could easily see this as adding busywork. Funders can require a lot. If you hold the purse strings you have the power to decide what happens. This can be good or bad. Why is this good? Imagine that I'm a skeptical reader who thinks: imagine the paperwork now - even before I get the grant!

Key point here could be that many of the bureaucratic layers have been built to address issues that do not manifest themselves the same way in open science, so if tackled properly, open science (a stick for many, a carrot for some) could actually be combined with a reduction in red tape, which should be a carrot for every researcher.

Too vague. Link directly to next sentence to get to what you concrete want to attain.

Consider some references on how current closed grant peer review is not very effective [1]. You want to stress that funders could desperately use help in selecting which proposals to fund.

Just get to the point: "We recognize ..."

Too long and vague. Don't tell me what you could hypothetically do. Tell me what you will do. "In the meantime, we will do everything to drive adoption by ..."

I think this belongs first, and that it should get worked into the proposed "Why will scientists participate?" section.

Agree.

Too much text saying too little. Again, nice of you to give credit to who got which ideas, but it waters down your proposal. In this case, where Ben came with the fundamental idea for the proposal, you could consider making him a partner.

Why do you say this waters down the proposal? I would imagine listening to the community would be seen as a good thing!

It is just unnecessarily wordy. From the perspective of a reviewer, I don't care who got which idea. "There are a number of benefits to this" says nothing that the heading "Benefits for grant writers" doesn't say. Last sentence says nothing that couldn't be said by just referring to the URL after the second-to-last sentence :-)

Casey Greene, a first time reviewer on this proposal, said: "The UI is very slick!"

This section seems largely redundant with the bullet list at the very beginning of the proposal.

any evidence?

No. I'll change the language to be less matter of fact.

How do you get a proposal in front of the right reviewers to make sure that it's well reviewed. There's a lot of feeling that the twitterverse is essentially a mutual admiration society. How do you keep this from becoming that?

Yes, well there has to be a lot of reward! I imagine you're reviewing this as a favor, because you've used Thinklab before, and because you'll be working with @dhimmel soon. But generally it is really hard to get people to take time away from their own work to give feedback. That's why I think funders should pay people for it. On top of that we add an impact points system so people feel they are being recognized appropriately.

Do I invite people, do the funders invite people, or do people self select? That was the bit that I was a bit unclear on.

Right now it's up to the authors to invite people. However, with funders involved that could change. I imagine it will always be open for self selected commenters as well.

Who is the community here? Other scientists, etc?

Let's say I'm a grad student or postdoc with a valid critique of a grant, but everyone who posted thus far loves this thing. What's the benefit to adding my (potentially negative) comment? Conversely - what's the benefit to reacting positively to a grant that is widely viewed as negative by earlier reviewers? How do you keep feedback independent of the first people to comment.

There may sometimes be benefits in both of these scenarios, but they might require a specific bit of knowledge (or occasionally even ignorance of mainstream views). I'd expect it to be more common, though, that if reviewers 1-3 agree, others would pile on comments that essentially amount to "+1".

I think it is risk/reward too. If 3 reviewers agree and a young grad student offers a dissenting opinion with a convincing argument that persuades the first 3 reviewers, this young grad student would gain a lot of respect (I would imagine).

Will there be an option for this?

Hm, I don't know. Let me know if you have a suggestions.

I could imagine someone wanting their grant text itself to be -ND. Would you like someone to copy a substantial amount of your grant to their own when applying for funding, even with credit?

I don't think anything more restrictive should be allowed, but CC0 would be nice.

Why not? What if we switch to this and thinklab fails. Would we lose the ability to apply for funding? Yikes!

I'm not sure what you mean here. How would you lose the ability to apply for funding? It's not open source because we are trying to create a sustainable business so that we can achieve our goal of making science much more open and collaborative.

Let's say that funders adopt thinklab to manage grant review. At some point, thinklab ceases to function. Now the entire platform has to be rebuilt to maintain the same approach to review. Is there a way that you could make it open source but offer a hosted/turnkey solution? This would give people the peace of mind that they could deal with a shutdown if they had to, but I bet the barrier to entry of issuing dois/etc would let you still price reasonably aggressively.

Hm, I don't know. The main concern of open sourcing now would be that a group of academics would decide this shouldn't be run as a for-profit company. They would be able to quickly launch an identical service and because of it's existence few people would signup on Thinklab. I believe it would also make it very hard for us to get funding from traditional investors. I will just say that we much prefer to have "impact investors" involved but the reality is we need to keep our options open at this point.

I see - makes sense! It probably wouldn't hurt to keep thinking about this in case there's a way to make it work. I could see some trepidation around the current setup. Perhaps there's a way to ameliorate that without removing your ability to find traditional investors. I'll try to keep thinking too.

I love everything about thinklab, except for this. Not being F/OSS is a dealbreaker for me. No way am I going to contribute to a platform that locks me in. F/OSS is completely separate from your ability to make a decent profit.

@michael_r_crusoe the content on Thinklab is CC-BY. In what sense are you locked in? And in what sense would you not be locked in if the Thinklab code was F/OSS?

I think you might want to play with the ordering of this. As I read, I encountered these questions (see above) before they were addressed. Easier to read if you supply answers as the questions are raised.

Do the reviewers see a revised proposal? Is there a way for the author to mark the places where a grant changed in response to specific comments? I might be willing to come back to see my notes overlaid on changes, but I probably wouldn't if I had to manually put them side by side.

It's a good feature idea. When editing the proposal we can set things up so authors will save a "commit", and have that commit reference a particular comment. In the meantime authors can just paste in a link to the diff. I'll try to do that with this proposal.

I don't have: "Add inline comment" Looks like it might always happen when you click "Note"

Yeah, same here - is the figure showing an earlier UI?

"Needs citation" would be nice.

If you're going to put this in here - how does it work? Does the open notebook platform integrate with the open proposal platform?

It's the same platform. The discussion on the proposal just becomes part of a larger discussion of the whole project as it moves forward. Is that more clear?

It is to me because I've interacted with @dhimmel's project. I'm not sure it'd be clear for your reviewers at this point, because they may have no idea how the notebook solution works.

for whom?

For science/society.. will clarify.

This is either an expansion or reduce. What's the purpose of including this here? If you don't have time to talk about it, I might remove it for now. You could mention it in a future directions, but is this within the scope of this grant? Feels a bit like scope creep.

Missing period after citation. Also the book can be cited by DOI: [1]

I might move this above just under Scientists and Funders and call it: Why will reviewers participate?

Rather than calling it a "big problem", perhaps rephrase that incentives will catalyze participation. I agree here with Lars's cart before the horse comment. I believe open science is incentive compatible currently, just few realize it. I think it's important you stress that Thinklab gives people the tools to take advantage of incentives, many of which already exist and that Thinklab doesn't have to pay for.

That depends somewhat on what I say as a reviewer. Not everything is nice to say in public.

The answer to this from reviewers could definitely be: "no." What if I'm busy and reviewing this proposal from an airplane where I can't focus enough to make deep comments? What if I'm without internet access? For the first: I realize we shouldn't review grants when we don't have sufficient time to think deeply, but we should acknowledge that this does happen. Would thinklab lead to fewer (but more successful) proposals reaching review panels? This could be a big selling point.

can replace with "became"

What if I'm an early career scientist, and I'm assigned Big Shot 5's grant to review? This seems like a situation with a lot of potential downside for an early career scientist. Is there a way to protect reviewers?

I don't think anyone would ever be assigned as a reviewer. People should only be reviewing if they actually have some expertise and expect their review to be of some value. We could consider adding anonymous commenting at some point in the future but in the near term it's not something we are looking at.

I very much share @caseygreene concern on this. It can be outright deadly to the career of a young scientist to publicly criticize a big shot. At the same time, the vast majority of scientists are early career scientists. If one cannot find a mechanism to protect them, one will very quickly run out of reviewers.

The road to openness is not all about fear. Intelligent comments on some big shot's stuff might actually get a newbie attention in a space where they currently get basically none, and if that attention becomes unpleasant, they might possibly have a better handle on it than in the current closed system. Plus, an open system would do the sorting into big shots and others in a more meritocratic way than the current system. The challenge is to find good ways to navigate these spaces. Are there examples from open-source that might be instructive in this context?

How does this not degenerate into a mutual admiration/criticism society? It feels like some twitter discussions certainly do.

Good question. The ratings are private. If it was public, I would agree: users would rate each other highly as thanks, or rate each other low as revenge.

Might be helpful to note this very briefly.

Link to the leaderboard?

Who gets the money? Does it go to me personally or to my science?

Personally. In theory it could go towards supporting your lab, but not everyone is in a lab. This is intended to reward participation from people outside academia as well.

Might be useful detail to add. I didn't realize the outside academia component, so this might be a good place to let readers see that vision.

Actually I never thought about having money go towards supporting the person's lab. It's something that could definitely be done that way if that's what funders want. (At least for those affiliated with a lab.)

Well - in this case my inclination would be to say that the incentive could go towards an individual or their research program, which allows academics with labs and members of the public without labs to participate.

Giving the money personally is certainly the strongest incentive. This does bring a few ethical and practical challenges, though. Is it fair that I spent work hours on reviewing for ThinkLab instead of working for my employer? Or does this turn reviewing into a side job? Do all universities allow their researchers to have side jobs?

Yeah, maybe cross those bridges when we get there :)

I can see numerous scenarios in which either the lab or the individual might not be in a position to accept the money (perhaps even both), but in some cases, it might work well. It's important to be flexible here, e.g. to allow active reviewers to have a say in how funds are spent in their broader area, or to donate their monetary rewards to some good cause (think a fund for minority scientists or so).

Though I'd say "comments that are valuable" - because it might be possible to write comments that peers find valuable that aren't actually.

Well, unfortunately we will not be able to detect comments that peers find valuable but that are not, in fact, valuable. So yes, you can game the system by writing comments that peers think are valuable but that actually are not. LOL

:)

This paragraph would benefit from a citation or two.

Without reading up on the overjustification effect, I do not understand this part.

I'm not sure that this is true. I'd say that a very small minority are already doing this.

What makes thinklab different than all of these others? Speaking of which - what is the related work to thinklab? Haven't seen it yet.

This comes across as awfully patronizing!

I agree. Rubbed me the wrong way too.

Will remove

I'm still not entirely sure that the case has been made that the proposed system is better. Is it valuable because it's different, or is there some evidence that it's inherently better?

I'm honestly not entirely sure that discussing the role of money in this is helpful. Sure, it may be a way to get people to participate, but it seems like refining the specific incentive structure is an experiment that needs to be performed. With some preliminary data, you could make an argument for why this incentive structure is good. Right now, it feels like this is one of many, w/o evidence, but it feels a bit concrete.

Considering that content will be copyright of the contributors, describing it as yours may rub some people the wrong way.

As you can see from my comments, I was wondering about alternatives earlier. What if you worked these parts into the envisioned future bits that I discussed earlier. You could envision what the future would be like with open grant review. Then you could discuss how much of this can be done now (and how difficult it is) with existing tools if a scientist was motivated to do this.

evidence?

I will rephrase this. Simply making the point that not all conversations have to be crammed into the sidebar.

Gotcha! I actually didn't even realize that there was a "discussion" beyond the sidebar until I got to the later categorization part.

evidence?

What kind of evidence are you looking for? This is more a statement of logic: if we direct people's attention to discussion that matches their interests then we will draw more people into the conversation. Google Docs does not do that. If you want attention on your Google Doc you have to share it with people. I guess the proposal needs to better explain that a "Thinklab Inbox" will surface content automatically based on a users's interests. Relates to this part of the proposal.

This seems outside of the domain of proposal submission, which this focuses on. Can you integrate w/ github/continuous integration providers to provide a verifiable record behind figures?

Consider changing to "the analog of a GitHub issue"

,

Not sure what you mean exactly here. This whole paragraph repeats already established concepts.

Needs citation

There's not a lot here to judge Jesse on. The specificity level is low.

Comes across as vague. How is Gleb related to ThinkLab?

Really? Which ones.

I was referring to the incentive to keep everything secret until publishing a paper. Will clarify.

What the the incentives though? Is it inertia or are there actual incentives?

Well they are concerned about people taking their ideas and publishing something first. This gets even more concerning if we're asking people to share proposals. I do think these concerns are overblown but nonetheless they are there. And I do believe there are many benefits to the researcher for being open that aren't fully appreciated. And yes, inertia, that's big.

What about using the term "challenges" and highlighting "inertia" and "fear"? Incentives (particularly aligning with how the term is used in this grant) feels like someone is paying scientists to be closed.

there are

I'm not sure that this is the case now - science definitely feels at least within-team collaborative. Can you make this a concrete example that is a bit more connected to the way things work right now?

Having both "enormous" and "massive" so close to each other comes across as overselling.

I would leave this out.

Think of evolution: sure, existing living systems are bizarre and often seem sub-optimal but if you just start making changes to the genetic code willy-nilly, it's probably not going to make the system more efficient. How are you going to measure your impact? How will you know if this is improving or harming the process of scientific research? How you will you adjust if it turns out that items need to be changed?

I see this proposal has completely failed to persuade you. I posted a response here: Has our scientific system been optimized by an evolutionary process?

I tried to read this as a skeptical grant reviewer. I actually like what you're doing, and I view your contributions positively. I wanted to give feedback that I thought would help you slightly reframe your proposal to make it more compelling to the interested but skeptical.

Thank you. I really appreciate you taking the time!

Add citations to sources with a "formal academic background" as well to lend credibility to the claim.

Consider citing RIO [1]
and the five deadly sins [2] either here or elsewhere.