Medical M&B Journal Club: Join the Discussion!

[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 into 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 into 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.

 

[Lars Laborious]

Hi. I just want to 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 consensus 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 knowledgeable 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 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 ...

 

[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
4. Published in mid 2005...so is current and has not been analyzed to death as of yet
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.

 

[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 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.