M&B Journal Club?

[hypnagogue]

I was wondering if any of the denizens of this forum would be interested in starting up an online journal club sort of thing. Essentially, interested parties would start new threads summarizing and discussing scientific papers pertaining to mind and brain sciences, and other members of the club (and anyone else who might be interested) could then discuss it further. We could organize it so that e.g. we have a new article to discuss every week, with different members of the club taking turns.

There's obviously a lot more that could be said about the details of how to organize this and so on, but first I'd just like to put the feelers out there. Would anyone be interested in participating in something like this on a regular basis?

[Mk]

I don't know much about Mind and Brain sciences, but I would be very interested in it, if the articles were good.

[somasimple]

Hi,

I'm very interested, too. I already summarized some good journals on this page. (but they're not all devoted to neurosciences :redface: )

http://www.somasimple.com/online_journals.htm

[Q_Goest]

Denizens? Is that like a den citizen? Do we get to lounge around on comfy chairs and smoke pipes and drink tea or must we knaw on uncooked bones rolling around the cave floor? Either is good for me I suppose, just want to know what's expected.

I'd suggest that emailing the paper's author and explaining our denizens are chewing on their paper and would like them to participate often gets the author's attention. I've done that a few times at different message boards, and it generally works out. Makes the conversation more interesting too I think.

[detta]

i'd like to be in a journal club

[hypnagogue]

OK, so some encouraging feedback so far, but I'd like to see if we can get a few more people in order to make this thing viable.

Just to be clear, my question is not so much who would be interested in following along with the journal club, but who would be interested in being an active member-- that is, would be willing to periodically search for interesting mind/brain science articles and write up summaries and discussions for them, and also to participate regularly in presentations created by other members.

[selfAdjoint]

Just to be clear, my question is not so much who would be interested in following along with the journal club, but who would be interested in being an active member-- that is, would be willing to periodically search for interesting mind/brain science articles and write up summaries and discussions for them, and also to participate regularly in presentations created by other members.

Well, I could help out, depending on how much my physics tasks keep me busy. Strings, Branes and LQG has already evolved part way to such a club. We spend most of our time reading and commenting (often arguing) about papers on the preprint arxiv. I have a couple of sources for M&B papers that I could exploit.

[cotarded]

If you all are accepting of the disparity between my background (high school) and yours and the limits it brings on the amount of insight and worthwhile discussion I can offer, I'm certainly up for participating in this. Another warning, though: I don't have any journal subscriptions, and the local college's (nascent, used to be a community college) database access doesn't offer near as many full text papers as I'd like, so I'll have to really scavenge about. However, I'm used to this.

I would be willing to discuss whatever the cat (or the somasimple,hypnagogue, or selfAdjoint as it may be) brings in whenever I have a clue as to what it is and feel like my thoughts would be a contribution. And I'd bet my own article/paper posting frequency would be at least once a week.

lates,
cotarded.

[hypnagogue]

cotarded, you would be a welcome addition. It's to be expected that everyone will have a pretty widely varying range of knowledge and experience with the kind of topics we'll be discussing. I'd say the only strong requirements are an enthusiasm for learning about and discussing mind/brain topics, and also a willingness to put in the time and effort to contribute.

It seems like we're approaching an acceptable number of contributors, so I think we can begin discussing some of the surrounding issues regarding the club, a number of which were touched upon in cotarded's post.

One thing is journal access. Once again, it's to be expected that different people will have varying degrees of access to journal resources. Optimally everyone would have a chance to read a given paper before the 'official' discussion thread on it is started, but practically speaking we can't expect everyone to be able to access every paper, and I don't think we should restrict the scope of what we can cover by only using articles that we're sure everyone can access. So we'll have to make do with what we can. We could begin by pooling together links for some free, publically available resources like the kind selfAdjoint mentioned so that everyone at least has some easily accessible resources to draw from if needed. (Some resources like this are already listed in the stickied M&B references thread.)

Another thing to talk about is how we should organize this. Originally I was thinking of a fairly structured setup where we would know some time in advance who would be presenting what article on what day, and we'd limit ourselves to one presentation per week so we could really focus on each article as it comes. (To help organize all this, I could create a stickied thread that keeps a running tab of who has presented/will present what articles at what times, with links to the relevant threads for past discussions.)

I definitely think we should still plan in advance who is presenting what on what day to give everyone time to track down and read the relevant articles. But perhaps we could loosen up the structure to the extent that we can have variable numbers of presentations per week, or variable orders in who presents when, or whatever. I think it would be valuable to have ample time before and after a presentation to really digest a given paper and then really be able to focus in on it discussion-wise, but I can also see merits behind flexibility as well. Thoughts on how we should do this would be appreciated. It would be best if we could strike on something that works for everyone, and of course we can tweak things as we go along if necessary.

[hypnagogue]

One other issue springs to mind, which is presenting graphical data. It would be nice if, where possible, presentations could display relevant graphs or illustrations from a given paper, either by way of linking to an online image or by attachment to the post. However, I'm not sure how copyrights and proprietary issues and all that might come into play here. Can anyone shed some light on what kinds of images we could and could not post, and under what conditions?

[Q_Goest]

cotarded, you would be a welcome addition.
I'll second that.

Regarding how often a new paper is presented, once a week seems a bit much. Cotarded's post regarding McFadden's paper is 3 weeks running now and still generating discussion. Not to say once a week can't be supported, but everyone might not have sufficient time to review in a single week. Which makes me wonder how those people that actually do this for a living manage to make time to read and understand the fresh work that arives at their doorstep on a daily basis. My job doesn't allow that unfortunately.
. . . and of course we can tweak things as we go along if necessary.
yes. Tweaking should not only be expected but be a priority.
One thing is journal access. . . . (Some resources like this are already listed in the stickied M&B references thread.)
There's a lot available. I like Chalmer's page (http://consc.net/online.html) the best.
. . . presenting graphical data.
Please correct me if I'm wrong, but any data presented on the internet is free for use as long as it is referenced. Check with Greg (I believe he's the PF owner) and verify.

[Moonbear]

This is a great idea Hypnagogue!!! I'd definitely be willing to participate (I wanted to start up something like this in biology a while ago, but didn't get much interest then...I think we didn't have enough people focused on any one area of interest at the time).

Just looking at how much discussion the CEMI paper generated, I think it's a viable option.

As for articles, we may just have to limit ourselves to articles over a year old if we want to keep them accessible to everyone. Many journals make their content freely available after a 1 year period. While I'm at home, I can check which are accessible because I don't use our university server from here, which means I see what the average person not affiliated with a university sees until I enter my login information.

For neuroscience topics, one of the top journals in the field is the Journal of Neuroscience, which makes articles over 1 year old freely available to anyone (you can open them in html or download PDF formats, depending on preference). This is a good resource for articles. http://www.jneurosci.org/contents-by-date.0.shtml

[neurocomp2003]

I'd be interested in a year or two.

Thats gonna be alot of a articles if you take the wide range of fields though...i especially found it fascinating to peruse through those brain journals(which really confused me because my terminology wasn't to par as an undergrad... and the AI ones(I found Nanokitty in one).

[hypnagogue]

Regarding how often a new paper is presented, once a week seems a bit much. Cotarded's post regarding McFadden's paper is 3 weeks running now and still generating discussion. Not to say once a week can't be supported, but everyone might not have sufficient time to review in a single week. Which makes me wonder how those people that actually do this for a living manage to make time to read and understand the fresh work that arives at their doorstep on a daily basis. My job doesn't allow that unfortunately.
Yes, it's a tenuous balance between having enough time to cover something adequately and not letting things drag on for too long. I don't think we need to make sure that all previous discussions are completely finished before we move on to a new one.

Can we get some other thoughts on the best amount of time to devote to each article before moving on to the next one?

Please correct me if I'm wrong, but any data presented on the internet is free for use as long as it is referenced. Check with Greg (I believe he's the PF owner) and verify.
I don't think there would be a problem for images posted on public webpages. I'm thinking more about e.g. an image found in an online article that one needs some kind of subscription in order to access.

[DocToxyn]

Count me in. I would think that at least a week would be required to get all interested parties to download, read and critique the papers, so perhaps only one new title per week. The subsequent discussions would progress as far, or as long, as the subject and/or reader interest support them.

[hypnagogue]

Count me in. I would think that at least a week would be required to get all interested parties to download, read and critique the papers, so perhaps only one new title per week. The subsequent discussions would progress as far, or as long, as the subject and/or reader interest support them.
Yeah, this is more or less what I had in mind. Q_Goest suggests we should follow a slower pace, and cotarded seemed to imply a faster pace. Anyone else want to chime in?

Also, I'm still wondering about the legality of posting images from articles that one needs a paid or university subscription in order to access online (of course, if we did so, we would provide references and so on). Perhaps DocToxyn or Moonbear would have some good insight into this?

[somasimple]

Hi,

On my site, we discuss about papers but often it is accepted to share them via a protected forum (private). It works like a room where members read a paper that one of us bought.

[hypnagogue]

Hi,

On my site, we discuss about papers but often it is accepted to share them via a protected forum (private). It works like a room where members read a paper that one of us bought.
That sounds like a nice solution, but I'd rather have our club out in public, where everyone who might be interested can learn from the presentations and be a fly on the wall (or participate) in the discussions. If we have to sacrifice the ability to post certain things in order to do that, so be it (though of course, I would prefer if we did not have to do that).

[somasimple]

Hi,

I enhanced the solution with a public forum by the creation of a public group which is the only available to download protected papers. In this case, all posts are viewable by public/normal members but papers/attachments, only but members of the group.

Papers have copyrights and need to be protected. Or you need to limit them to sample issues and free full text access journals.

[Q_Goest]

I'd like to know if people would prefer to have the paper's author invited or not.

Thanks.

[neurocomp2003]

an article a month/biweekly sounds about right...just to get the club started since its almost the start of the new year.....onces the club gets going you can jump to biweekly/weekly.
Exactly what fields will you be exploring in M&B club? any? strictly human intelligence from AI/Cogsci/Neurosci-human brain/Lingu/ and the other sciences
or are we talking about general intelligence like ALife, Adaptive Learning Techniques, other types of brains, evolution of the mammalian brain, self organizatino of other species like ants? etc

[cotarded]

I was too hasty when I last posted. I underestimated the depth of the discussions and the care with which the material will be selected. I thought it'd be more of a napster for compelling papers, with the option of exploring it further in a separate discussion left to those interested. I still think there should be someplace people can deposit papers and articles that they either don't have time to thoroughly discuss, or when the appeal to the rest of us is uncertain - a sticky, maybe? The popular items could migrate to our intensive discussions. It'd be a communal paper drop box and screening area.

As far as the focus of this thread goes, now that I better understand what we're really talking about, I completely agree that we could need quite a bit more than a week to really address everything. Though I don't think we need to bring a discourse to conclusion to begin a new one. I think biweekly would be a fine balance. We could always defer the next paper if the current discussion isn't showing signs of deceleration.

q_goest:
I'd like to know if people would prefer to have the paper's author invited or not.

Having McFadden come in on our CEMI discussions was a delight - though I wish he'd stayed a tad longer to see some of your later posts - and certainly the sort of thing that I'd like to see repeated (whenever possible). Although we should probably hold on invitations until we get deadlocked or find ourselves arguing interpretations; after all, we want to have something to attract the author. People tend to want to rectify misconceptions concerning their work; presenting your paper to people on the internet at random probably isn't quite as enticing.

edit: I really want to see johnjoe's response to moonbear's most recent connexin-36 post.

[cotarded]

Hi,

I enhanced the solution with a public forum by the creation of a public group which is the only available to download protected papers. In this case, all posts are viewable by public/normal members but papers/attachments, only but members of the group.

What do you all think of this idea? Sounds like a good compromise, provided matriculating to the privileged group isn't too difficult.

[hypnagogue]

Exactly what fields will you be exploring in M&B club? any? strictly human intelligence from AI/Cogsci/Neurosci-human brain/Lingu/ and the other sciences
or are we talking about general intelligence like ALife, Adaptive Learning Techniques, other types of brains, evolution of the mammalian brain, self organizatino of other species like ants? etc
Basically, any paper that covers a topic appropriate for posting in this forum (as explained in the sticky) would be acceptable. (I think pretty much all of the things you listed would fall under that umbrella.) This would allow for quite a wide range of topics and fields for us to explore.

[hypnagogue]

What do you all think of this idea? Sounds like a good compromise, provided matriculating to the privileged group isn't too difficult.
Yes, that does sound like a good solution. I'll talk to Greg to see what we can do about setting up something like that, but I'd still also like to be more assured one way or the other what would be an acceptable way to handle stuff like this (legally).

[hypnagogue]

I thought it'd be more of a napster for compelling papers, with the option of exploring it further in a separate discussion left to those interested. I still think there should be someplace people can deposit papers and articles that they either don't have time to thoroughly discuss, or when the appeal to the rest of us is uncertain - a sticky, maybe? The popular items could migrate to our intensive discussions. It'd be a communal paper drop box and screening area.
That sounds like a good idea. Perhaps what we could do is set up a sticky like that anyway, just for general interest purposes, and members of the club could select papers from the list to present if they so chose. I was also thinking of making a sticky for keeping tabs on news articles involving m/b stuff (independently of the journal club), so perhaps that could somehow be integrated into the journal article reference source as well.

[CosminaPrisma]

I would be very excited to participate in a Mind and Brain Sciences Journal Club or message board. I think it would be a great experience even though I don't know much about the subject matter. I am very eager to hear more and would be delighted to participate in such a forum.

[somasimple]

Hi All,

Yes, that does sound like a good solution. I'll talk to Greg to see what we can do about setting up something like that, but I'd still also like to be more assured one way or the other what would be an acceptable way to handle stuff like this (legally).

It is legit and at the fringe, at the same time.

Having a public group is a good way to advertise members about usage of protected materials. Many papers may be shared for research.
The paper is only discussed, not sold, neither used in a malignant way.
You get the right to buy a journal and tell some friends that the journal is at home, in a room where they could read it. It is perfectly legal.
Institutions buy articles and they are read by teams. This is legit.
But the paper is reproduced since it is stored on a server. It is why, it may not be accessible directly without an agreement of the group's moderator.

[fuzzyfelt]

I'd like to read the discussions, but I don't think I'd have anything much to contribute. Would I have to join the club in order to read the papers? And btw, I really enjoyed the links Somasimple gave to some of Domasio's papers. Hope papers like that will be included in your discussions.

[hypnagogue]

Just a quick note here-- due to the nearing holidays, I think it would be best to wait until a couple of weeks after New Year's to officially kick off the M&B journal club. In the meantime, we can continue to discuss relevant organizational issues about how the club will work (more to be said here, but I don't have the time right this instant), and we can also begin hunting down some articles that we can use for presentation purposes when we do get started.

[Moonbear]

Yeah, this is more or less what I had in mind. Q_Goest suggests we should follow a slower pace, and cotarded seemed to imply a faster pace. Anyone else want to chime in?
I think the 1-2 week per paper timeframe is reasonable. More often than that and you'll lose participants just because they don't have time to read the article, and any longer than that and the topics will drag on too long or we'll lose momentum in selecting new articles. Perhaps we could always have two topics open at the same time...one where the paper is introduced about a week in advance of planned discussion (the discussion "leader" can provide the source of the article they will discuss, and perhaps a brief intro of why they find the paper interesting), which will give everyone time to get the article and read it and think about it, and then the other topic that was started a week earlier that is being actively discussed. If the discussion continues longer, that's fine, but we'll open up the new topic to discussion in that time. We can "sticky" the active discussion and the upcoming topic, and "unstick" the previous discussion after the week is up. How does that sound?

Also, I'm still wondering about the legality of posting images from articles that one needs a paid or university subscription in order to access online (of course, if we did so, we would provide references and so on). Perhaps DocToxyn or Moonbear would have some good insight into this?

We can't post those images without permission from the journal (and my experience is the journals are reticent to grant permission without charging an exhorbitant fee...even if you're an author on the article! This came up when we wanted to include a figure in a review article that we had previously included in another publication). It's a fine line because we are using them for educational purposes, which generally is considered "fair use," but because this site is funded by contributorships and advertising, it could be viewed as using their articles to make a profit (even if Greg doesn't make any actual profit). Besides, since we can't control who views this site, a publisher would have a legitimate gripe that we're making their copyrighted material available to people who haven't paid either through an institutional or personal subscription.

What we can do is re-draw the highlights of a figure rather than copy the exact figure and provide reference to the source with a statement such as, "Based on: Author(s), Journal Title, Year, Vol: Pages." Alternatively, we can describe it in words and refer to the original source..."If you look at Fig. 1 in (article reference), you'll note that there is an increase in..."

[Moonbear]

I'd like to know if people would prefer to have the paper's author invited or not.
Thanks.
I'd rather not have the authors invited. For starters, this isn't even going to be feasible in most cases. Second, it really hinders discussion to have the author hanging around and having to worry about hurting their feelings when you find some fatal flaw in their reasoning.

Just a quick note here-- due to the nearing holidays, I think it would be best to wait until a couple of weeks after New Year's to officially kick off the M&B journal club. In the meantime, we can continue to discuss relevant organizational issues about how the club will work (more to be said here, but I don't have the time right this instant), and we can also begin hunting down some articles that we can use for presentation purposes when we do get started.

I agree. I wouldn't have time to seriously contribute to such discussions until after the first week of January.

Also, I think we can be somewhat flexible in how we address papers and what topics we choose. I think the person who chooses a paper should be the discussion "leader." I think they should have the role of initiating the discussion with the background on the topic, and jumping in to steer the direction of discussion if necessary, and presenting their initial thoughts on the strengths and weaknesses of the paper.

Neurocomp asked about the range of topics for discussion. I think that's what interests me most about having a journal club here, that we'd have a much wider range of topics guided by member interests than what I'd get to discuss in a local journal club. Though, for that reason, we have to keep in mind that the person introducing a paper may be the ONLY person here with much background on that particular subject, so they will have to take on the responsibility of providing the necessary background for others, letting us know if a particular method is done correctly, is typical for that field, etc. We all stand to learn a lot from this approach.

For those who are expressing concern that they don't know enough about the subjects to be discussed to contribute to discussion much, feel free to just read along and see if you learn something, but also feel free to ask questions! The whole point of a journal club is for people who are not experts in a field to learn more about it, and for the experts to help them along. Questions are essential for the discussion. You might wonder about anything from how they came to a certain conclusion based on the results to why a particular reagent was used in a method. Those are all opportunities for learning.

[hypnagogue]

I think the 1-2 week per paper timeframe is reasonable. More often than that and you'll lose participants just because they don't have time to read the article, and any longer than that and the topics will drag on too long or we'll lose momentum in selecting new articles. Perhaps we could always have two topics open at the same time...one where the paper is introduced about a week in advance of planned discussion (the discussion "leader" can provide the source of the article they will discuss, and perhaps a brief intro of why they find the paper interesting), which will give everyone time to get the article and read it and think about it, and then the other topic that was started a week earlier that is being actively discussed. If the discussion continues longer, that's fine, but we'll open up the new topic to discussion in that time. We can "sticky" the active discussion and the upcoming topic, and "unstick" the previous discussion after the week is up. How does that sound?
The rolling scheduling idea sounds great. I think that's the best proposal yet, so unless anyone has any strong objections or alternative ideas they'd like to discuss further, I think we can go with that setup.

As for the stickying, I was actually thinking of having a journal club 'index' stickied that would have links to all current and past journal threads (and maybe a blurb about what the journal club is all about and how it works). That might mitigate any need to stick the current journal discussion itself, but we'll see how it goes.

We can't post those images without permission from the journal (and my experience is the journals are reticent to grant permission without charging an exhorbitant fee...even if you're an author on the article! This came up when we wanted to include a figure in a review article that we had previously included in another publication). It's a fine line because we are using them for educational purposes, which generally is considered "fair use," but because this site is funded by contributorships and advertising, it could be viewed as using their articles to make a profit (even if Greg doesn't make any actual profit). Besides, since we can't control who views this site, a publisher would have a legitimate gripe that we're making their copyrighted material available to people who haven't paid either through an institutional or personal subscription.
Thanks for clarifying that. I assume that only holds for figures found in online articles requiring some sort of subscription, correct? i.e. if an article is available to the public online, there should be no problems with direct linking to images, right?

As for images that would require permission, do you think somasimple's idea would do the trick? Actually, ultimately it might be preferable to just go with redrawings or descriptions of such figures, because optimally I would like everyone on PF to have the same kinds of access to whatever things we'll be talking about.

[hypnagogue]

Also, I think we can be somewhat flexible in how we address papers and what topics we choose. I think the person who chooses a paper should be the discussion "leader." I think they should have the role of initiating the discussion with the background on the topic, and jumping in to steer the direction of discussion if necessary, and presenting their initial thoughts on the strengths and weaknesses of the paper.
Agreed, but...

Neurocomp asked about the range of topics for discussion. I think that's what interests me most about having a journal club here, that we'd have a much wider range of topics guided by member interests than what I'd get to discuss in a local journal club. Though, for that reason, we have to keep in mind that the person introducing a paper may be the ONLY person here with much background on that particular subject, so they will have to take on the responsibility of providing the necessary background for others, letting us know if a particular method is done correctly, is typical for that field, etc. We all stand to learn a lot from this approach.
What if someone would like to present an article on a subject that they don't have much background in? One could always do some preliminary, extra research to help get filled in on such things (review articles are always good), but there's a limit to how much background one could accrue that way and how well one could understand it, especially if time constraints are a factor. It would be nice if people were free to stretch their horizons a bit with this, even for the articles / topics they themselves present.

For those who are expressing concern that they don't know enough about the subjects to be discussed to contribute to discussion much, feel free to just read along and see if you learn something, but also feel free to ask questions! The whole point of a journal club is for people who are not experts in a field to learn more about it, and for the experts to help them along. Questions are essential for the discussion. You might wonder about anything from how they came to a certain conclusion based on the results to why a particular reagent was used in a method. Those are all opportunities for learning.
Yes, definitely.

[Moonbear]

Thanks for clarifying that. I assume that only holds for figures found in online articles requiring some sort of subscription, correct? i.e. if an article is available to the public online, there should be no problems with direct linking to images, right?
If it's freely available, and we just provide a link rather than re-posting the image, I see no problem with that.

As for images that would require permission, do you think somasimple's idea would do the trick?
I'm not really sure it would. All it does it make it a more elite group, but we'd still be providing copyrighted material to people who wouldn't otherwise have access to it. On the other hand, it would be easier to argue we're using it only for educational fair-use if access is limited to those actively participating in the discussion. It would be different if we were all at the same academic institution and were just providing a convenient copy of an article we all already had access to. Ultimately, we have to abide by US copyright laws. Things might be different for somasimple since he's in France. I don't know how much the laws vary from country to country.

Actually, ultimately it might be preferable to just go with redrawings or descriptions of such figures, because optimally I would like everyone on PF to have the same kinds of access to whatever things we'll be talking about.
Yes, I'd prefer a method that doesn't limit participation. Since most people here are trying to broaden their knowledge in areas outside their own research area, I don't see a problem if we have to limit our sources to free access journals, even if it means they have to be a year or so old. It would be different if we were trying to keep up with the cutting edge in our own fields.

[Q_Goest]

Moonbear, thanks for the feedback.

I'd rather not have the authors invited. For starters, this isn't even going to be feasible in most cases. Second, it really hinders discussion to have the author hanging around and having to worry about hurting their feelings when you find some fatal flaw in their reasoning.

Yes, it certainly would be embarrasing for the author of a paper published in a peer reviewed journal to be shown a fatal flaw in their reasoning here at physics forums. It seems quite clear that the vast majority of people here do not want the authors invited in any case, so I'll refrain in the future. Thanks again.

[neurocomp2003]

can we have a seasons thing? where its like
first season: psychology(ling/cogsci)/ Philo
second season: neuropsych/neurochem
third season: AI/ALife/Adaptive Learning
fourth season: mmm physics-based or non-human based biological intelligence

[hypnagogue]

can we have a seasons thing? where its like
first season: psychology(ling/cogsci)/ Philo
second season: neuropsych/neurochem
third season: AI/ALife/Adaptive Learning
fourth season: mmm physics-based or non-human based biological intelligence
Not a bad idea, but my vote would be not to have something like this. I'd like to give everyone maximum flexibility in choosing what they'd like to present. We could go with something more structured like this if enough people wanted to do it though.

[Moonbear]

can we have a seasons thing? where its like
first season: psychology(ling/cogsci)/ Philo
second season: neuropsych/neurochem
third season: AI/ALife/Adaptive Learning
fourth season: mmm physics-based or non-human based biological intelligence
In theory, that would be nice, but I think for maximum participation, we should just go with what people are willing/able to present at any given time.

Though, that suggestion made me think of something else...maybe once we get a list of willing participants, we could get them to list the papers they're interested in presenting (to whatever extent anyone is ready to list those), and if we see two that are similar on the list, we could try to put them back-to-back for more continuity of discussion.

I think there will be some things we'll just have to work out as we go along too. I've certainly never done an online journal club where a topic was discussed over a week before. Usually I sit in a pub with a group of people and we spend an hour or two discussing a paper and then decide whether it leads to any interesting new ideas for our own group, or if we should have tossed it to the rubbish bin. :biggrin:

[Lars Laborious]

Hi. I just wanna add my name to your list. Also, I vote for maximum flexibility in choosing what to present, 'cause I think that will generate more new ideas.

[shruth]

Hi all...Please count me in.
Also, the journal Neuron is also free access for articles which are a year old. http://www.neuron.org

Also arxiv server also has a lot of computational neuro papers but are not peer reviewed. So getting papers which everybody can access should not be a problem.

[shruth]

Would it be illegal if the paper were emailed to a mailing list including all the people who are in the journal club? If legal, could some system be feasible?

[somasimple]

Shruth,

It may be possible but email system on standard Vbulletin forums doesn't allow attachments on email messages.
But this feature exist and will be a legit way to transmit papers.

BTW, it doesn't respond to the original asking. Papers need to be shared by all users?!

[shruth]

If email sharing is legit, then couldn't we make a list of the email addresses of the participants which could be updated, say, every fortnight. Then couldn't the person who does the OP send out a private email (not the forum one) with the said paper as attachment to that list?

[hypnagogue]

OK, so to summarize where we stand and what we still need to figure out:

Member list

CosminaPrisma
cotarded
detta
DocToxyn
hypnagogue
Lars Laborious
Moonbear
neurocomp2003 (?)
Q_Goest
selfAdjoint (?)
shruth
somasimple

A nice group there!

Format

We'll be having a sort of rolling format where in any given week, there will be two articles to mull over. One article (call it A) will be the primary one for which everyone has read up and is focusing on discussing. The other article (call it B) will have just been introduced to the group that week, so everyone can begin to digest the contents and perhaps pertinent background information, etc. The following week, focus on A will be dropped (though discussion may still carry on indefinitely); B will become the primary topic of discussion for the club; and a new article will be introduced and earmarked as the primary topic of discussion for the next week; etc.

Article access

I think the concensus is that we should try to get articles that are freely available for download on the internet. Sources of such free articles that have been mentioned thus far are http://www.neuron.org and http://www.jneurosci.org/contents-by-date.0.shtml ... do we have suggestions for others? Please keep in mind that any articles to be discussed should already have been accepted for publication in a peer reviewed journal.

Although it is highly preferable to draw from such free resources, I think we should also permit members to present articles that are not publically available on the internet if they feel they would really like to present such an article. In this case, the member in question should provide a detailed summary of the paper contents, and if necessary can draw and present a depiction of any key graphical data in the article, while giving due credit in the image itself (e.g. "based on figure 1 from Smith et al, 2003").

We still do not seem to be entirely settled on the issue of distributing such articles. I believe the default position should be that we will not distribute non-publically available articles among club members, even by using a private distribution system like email. We may decide to do differently at some point, but I would not be comfortable in doing so until given strong, authoritative evidence that we would not be violating any rules or laws by doing so.

Organization

To help organize the club, there will be a stickied 'directory' thread explaining what the club is about and how it works, listing members and their orders for upcoming presentations, and containing links to past and present presentations. We may also choose to sticky the two current article presentations for a given week.

Further issues

* I suggest that we should also come up with a regular scheme for titling threads for the journal club. Something like this:

JC #X: Paper title

Where this thread would be the Xth installment of the journal club presentations. "JC" stands for "journal club" and "Paper title" is the name of the paper being presented in this thread.

* When do we officially begin, and how should we assign the orders for which members present at what times?

I think a good time to start would be January 15th. (During the first week, we would only have one article on tap, in the 'introductory' phase; the following week, the regular rolling schedule of 2 articles per week would begin.)

As for deciding presentation orders, hopefully we can sort this out largely by self-nomination. However, I think it would be helpful if we could set a good tone by starting off strongly, so it might be best if one or two of our more experienced and knowledgable club members could do the honors of inaugurating the club.

[Q_Goest]

Sounds good H, I'd agree with the outline you've provided.
I think a good starting point would be Chalmers' paper "Facing Up to the Problem of Consciousness" (http://consc.net/papers/facing.html). I'll volunteer to do that one.

[shruth]

Should we all declare our educational level and field of interest so that an informed choice can be made about the kind of papers that are picked for discussion?

Also, maybe it would be better if we allotted 2 weeks for each paper. This would give everyone enough time to read it and formulate their opinion...The second paper can be introduced a week after the first one....but discussion on it could only start after a week....

[Lars Laborious]

Should we all declare our educational level and field of interest so that an informed choice can be made about the kind of papers that are picked for discussion?
Also, maybe it would be better if we allotted 2 weeks for each paper. This would give everyone enough time to read it and formulate their opinion...The second paper can be introduced a week after the first one....but discussion on it could only start after a week....
Sounds like a good idea to me ...:smile:

[hypnagogue]

Would anyone mind if we pushed back the debut of the journal club a week? Originally I set a start date for Jan 15 but I haven't been around much lately and overall it seems like we're still a bit unprepared to begin in earnest.

In the meantime, just to clarify something I said earlier-- if possible, I'd like if we could start off with a paper presentation or two from folks who have considerable academic experience doing scientific research about, or directly related/applicable to, mind/brain science. Presumably such people will be experienced in both the details of the some portion of the field in particular, and also with scientific article presentations in general, which would make for an ideal example for everyone else (me included) to look up to for future presentations.

Also, Q_Goest proposed to present David Chalmers' paper, "Facing Up to the Problem of Consciousness." That's a fine paper and there's much to be discussed in it, but I'm wondering if we'd be better off focusing explicitly on scientifically oriented articles rather than incorporating philosophical ones as well. I kind of lean in this direction just so we could maintain a strong focus on scientific approaches, but I'll open it to the floor for everyone to give their 2 cents.

[neurocomp2003]

i think its a great idea that the first paper be philosophic than scientific...just so people can get a perception of others views of what it would means to study brain sciences: cogsci/neurosci/ai/alife/ling etc. This gives us a generic view of where people are interms of knowledge and perhaps academicly and what goal they would aim for in particpating in such a journal club.

But i'd have to agree after the first, that all the papers be of some scientific nature(any science relation or math/cs).

Also how would this M&B club take place? just on these threads? or are there other methods like msging systems? I should be able to participate end of jan/mid-feb.

[selfAdjoint]

Also, Q_Goest proposed to present David Chalmers' paper, "Facing Up to the Problem of Consciousness." That's a fine paper and there's much to be discussed in it, but I'm wondering if we'd be better off focusing explicitly on scientifically oriented articles rather than incorporating philosophical ones as well. I kind of lean in this direction just so we could maintain a strong focus on scientific approaches, but I'll open it to the floor for everyone to give their 2 cents.

I would agree with you. We have philosophy forums for the philosophical discussion of consciousness; let's not do that in this club.

[shruth]

I too feel that we should focus more on experimental neuroscience. And I found one paper that seems to have something for everyone.
Ongoing Spontaneous Activity Controls Access to Consciousness: A Neuronal Model for Inattentional Blindness
Stanislas Dehaene, Jean-Pierre Changeux
PLoS Biology, May 2005 | Volume 3 | Issue 5 | 141
http://biology.plosjournals.org/archive/1545-7885/3/5/pdf/10.1371_journal.pbio.0030141-S.pdf
I have just browsed thru the paper and on first look,
The pros of this paper:
1. From two leading scientists in the field in a leading scientific journal.
2. Has theoretical modelling...which should interest the computational neuroscientist....and correlates to other experimental approaches...which should interest the rest of the neuroscientists....and at the same time touches on the subject of consciousness which should interest the informed non-neuroscientist
3. OPEN ACCESS! Let us all support the PLoS journals by spreading awareness about them :smile:
4. Published in mid 2005....so is current and has not been analyzed to death as of yet :smile:
The cons:
1. The paper is on the longish side...18pgs
2. On first glance, the theoretical modelling seems to require quite some effort to understand
Theoretical neuroscience is not my area of expertise. So if you guys think that this is a good paper, someone with the relavant expertise could make the OP. Or if someone starts the thread, and nobody else makes the first analysis by the end of this month, I'll volunteer.:smile:

[Moonbear]

After much time getting side-tracked by articles that aren't accessible to all, I finally found something I'm willing to present for the journal club format and can volunteer to kick it off.

shruth, I haven't looked at your paper yet, but why don't we add it to the queue since it's outside your area of expertise and you indicate it will take some time to understand. I'm sure any article will present difficulties to those who are outside any given field, so I propose that I begin with one that at least is sufficiently within my field that I can provide guidance in how to read and interpret it so those unfamiliar with reading journal articles can get more gently eased into the process.

This is the article I've found:
http://www.pnas.org/cgi/content/full/102/5/1761

Messager S, Chatzidaki EE, Ma D, Hendrick AG, Zahn D, Dixon J, Thresher RR, Malinge I, Lomet D, Carlton MB, Colledge WH, Caraty A, Aparicio SA. Kisspeptin directly stimulates gonadotropin-releasing hormone release via G protein-coupled receptor 54. Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1761-6.

The abstract:
We have recently described a molecular gatekeeper of the hypothalamic-pituitary-gonadal axis with the observation that G protein-coupled receptor 54 (GPR54) is required in mice and men for the pubertal onset of pulsatile luteinizing hormone (LH) and follicle-stimulating hormone (FSH) secretion to occur. In the present study, we investigate the possible central mode of action of GPR54 and kisspeptin ligand. First, we show that GPR54 transcripts are colocalized with gonadotropin-releasing hormone (GnRH) neurons in the mouse hypothalamus, suggesting that kisspeptin, the GPR54 ligand, may act directly on these neurons. Next, we show that GnRH neurons seem anatomically normal in gpr54-/- mice, and that they show projections to the median eminence, which demonstrates that the hypogonadism in gpr54-/- mice is not due to an abnormal migration of GnRH neurons (as occurs with KAL1 mutations), but that it is more likely due to a lack of GnRH release or absence of GnRH neuron stimulation. We also show that levels of kisspeptin injected i.p., which stimulate robust LH and FSH release in wild-type mice, have no effect in gpr54-/- mice, and therefore that kisspeptin acts directly and uniquely by means of GPR54 signaling for this function. Finally, we demonstrate by direct measurement, that the central administration of kisspeptin intracerebroventricularly in sheep produces a dramatic release of GnRH into the cerebrospinal fluid, with a parallel rise in serum LH, demonstrating that a key action of kisspeptin on the hypothalamo-pituitary-gonadal axis occurs directly at the level of GnRH release. The localization and GnRH release effects of kisspeptin thus define GPR54 as a major control point in the reproductive axis and suggest kisspeptin to be a neurohormonal effector.

So, I'll give everyone a week to get ahold of the article who wishes to participate and read it over. On Saturday, Jan 28, I'll open the thread for it (this gives me the weekend to focus on the initial discussion) and some relevant background material, and kick off the topic. When I open the thread, I'll post an introduction to the topic, a little bit about why this is an interesting topic to me, and provide some background to help folks understand the content. I thought a PNAS article would be a good one to kick off the topic, because those are usually very thorough, and give a good example of high-quality, cutting-edge science.

[Moonbear]

Oh, I just noticed that Hypnagogue has requested we post the topic and intro in a separate thread a week ahead of discussion. Okey-dokey, I'll get right on it!

[hypnagogue]

Please note that an official M&B journal club (http://www.physicsforums.com/showthread.php?t=107956) thread has been created and is stickied in this forum. In this thread you can find up to date information on how the journal club is organized, links to good resources for free journal article access, and scheduling info for past, present, and future journal club entries.