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How much domain expertise and network does a special issue guest editor need?
I have been invited as a special issue guest editor.  The journal is genuine (I have both published and reviewed there multiple times) but not very prestigious and sometimes seen as "easy" to get into.  So far the special issue has a title and a deadline, but the scope is yet to be defined by the guest editors.  The title is broad enough to be its own journal.  Within the fields that would fit with this title, my expertise and network range from "a little" to "none at all".
I've been a little surprised by the invitation because I thought guest editors were senior researchers in their field, and no matter how much introspection I do on the impostor syndrome, I'm not a senior researcher in this topic.
I tentatively accepted, because being a guest editor could be a great learning experience and would enhance my CV, and perhaps I don't need that much domain expertise if the other guest editors are more experienced experts and my role would be rather to carefully read papers, reviews, replies, and more reviews, before accepting a paper (or not)?
Now it turns out nobody else has accepted yet and I've been asked to find others, and I'm getting cold feet.  Could people who have experience being special issue guest editors, or who are otherwise familiar with these roles, give some advice?

In special issues, are guest editors usually senior researchers with a lot of domain expertise and an extensive network in the field?  Or do you also encounter those whose expertise is at best tangentially related?
How much of a handicap would it be to lack the in-depth expertise?  Is this a debilitating limitation or one that can be reasonably accommodated?

The field of Earth Observation / Remote Sensing.  The publisher is based in Switzerland, specialises in open access, and its journals are indexed by the usual places,

If you are the only guest editor, why not change the topic to suit yourself?

@AnonymousPhysicist I don't know what to do with so much freedom.

Why the downvote?

In my experience, special issues of respectable journals are usually connected to some conference. The guest editors are the organizers or program committee (or a subset thereof), and the authors are people who either spoke at the conference or were invited to speak but couldn't attend. The situation you describe looks quite strange to me.

but not very prestigious and sometimes seen as "easy" to get into (Impact Factor 4.1) --- I guess it would take someone familiar with the field of Earth Observation / Remote Sensing to know what exactly what "not very prestigious" means, because 4.1 is stellar high in some fields. For example, one of the top 2 or 3 most prestigious journals in all of mathematics has an impact factor of 3.027.

@DaveLRenfro you're right, academia varies more than I think.  I have removed the impact factor from the question because it doesn't really add important information and is without sufficient context.

For what it's worth, I had no idea what was good or bad for impact factors, even in mathematics (my few papers came out before this started being something people worried about), and thus I googled a few OK but not top journals I know of to get an idea, and was getting impact factors under 1. So I decided to look at one of the most prestigious journals I knew offhand (it's associated with the Institute for Advanced Study in Princeton), and at this point I realized that impact factors must vary drastically with field. Prior to this I would have guessed they varied a bit, but not to this extent.

I've edited journals without holding a PhD in the past (don't ask). Doing a mediocre job is not that hard - to invite reviewers for example you just need to do a literature survey of the paper's field, which is standard Masters-level work. You can then invite reviewers even if you don't know them. The success rate is quite good - I think roughly 50% of the reviewers I invited responded to the invitation (although a substantial number decline). Doing just this, it's possible to keep the journal operating, although of course it will not do well. Since you know something about the field you should be able to do better: for example you can desk reject with more confidence, make sure every accepted paper has something interesting to say, and so on. If you can understand what the papers are saying on a high level, you should not have to worry about not being able to do a good job.
However, there are several potential problems I can see:

You've said it's an open access publisher based in Switzerland, which pretty much identifies which publisher it is. It doesn't have a great reputation. You could meet people who disapprove of you working with that publisher.
More concerningly, you are very likely to be asked to help solicit submissions. This is very different from reviewing submissions, and here a wide network will be helpful. You may also feel like the publisher is exploiting you - viewed one way, you are using your contacts to help them make money. If this troubles you, then that feeling could be exacerbated by the low response rate from other potential editors.
Yet another potential problem is "The title is broad enough to be its own journal". I would guess from this that the initiative for the special issue came from the publisher's staff, not the editor-in-chief. Although this isn't a red flag - there's a good chance the publisher got the editor-in-chief's approval before approaching you - it is something to keep in mind. Another issue is the broad scope could make it difficult for you to even put together a special issue since so many topics would be relevant. You could talk to the publisher and/or the editor-in-chief to narrow down the topic, if you feel it's appropriate.

One more thing probably worth mentioning is that you'll likely have a lot of scope to define what you want the special issue to look like. If the initiative really is from the publisher, chances are they will be willing to defer to your expertise, and the editor-in-chief won't object.
So, what to do now? If you don't care about doing a good job, you can go ahead. Leave the scope, invitations, marketing, etc to the publisher (they'll undoubtedly do a mediocre job at best, since they have no domain expertise) and just review any papers that actually are submitted. The special issue will not be pretty, but the amount of non-review work you need to do will be minimal. If you care about doing a good job, I'd suggest thinking it through before committing. Talk to the editor-in-chief, talk to a senior colleague, think about what you want the special issue to be about and who you might invite to contribute.
By the way: if you do go ahead, I'd recommend asking the publisher if they can offer free open access for your invited submissions.

In my experience, the main role of a guest editor is to find reviewers for submissions—and perhaps to solicit submissions.  Can you think of some interesting work you'd like to see in a special issue?  Do you know who you'd ask to review it?  Then you're ready.
But you don't need our help with this, and you can get much more specific and exact advice—pick up the phone and have a chat with the editor-in-chief (or whomever asked you to serve).  You were invited for a reason, and you may as well find out what it is.

Can the authors of the special issue serve as reviewers for each other?

@Philosopherofscience Just stumbled on your comment. There's a question on that topic: https://academia.stackexchange.com/q/15903/17254


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Are fixed-term research funded staff such as post-docs entitled to redundancy rights, such as severence pay at end of contract?
According to Fixed-term employment contracts at gov.uk:

Anyone who’s worked continually for the same employer for 2 years or more has the same redundancy rights as a permanent employee.

When ending a fixed-term contract specifically:

If a contract isn't renewed, this is considered to be a dismissal, and if the employee has 2 years’ service the employer needs to show that there’s a ‘fair’ reason for not renewing the contract.

Redundancy rights include redundancy pay and a notice period, among other things.
Do those redundancy rights apply for research funded staff on fixed term employment contracts at universities in England?  My question covers both postdocs (Grade 6) and other research funded staff (Grade 7).
(There are also other rights, such as Any employee on fixed-term contracts for 4 or more years will automatically become a permanent employee, but those come with caveats already on the gov.uk page; my question is specifically about redundancy rights)

Edit: It appears this may depend on whether postdocs are legally considered trainees on a work-experience placement or not.  Since my question covers both postdocs and other research funded staff, the trainee-or-not status of postdocs would need to be established in order to answer the overall question.

"Workers don’t count as fixed-term employees if they: ...are a...trainee on a work-experience placement" (source: https://www.gov.uk/fixed-term-contracts/what-counts-as-a-fixedterm-contract). So post-docs might not be considered fixed-term employees. Hence, would not be entitled severance pay.

You might want to clarify whether you are considering trainees or non-trainees, because the answer will differ.

@user2768 I have no clue whether postdocs in the UK are legally considered "trainees on a work-experience placement".  Certainly my employer does not describe me as such in my employment contract.

I don't know whether "trainee" is legally defined in the UK, but definitions of postdoc include the word training, e.g., "[a] postdoc is a person...who is pursuing additional research, training, or teaching in order to have better skills to pursue a career in academia, research, or any other fields" -- https://postdocs.cornell.edu/structure-postdoctoral-study

@user2768 But they're also employees, and your link is from New York, USA.  There must be many precedents of postdocs leaving employment at end of contract after >2 years in the UK that can inform an answer to my question.

The definition is from a prestigious academic institution and I believe it will be accepted internationally, by academics at least. Regarding the "many...postdocs leaving employment at end of contract after >2 years in the UK," I am sure there are. But, those that didn't receive any severance pay can't help you. (They may not have insisted that their employer's obligations were fulfilled.) And any that did might not be able to help either. (They may have had a different contract.) In any case, your question relates to UK law, rather than whether particular postdocs received severance.

Try contacting the Citizens Advice Bureaux.

@user2768 I have contacted the UCU (where I am a member) with this question, they might know.  See also https://www.ucu.org.uk/legal-dispute-at-stirling and https://www.ucu.org.uk/article/3547/The-ending-of-a-fixed-term-contract---some-information

the UCU looks like an excellent organisation to contact. Making several assumptions, I presume that you aren't expecting/haven't received severance, when you believe it is legally due. Moving forwards, you should consider whether you want to chase what you believe is legally due. It might well be expensive in terms of your time and finances (a lawyer might be required), and it might well damage your reputation (your supervisor, head of school, dean, ... might be involved and that could be damaging, this could be mitigated if they believe you're right).

@user2768 My end of contract is only in two years (unless renewed by another fixed-term contract), but it never hurts to know what to expect, so the hypothetical situation of a legal conflict is not currently applicable.  I only learned about those rights outlined at gov.uk recently (see also this question), so now I'm curious as it would mean the armies of fixed term staff employed by the university may be in a slightly better situation than I thought we were.

See https://www.ucu.org.uk/article/3547/The-ending-of-a-fixed-term-contract---some-information and specifically "employees with more than 2 years' service are entitled to redundancy".

I'll tell you this much: They are if the academic staff unions in the UK demand that they are, and stick by this demand. And if that's not the case I'm sure the universities can come up with some legal fantasy they declare to be the truth to avoid paying.

@user2768 the most common official job title for a postdoc in the UK is "Postdoctoral Research Assistant" or "Postdoctoral Research Associate". Unilke in the US, a postdoc is considered a member of research staff and not generally a trainee (unless on a speicfic "Postdoctoral Training Fellowship").
Many PDRAs don't receive redundancy because they leave to take up a new position before the last day of their old position, but universities do pay up, without argument, if you are still in place on the last day of a contract of more than 2 years.

Yes. If you refer to your contract, you will find it is a contract of employment (and probably explicitly states that you are an employee of the university*). Indeed, some universities issue permanent contracts, with a "we'll make you redundant once the funding runs out" clause, to their postdocs.
A few other points:

If you wanted to claim redundancy benefits, you would have to wait for the university to actually let you go. This prevents you leaving before the end of your contract, so will limit your ability to look for a new job in a timely fashion. The university could just shift you into another role to avoid the redundancy costs (especially if it's one you'll want to leave); although, hopefully, most wouldn't be that cynical.

(There's a possibility that they could also require you to apply for suitable, open internal positions, but I don't know whether they could seriously claim your failure to do this equated to leaving voluntarily.)

From your own link, there is no notice period on the non-renewal of a fixed term contract; so a notice period on non-renewal of the contract would only apply to people who, by virtue of over four years of service, have become permanent employees:

Fixed-term contracts will normally end automatically when they reach the agreed end date. The employer doesn’t have to give any notice.

Postdocs are not students or trainees. Here's the definition of those two categories, from the Fixed-term Employees (Prevention of Less Favourable Treatment) Regulations 2002 (part 5, exclusions) (emphasis added):

18.—(1) These Regulations shall not have effect in relation to a fixed-term employee who is employed on a scheme, designed to provide him with training or work experience for the purpose of assisting him to seek or obtain work...
[cut, funding info]
(2) These Regulations shall not have effect in relation to a fixed-term employee whose employment consists in attending a period of work experience not exceeding one year that he is required to attend as part of a higher education course....
[cut, references to the acts that define a HE course]

The pay grade is irrelevant.

*Weirdly, I have seen employment contracts that state you're not (and not for self-employed contracting arrangements). I don't know why because a court wouldn't find someone not to be an employee just because the contract says so.

Excellent answer. Just like to add 1) Employers are required to offer you internal redeployment opportunities if your services are no longer required. 2) Many universities will offer two levels of redundancy, an enhanced redundancy if you can show if engaged in good faith in the redeployment system and the legal minimum if you don't. Often if you take enhanced redundancy you will be barred from working at that uni for a specified period.

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Apply PhD with no recommendation
Please allow me to ask for suggestion about no recommendation problem.
I graduated my master with distinction and my paper was published in nation wide journal, everything seems to be perfect. But after the graduation,  my thesis supervisor has a personal problem with me and we've never talked since then. So now I want to apply for PhD and when it comes to recommendation, I really don't know what to do and I don't think my supervisor will write a good thing about me since we are in personal conflict.
Do you have any suggestion for this situation?

Have you tried e-mailing your thesis supervisor requesting a recommendation? A professional may be prepared to put personal conflict aside and just write about your master's degree work.

I hope that your adviser will be able to put aside personal differences when you ask him and write the recommendation that speaks to your abilities in an academic setting.

If you can be open with your formal supervisor about the "personal problem" s/he has with you, you could simply ask, "I am interested in pursuing a PhD. I know that we have disagreed about XYZ and so I wanted to ask you if you believe you could write me a fair recommendation."
Note, that this is still risky - the supervisor can write a bland recommendation (which holds little weight) or agree to write it and write a bad one anyway.
What about the director of the program you attended? That could be weighed more favorably. Other faculty members? My PhD dissertation chair never wrote recommendations for anyone, so I never even asked him (we never had a falling out or anything, it was just his personal policy). It never hurt my chances of jobs or other things because I had other faculty and references write litters for me instead.
Good luck!

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Manuscript status "Submitted to Journal" over a week in an Elsevier Journal
I submitted a manuscript to an Elsevier journal on 8 days ago. However, the "Current Status" of the manuscript is still "Submitted to Journal".
Is it common that the status "Submitted to Journal" lasts over a week?
When I click "Send E-mail" in the "Action Links", it shows that "This letter should not be used at this time. This submission is not in a status that would allow this letter to be sent to the intended recipient."
I cannot even withdraw this manuscript now because the Action Links do not contain "Withdraw" button. I submitted several manuscripts to this journal about three years ago. I checked the email at those moments. When I approved the submission of PDF files built by the submission system, I would receive a confirmation email from the editorial office. However, this time I did not receive any such email.
What should I do at this moment?

Wait, it can take weeks.

@Zenon Thank you. But may I ask why it lasts so long?

I can take months, even years. Any given editor uses the editorial manager as the editor sees fit. In some cases the status does not change from "submitted" until a decision has been made on the article.

@DanFox I understand what you mean. I cannot even withdraw this manuscript now because the Action Links do not contain "Withdraw" button. I submitted several manuscripts to this journal about three years ago. I checked the email at those moments. When I approved the submission of PDF files built by the submission system, I would receive a confirmation email from the editorial office. However, this time I did not receive any such email.

@scaaahu That is fine. Thanks.

Have patience -- you're asking that many things happen within a short amount of time. Your paper needs to get through an initial administrative check whether the formatting is correct and/or whether there is any plagiarism. Then the editor-in-chief needs to assign the paper to an associate editor. And then the associate editor needs to assign reviewers. Only then does, in most system, the status change to "Under review".
So it requires three people. Any one of them might be on vacation for the week. Or they have a paper or proposal deadline themselves. Or they have a family emergency. Or they need to grade a term paper. You can't expect that they stop everything they do and turn to handling your paper. They'll get to it in due time -- I'd say you can start to get upset if it's been 3 weeks, but before that my recommendation is as stated at the top: Have patience.

8 days is nothing in academic time.  Like the blink of an eye.  It is not uncommon for reviews to take months. Just be patient. I know it's hard, but just move on to your next project.  If there's no movement in a month or two, then maybe e-mail the editor and ask for a status.

Thank you for your answer. I know that it takes months to review a paper. However, it seems that my paper has not been sent to the editor yet.

@Hebe: I would guess that it has been sent to the editor, but that the editor has to take some action to acknowledge and has not yet done so.

@NateEldredge Hence, it is possible that my paper is already under review by the referees, but the status in the system never changes  until the decision is made, right?

It's possible.  What I'm saying is that it could be that the editor has already done something with the paper (anywhere from "initial skim" to "considered some possible referees" to "actually sent it out"), but hasn't clicked the corresponding buttons in the editorial manager software to acknowledge having done so.  For this reason, I think it's always misleading to assume that the status in an editorial manager actually reflects what's going on.

@NateEldredge I see. Thanks for your explanation.

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Need clarification on the status of my manuscript in ScholarOne
I recently submitted a manuscript to a journal using the ScholarOne submission system. After the second round of review, the editor provided some minor language revisions, and all three reviewers had no further comments. However, after we made the revisions, the manuscript status changed to "Awaiting Reviewer Invitation." Does this mean that my manuscript needs to go through another round of review? Or it is just a brief status which actually means the paper is going to the chief editor?
I would greatly appreciate any insights or advice on this matter. Thank you in advance for your help.

Manuscripts will go as many rounds of review as needed, until the reviewers (and ultimately, the editor) is happy with the manuscript status. I had papers published with 1 review, and papers published with 5. There is no way to tell.
When you review papers for such system, you are explicitly asked again if you would like (again) to be the reviewer for the second (nth) time.
The system is telling you that the invitation has been sent to the original (and perhaps new) reviewers and they are waiting for them to confirm.
In essence, there is no way to force the reviewers of the original submission to be a reviewer again, so they asked, again.

Thank you for you kind reply! I feel less anxious now. Thanks !! Hope things go well for you!

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On the verge of being "fired" from post-doc position, how to act towards supervisor?
I am in month 5 of an extremely unfulfilling post doc position in France. My sole responsibility is debugging 10k+ lines of spaghetti C++ code. I am a mechanical engineer and although I did my PhD with a focus on numerical simulations, debugging isn't what I envisioned myself doing.
My current supervisor has been "controlling my life" by controlling when I leave from work by strategically placing meetings at such times. He has also suggested on numerous times, quite explicitly that I must not leave work until he does; and he is a workaholic - works 12 hours a day. This has continued for the last 4 months and this has severely affected my health. I am now depressed, balding and have lost 15 pounds of body mass.
Today I had a conversation with the director of my research lab and he hinted that since things aren't working out, "I may be given enough time to find employment" and leave.
I am confused, hurt and extremely displeased to say the least.
Losing my job would be very problematic for me, as I am an Indian citizen and it would affect my ongoing H1B processing for a faculty position in the US starting next fall.
My current contract doesn't state what the "rules of being let go" are. All it says is that I am required to work 35 hours a week. I have consulted a lawyer "friend" and he tells me that most contracts are at will anyway and for foreign nationals, once your contract AND work status are revoked, you may not be able to fight the system.
Considering that I will be given a few weeks to a month or so perhaps, how do I behave towards my supervisor. Should I show up for work or just say screw it?

You need to consult an immigration attorney as soon as possible. Any other advice to this is superfluous to you figuring out how to handle the current situation.

@aeismail Career wise, how do I handle this? Have I failed? How do I show that on my CV or have conversation with potential job offers (if I even get offered something in the future - fat chance)

Isn't a 12-hour work day/60-hour work week explicitly illegal in France? Seems like you need a French employment law attorney as well.

@BillBarth See edit. Contract says 35 hours a week. I cannot go around searching for an attorney now.

I think it's a given that consulting an attorney is a good idea, if you can manage it. I've edited the rest of the post to focus on the question of how to act, now. (And I do think the question about the CV is a very good question, and you should definitely ask it separately)

@ff524 Thank you for doing my work for me. I appreciate it even if it is from a stranger.

Why not? You might have to sue your current employer after they let you go for not doing the illegal and anti-contract thing they've asked you to do.

@BillBarth Lets look at what you said:1) I get fired 2) since I don't have French employment, my visa is invalid (it is not just an entry document in Europe) 3) I go home to India and then search for an attorney to fight my case from... INDIA? Right. thats going to work.

You wrote "You're on a leave of absence from a US university for 1 year" and then "I will return to my university in May 2015 to take up a non-tenure track lecturer position." Cannot this university help you, and the remaining time is like 7 months or something. Can't you ask them to let you stay for 7 months till your new job kicks in, or am I missing something? Anyway, sounds like a bad situation. I've also been there - Indian citizen in the US... lots of scope for abuse. Though this is France...

@FaheemMitha Good point. However, I don't have a visa to the USA. They would petition my visa only if I returned next year in May. Not before, not later. Petitioning for a visa takes place in the city of current residence. in my case that is Paris. However, not for long. So if I am "cityless" as far as visa procedures go, my visa dossier would have defaulted and will be rejected.

@drN Sheesh, that sounds nasty. I assume you have asked your "home" university for help? If not, I suggest doing so immediately. It does sound like your best bet is to try to keep the people you are working with happy for the duration if you can. I suppose you had no idea it was going to work out like this? Sounds like something went badly wrong. I was in a somewhat similar situation once that went on for years. I'd have thought stringing these people along would be possible for 7 months. Try to act all enthusiastic about your job if you can.

Which is why you should get the local employment law attorney now! I doubt it's legal for your employer to fire you and have you deported while your lawsuit unlawful working conditions is pending. You might not be able to work, but I suspect you can find a way to stay in France while you work out your dispute. It's also possible that your advisor/university will back off and not fire you if your attorney points out to them that what they are doing is illegal. GO GET SOME GOOD LEGAL ADVICE!

At the risk of being superfluous, Bill's advice sounds good. Since (if I understand your situation correctly) all you basically need is to stay put for 7 months, and you have a job waiting for you after that time, legal action (or even the threat of legal action) might be enough to swing that. It is quite likely the adviser/university will back off under the circumstances. After all, they have little or nothing to lose by letting you stay on in the area (or even stay employed) for the next 7 months. I would certainly try to stay employed if you can, even if you don't enjoy the job.

You get money, looks better on the CV, possible health benefits implications etc. This is an obvious thing to say, of course. Sadly, it sounds like you are not going to get any publications or even a reference out of this, but at this point those are probably low on your list of priorities.

You need to talk to a lawyer in France and maybe to the US school about whether a January start is possible, there's no point talking to random academics on the Internet about this further until you understand your options better.

Was your lawyer friend French?

@NoahSnyder Yes. He is French. He couldn't say more since he has a conflict of interest.

Assuming that the legal work contract situation in France may be somewhat similar due to EU: In Germany, the fixed time contracts that are usual for postdoc positions usually cannot be canceled  without mutual agreement. Important exceptions are: 1. probation period is possible (up to 6 months) - within that time, no reason is needed to cancel the contract (both sides). 2nd exception: there are situations where the employee is entitled to the employer's agreement, e.g. if they have a better job offer. IANAL: I'd seriously suggest to get a lawyer that knows both about immigration and employment

There are two problems here. An academic dilemma and a legal issue. The latter is specific to country's immigration, workplace rules, your residency status, etc., therefore I will politely keep the focus to the first one. There are also good comments to your post, so keep them in mind as well. Needless to say, the legal problem could be more intimate to your situation but you will find actual support from a legal authority as you yourself have stated. Now, to the academic dilemma at hand: first of all, I suggest talking with your supervisor and make your position clear in an honest sober way. Your problem is a practical one and need not to be emotional. Here, I would suggest and stress on keeping the best of relations with your supervisor (even if you decide to leave or they decide to let you go), especially if this is your first ever post-doc position. This is important for two reasons: first, you want to leave on good terms even if it didn't work out for you and so you don't need to give an impression of personal grudge. Second, there might be opportunities in future where you will have to work/collaborate with the said supervisor or the university. You also don't want to ruin the possibility of good references for your own future work from this university - hope things will work out for you, and my two cents help. Good luck.


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Cancellation of certificate of course completion
I took a 4-month online course in London. Upon completion, I received an email congratulating me for passing the course with the course certificate attached. The following day, I was told that there was a mistake in the grade given and that I did not pass the course. There is no plagiarism involved. Is it legal to revoke the certificate and change the grade from pass to fail?

For legal questions, consult a professional.  Personally, I doubt such cancelation was illegal.

It would be normal procedure for an institution to correct a grade if an error is found afterward, no matter whether the new grade was higher or lower, and no matter if the student had already been issued a certificate.  The goal is to "get it right".
The institution may have internal time limits as to when this can be done, or how much internal review is required, but those limits would typically be months to years.  One day is practically no time at all on academic time scales.
Of course, if you think the newly assigned grade is not actually correct, you probably have a right to appeal or request a review.  You would have to refer to the policies of your institution to find out how to go about that.  But if you acknowledge that the new grade is correct and the original one wasn't, there isn't really anything to be done.
Legal questions are outside the scope of this site, but since this is common practice, I would be very surprised if it is illegal in any country.
It is certainly unfortunate and frustrating that the mistake was made, but at the end of the day, the grade is what it is.  I wish you better success going forward!


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Are there any acceptable reasons for omitting data in a publication (i.e. "data not shown")?
I was recently going through an article (which I was told is fundamental in the area of my new project) published in a respectable medical journal. In short, the paper is about the similarities between a particular sub-type of tumor cells versus a particular type of stem cells in the body, then they go on to investigate what that similarity might indicate.
Barely two pages in and I realize that the authors omit what I consider to be critical data when motivating the use of two particular proteins as markers in establishing their fundamental assumption, that their immunohistochemistry findings are representative of the reality and that their model is valid:

Accordingly, we screened all known ..... markers against our ..... data to determine which, if any, decrease with differentiation (data not shown). Of all the potential ... markers, we found that X and Y are the best candidates, and they were therefore used in this study.

Now it might not be a big deal to some but I find it important to see that omitted data, since:

I am not that informed in that particular type of biology
Seeing that their "real" findings are built on the results of the aforementioned screening, the validity of their research is practically depending on the decision of using those two markers.

Which brings me to my question: Are there any cases where not showing "critical" data in such a manner is acceptable or common? I know that some journals do not accept "data not shown", but obviously it does happen in better journals as well...

I am not in any way familiar with biology, but it seems odd to refer to "all known...markers" when, apparently, there are only two markers of interest. Are you sure what you quoted from the paper is accurately reflected by what you understand is the authors' methodology?

I think I got the methodology right, I had skipped the next line which might have caused the misunderstanding. Please see the quote now.

I think it is perfectly reasonable to not "show" data. For example, consider a multivariate randomized control trial with two groups. If there are a large number of partially correlated dependent variables, the data are not suitable for graphical or tabular presentation. What we are potentially interested in is if there is a difference between the two groups. We can "see" that from a single sentence about a statistical test and a comment that the data are not shown (so people do not go looking to find the figure).
In a biology example, maybe you are counting the number of intact cells after two different treatments. There may be hundreds of slices that result in two numbers. What exactly do you want to see?

Interesting, I had not thought of the data presentation problem, even though I doubt that is the case. This field of biomedical research is riddled with HUGE pdfs with cluster graphs and heatmaps, you name it... It has not hindered people from having 900+ pages of supplementary (yes, I did come across such a paper). Long story short, yes I guess it might be an issue in some cases.

Critical data?  Probably not.  But, I have seen many papers with data left out simply because of paper length restrictions, and in all cases other graphs and data appropriately contributed to the papers' fundamental arguments.
In the cases where I wanted to see the data that was omitted, I've written one of the authors and they have almost always forwarded it along.

how about supplementary data then? I mean there usually isn't a limit on supplementary data, right?

@posdef I think it goes back to the question of whether it is critical or not.  If the authors didn't think it was critical, and the reviewers/editors accepted the paper, then the peer-reviewed answer is that it wasn't critical.

What constitutes "data" is a highly subjective issue. If "data" means "all scientific output," in many cases this exceeds what can reasonably be shown in a paper.
In molecular simulations (my particular field), we may generate gigabytes or even terabytes of data for individual papers. This data needs to be crunched down and represented in figures that process the data and make sense of it to the reader, as it is plainly impossible to show the reader the same data over and over again. Thus, we choose to show only the most essential information, rather than deluge the reader with more information than can be handled either visually or in tabular form.

I sometimes start with gigabytes of measured raw data, even before any bootstrapping of models or whatever takes place... Clearly outside usual sizes for supplementary material.

It is of course difficult to judge this particular paper without having seen it so I will stick to general terms.
I do not see any reason for not representing all data in some form. When I say represent I mean that the complete data set can be given in terms of, for example, statistical measures which would at least provide some way to see or judge whether the subset shown is truly representative. But, I still have a hard time seeing a good reason for omitting it without clearly explaining on what grounds.
Journals allow supplementary information and so it seems reasonable to use that option if it exists in th eparticular journal. In very old papers where plots were mae by hand, there may be some excuse if not everything is included.
As I see it one of the fundamental principles of scientific publication is reproducibility. That requires access to all data. There are of course instances where this i snot possible such as when patient journals are involved.

From the way you've described it, it sounds like the choice of markers was somewhat arbitrary.  Presumably they had figures that demonstrate that the markers they did choose are good at marking whatever-it-is that needs to be marked.  Thus, the fact that they looked at howevermany others is immaterial to the scientific content of the paper and is rightly omitted.
Now, that data could well be useful to someone else for whom markers X and Y are inadequate (maybe because of expression problems or tissue type or whatever).  It would be useful to the scientific community to know what that data is (if indeed it was done carefully enough to be worth anything--maybe it wasn't, but it didn't matter because X and Y checked out).  But there's no requirement to be especially helpful to the rest of the community (or to avoid being sloppy in some areas as long as you go back and do it carefully/right once you know what you're doing).  So it seems reasonable to me.
(Again, inferring from what you've said.  If that screen was what told them that X and Y had the properties that they thought, and there is no other confirmation, then they'd better show that data in convincing detail!)

"Thus, the fact that they looked at howevermany others is immaterial to the scientific content" not necessarily: looking at howevermany may constitute a multiple testing situation. And then it does make a difference whether 10 markers or 100s or 1000s were screened. See e.g. http://www.nature.com/news/2011/110323/full/471428a.html However, the fact that they are not reported points to rather larger numbers I guess. The question is whether later on comes a really independent confiramation of the required properties or whether this is not independent of the screening data.

@cbeleites - It's irrelevant how many you look at if your screening criteria are different from your criteria used to confirm.  Otherwise, yes, the statistics are rubbish.  I said as much in my last paragraph.

I read that last paragraph. But I think data dredging  is so widespread a problem that it needs to be emphasized far more than by a paragraph in parentheses. I'm biased, for the moment I tend to believe that if such a paper doesn't have an explicit sentence stating that there is no problem because the final testing was independent of the screening, I tend to assume that it probably wasn't. This may be wrong for the biological field in discussion, though (I'm not a biologist, but my field interacts with biological/medical questions).


text:
What are the super cool tricks to getting published in high impact journals?
I am starting a post-doc in Cognitive Neuroscience and I am interested in publishing my work in high impact journals (e.g., Nature, Science, Behavioral and Brain Science). I have already published review articles in not-so-high impact journals, and I would like to know your thoughts and tips for publishing in high-impact journals. I will be responsible for submitting these papers to these journals and I will be seeing them through to the end. Ay helpful advice and tips would be greatly appreciated!

Do you mean Science-Nature or more regular journals with high impact factors? depending on which the answer may differ.

Also some hint on which research field we are talking about would be great.

I think you will learn more (and easier) from the opposite question: What to do to a great result to be sure that some high-impact journal will never ever accept is?

If your postdoc contract specifically asks you to publish in Nature and Science -- good luck.

@Joe Really? Or is that the fact that a paper is accepted increases its chance to have a colon in the title?

Sad, dishonest, but important to know about in this context: Check a recent Science article on how to fast-track to publications in reasonably good journals (Science 29 November 2013:
Vol. 342 no. 6162 pp. 1035-1039). TL;DR: money buys it for you!

Here is another way: http://academia.stackexchange.com/q/72680/4484

There is no 'super-cool tricks', I guess. Just do a breakthrough which could a show the world something very crucial.

I’m voting to close this question because ... it is a stupid trolling question, whether or not intended such by the questioner.

High impact journals, or in other word, top ranked journals (based on IF) are those publishing the state-of-the-art research works with high percentage of novelty and originality. In my own opinion following tips are very important in getting into the high impact journals:

Select a real challenging problem whose solution/amendment significantly impacts on the domain.
Formulate the problem (using mathematical modeling, visualization, or empirical experiment depending on the domain) and let peers/reviewers see the significance of the problem.
Propose a solution with high degree of novelty in a way that has not been undertaken before for the same problem.
Throughout the research try to follow the conventions of research in your domain in the highest possible level, especially when it comes to evaluation and validation of your work.
In data collection phase, try to follow the most appropriate approaches and use accurate tools to measure/quantify. Maybe looking at similar papers can help you in this.
Avoid silly mistakes. Usually reviewers do not expect to see silly mistakes in the work. If you make small obvious mistakes, how can reviewers ensure the rest of your work is error-free.
Show high level of confidence in understanding and expertise over the domain. If you need to review related works in your paper, try to select those closely related to your work; not any work.
Present your work nicely. Avoid English errors (no grammar and no spelling). Use professional drawing tools to draw high quality figures, draw nice tables, use proper sizing for objects in the paper, not too big, not to small.
There is an approach by some young authors that leave some works to be done in revisions stage, which is not correct to me. Don't send incomplete work to any high quality journal. There will hardly be any chance to correct mistakes. The review is more to evaluate the significance of the work, the novelty, relevance to the journal, and research practice presented in the paper. Reviewers are not English proof reader and their job is not to correct you.

There may be lot more tips that I will compile as I noticed. Hope it works.

For an (extreme) example of a paper that does things like this, take a look at the paper that announced LIGO's discovery of gravitational waves. It's around 2-3 pages of "we've seen this", followed by 10 pages of "and this is why the measurement is valid and not an error."

Others have asked and tried to answer this question before. Here is an ad-hoc list of resources relevant to your question, both print and online.

Sternberg, R. J. (Ed.). (2000). Guide to publishing in psychology journals. Cambridge University. (field: psychology)
Bem, D. J. (2003) Writing the empirical journal article. url. (field: psychology)
Roediger III, H. L. (2007). Twelve tips for authors. APS Observer, 20. url. (field: psychology)
King, G. (2006). Publication, publication. PS: Political Science & Politics, 39, 119-125. doi:10.1017/S1049096506060252 (field: political science)
Senturia, S. D. (2003). Guest editorial: How to avoid the reviewer's axe: One editor's view. Journal of Microelectromechanical Systems, 12, 229-232. doi:10.1109/JMEMS.2003.814319 (field: mechanics)
Manuscript review histories of the Journal of Consumer Research. One can track the whole review history of a couple of papers including the submissions, reviews, resubmissions, etc. (field: consumers)

There is really nothing special that causes your paper to be accepted in a high-impact journal. If we start by looking at Science and Nature, they publish material more like a newspaper would than a scientific journal ( I am not saying it is without worth, they just have different criteria for their selection). The material needs to be extraordinary by, for example, being "sensational" in some way, by affecting many, or by causing a change in paradigm. It is really hard to design your research to obtain such results. They may be a result of good design but also luck. So if we disregard from results that fall into the science/nature categories and focus on more normal science output the following (adapted from Lichtfouse, 2013) will be the basis for high-impact publications:

Select your journal carefully
Be careful to follow the instructions for authors
Focus the article on one finding
Prepare one figure that shows or illustrates the main main finding
Explain your new finding in the abstract, the discussion AND the conclusions
Delete any irrelevant results or those that are not explained
Distinguish clearly between the results from your study and those of others
Include a good dose of education and dissemination
Read your article at least five times before submitting it
make sure your manuscript is written in good English

While this may look like generic advise, it is followed by so few that it will set your manuscript apart from the majority. Some of the points also involve serious work so it is perhaps a deceptively simple list.
Lichtfouse, E., 2013. Scientific writing for impact journals. Nova, New York.

really nothing special that causes your paper to be accepted, but I think you missed two most important things top quality journals are looking for. They are looking for a paper 1- reporting results of a research on the state-of-the-art domain, 2- addressing an original problem using a novel approach. As an example, I was attending a talk by an EiC of top 1 CS journal where he discouraged submission of papers on routing in MANET since this is not he trend and there are already very large number of articles in this domain. Top journals do not publish a 50's research for sure.

Let me give you another example. I prepared two survey articles with identical theme. One on the state-of-the-art domain and another one on a 20-year old domain. The first one published in the journal with the highest impact factor and the second one got rejected from the 30th journal because the topic was old. Timeliness is VERY VERY much important.

If you are publishing in emerging fields where much research has not been done, you have good chance to get published, even though its not groundbreaking. First movers are always at an advantage. Just like patents.

Isn't publishing something interesting in an unexplored field the very definition of 'groundbreaking'?

Well, if "super cool" ... There was a history when one laboratory has published a highly impressive discovery in a very reputable journal. Then they found a mistake in they experimental setup, and applied with another paper to the same journal, just to say the previous result is wrong. This was also accepted and now they have two publications in highly reputable journal ... for nothing.
But I believe this "trick" was not intentional and I am far from recommending it.

Then one found by a PhD student, right? Yes, that was cool. I believe, lack of further amendment, is what is missing in today's publication, at least in online-only versions. Publishers may look at this issue seriously.

1) Produce good science
2) Go to groups which already published in Science, Nature, etc.
Both conditions are necessary (especially the second).
Slots in journals with IF>10 are practically "inherited" (you can publish there sth if your PI already published there etc.) - thus you need be very selective in case of where you want to do PhD, postdoc.
In simple words, if you are independent scientist without publication record in Science, Nature, Cell, ... Editors will reject your manuscript in one day without reading it (you will get this nice courtesy letter, that your work is nice, but does not have wide impact ble ble). Sad, but true.
This is hard rule, I know only one exception in which one scientist broke it, but it is single case in the 20-year history of science in my country and it was celebrated almost as national holiday, but he was already established scientist, EMBO member etc).


text:
How to make the most of a currently unfulfilling post-doc experience
How to make the most of an nnfulfilling post-doc experience
Before I pose my question, I would first like to describe the circumstances and provide as much "quantitative data" relevant to this as possible.
Background
I am on a leave of absence from a US university for 1 year (2014-2015) and currently working at a lab in France as an Engineer II (let's face it, E2=fancy_way_of_saying(post_doc)). I posted a question about the merits and demerits of doing this a few months back and received some useful feedback (in hindsight obv.!)
I am at an early stage of my career. I received my PhD in Mechanical engineering in 2013. From Aug 2013-May 2014, I worked as a non-tenure track instructor at my US university. I will return to my university in May 2015 to take up a non-tenure track lecturer position. I prefer teaching track to research track. The idea was to diversify my portfolio to work and hence the leave of absence to work as an E2 in France. I am in month 3 of my E2 position.
Gist of current position
To introduce major modifications in a "spaghetti code" developed by my E2 supervisor some 6-7 years ago. The code itself is quite obfuscating and models certain thermal engineering physics problem.
My perceived failings as an E2
The code is obfuscating! No, I am not making excuses but the previous two E2 quit to go on to purportedly greener pastures.
I was given tasks to modify certain aspects of the code and in my opinion (I have no yardstick for comparison), I have not done the best job at it.
Result (for now)
My supervisor has hinted that "we must hurry as there is a deadline next month we must meet" (I did not know of this deadline prior to taking up this position).
I am making a sincere effort to accomplish the tasks but I am not sure if it is my ineptitude or lack of scientific maturity that I constantly see myself failing at my job.
Over the last couple of weeks, my supervisor has not asked me to do any important things with this code/project and I think I have been relegated to "just check the code for mistakes".
Also I find that unlike my previous department head, my current supervisor treats me like a student and is sometimes disparaging in his comments. I suppose this is normal.
Also, what is normal in my current lab is that post-docs share the office space of their supervisors and the supervisors LITERALLY are looking over their shoulders at all time. Yes, I know what LITERALLY means.
I understand that this is a character building exercise for me and I'll treat it as such.
Future

Do I have a future or am I looking at a premature "pink slip"? My contract doesn't mention conditions of being fired.
How should I make the most of this situation? I want to have a positive impact on this project which in turn will have a positive impact on my career. Although I am in a teaching track from 2015, I feel that this research experience will only enhance my teaching capabilities.

References I have used to understand this better
A postdoc experience
Making the most of your post doc
However, I would feel better if I got "real time advice" from the diverse membership of this forum.

Any particular reason for a -1? Can I improve this question?

The main problem with this question is that it isn't really one. "Any advice?" style questions are just a very bad fit for SE. Further, the question is probably way too localized. See for instance this meta discussion (http://meta.academia.stackexchange.com/questions/1093/time-to-expressly-ban-i-want-to-do-x-heres-my-life-story-questions) - not exactly the same, but closely related.

@xLeitix Thank you. Any suggestions?" When a user wants to do X and asks for help without giving life story, users automatically ask for details regarding the professional life as comments and the author edits the question and adds asked details. So it is essential for us users to read a life story or detailled paragraph to consider different aspects and give a good answer."

The problem is not so much that the "life story" is given by itself, but rather that the need to tell said life story is a good indicator that the question is of little value to anybody aside from the OP, and hence off topic on SE. I think this is also true with your question. That is why I also don't have a good way to fix the question.

@xLeitix Thats one way of looking at it. The way I look at it is that it is perhaps a unique situation in the world of academia and there is little or no way to predict if this will NOT happen again and solutions for this will NOT be sought in the future. Hence a solution to this problem may be useful in the future.

+1 I think in this case the "life story" helps highlight the issue and I think the issue is one that many post docs face.

it is perhaps a unique situation in the world of academia — You can't have it both ways. If this is a unique situation, then the question is relevant only to you and should be closed. If it isn't a unique situation, the details of your life story should be deleted to better expose the useful question.

@JeffE that would be ideal, but presenting a life story which allows someone to understand the issue is much easier (for the asker) than distilling the life story and presenting only the isolated issue.

I agree with @StrongBad: the question is fine.  Let's show some self-awareness: many of the details disclosed by the OP would, if absent, be inquired about by us in the comments.

Do I have a future or am I looking at a premature "pink slip"?

This is unlikely, especially in France. The financial savings from firing a one year post doc is pretty small compared to the hassle and bad blood that will result from doing it.

Although I am in a teaching track from 2015, I feel that this research experience will only enhance my teaching capabilities.

Is this really your goal of the post doc? It is not clear to me how a year spent disentangling spaghetti code is going to enhance your teaching capabilities. Most engineers do not take up a non-teaching post docs to enhance their teaching. I am not sure that most post docs would spend a year disentangling spaghetti code with supervisors hovering over their shoulders. Are you sure that an E2 is really the equivalent of a post doc? It is probably worth talking to your supervisor, hopefully again, to make sure you are both on the same page.
Realizing that you are unhappy with the current state of affairs does not really help you to change things. I think grad students and post docs sometimes have unfulfilling experiences because they do not know what they want. You need to figure out what it is you want to get out of the post doc and then figure out a way to work towards that goal. Often once you know what you want the road to obtaining that goal becomes clear.

The fact that my primary goal would be disentangling spaghetti code was not mentioned in any discussion or contract. Since I am a mechanical engineer and not a computer science person (tried and tested excuse), un-obfuscating code is not my strong point. However, it is a challenge that will enhance some aspect of my teaching abilities-the courses I have taught have focused on numerical methods for PDEs etc. Yes an E2 apparently gets paid the same as a post-doc. Coming back to the point: I don't mind disentangling code for one year if that is what I am required to do.

...contd. How should I make the best of this situation really? Make lemonade from the lemons bestowed on me.  Supervisors hovering over the shoulders of their wards is then uncommon??

@drN: "The fact that my primary goal would be disentangling spaghetti code was not mentioned in any discussion or contract."  What were you told was the primary goal of the job?  Also: "Yes an E2 apparently gets paid the same as a post-doc." Just because two jobs get paid the same does not make them equivalent.

It's an interesting question whether it matters whether your job is actually a postdoc.  One could argue that it does: postdoctoral positions are supposed to offer advanced training and career development.  If all you are doing is working on someone else's project under their direct (literal!) supervision, it doesn't sound like you're getting that.  It sounds more like a "real job".  Finding out what the parameters of the position are and could be seems like a key point for you: if it is really not what you expected, maybe you shouldn't continue with it.

@PeteL.Clark Thank you for the perspective. Just checked about E2. E2=Ingnieur/Chercheur-Postdoc. So An E2 is a postdoc per my lab. Yes, I am definitely not developing something new here. I pretty much have "strict orders" to "do this and then do this and then this". I have made suggestions such as "what about this?". They were shot down quite swiftly as being "bad ideas" without quantitative proof that they are "bad ideas".

@PeteL.Clark As for not continuing with it, not quite an option. I am a foreigner and my University in the US has just applied for an H1B work visa and petitioned for me to go to the consulate in Paris. Essentially I have to be here and work here at least to ensure I get my US visa and head back :( next May.

@drN: Okay, I'm glad you checked.  Although what you describe is not what a postdoc ought to be, I strongly doubt you are the only, or almost the only, postdoc who is in a similar situation.  The visa stuff is key information too.  Actually I worked as a postdoc in a foreign country (Canada) and learned that such issues are not to be messed with.  I agree with StrongBad that it seems unlikely that you will get fired from such a 1-year position...though of course I can't guarantee anything!  A frank talk with your supervisor seems to be in order: at least you know where to find him!

@drN to make the best of the situation, you need to define "best". Once you can articulate "best" you can ask your supervisor, friends, and AC.SE how to obtain that goal.

@PeteL.Clark in my experience post docs have a lot more freedom and responsibilities in NA compared to Europe. I wouldn't go so far as to define what a post doc should or shouldn't be.

@StrongBad Yes. Should ask my friends who I haven't yet approached about this. However from the horse's mouth (my supervisor). To make the best of this, I should "change the (computer)code" that I am working on. I suppose I am just a "research tool" but not quite "research".

StrongBad: A former PhD student of mine is currently doing his second European postdoc.  Both of them involve at least as much freedom as most cognate North American postdocs and significant time to devote to his own projects.  I feel confident that there are some NA postdocs who would identify with the OP's plight.  In terms of defining what a postdoc should be on a global scale: that is certainly not within my power!  However, most people (that I know) take postdocs with expectations like the ones I mentioned above.  Surely the moral here is: find out the parameters of the job in advance.

@PeteL.Clark Yes. Finding out the parameters in advance was an attempt I made. I suppose that the lab too liberties after I left the united states and came to Europe since it's not like I can just leave and go back to the USA since I am not a US citizen.

@StrongBad My experience is consistent with Pete Clark's.  The European postdocs I've known were all given significant freedom and independence, just like North American postdocs in the same fields.  This may be more a cultural difference between math/algorithms and other fields of science/engineering than between North America and Europe.  +1 for "Find out the job parameters in advance", and not just by asking the supervisor.


text:
Decision making paradigm for career planning
Despite receiving a job (post-doc) offer in January I have kept applying to other positions (post-doc and teaching track jobs). This was not a bad idea in retrospect, I suppose
This post doc job offer I received is in Europe (France) and required me to apply for a "long stay visa". I am currently a visiting faculty in a well known mid-western university in the USA. My citizenship is "Indian".
I did apply for a long stay visa and have not received it yet. In the mean time I have received a job offer for one teaching track (non-tenure but "long term" contract) job at my current university.
I have not been offered tenure track jobs anywhere since I have a backlog of publications right now.
Here is the problem:

My post doc job starts in 3 weeks time and I haven't received my visa yet. I have to make other arrangements too (air tickets, housing in Europe, other stuff for a trans-continental move).
I have been given 3 weeks to decide and confirm my availability for the teaching track job.
I prefer the post doc since it is a more appealing challenge. The downside is I have to exit the USA if I get my visa and go to Europe.
The teaching track job offers me stability, a full time employment and a salary that is difficult to beat in the post doc job and in my home country of India.  The downside is that teaching track lecturers are treated as "mules" in the USA and are burdened with courses that "tenure track" do not want. This would mean that any research aspirations I have go down the drain since I won't be afforded time to do research.
For me as a foreigner, it is not just working on my "passion" but also getting a lucrative position with which to support my family. I have to strike a balance between working on my passion and living in a developed country with a good salary.

I am confused as to what to do.
Here are options that occur to me (deferment of either position is not a possibility):

Wait for 3 weeks and irrespective of the visa decision, take a risk and say "no" to the teaching track job and take my chances with the European visa and miss an opportunity to have a full time job in the USA.
Wait for the next 3 weeks, if EU visa is not delivered to my house, just tell the lab that I cannot wait any longer since I have to make a career decision and take the teaching track job and miss a fantastic research opportunity for a great salary but a job that could very easily become flavorless.

Some more detail that I need to factor in:

I love to teach and have received some teaching awards for graduate and undergraduate courses I have taught as a visiting faculty.
However, I love research as well and understand that teaching and research are symbiotic activities and that the EU postdoc (which is a research position) allows me to do research and develop as a better teacher.

My question:
I am not asking this forum to make my decision for me; I just want to know how to weight this situation rationally and try and cut my losses if things go to pot. What are some of the decision making paradigms that one would use in such a situation?
If there are other details that may not have occured to me, would prove useful, do let me know via a comment below and I will try to include them.
Amendments to question:
"what is the likelihood that the visa will appear in the next three weeks, and what methods do you have to estimate this likelihood?"
The consulate tells me that it takes between 2 weeks and 2 months for a decision on "long stay visa" to be made. It is week 3 of my wait.
There would appear to be no way of estimating the likelihood other than tracking the status on a status page. All it says right now is: "Your application is under consideration". Contacting the consulate yielded the same answer.

One data point that I'd need for a decision is: what is the likelihood that the visa will appear in the next three weeks, and what methods do you have to estimate this likelihood ?

@Suresh Good point. Pl see amended question.

I asked because with visas (and I have a fair bit of experience with this) some processes are routine but long, and others are long and have nontrivial outcomes.  Have you been able to get a sense of a) whether visas are ever rejected for cause b) how long it's taken others in the past to get visas for the country you're applying to c) what your putative employers have to say about the visa process and their experience with dealing with it ?

...continued. My point is that from your question it's clear that you'd like to go to this European location. So all your efforts should be directed at getting good information about the visa processing (or at explaining that information to this forum)

@Suresh it would seem that the visa process and ETA for a long stay visa would seem to be variable. The lab that has hired me in the EU is confident that I will receive my visa but as I see it, they are (and have to) be positive about it and present an optimistic front! There is little to no official information available on the visa process itself wit regards to "timing".

@drN I sympathise with your predicament. However, I notice you have not specified the European country. I can't think of a reason not to do so. I don't know whether it would help you get better information from the forum, but it couldn't hurt.

@FaheemMitha It is France. Have updated second paragraph of question with that detail in bold

@drN Ok. Can you also say how many years the post-doc is for? Also, one thing that is not clear from your answer is whether your post-doc employers are willing to wait on your visa decision, which might take longer than 3 weeks. ADDENDUM: I see your earlier question says 1-2 years. So it could be just for 1 year?

@FaheemMitha The post doc is for 2 years. The employers delayed my joining date to May 2014 on request as I was unable to join them in January 2014. I will however ask them about the effect of this delay. This has not occurred to me but wouldn't it not be "equal opportunity" if reasonable delays are not accommodated?

@drN Ok. two years is not a very long time. Is there any possibility it could/would be extended? Your earlier (February) question says "I have been offered full time faculty position at two other universities in the USA." Has the situation changed since then? Another relevant variable - you talk about a backlog of publications. Giving more details of these might be relevant if you feel comfortable with it.

@FaheemMitha No, these are teaching track positions that I was offered. I have realized since february that although teaching is a good option, I will be relegated to a lower rank and my contract would be dispensible in favor of tenure track faculty -- this I would like to avoid and the post doc gives me a way to do that.

@drN Yes, it makes sense to avoid that.

Since the purpose of this question is to ask for general decision-making strategies that might apply more generally, here are some (that also impinge on this case):

Acquire information: Get as much information as you can that would affect the decision: in your case, estimates of time for the visa process, and so on.
Determine the "real" timeline for decision making: in this case, do you really have to decide in three weeks ? can it be delayed slightly ? and so on.
Determine how "permanent" the decisions are: can you negotiate a 1 year contract ? Can you defer the postdoc ?
Separate out facts that affect the decision from feelings/opinions: Is it true that "if the visa comes through I'm going without a doubt" ? If so, then everything depends on facts regarding the visa. Is it instead true that "if the visa comes through I have a preference, but I do enjoy teaching and like staying in the US" ? In that case, there's a personal preference coming into play that isn't usually resolved by "facts", and so timelines and data collection don't matter as much as (or are influenced by)  some soul searching.

Thank you for your answer to a rather tricky question. Yes, I may be able to delay my decision on the teaching track job by 4 weeks instead of 3 weeks. Little but useful breathing space. The post doc job is for 2 years and neither position may be defered (I would love to defer the teaching track job!)


text:
Pros and cons on commenting on public review papers
Journals such as AMTD and ACPD contain an open discussion where anybody can comment on papers under review. The peer-reviewers are still anonymous, but other people commenting are not. If I'm reading a paper and have questions about it, what are the pros and cons on posting them as public comments versus writing an e-mail to the author directly? On the one hand my comments may improve the paper; on the other hand, if I write something stupid or step on somebody's toe, that may harm my future career.
What do others think?
(Edit: I might add that in the case I have in mind, I am already in contact with the author)

As I pointed out recently in http://nuit-blanche.blogspot.com/2012/07/problem-with-pre-publication-peer.html , the problem with the current peer review system is not the rejection and all the horror stories that go with it, it is the secrecy that goes with the process. Make anonymous the reviews but hold the reviewers accountable is the surest way reviews can be both effective and provide some "currency" as +David Ketcheson points out.
In short If I were you, I would send the author some questions, then (after her/his approval) make the whole discussion available on the interwebs (after you have edited the parts that are sensitive or the ones that make you look really clueless). I do this often on Nuit Blanche with good results. Make sure you run the whole thing you are going to publish through the person you talked to as you are not a journalist. If you ask questions, you surely are not the first or the last one and remember what you publish must enlight both the people of your community and your future self.

What I finally did was simply proposing the questions to the author and asking his opinion if he would prefer private or public, and following his preference.

I would try to answer this from the standpoint of a cost-benefit analysis.
A private conversation with the author will benefit you in that you now know the answer, and can harm you in that if your question is completely boneheaded the author will think you're an idiot.
A public conversation has the added benefit that you and other people both benefit. This is somewhat of a questionable added benefit, as oftentimes the question being asked isn't relevant to most people, but still, added discourse is often a good thing. Public discussion also has the added cost that more people can see your boneheadedness. While typically this wouldn't be a problem, as most people wouldn't ever encounter the discussion, anything on the internet can go viral, even if only within a smaller community (such as your research field). Personally, that cost strongly outweights the potential benefit. I would definitely stick with personal correspondence.

By openly and intelligently commenting on many new papers in your subfield, you might gain respect among your peers, which is the currency of the academic world.  I can give at least one example: http://nuit-blanche.blogspot.co.uk/.

The first advantage that comes to my mind is that emailing the author and getting an answer will only help you, while commenting on the paper and getting an answer in the open discussions might help other readers as well.
But I really understand your concerns. One does not want to embarrass oneself or the author.
Which leads me to the inconclusive result of +1 for both methods.


text:
Should I post a response to reviewers online?
I usually spent an incredible amount of time answering the questions raised by reviewers when submitting research manuscripts to a journal. The length of the response is often longer than the paper itself. Such a process, albeit time consuming, has significantly improved the quality of the work.
Since there are many thoughts that can not be delivered in the paper, which are elaborated in the response of the reviewers, I am wondering whether it is good to upload the response online along with the paper? (e.g., research profile page) I think this will benefit the readers but am not sure what might be the consequences resulting from that? Do note that I don't have any clue as to the reviewers' identities.

In case you're interested, there are some journals in the biological sciences where this is standard. For example, at the EMBO journal you can click "Review Process File" under "Transparent Process" http://emboj.embopress.org/content/33/16/1740.transparent-process and at eLIFE you can click "Decision Letter" http://elifesciences.org/content/3/e03245/article-info#decision-letter to read the editor/reviewer comments and the author responses.

Could you give some examples?  In most cases, I would think review responses would correspond to stuff that can and should go into the paper.

@NateEldredge Agree. Either it's irrelevant misunderstanding, or it should go into the paper. Or not?

@NateEldredge Thanks for the suggestion, the time I spent most for respond is exactly like the question New_new_newbie has raised: "why the approach in the paper conflicts some sacred tenet?" These discussions are not supposed to be incorporated in the paper, but are useful for the readers as they may think in the same way.

I added a relevant comment to new_new_newbie's answer.

You are free to post your response as you see fit, If you know who the reviewer(s) is/are then you may need to think twice about mentioning their name(s) since. I am not sure how you may be thinking of posting such comments but I assume you will rewrite them into some form of self-contained text. As such it would not be very different from a blog entry and so one suggestion would be to use a blog type web to add comments around your publications. You may also provide means for commenting on your papers and associated posts.
But, in short, no problem posting your own thoughts but stay clear of adding the thoughts of others that may be given in a context other than open posts.

And if/when they are known, you can just ask them if they let you post their comments.

Yes, asking is always a good strategy

(I request that this answer may be viewed as an addendum to Pete's nice answer here, in light of Nate's comment above.)
As Nate pointed out, most of the typical referee responses would be concerned with stuff that should enter the manuscript. So, assuming that all his useful suggestions were incorporated in the text itself, there isn't generally more meat from that conversation that could warrant a separate 'response log' to be uploaded anywhere (I'm assuming on arXiv, for example).
But the impression that I get from the question is that, OP is inquiring about suggestions that go deeper than the above paragraph. In some cases, it is possible that referee queries stuff on the lines of

How is [a fact that you established on the basis of your calculation in the manuscript] consistent with [a sacred tenet, or a well-established or experimentally verified result] ? Aren't the two incompatible because of [some qualitative reasoning, devised by the referee]?

The reasoning looks valid to you, so you sit down and calculate the implications of your calculation on the established fact, and find that the two are indeed compatible. Then, you identify a weakness in the qualitative reasoning, and let the referee know about this. Now, all this isn't worthy of being included in the text of your manuscript, since it is off-track from the overall theme of the work. Yet, this is a valuable piece of information, and is likely to help future readers because they may also reason this apparent contradiction. Responses of this kind are worthy of being put up. Occasionally, one encounters those one-page or two-page ''Comment on [a paper]'' sort of things on arXiv, so these can definitely be put up too. It doesn't necessarily have to be journal article manuscript always.
Lastly, regarding acknowledging the referee, there are two options - either take their permission (ref - Pete's answer), or you simply acknowledge ''the anonymous referee'' for pointing it out, in case option 1 doesn't work out. I know some instances where this has been done in my field, but one example that I can find is over here. Sorry, there isn't any corresponding arXiv version for this, so if you can't access it directly, here's the relevant excerpt:

The author would like to thank the anonymous referee for making insightful comments which have been helpful in improving and updating the manuscript.

But seriously, option 1 is the better option (why strip the poor guy of his due credit!).
Hope that helps.

Well, I don't know the details, and this could be culture/field dependent, but in such a case I'd be tempted to say something in the paper anyway.  "The reader may be concerned that our result appears to conflict with [sacred tenet] because of [referee's reasons].  However, this is not the case, because of [brief sketch of why the conflict doesn't really exist]."  If the referee had this concern, surely other readers might as well?

@NateEldredge - You are right, that could be an option.  But like I'd said in the answer, it will mostly be off-track from the theme of the paper. Also, if the paper is something like a letter communication, where there is a word or page-restriction, you can't go on and on. The way I'm imagining this question being posed is the way it goes in PhD qualifying oral exams - you describe, e.g. how your devised plan is going to work, and there is a big prof on the other side of the table who stumps you with a plain ''But this is inconsistent with ...  How can this be right?'' remark.

@NateEldredge - (contd.) So, while proving consistency is a very important requirement in such situations, it isn't that in a subsequent presentation, you include this consistency argument. The way it goes is - I've shown that there is an overall consistency, now believe rest of what I say! Thus, while consistency is important, that's not the subject you are addressing. But, of course, you may be right, maybe it could be field-dependent. Nevertheless, thanks :)

Yeah, okay.  In my field (math) it's not unusual to write with a more pedagogical tone, where you really try to help the reader follow the argument, and point out possible pitfalls.  Also, we rarely have strict page limits (and if one journal does, you can usually find an equally good journal that doesn't).

@NateEldredge - I'm not saying that mine (Physics) doesn't have pedagogic papers, but it is a mixed bag - some pedagogic and some totally cryptic. However, cryptic and concise aren't really synonyms (to me at least). And conciseness is appreciated in letters (page restrictions etc.) and even otherwise.

@NateEldredge - But I must add that some of them, like Physical Review Letters, do allow for supplemental material (where there isn't any such restriction). So, people can move big derivations etc. over there, and have only the important steps in the 5 page text. But of course, all of them don't, which is why some papers are cryptic.


text:
What advice would you give students applying for graduate school in mathematics?
I work in the mathematics department of a university that has a new, small, mathematics bachelor's degree program, and no graduate mathematics programs.  Some of our students are looking for advice on how to successfully apply for graduate school.  I don't know what to tell them.  Everyone in my department (myself included) applied to graduate school so long ago that I think our advice may not be relevant.  I don't think anyone else who works for my university knows more than my department colleagues do.
What are good things for students at a small school to do to get into graduate school in mathematics?  In particular, what are some things that might not be obvious to mathematics professors who've been out of graduate school for a few decades?
EDIT: In response to this question being put on hold for being "too broad", here is my modified question: What advice would you give students applying for graduate school in mathematics in 2014 that you would not have given them a decade or two ago? In other words, how would the advice differ?  I am thinking both about what students have to do as undergrads and about the application process itself (which I assume is done online nowadays).

I think this question is too broad for stackexchange.  Perhaps you could break it up into more specific questions.  You might also look at the questions and answers already available, which contain a lot of good advice.

It is a little on the broad side.  Here is one idea for sharpening it: you write "Everyone in my department (myself included) applied to graduate school so long ago that I think our advice may not be relevant." But that's clearly an exaggeration: e.g. I'm sure you know that taking challenging course and doing well in them is good advice.  It might be interesting to ask: "What advice would you give in 2014 that you wouldn't have given N years ago?"

(Also, do you mean advice on what to do during one's undergraduate career in order to successfully apply to grad school or advice specifically about the application process?  The latter is much less broad.)

@PeteL.Clark : thanks for your comments.  I modified my question.

@Stefan: I may not have fully grokked the ethos of this site...but I voted to reopen your question anyway.

Graduate level
It is important to work hard, and work professionally. But it is also important to enjoy your work.
Think ahead to understand the way forward; ask yourself dumb questions to understand the way before.
Attend talks and conferences, even those not directly related to your own work.
Talk to your advisor, but also take the initiative.
Don’t prematurely obsess on a single “big problem” or “big theory”.
Write down what you’ve done, and make your work available. In this regard, I have some advice on how to write and submit papers. Terence Tao, Fields Medalist

I personally had the experience of applying to graduate school from a very small college that has not produced many math Ph.D.s (though oddly enough, I'm not the only 2002 BA graduate working at an R1 university in North America) not so far in the misty depths of time.  Of course, I only have a couple of data points, but let me try to give my thoughts.
I think one thing is you've really got to get the basic stuff right: take the hardest classes available to you from the selections you have (and you should note in your letters that the student did this!) and ace them.  Do well on the general and subject GREs.  I assume you could have told them those.
I think the biggest non-obvious thing is that it's essential to seek out experiences outside your small program.  If you're at a large school with its own graduate program, probably you have all the resources you'll need at your fingertips, but in a smaller program, I don't think you really have the ability to fully prepare someone for graduate school.   Study abroad is good for this (I went to BSM in Budapest, but there are other programs).  So are REU's (I did the one at LSU).  On a smaller scale, you might be able to take more advanced courses at a nearby college (for example, students at Smith and Amherst can take graduate courses at UMass), or do a guest semester somewhere in the US (like at the Penn State MASS program).
These will, of course, be generally enriching experiences, but they also help by giving some real points of comparison.  Graduate schools know what an A at BSM means (where they might not know it for your school); a professor who supervised you at an REU can speak with authority about having supervised many talented young people, and having some experience with which of them succeed in grad school.
Another possibility is working at summer mathematics program like PROMYS  or Canada/USA Mathcamp (there are many other) though I think you should give some weight to activities like REU which are more likely to result in letters.
EDIT: I'll just note that what I've written about is still advice from the Web 1.0 world, but it's not so clear to me what Web 2.0 has changed about the admission process.  I think it has made communicating with other people going through the process easier (for example, you can see in essentially real time which schools are sending out acceptances and rejections.  This seems more likely to drive you insane than help though).  I think for students at a smaller school this can be a boon (for example, the applicant profiles in this thread could be helpful for understanding where they might get in, though it's worth a reminder to take things with a grain of salt).
I think one thing I didn't know was that it's very reasonable to contact the Director of Graduate Studies at programs that interest you if you have questions.  Don't be a pest about it (only email if you have a real question), but communicating with applicants is part of the job, though my DGS may not appreciate me telling the internet that (sorry, Tom).
The Web, of course, has also changed research about grad schools a lot.  In theory, you can know a lot more about individual professors now than it would have been easy to figure out even 10, but especially 20 years ago.  It's not super clear to me that this will help very much though.  I generally feel like researching individual professors before starting grad school is a mug's game, since you're so likely to shift interests.  I think it's much wiser to choose based on the program, and then worry about getting an advisor after a year or so of grad school when you know a bit more.

You've left out a crucial verb in the phrase "it's essential to outside your small program."

@BenWebster : What's BSM?

Budapest Semesters in Mathematics (I had linked to it earlier, but not with the name).

@BenWebster : sorry, I didn't click on the link.  As far as the Web 2.0 world goes, LinkedIn and maybe ResearchGate might help undergrads make contacts.  I don't know.  It wouldn't hurt, unless they wrote something inappropriate.

I suppose in theory, but I'm not sure how.  I don't know any academics who take those sites seriously.  It probably is true nowadays that you want to try googling yourself, and putting up a website in order to control the top google hits a bit isn't a bad idea.  But I wouldn't have any high hopes for the effect of such a site.

@BenWebster : A lot of people have downloaded or viewed my papers on ResearchGate (I don't think anyone ever looks at my personal Web page).  I've found some other researchers there with interesting papers and downloaded the papers (haven't had time to read them yet).  I have met a good senior mathematician through LinkedIn, and we correspond.  I don't know if it will ever get me a new job or a raise, etc.  I think the "endorsements"/whatever systems of both LinkedIn and ResearchGate are silly because anyone can recommend anyone for anything.  I hope no one takes them seriously.

Ben Webster has already wrote a great answer about how to get into a good math grad school, so I will not repeat that answer here. I do, however, want to interpret your question more broadly (what advice would I give to seniors applying for grad school?) and give you some advice. In particular, most of the things that I am about to talk about were not so much of problems back in the 70s, I think.
No one tells you about the darker side of academia when you are an undergraduate student. But academia is really, really hard. Here are some cons of becoming an academic.

the most serious problem by far is the fact that you do not have any choice on where you live. You just go to the best grad school that you got into, then after that, you apply to around 60 institutions for your postdoc job, and cross your fingers. Most schools give you two weeks to decide on your position, then off you go to some random city that you have never thought of. The same deal repeats for your second postdoc (if you are unlucky), or tenure-track. If you fail to obtain tenure, you might have to do another postdoc or tenure-track. So you are actively changing cities every 2-3 years for the next 10-15 years of your life. As an undergraduate student, this is not a serious problem, but when you have a significant other, and you are past 30, you really do want to settle down.
academia is an extremely hierarchical society. Whether you get a job or not depends on your letter writers, one of which must be your advisor. As you obtain letters from people senior to you, it is often very difficult to express your opinions, as it is very easy to burn bridges. Academia is also very small; words travel fast. If you mess up in one place, chances are, everyone knows about it. Sometimes, it's not even your fault, but people can get very, very upset at you.
the job market is very tight these days. The schools that I consider to be the top grad school are Harvard, Princeton, MIT, Stanford, Berkeley, Michigan and Chicago. These schools alone produce about 100 PhDs a year. I think that there are around 300 research postdocs available each year in the US (if you apply to every PhD producing institution, I think that you would send out around 80-90 applications; let's assume each school hires around 3 people, which I think is being generous). You can do the math.

These are only the universal issues that apply to practically every PhD student. Then there are issues that apply more strongly to some people than others (elitism displayed by some mathematicians, competition among peers, difficult advisor, your thesis problem being scooped, etc.)
So I advise that you need to be very, very sure that you really love math. I have been through many of these issues, and honestly, your love for the subject is the only thing that will keep you going. If you don't have the passion, you will regret your decision very quickly.
There are also perks of being a mathematician, of course. I do enjoy the flexible schedule (aside from teaching and committee work, research can be done any time, anywhere), being able to travel to conferences, and the job security that follows, if you make it to the ranks of a tenured professor.

@NoahSnyder I don't think what you are claiming is correct at all. If I am reading the AMS job survey correctly, they in fact claim that 573 of the new PhDs are now postdocs (which I think is too high, and I am probably missing something). But 100 is way too low.

The number the AMS gives is 525 (not including statistics), though it's worth noting that only 249 are in math departments in the US.  127 are outside the US, and 149 are in government, industry and research institutes in the US.  I wish I understood better what that really meant, since this is contrasting postdocs with other industry/government jobs.

Indeed I was looking at the wrong number.  I think your 300 is roughly right.  The number of math postdocs at universities (i.e. postdocs in Groups I-III+Va) is 228, but some portion of a few of the other small categories are math postdocs too (e.g. IAS, MSRI, Microsoft research).  So between 250-300, plus another hundredish getting postdocs overseas.

@user45756 : Thanks.  I am well aware of the facts you describe, largely because of my own experiences. You stated things more eloquently than I might have.  When I help my students get into grad school, I will ask them why they want to, and inform them of these realities.

@StefanSmith It is a sad fact of academia that your initial starting point matters a lot. As much as I wish that I didn't have to say this, I think that it is significantly harder for a student from a small school to make it to the tenure level. Although there are some exceptions (as Ben Webster said), I assume that it is quite a bit of struggle. I have seen too many mathematicians who have reputations of being "nice" completely ignore students from smaller schools, for example.

@user45756 : Thanks.  I had always thought that academic employers didn't care much about where a person got their undergraduate degree, and cared a lot more about more about where they got their graduate degree and what they did there.  Was I wrong?  If so, is there any way I can verify or document your assertion, in case the students don't believe it?

@StefanSmith: I think you're right that once students get their Ph.D. the undergraduate institution doesn't much matter.  The harm of a small school is going to come at the getting into graduate school stage.

From experience, I can say that having gone to a tiny undergraduate school is just a piece of small talk once you're in graduate school, whereas where you went to graduate school sets the tone a bit more.  That said, I think the networking possibilities of going to a fancy school vastly outweigh any snobbish valuing of the name.  A nice pedigree will get your application a look, but people have to like what they see.

"These are only the universal issues that apply to practically every PhD student." Actually, I think some of your comments must apply only to your field, ie math. E.g. the para starting "the job market is very tight these days." Presumably some job markets are less tight than others. The rest fo the para also seems quite math specific.

@Faheem The job market is tight accross all of academia.  My impression is that most academic fields have even worse job markets than math.  (Certainly the humanities, but also theoretical physics for example.)

@NoahSnyder yes, both the areas you mention might actually be bad too, or maybe worse, but academia spans a very wide range of subjects, by definition.

Is it really that common to apply for 60 (or even the 80-90 mentioned) postdoc positions (maybe @NoahSnyder can weigh in on this)? I felt lucky to get a position without having to apply too many places, but I did not expect the number to be an order of magnitude smaller than what prospective american postdocs generally apply to.

@TobiasKildetoft I think it's pretty common for people to apply to a lot of postdocs.  I "only" applied to around 25 myself, but I think that's definitely on the small end.

@Noahsnyder thank you. Now I feel even luckier that I only had to apply 7 places.

This is too short for an answer. However, I do think it is worth an answer.
Tell your students to get on this site ! There are plenty of questions and answers about graduate school admission. If they don't find their questions answered, then ask their own questions to get useful advices.
Your students may have the same general questions as how to apply for admission. They may also have specific questions regarding their individual situations. The best advice is, get on an excellent, informative and reliable Q&A site and that's us!

Matt Might's advice page here provides some really useful tips of the kind you're looking for.  The three of his tips that I found really useful for when I applied to graduate school two years ago (that weren't mentioned above) are as follows:

Consider emailing professors whose research interests you with a brief statement asking them about their work. As Might states on the linked page above,

Tell them you were considering applying, and you're curious about the research opportunities available in the field. Comment intelligently on some research that faculty member has done. Attach any research you've done, and briefly summarize your research interests. That faculty member can then make sure your application receives a thorough review. Bear in mind that professors receive lots of form-letter spam from prospective students. It's painfully obvious when the email is form-letter spam, and most professors will summarily discard it.

He suggests to email a month before the application deadline, but I emailed maybe 2-3 weeks before and it was still fine. He also has tips on how to send professors emails here.
Consider writing your essays in LaTeX.  You'd need to learn how to use it in graduate school anyway, and it makes you look more like a mathematician, so to speak.
In your essays, put really important words in bold.  I used this to emphasize the names of the faculty I was interested in working with, awards I had received, and my particular research interests (partial differential equations for example).

I've never understood why people bold words in their essays. It's annoying and makes them harder to read. I haven't seen a single professor do this, yet it seems popular among undergraduates for some reason.

Different strokes for different folks, I guess, but I'm taking it directly from a reputable professor's page himself.