publications - Why become a journal editor?

I know peer-reviewing research papers is a lot of work, but it is something that as a scientist in academia you must do. However, you are not required to become an editor of a journal. It seems to be tons of work, and I am trying to understand what people gain from it and whether it is worth the effort.

I mean, I can understand how being an editor for Science or Cell would be helpful in terms of prestige, connections, and exposure to top science, but what about for lesser known journals? And how is that integrated with research and other duties?

Answer

As you alluded to in your question, there are several things to be gained by being a journal editor:

• Greater familiarity with ongoing research in your field



• Credit for "service" within your department institution


• Greater visibility within your research community


• In some cases, monetary compensation (some editor positions are paid, some are unpaid)

Being a journal editor can be a very time-consuming job, and it's certainly not for everyone. However, it can also be an interesting and rewarding experience, even if it's not a journal at the level of Science or Cell. (Then again, many of the journals at the level of Science have in-house professional editors, rather than part-time staff from academia!)

Editing a minor journal can also offset other forms of outreach service, particularly if you are still developing a tenure dossier. In those situations you may find editing more (or less) rewarding than the duties you would take on (or be assigned) otherwise. (You should check with your department chair, however, that such service would be considered acceptable before committing to a position!)

Whether or not the connections are worth it at a particular level of journal is not something we can directly answer. You should consider the time commitments relative to other priorities that you might have, and make a decision accordingly.

genetics - Effect of a doubling of the start codon in a gene

I am learning about frameshift mutations. Frameshifts can occur due to a nucleotide deletion. Suppose that due to a frameshift, because of a deletion somewhere upstream from the original start codon, two additional start codons are generated, just before the stop codon in the new reading frame. What would happen in terms of translation?

AUG-GCC-AUA-AUG--------UAA Start Start then stop

Answer

There is a basic misconception in the question you have asked, which @biogirl has explained. There is only one start Codon in any mRNA and it defines the open reading frame.

All other AUGs in the open reading frame are simply codons that encode for the Amino Acid Methionine and have no function in the start of translation. There are factors other than AUG that determine the start of translation.

So a frame shift that gives you an additional AUG only means that you will have a different Amino Acid encoded for in the resulting polypeptide. A frame shift will generally completely alter the protein product of the gene. If however the frameshift does disrupt the start codon, then it is unlikely that you will have any translation what-so-ever, as the other elements necessary for determining the start of translation will likely not be present in other areas of the coding sequence. In prokaryotes, you need a Shine-Delgarno sequence to initiate translation, and in Eukaryotes, though all of the factors for translation start are not well understood many genes carry a Kozak sequence that indicates to the ribosome the start of the open reading frame.

The more important codons to look for are introductions of stop codons. These three codons, UAA, UAG, and UGA do not have tRNAs with complementary anticodons (for the most part, as tRNA genes can also sustain mutations that change their anticodon) and therefore all result in the termination of translation if the shifted frame results in the ribosome reading one of the three stop codons in frame.

cell biology - How is the diploid chromosome number maintained at mitosis?

A normal human cell is diploid that contains 46 chromosomes in 23 pairs. Thus, when the cell undergoes mitosis, the cells still has the full chromosome with the two sister chromatids. What is it doing in interphase when it produces the other chromosomes?

I thought that the sister chromatids were pulled apart and, in interphase, the single sister chromatid grew another one. How is this possible if a human diploid cell contains 23 pairs of 2 chromosomes each?

job search - What are paths that physics majors/PhDs can follow?

I’m currently a high-school student that has been aspiring to be a physicist for quite some time. However, after much research I have found the following to be stakes in that path:

• 
  

  There are about twice as many physics PhDs as tenure-possible jobs in academia for them, and those who make it don’t usually get tenure.

  
  


• 
  

  Physics majors lack the skills in life that others do, like engineering majors or math majors. This makes it very difficult to find a job where they are competitive applicants.

  
  



• 
  

  Job prospects for future physicists is at 10 %, slightly below average, meaning that this situation won't get better in the next decade.

  
  

I’ve always been interested in the sciences, but this is rather depressing. With a physics major, and no PhD (which would otherwise put you in the above position), the best possibility seems to be a high-school teacher. That’s respectable, but I would like to know what other options there are for physics majors (BSc, or MSc). Be as creative as you’d like – include options like moving to another country with better job prospects for physicists (I checked and couldn’t find the job prospects of other countries).

citations - Is it accepted to refer to your own published result by your own name?

Assume that Jane Doe has published a paper in 2010 where she has developed a model or a theorem or a similar result, let’s say, that it relates to growth.

Now assume that Jane Doe is writing another paper in 2015, where she refers to the model/theorem from her paper in 2010.

Is it acceptable for Jane to write something like the following?

Doe’s growth model (2010), implies that ...
Doe’s growth theorem (2010) implies that ...
The Doe growth model (2010) implies ...

job search - How to show interest in a candidate when no positions are available?

I occasionally receive "cold-call" applications from graduate or postdoctoral candidates interested in working in my research group. Most of the time, they are of no interest—it's just a "form letter"-type application. However, once in a while, I get an application from someone who I would consider giving an interview to—if I actually had an open position.

What I want to do is to let people know that I am interested in such candidates, even though I don't have an open job for them. Is there a way to express this interest, and to encourage them to apply again when a new position becomes available. Is there a good way to do this—most of the time, such emails sound very trite, and that's exactly what I'm trying to avoid.

Answer

Being in the situation of looking for postdoctoral positions, I can at least give you my feelings of how I would understand that the person I contacted is interested, but cannot provide a position right now:

• 
  
  

  First of all, replying is already a good sign of interest. There are many persons who don't even take the time to answer to an official application for an open position (apart from the standard acknowledgement email), and you have to consider that you don't get the job if you don't hear from them. So, if you take the time to answer, that shows that you have at least a bit of interest

  
  


• 
  

  Then, if you provide a "personalized" answer, that shows that you took the time to read some of the applicant's papers, then it's clear that you are interested, and even if you can't provide a position, you might be interested in a collaboration.

  
  


• 
  

  The ideal would be if you can invite the applicant to give a talk, even though it's clear that there is no job following It would be a good opportunity for the applicant to talk about his work, to get some practice, meet new people, and that can also give you the opportunity to talk about creating a project together.

  
  

Basically, when one contacts a professor even though there are no official open positions, there are no really high expectations. But knowing that the professor is interested, but has no funding, is great, because it also opens the possibility to apply for a position in one year or two, when some funding is available. In order to show your interest, you can consider it as offering a potential collaboration: you can't provide money, but you would be glad to work with the applicant.

peer review - How to deal with rote "publication shopping"?

I spend a lot of time peer-reviewing paper submissions to conferences, workshops, and journals in my field. Sometimes I end up getting assigned a paper that I had already rejected from another venue. Usually the authors of the resubmission have at least attempted to address the flaws pointed out in the past reviews. But sometimes the paper is submitted in much the same form. That is, the authors have failed to correct the major errors and gaps identified and agreed upon by the reviewers. They may not even have bothered to fix simple mistakes such as typos (even when the reviewers helpfully itemized these). It seems that these authors have no understanding of or respect for the peer review process. Rather, they are adopting a rapid-fire approach of submitting the same paper to different venues in sequence (or in parallel, for all I know) until they luck out on a suitably unqualified or neglectful reviewing panel that happens to clear it for publication.

What I normally do when I receive such a resubmission is to copy, paste, and resubmit my previous review. After all, if the authors haven't bothered revising their paper, why should I spend any extra time re-evaluating it? But I wonder if that's all I should be doing. Does it make any sense to alert the journal editors/area chairs about these time-wasting shenanigans? Do serial "publication shoppers" ever get blacklisted, or at least a stern talking-to? Or is dealing with the same submissions over and over again just an inevitable and unmitigatable part of the whole peer review process?

What can PhDs offer to high school teaching that Masters graduates can't?

I refer only to academic PhDs, not doctorates in education. Many swanky fee-paying schools in England and the US hire PhDs as teachers. So what qualities are likely unique to PhDs and may not be mastered (pun intended) by teachers whose highest degree is a Masters?

Charterhouse's PhDs in math include:

Dr Graham Kemp, MSc, MMath, PhD
Dr Philip Langman, PhD
Dr Stephen Marshall, MMath, DPhil

Phillips Exeter Academy:

Zuming Feng, "Ph.D. from Johns Hopkins University with an emphasis on algebraic number theory and elliptic curves."
Panama C. Geer, M.S., Ph.D.
Filip Djordjije Sain, PhD Applied Math

St Paul's Girls' School (in London):

Damon Vosper Singleton (Head of Department) — MMath (Oxon), PhD (London)
Pip Bennett BSc, MA (Durham), PhD (Bristol)
Alexandra Randolph MMath (Oxon), PhD (Nottingham), MIMA

Tonbridge:

Head of Department
Dr Ian Jackson
MA (Hons) Mathematics : Trinity Hall, Cambridge
MMath : University of Cambridge
PhD (Radial Basis Function Methods for Multivariable Approximation) : University of Cambridge

Dr Jeremy King MA (Hons) Mathematics : St. John's College, Cambridge
PhD (Finite presentability of Lie algebras and pro- groups) : University of Cambridge

Dr Zi Wang MA (Hons) Mathematics and Statistics: Christ Church, Oxford

MMATH: Christ Church, Oxford
PhD (Sparse multivariate models for pattern detection in high-dimensional biological data): Imperial College London

evolution - How do I calculate the change in allele frequency in a haploid population under selection?

From this book

For simplicity, let us consider a haploid organism and assume that the frequencies of alleles $A_1$ and $A_2$ are given by $x$ and $y=1-x$, respectively. We also assume that the fitnesses of $A_1$ and $A_2$ are $w_1 = 1$ and $w_2 = 1-s$, respectively. In this case the mean fitness $\bar w$ is given by $x + (1-x)(1-s)= 1-sy$, and the allele frequency change per generation becomes

$$\Delta x = \frac{dx}{dt} = \frac{sxy}{1-sy}$$

If I would have to find what $\frac{dx}{dt}$ equals I would use the Wright-Fisher equation and find that:

$$\frac{dx}{dt} = \frac{w_1 \cdot x}{\bar w} = \frac{x}{1-sy}$$

, which is obviously not the same result as what the author found...

What am I missing? How did the author find out this result $\frac{dx}{dt} = \frac{sxy}{1-sy}$?

Answer

Here is my full derivation to the book example you gave, hopefully it'll help you clear up what went wrong:

You need to remember that after there is selection acting on the population, you no longer have a total of 1 after selection. Think of selection as "killing" individuals, which means the total is now 1 minus what has been "selected out". sy is what is selected out, therefore the new total is 1-sy. Which means you now divide each of your frequencies by 1-s*y (see picture).

Please comment if you need more explaining.

advisor - My professor is rigging data and plagiarizing. What can I do?

My department head is manipulating data in his research papers and skillfully alters plagiarized text to avoid detection. I found this out while working with him on a journal article. I politely confronted him but he did not concede and I backed off from that paper. Later other professors confirmed that most of his papers are bogus and results are fabricated.

He mentioned once that the reason for choosing nanotechnology (which he is not familiar with) is that there is very little literature available and few experts to review the paper. He gets through the review process by using a plethora of statistical analysis results (with fabricated data) to support his claim and gets through (some) editors by using fancy terms like neural network and fuzzy logic. The irony is that he does not even know the underlying theory of whatever analysis he is doing. How do I know this? I uttered a few doubts and the responses were extremely poor. He uses Minitab and Matlab tools to get things done. He once jokingly told me that he gets a paper ready overnight. Maybe it was not a joke after all.

Reporting to the management is useless as they won’t listen to me. I cannot challenge his paper, because I barely know anything in nanotechnology (neither does he). Editors won’t take me seriously since he has considerable reputation due to articles in high impact journals. So what should I do? I could not tolerate his insanity and literature pollution.

[Edit 1] More info: I am about to graduate and leave the department for good. The paper in which I was involved was shelved because sometime later I pointed out to him that the hypothesis is fundamentally wrong. I still have the original manuscript he mailed to me from his unofficial mail id. Institutional routes are closed, I tried complaining about his poor lecture quality once (anonymously) and it backfired for the entire class. He has 15 years of experience, 20+ journal article and numerous conference papers. I don't stand a chance against him.

Update I will try to report this issue to retraction watch or through any other means possible. Still it is not possible to disprove his claims without repeating the experiment. Will update here, if there is any progress on this issue.

Answer

Your backing off reaction is the appropriate one: cease any form of association with him right away.

The description of your first-hand witnessing of him fabricating data is more than enough to ascertain his academic dishonesty. You don't need to know about nanotechnology to know that manually modifying data to make it pass a statistical test is idiotic and fraudulent. Also, experts in that field will assume the data are real when conducting peer review, so it's not something they can easily detect without repeating the (alleged) experiments.

His 'results' are unwanted. By publishing bogus science he makes people lose time and money, he's robbing legitimate researchers of their funding, he is adding noise that masks the signal. If you can afford to report his behavior please, do it. Depending on where this story takes place, you might lose a variable number of feathers in his striking back, but at the end of the day he is the one who is wrong.

Taking direct action to publicly expose his fraudulent behavior is risky for you, especially since he is your hierarchical superior. But, when he will get caught (because he will), if it is apparent that you were aware of his wrongdoings and still accepted co-authorship or credit for his publications, his bad reputation is going to stain your career. If you fail to prove your claim, it's your career that will be at risk. So, proceed with caution. Note that it is ethically perfectly fine to report scientific wrongdoings anonymously.

• 
  

  Make sure that all institutional reporting routes are inefficient before bringing the issue to another level. It is not clear in your post if you actually tried or if you just assume 'they won't listen to you'.

  
  


• 
  
  

  Since you provided the content of at least one paper, and know about its fake nature, if he submits the paper despite your protests, notifying the editor is a thing you could do. Editors will take you very seriously in reputable journals.

  
  


• 
  

  You can also take part (anonymously if relevant) in a post-publication comment on his papers, on websites like pubpeer.com or retractionwatch.com.

  
  

graduate admissions - Is it a bad idea to say in my statement of purpose that I want to pursue a PhD in applied mathematics primarily to work in industry?

I am seeking some general advice from applied mathematicians at American universities. In my statement of purpose, would my stating that I want to pursue a PhD in applied mathematics primarily for the purpose of working in industry be a bad idea, in general?

This would be sort of "keeping it real" and being honest, when knowing that the vast majority of phds will end up in industry and not in academia, where jobs are extremely scarce.

Or is it still better to tell them what they want to hear? I am assuming that what they want to hear is that I want to be an academic and make contributions to teaching and publish in academic journals, etc.

masters - What are my obligations as an MSc holder?

I hold two degrees, a BSc (2011) and an MSc (2013), from the University of Waterloo. I noticed recently that on my BSc it reads "[...] and has been granted admission to that degree with all the rights and privileges thereto appertaining.", whereas on my MSc it reads "[...] with all associated rights, privileges and obligations." I'm a bit curious about the difference. First of all, I wonder what these obligations might be. Off the top of my head I can think of a couple of rights and privileges that would apply to me as a degree holder, but nothing that I might be obligated to do occurs to me. A quick search for an explanation of the text didn't turn anything up either. I also wonder whether the association of obligations to the degree is peculiar to the MSc for some reason. Would also be curious about the ubiquity (or not) of such statements at other institutions.

Answer

Some insight can be gained from considering the Oxford degree day ceremony, which is still conducted in Latin and uses fairly traditional formulae in admitting graduands to degrees. The descriptions used indicate various rights and responsibilities (all translations from here):

Candidates for the DD, DCL, DM and MCh (all higher doctorates) swear to the following:

Doctors (Masters or ladies/gentlemen), you shall swear to observe the statutes, privileges, customs and liberties of this University. Also when you shall have been admitted to the House of Congregation and to the House of Convocation you shall bear yourselves in them well and faithfully to the honour and profit of the University. And especially in those matters which concern Graces and Degrees you shall not impede the worthy or put forward the unworthy. Also at elections you shall record and nominate one only at one time and no more in each scrutiny, and nominate no one unless you know certainly or believe firmly that s/he is fit and proper.

For other higher degrees:

You shall swear to observe the statutes, privileges, customs and liberties of the University, as far as they concern you.

They are then admitted to the degree by the Vice-Chancellor, with the wording (for the DD, DCL, DM and MCh):

To the honour of Our Lord Jesus Christ, and for the profit of our Holy Mother Church, and of learning, I, by my own authority and that of the whole University, give you licence to incept [begin to teach] in the Faculty of Arts (or Faculty of Surgery, Medicine, Law or Theology) to lecture, to dispute and to do all the other things that pertain to the rank of Master (or Doctor) in the same Faculty, when those things have been completed which the Statutes require, in the name of the Lord – Father, and Son, and Holy Ghost.

(A non-Christian formula is available if graduands request).

Other higher degrees have a formula either conferring permission to incept (begin to teach) in the faculty, or just admitting them to the degree.

For the MA, graduands swear an oath "binding them to be loyal, obedient and faithful to the University and its interests, and to comport themselves circumspectly at elections to University offices" before being admitted by the Vice-Chancellor.

Finally, BA graduands are admitted with the following formula:

Ladies/gentlemen, I admit you to the degree of Bachelor of Arts: furthermore by my own authority and that of the whole University, I give you the power of lecturing, and of doing all the other things which concern the said degree.

To summarize, traditionally degrees were about membership in a Faculty of the university, and came with responsibilities to uphold the rules of the university, and participate fairly in elections. (These aren't empty words at Oxford, where they still confer 'MA status' on faculty members who do not have an Oxford MA so that they can participate in the governing bodies, and which still allows all graduates to vote on the Chancellorship and Professorship of Poetry). It may be that something similar is indicated in the University of Waterloo's ceremony or statutes, although it's also possible it's just traditional phrasing without anything formal behind it nowadays.

working time - How to be efficient as a graduate student juggling classes, TA and research?

I am a first year PhD student, and it's the fourth week of school. I am taking two classes, doing one grad class TA and doing a lab rotation. I am in Electrical Engineering (Controls and DSP).

I start my day thinking- "I'll go to class from 10 am to 12 pm, solve 5 homework problems from 1 pm- 3 pm, do some TA work from 4 pm to 6 pm, and read a bunch of papers from 7 pm to 9 pm, then cook and sleep. How optimistic.

In reality, when I start the homework problems at 1 pm, I end up having to read a bunch of textbooks to understand stuff in it (I'm doing Convex Analysis), and by the time 3 pm rolls around, I have finished only one problem. Feeling discouraged, I keep at this homework, vowing to stop only when I'm done with my quota of 5. My efficiency starts to drop severely after a few hours, but since I'm in school with my laptop and stuff, I can't go anywhere to 'relax', so I just keep sitting and start redditing or something. And then my concentration further drops when I try to resume real work. This goes on, I miss dinner, I sleep late, and the efficiency just plummets through the week.

My past couple of weeks have been so inefficient, I want to do something about it before it's too late.

In short, my question is, when your work is way too difficult to achieve your goal of the day in your allotted time, do you switch work, or do you keep going? I have always believed that output is more important than input, that is, putting in two hours for each task without achieving much in anything is not as good as putting in, say, eight hours for just one and finishing something in it nicely. However, this strategy of mine is failing me for the first time in my life, because even if I put in eight hours, I am not able to finish anything. The work is so difficult. I'm not complaining, just really need guidance.

molecular biology - In what sense is the "histone code" a code?

Since I started learning about molecular cell biology, I have witnessed an increasing amount of attention to this thing called a "histone code." However, unlike the central dogma of molecular cell biology (i.e. DNA RNA Protein), I still feel very confused about what exactly constitutes the histone code. Is this term code being used rigorously like it is for the central dogma? That is, is there an actual code? If so, what is its alphabet (e.g. GTAC for DNA, GUAC for RNA, the amino acids for proteins)? What kind of words does it encode (e.g. codons for RNA to protein)?

If these things are not known, how do we know it's actually a code then?

Thanks!

Answer

As already mentioned by Stefan, the "histone" code is not really a universal code; it is restricted to eukaryotic systems and even then, not unambiguous. It is, at present related to two kinds of histone modifications and their correlation with the transcriptional activity at that locus:

• Methylation


• Acetylation

Other modifications such as phosphorylation and ubiquitylation also exist but they are not generally considered in this "code".

Acetylation masks the histone's positive charge and thereby loosens the chromatin (DNA wrapped around the histones), which in turn facilitates transcription. Therefore acetylation is almost always activating in the sense of gene expression.

Methylation, on the other hand has different effects. Methylation on Histone-3 at 4th lysine (H3K4) and H3K36 causes activation whereas H3K9 and H3K27 are repressive. There is also some difference between different extent of methylation i.e monomethylation, dimethylation and trimethylation. The effect of methylation is executed by proteins that have domains such as chromodomain and PHD fingers, that identify these modified histones. Sometimes the histone can carry both kinds of methylation marks H3K4me3 and H3K27me3 and these are called bivalents.

Other histones of the octameric nucleosome can also be modified. However as with other kinds of modifications that I mentioned previously they do not seem to be very common and are therefore not generally considered in this "code".

statistics - Is it necessary to conduct a power analysis before beginning an experiment?

I know that power analysis is the statistically valid way to ensure you use the correct numer of samples or repeats in an experiment. But I have never seen any biologist actually conduct a power analysis. Mostly, researchers seems to use a rule of thumb (three technical, three biological replicates is a common one).

Should I be doing a power analysis each time I design an experiment, or can I just use one of the common biology rules of thumb? If not, what are the consequences for the validity of my results? And is there a situation where I will be required to use power analysis, which makes it advantageous to get used to doing it now?

Answer

You've already gotten a decent answer to this, but I'll provide my own thoughts on the subject.

Yes

It's necessary. It is absolutely something you should do before beginning an experiment, and preferably something you should do in collaboration with the person who is going to be helping you analyze your data. To address a couple points:

1. You'll see all kinds of researchers doing all manner of sloppy things when it comes to statistics and data analysis. Reading some journals makes me groan. You won't necessarily find it a problem for your field, but one should ask oneself if the goal is merely not to get called out by your peers, or to actually run a well designed experiment.


2. The consequences to the validity of your results lie in an increased risk of Type II error - the incorrect failure to reject the null hypothesis, or in slightly clearer English, finding no effect when an effect exists in reality. Which means, if you run an under powered study, you run the risk of doing the entire experiment, finding nothing, and being wrong. The consequences of that are myriad - first, it likely harms your chances to get published, as null results are often quite difficult to get into press. Second, if it does get into press, you've managed to get an incorrect finding into the literature, which will then be propagated in meta-analysis, reviews, and the minds of impressionable future readers. And then there's the chance you'll abandon a potentially productive line of inquiry because you couldn't be bothered to do power analysis.


3. One thing to also consider is that not having conducted power analysis somewhat limits your ability to chase after interesting sub-findings. If you've built your experiment on a shaky foundation, and then want to do a second analysis on a sub-set of your results, you almost certainly don't have the power for it.


4. There are times when you'll be required to do power analysis. If you do research that's clinically relevant, and you ever want it to appear in one of those journals, you may very well be required to show you had a properly powered experiment. And many grant applications require you do so. Even if they don't require it, some people will do a napkin math estimation of your power if they don't see it appearing in your application anywhere.

sjcockell is partially correct. To do power analysis, you at least need to have some notion of the effect measure you're likely to see. And these are indeed just estimations of what you'll see. But in nearly all circumstances, you'll likely have some ideas already. Are there similar experiments you can draw from? Your own pilot studies? A "feel" born of experience in your particular system?

It's also trivially easy to calculate power under a number of difference scenarios, to ensure your experiment is sufficiently powered if things go considerably worse than expected. For example, in a study I once did the power calculations for, we weren't sure what the ratio of exposed to unexposed subjects would be. So I ran it over a large range:

Which left me with the confidence that even if I was in my "worst case" scenario, I'd have reasonably good power at realistic effect sizes.

That's the true strength of power calculations. They'll tell you things about your study. What you need. What doesn't matter. Whether or not before you spend time and money pursuing an idea if you have a reasonable chance at success. Sit down with someone, take an hour or two (at most for a simple experiment) and do it right. Or ask CrossValidated for advice.

For a master-degree student, how influential a role do publications play in his phd applications?

I am a prospective student for phd programs in STEM. In my field F of study I have published a paper (unique author) in a journal included in the international F society, a paper (with a classmate of mine) in an annual conference of the representative local F society, and a paper (unique author) in a centenary conference about F. Besides, I have several manuscripts that are either under review or nearly done.

I am wondering:

1) How would an admission committee weigh these records? More specifically, would them weigh publications higher than other records?

2) How would an admission committee value manuscripts?

Though there are ''similar'' questions here in this SE, I still feel the need to ask this question. For these questions are subtly different in nature.

Answer

Disclaimer: I am a current doctoral candidate with 2 years of experience as the graduate student representative on the admissions committee of my department (in STEM) at a major R1 university in the USA and so, write this answer from that context.

Simply put, a strong research record matters. However, this comes with several caveats. For a successful doctoral application in our department, we look at

1. Standardized Test Scores: These (GRE/TOEFL) will not get you in but can keep you out. Mostly, they serve as preliminary filters and to fulfill certain graduate school minimum requirements.

2. GPA/Academic Record: This matters significantly. Relevant grades in relevant courses matter more. A 4.3 GPA from MIT in Mathematics and Computer Science is great for a Mathematics or Computer Science application. We tend to look at overall GPA's and then at relevant courses to catch red flags. For instance, you want to develop novel machine learning algorithms but have a C+ on "Introduction to Discrete Structures" and B- on "Statistical Data Mining". Red flag !

3. Research Experience: Research experience is important but more so in different sub-fields. This is the same as publications but there are important variations. For instance, in the field of Human-Computer Interaction (HCI), having a first author paper in CHI or TOCHI matters more than a first author paper in a conference the admissions committee most probably haven't heard about. If you want your research to speak up, then get published in the best conferences in your field. This is not a requirement but is a very good sign of your nascent research potential. Over the past few years, I have seen increasing numbers of applications to our department come from well qualified undergraduate and masters students with such records. Its a competitive world !

4. Letters of Recommendations: This should be correlated positively with research experience. If your letters talk about your wonderful performance in coursework, admissions committees are generally not very interested (they can already see that from your transcripts). If, on the other hand, you have detailed letters of recommendation from researchers that the admissions committee might know and which attest to your research performance with them, then that is a very good sign indeed !

In other words, its all about signals, signs and red flags. Specifically, in response to your questions:

1. 
   
   

   It varies.

   
   


2. 
   

   Unpublished manuscripts are not worth much but can serve as a good writing sample in case you do not have any other publications.

   
   

teaching - Should students be shown the grading rubric?

I teach a practical class which is assessed by a lab report. I grade the lab reports based on a rubric. The rubric has 6 sections (abstract, introduction, methods, results, discussion, conclusions) with a number of items that I generally expect to see in each section. Historically, about 95% of the lab reports can be accurately graded based on the rubric while the remaining 5% of the lab reports go in unique, often very good, directions and therefore do not tick many of the boxes on the rubric. I am considering showing the students the grading rubric in advance of writing the reports this year with the hope that this will key them into what is important so that they can better demonstrate their understanding of the key issues. Is there any research that looks at the benefits and consequences of showing students a grading rubric in advance?

Answer

Being open and clear about your grading policy is a large part of what makes the grades you assign meaningful. In that respect, it is generally helpful to share the rubric with your students if you work from one. At minimum, a good grading system should meet three criteria:

1. it should accurately reflect differences in student performance


2. it should be clear to students so they can chart their own progress


3. it should be fair

Sharing your rubric directly enhances the second criterion, and presents a context for evaluating the other two. You might also consider using some of your lecture time to go over examples of what an excellent lab report should look like and then discuss the rubric with your students. This would give you an opportunity to point out that lab reports should cover key points, but good lab reports don't necessarily follow a rigid cookie-cutter format.

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Since you asked about sources on sharing rubrics with students:

The authors of Introduction to rubrics, mention discussing the grading rubric with students and even include a chapter on constructing/tailoring rubrics directly with student feedback.

[Stevens, et al.] "... because we discuss the rubric and thereby the grading criteria in class, the student has a much better idea of what these details mean ..."

However, you may be interested in this paper which examines the learning outcomes for different peer groups when they're given details about assessment criteria. Evidence for their conclusions is based on a very limited number of samples, so the usual cautions apply, but they found that simply sharing explicit grading criteria was not sufficient to positively influence learning, while making time for the students to work more intensively with the rubric did yield benefits.

[Rust, et al.] "... it is being engaged with the process of marking as well as seeing examples of other work that significantly contributes to the students’ subsequent improvement in performance."

biochemistry - During starvation, does the human body do anything to prioritize which organs receive nutrients?

When food is scarce, the body slows its metabolic rate to conserve energy. Are there any other systems or processes that prioritize which organs receive nutrients?

Answer

Glucose is prioritized for the brain and erythrocytes over the muscle and adipose tissue, for example, by hormonal control.

The hormones insulin and glucagon respond to strarvation, insulin secretion falling and that of glucagon increasing. The glucose transporter, GLUT4, in muscle and adipose tissue is dependent on insulin, so that in starvation less-essential uptake of glucose to these tissues declines. The glucose transporters of erythrocytes and brain (e.g. GLUT1) do not depend on insulin, so the supply of glucose to these tissues, which absolutely require it, is not cut off.

References

Hormones and Starvation: http://www.ncbi.nlm.nih.gov/books/NBK22414/

Insulin and the GLUT4 Glucose Transporter: https://en.wikipedia.org/wiki/GLUT4

GLUT1, insulin-independent Glucose Transporter: https://en.wikipedia.org/wiki/GLUT1

graduate admissions - MS in Physics after Bachelors in Mechanical engineering

I am in the final semester of my mechanical engineering bachelors, though I could have finished my bachelors about 4 months ago, but I failed to clear 2 of my subjects, for which I would appear again in the December examination. Physics has always caught my attention, but then, everything I see catches my attention.I want to study physics now after I get my degree. The problem is my grades. I have scored an aggregate of 65% in my bachelors, but I can learn and understand things once I decide to do so. I am from India. How can I apply in foreign universities for MS, considering that they take engineering graduates for MS in physics, what kind of entrance/competitive exams would I have to give. Thanks.

etiquette - Is ignoring emails acceptable in academia?

As a grad student, I just find it tremendously frustrating when emails are ignored by faculty (both at my institution and at other places). Is this acceptable? I'd be content with a simple response with one line along the lines of "I have read this email and am busy right now, will respond in X days when I can write a more detailed email." I understand that, as a first year student in my field, I'm not really in a position to request anything of anyone, but it just seems like common decency.

Instead, I never hear back, as if my email has been jettisoned off into oblivion.

research process - How much is the normal salary of a postdoctoral fellow in North America and Western Europe?

I understand that the salary of a postdoctoral fellow depends on the field, project, contract, and so forth, but I am curious how much is the normal range for a fellow. Someone told me that he prefer to continue postdoctoral fellowship, as he gets the same salary of assistant professorship with less official duties.

In my experience, the range of salary for a postdoctoral fellow is much less than an assistant professor, something between $25,000 - $50,000. In Europe, it is in the lower side, but it is usually higher in the US.

I am curious to know what is the actual rate, and is there a norm for estimating the salary of a postdoctoral fellow?

In other words, when looking at postdoctoral openings, how much is an excellent/good/normal deal?

Answer

Let's find some official numbers and statistics. From this article:

As a baseline, in 2012, the National Institutes of Health (NIH) National Research Service Award (NRSA) postdoctoral stipend for new postdocs was $39,264, increasing to $54,180 for those with seven or more years of experience. Funding levels at universities are broadly similar.

Post-doc salary guidelines depend on individual institutions, and benefits vary widely from place to place. In addition to salary, checking the benefits is important in the US, but less important in more civilized/socialistic (strike out the inapplicable term) countries.

A job site that gathers salary information from US job advertisements has the following for post-doctoral fellowships:

Post-Doctoral Fellow average salary is $39,302, median salary is $38,000 with a salary range from $20,779 to $961,896.

I think it's safe to say that $961,896 is an outlier, but apart from that, the median matches the NRSA number. It also shows that there is a broad range of salaries, even by browsing the job listings on that site.

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For Europe, as I've said the situation is heterogeneous. I know how to find numbers for UK, at least. If you look at jobs postings from jobs.ac.uk for post-doctoral positions, the range appears to be £28,000 – £37,000 (apart from a few outliers). This would be roughly $44,000 – $58,000, but you have to adjust for taxes, health insurance, and then cost of living (which can be quite high in UK).

In France, CNRS is the largest scientific employer, and its post-doc salary is:

The gross monthly salary of a CNRS postdoc is 2,500 €

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As an anecdote, when I started as assistant professor, my salary was significantly lower than my post-doc salary. And even some of my post-docs in my group had higher pay than me (as well as some industry-employed PhD students). But money's not everything…

publishers - Is ProQuest a reputable company?

What are the possible benefits or consequences of submitting my dissertation to ProQuest?

My university recommends submitting dissertations to ProQuest. I am wondering about the practices and academic reputation of this company, and whether or not it is in my best interests to follow the recommendation of my institution.

Does ProQuest support academic work? Do they charge exorbitant fees to access their content?

publications - Can I make a case for authorship if I spend two weeks running a series of repetitive experiments for my PI?

I am a postbac working at a national lab. I have a project that is funded through an outside source, but my PI and postdoc informed me that they need me to spend the next two weeks completing a series of repetitive experiments they don't have the time to do for an alternative project. These experiments are required to satisfy the peer review criteria of the paper. Can I make a case for myself to attain authorship within the paper?

Advantages and disadvantages of doing PhD research at a non-academic lab

What are the advantages and disadvantages of doing your PhD research (in science, math, or engineering) at a non-academic lab (like a government or industrial lab) vs. the traditional academic setting? (Of course, the degree is granted by a university.)

When is one option better than the other if you have the choice between doing your research in an academic or non-academic setting?

A few potential advantages I can think of:

• You're likely to be hired by the lab after graduation. If you don't want to enter academia and are happy with the lab, this could be your career. If you do want to enter academia, often you're in good company because leaving research labs for academia isn't uncommon.


• You can work with more people (your school's students and professors and the lab's researchers). This'll expand your professional network and expose you to different perspectives.



• Your affiliation with the lab could add some credibility to you and your research.

A few potential disadvantages:

• Travel could be problematic if your school and your lab aren't close. This could be mitigated by taking care of the coursework first.


• The research topic is often dictated by someone in the lab if you are funded by them. If you decide this topic is not worth researching or not interesting then you might have a problem. Politics in the lab could change the research topic in the future and that might also be a problem.

Answer

Throughout graduate school I worked at and was funded by a university-run laboratory that operated somewhat like a government laboratory and was largely funded for applied research. I now work at a UARC (which is similar to an FFRDC). Given that my graduate school lab was already affiliated with the University, though, my situation is slightly different than yours.

At least in the US, it is relatively hard for non-academic laboratories to find funding for basic research; funding agencies like the NSF have a prejudice toward funding degree-granting institutions. Therefore, in my experience, much of the flavor of the funding at non-academic laboratories is geared toward applied research. This might not be a problem, but it can be a challenge to find a deep, Ph.D.-level problem to solve when your sponsors are interested in seeing more concrete results.

In my case, working at an applied research laboratory to fund my graduate degrees was actually somewhat of a benefit. Due to the reasons I listed above, it was difficult for me to latch onto a deep problem to solve for which there was stable, direct funding. Therefore, I used my position at the laboratory to basically "pay the bills" (it covered my stipend, tuition remission, &c.). That gave me the freedom to work on related—but not directly funded—problems that interested me. This of course had the overhead of essentially working two jobs at once, but it had the added benefit of providing visibility to my "side" research to the sponsors who were funding my "pay the bills" research. It also paid for my trips to relevant conferences, at which I was able to present both flavors of my research.

Now that I am working at a UARC, I see others here who are also pursuing part-time Ph.D.s. Most of them seem to have found a similar model to mine: They use their position at the non-academic lab to "pay the bills", and then focus their actual research on a related but independent problem. If you are able to fund yourself (i.e., if your Ph.D. advisor doesn't have to worry about finding funding for you), then many advisors will be willing to take you on as a student.

microbiology - How many diseases can be linked to disruption in the microbiome of a human?

I was listing to the radio and heard recent research found a link between children and higher cases of asthma when certain bacteria are missing from the microbiome. How many other diseases can be linked to a disrupted microbiome and are there ways in repopulating missing bacteria?

Answer

It is an open question and an active area of research. You will not be able to get a definitive answer to your question of number, as each new discovery will add to the total.

As for repopulating, we have not even determined all of the strains of microbes that populate us, many are very difficult to culture in vitro, and we do not know of all the functions for each species, so we do not have a clear picture of which need to be there, which don't, and whether or not some species work together to provide us with a benefit. For certain conditions such as Irritable Bowel Syndrome, one of the treatments that has been tried is fecal transplant.

Do a literature search for recent reviews. Nature Reviews tend to do detailed reviews, especially on topics as in the news as the Human Microbiome. That is probably the best first place to start. Then you can start to drill down into the reference papers that are cited in the review. That will generally give you a good state of play in the field.

publications - Can I present the results of a paper that is currently under review?

Among the presentations in a major conference, I attended one where the author cited a paper (of theirs) under review in another major conference. Not only cited it, but showed some of its results.

I have the impression that it should not be possible, since there's the potential risk of influencing reviewers who could also be in the room during the presentation. Or is it only "good practice" not to do so?

Answer

After thinking about the answers provided so far and the discussion in comments, it seems to me that the point of view favouring dissemination of research results unrestricted by the double-blind peer-review process needs a stronger case. I believe that the answer can be derived from higher-level, rather philosophical, principles.

... Or is it only "good practice" not to do so [to present results under review]?

What is the purpose of developing and disseminating research results?

I am an idealist in these things and argue, that it is first and foremost the advancement of human knowledge and ultimately improvement of the conditions of the human society, as well as the world around us -- regardless of what exactly "improvement" means, I have in mind something like a wider social consensus that the change has a positive vector.

Given this stance, unless there are other considerations in the game, there is no reason which could obstruct our advancement of human knowledge, which ultimately rests on dissemination of quality results to the wider public. Of course, we should be careful and act in a good faith so as to be cautious about validity, significance and originality of our results. Peer-review process is only an auxiliary mechanism helping us to filter out ideas/results in violation of these principles, i.e., helps us to recognize and fix our own misjudgements and mistakes, as well as (in the worse case) dissemination of results not advancing knowledge of humankind, but produced for other primary purposes. After all, the ultimate metrics for the results of scientific research is not the outcome of the peer-review process, but rather the long-term impact on the society and the world around us. That is, whether other people will learn something from the results and whether it eventually helps them to build something beneficial to the society.

Unfortunately, thanks to the recent proliferation of the publish-or-perish attitude and its intertwining with the need to advance human knowledge, as well as interactions of these two conflicting forces, gradually peer-review becomes primarily a mechanism to filter bad-faith products - think plagiarism, results falsification and all sorts of other scientific misconduct. Yet, I maintain, the process of filtering should not gain a higher importance than the objective of our pursuit itself. To conclude, if executed with caution, restrictions imposed by double-blind review process should not restrict our ability to disseminate our results.

health issues - How to deal with an abusive advisor?

I am a graduate student in mathematics. I've been having a difficult relationship with my advisor, and I need some help on the matter.

Some background

When I just started my graduate studies, my advisor warned me that he tends to be strict, and that sometimes he can have anger outbursts. I thought (and still think) that a strict advisor would be good for me, and didn't think the mentioned anger issue would be as bad as it turned out to be.

In the beginning, our relationship was good and (professionally) friendly, and I looked forward to every meeting with him. Our discussions gave me motivation in my studies and research.

About half a year later, I was going through depression unrelated to academic issues (and started being treated by medications), and was completely unproductive and not concentrated on my work for a few of months, which my advisor was unhappy about. He said that he didn't care about my personal problems, didn't want to hear excuses, and that he expected me to work regardless. From that point on, our relationship completely changed. He stopped being nice and supportive, and started accusing me of not being serious and not working hard enough. This seems to have been the main trigger for his behaviour which I am to describe next.

The problem

If I don't get results, and try explaining that I've been working hard and just couldn't come up with a solution, my advisor starts yelling (yes, really yelling) that my progress is too slow, that he's sure he could have solved it in a month/week/hour himself if he tried, etc.

He also tends to interpret everything I say as a personal accusation, even though I always try to formulate my questions carefully and politely. For example, if I ask whether I should stick with a certain approach even after being unsuccessful for a while, he responds by yelling that he's an experienced researcher and that if he suggested it there must be a reason, and how dare I, a student, question anything he says.
A similar situation happened when I pointed out a mistake made by another researcher (and which was checked, per my request, by a third party after the incident). My advisor didn't check my claim thoroughly, and yelled that how dare I "accuse" a well-regarded researcher of making a mistake, and that it makes him angry that I "don't check my facts" before making such a claim, and compared me to mathematical cranks.

[To clarify: I pointed out the mistake in an email to my advisor, not in any arrogant way, and without involving anyone else at that point.]

It is difficult for me to work, because every time I'm stuck on something, I panic thinking about our next meeting and how he would yell at me again for lack of results. It also makes me look for "shortcuts" instead of really understanding what I'm studying for my research (even when those are basic things that he would agree I should understand) to save time.
When I explained to my advisor that this slows down my progress, he said that he's not a psychologist, and it's not his job to deal with my psychological problems.

Another problem is that almost all of our conversations revolve around my lack of progress and him yelling repeatedly the same things, while I'm trying to pull the conversation back to the math, as I need his help, and as there is no-one else working in this area at my university (and perhaps in the country). He had another graduate student who just graduated and switched to a different field, telling me that he would not continue for a PhD with this advisor because "he can't survive this psychological pressure for several more years".

I don't see a feasible option of switching advisors for the reason stated above, and also because based on his past PhD students and on what he told me, he could significantly help me in finding positions after I graduate. Also, I regard him as a good advisor in other aspects (much better than other advisors I know at our department), and I do believe that after all he cares and would help me if I made progress.
As much as possible, I would like to have a good relationship with him, and I definitely don't want to harm him in any way (such as reporting it - which would have been counter-productive anyway).

Our relationship quite reminds me of the movie "Whiplash" (without the physical abuse)...

Since the situation seems to have been worsening recently, I would very much appreciate some input on how to deal with this situation.

Answer

I cannot stop typing this long response.

I'm sorry to hear that you are in this situation and I have lots of sympathy for you. Your story sounds similar to but not as horrible as mine in the previous university and the department I was in (NOT the one I list in my profile now, that is the one I'm currently in, the one I enjoy so far). I'll first give you a one line advice, then answer your question in detail. In the end, I attached my story just for your reference (can't resist telling it!).

One-Line Advice

Most likely, the best option is to peacefully walk away and find a new advisor.

Detailed Answer

Based on your description, I can hardly imagine things will be better later on if you don't take action now. You've worked reasonably hard, but have slow progress for the reasons you don't have control. There are many misunderstandings in the communication with your advisor, and most importantly you're scared of meeting with your advisor. It's impossible to produce any good research work under a scenario like this. Time to look for someone else that fits you better.

You do not specify which stage of graduate study you are in. This may affect your approach now. If you are in the early stage (before passing preliminary/qualify), you should simply walk away, pass the exams, claim your interest change and convince someone else to be your advisor. It's not unusual at all for students to change advisor at this stage. If you're in the late stage (all but dissertation), you might consider enduring the pain for another year to get your degree, the potential cost (like dropping out) of making any unsuccessful move is too huge at this stage. If you're in the middle stage(pass qualify not yet advance to candidacy), the situation is awkward. You probably should talk to some department/university authority, and find out what's the best way to continue your study. However, you need to be very careful about who you talk to and how you talk.

When you describe your scenario to any third party (other professors, department chair, ombudsman, etc.), focus on the key issues you're facing and give them enough information so they can offer reasonable solutions. Avoid ranting and complaining, even if what you're saying is absolutely correct and can provide evidences. You run into danger of convincing other people you're a lazy student with many excuses. For example, you should avoid suffering the things I suffered (see my story+rant).

Last but not least, when it comes to advisor, you should have doubts on words of senior students and most recent graduates, they are the people who rely on advisor's letter to find jobs, therefore are unlikely to tell you any bad words, even if they don't like the advisor themselves.

End of Detailed Answer

My story+rant (only for reference)

Almost the same structure as your story, three years ago I was a new graduate student (in Ph.D. program) working in computational chemistry. It was OK in the beginning. About a few months later, I found out the software and source code I was supposed to use to do the calculation of my main project was fundamentally flawed. Some physical quantities were calculated on a non-trivial wrong way and it was clear to me that any data outputted would be meaningless unless the problems were fixed. I temporarily stopped working on the project to resolve the issue with my collaborators (one postdoc., one software engineer). It was a much slower process than I expect, because the person who wrote the code, although an expert software engineer, knows relatively little about the research I did and couldn't understand why the code was wrong for a long time.

My former advisor then behaved the way like your current advisor. In our meeting, he ignored the issue I faced and only blamed me on slow progress. Very often I found the suggestion he made was wrong and the solution I figured out myself was right. Whenever I pointed out the errors in other papers, providing more than sufficient evidences, he thought I must make up excuses for failing to reproduce the result in the paper. When I wanted to pull the discussion back to the research and seek for advises, all I got is "This is not undergraduate, you're supposed to figure it out."

After many meetings like that eventually he kicked me out of the lab(where he had already kicked out more than half of his students for many different weird reasons), originally with the promised of funding me finishing masters. He gave my research project to another student. Later on he blocked my access to all the data I had, and requested me to come back to lab if the student continue on my project had any problem, otherwise he was going to cut the funding. Even worse, I worked as a TA of my former advisor the academic quarter he kicked me out of his lab, he simply found every chance I made an insignificant mistake in TA job to blamed me, and sent abusive emails.

(Here is what I did, and don't want you to repeat) Finally, I cannot endure many abusive emails like that, decided to response one of them rudely (no personal insult and threat though), accused him lying and attached with evidences. The email was cc to all his group members and some department faculties and staffs. He was scared, he turned into the graduate community center (something equivalent to counseling center), described me as a potential criminal, and asked them to physically isolated me from the department. It took a while for me to convince them that I was the victim, not the other way around. After a few weeks of long conversations via the third party, we finally achieved some compromise- He agreed to do what he promised originally (fund me 2 more months to finish M.S.).

On the other hand, despite the evidence, it was impossible for me to convince other faculties in that department to be my new advisor. Most of them believed my former advisor's words and thought I was a failing student with excuses. They set up an "advancement exam" for me, at the date one faculty who potentially supported me had a doctor appointment, to find an official reason to kicked me out of their Ph.D. program.

End of my story+rant

presentation - Is it more acceptable to list interview talks on CV if they're also part of a seminar series?

Consider someone invited on a job interview (in the sciences) at a university or a national lab or something of that sort with a regular seminar series. As part of the interview, the person is asked to give a talk as part of the seminar series.

Is that appropriate for inclusion on the CV as an invited talk?

I saw one related question to this but it was different enough that it didn't really answer my question: Do presentations given during interviews count as invited talks?

However, the thread really just has a couple answers with equal support for opposite positions. The difference here is the distinction that the talk is given as part of an interview but also is part of a regular seminar series. I was wondering if this changed people's feelings on the matter at all.

It seems to me that any other person would list that as an invited talk. It also just seems to get grayed a bit by the fact that it is technically being used as part of a job interview.

Answer

I think there are two points of view in regards to talks related to a job search. The first is everything associated with the search should be lumped together, and if listed on your CV, it would be under something like "positions interviewed for". On my full CV, which I use for keeping track of my activities, I group positions interviewed for into off-campus and on-campus. The other approach is to separate out the "public" aspects of the job search and list them separately (e.g., under research seminars and guest teaching). I take the later approach since an issue with the former approach is that sometimes after giving a research seminar (or potentially guest teaching), you might be asked to apply for a job, which of course then blurs the lines.

In general, prior to making a campus visit, I ask for information about the audience of at the different activities (e.g., teaching demo, research talk about past research, and chalk talk about future research). The response about an activity is usually something along the lines of "it will just be the search committee" or "it is open to everyone and their might be a couple of interested undergraduates in the audience." From that I can usually decide if it is a public or private activity. Once I decide an activity is "public", I think it is not only entirely appropriate to list it the same as any other talk on your CV, but that leaving it off is misleading. I would consider it the same as if I found out someone was leaving "questionable" publications off of their CV.

research process - Can I do experiments on humans without a degree?

I have several ideas for research that I believe would advance our understanding of psychological priming. It won't involve anything extreme - just reading non-offensive words on a screen.

But I have only a bachelor's degree. Will that preclude me in anyway from doing research of this type, and publishing?

I know I'll have a greater challenge finding participants, and designing the experiment, and correctly formatting my paper without guidance, etc. I can work with that.

But is it even possible to get IRB approval without being affiliated with a university?

Is there any way that my current affiliation status will formally prevent me from going forward?

Answer

It is possible to get IRB reviews without an academic affiliation. Commercial IRBs (companies that, for a fee, review trials for third parties) exist; that's one way that industry manages to perform clinical trials.

Commercial IRBs have multiplied in recent decades, reviewing and passing proposals for profit. Their creation was spurred partly by an explosion of industry-sponsored clinical trials, but they are increasingly passed business from academic centres, to relieve overstretched in-house ethics committees. There are now dozens of these companies and they will see potential business in the proposed shift to single-IRB oversight of multi-site trials.

--Who watches the watchmen? Nature, 2011

Some of these IRBs are listed at the Consortium of Independent Review Boards (CIRB).

The absence of a graduate degree and of academic affiliation don't prevent you from publishing either, although they may present some complications during the process. There are other questions in Academia SE that discuss this:

writing - Where to locate authors’ names in sentences?

Is it or is it not good practice to make an author the subject of sentences in a paper? When should their name be central, discreet, or absent in the sentence? Here are five variations showing different approaches, four of which include the author’s name. Are there particular identifiable use cases for these styles?

1. Johnson argued that this will never work.


2. Per Johnson, this will never work.


3. The argument was advanced by Johnson that this will never work.


4. This will never work (Johnson).


5. This will never work [42].

Answer

There is more here than style: the first and third options mean something quite different from the fourth and fifth. In the former cases, what you are asserting is that someone else argued for X. In the latter cases, you are asserting X and using the citation as evidence/support/proof. (That I can't quite tell where the second one fits into this dichotomy is a strike against it.) In an academic paper, that is a not so subtle difference.

I find the style question less critical. It is a matter of general good writing rather than anything specifically academic or it is specific to the journal at hand (so we need not discuss it here).

Of course you can use an author's name as a subject of a sentence: you can write what you want, you know! As a matter of style, to my ear the first option sounds good, the second option sounds weird, and the third option sounds weaker and wordier than the first, but maybe the surrounding text gives you a good reason to write it that way.

The difference between options 4 and 5 is just a difference in citation style. First that is very field dependent; in my field (mathematics), we would do 5 rather than 4; in much of the humanities it would be the other way around. Second, unless your choice is so so strange that it prevents your readers from finding the references in your bibliography, the whole issue can probably wait until your paper gets accepted, in which case they'll either do it for you, tell you exactly what to do, or tell you that you did it wrong (and ask you to fix it).

undergraduate - Cons of graduating quickly

I read this question Does rigor/thoroughness of undergraduate program matter (for graduate/PhD applications)? and became very worried when I saw everyone blasting the OP for contemplating graduating in three years. The general consensus was that there was no reason at all to graduate early and that the lack of additional experience would hurt your chances at graduate school. I am concerned because I am graduating with only 2.5 years because I can only barely afford this by maxing out all loans. I would love to be able to develop greater depth in my field. Instead it has been a constant sprint to finish before I run out of money completely. I was rejected from every top ten university, and the one token safety school I got into jacked up the price as soon as they found I had nowhere to go.

Are the criticisms that finishing too fast valid in the context of extreme debt? I am saving over $100,000 by finishing early, will this reason be accepted by graduate schools? I see that graduate students do not have to pay tuition and get a small stipend, this sounds like a wonderful way to pursue an education and is very attractive to me right now. I feel that my education is rushed and I have not had the time to contemplate open research questions which are very important for graduate admissions. Graduate school is also the path to a job in research labs or academia.

edit: I have done well enough (6th in graduating class unless I mess up). They offer to tack on a year for a masters at your current rate, which is touted as a way extend finiancial aid. This is untenable for me.

Answer

Are the criticisms that finishing too fast valid in the context of extreme debt?

Yes, the criticisms are still valid: the world, unfortunately, does not care about any particular person's debt problem.

The answers/comments given at the linked question in the OP are spot on; thus I would encourage you to try to find other sources of aid to fund your full-length undergraduate studies, if you haven't already done so (scholarships, etc.).

Having said that, some schools have a diversity statement that you are to submit along with your application. In this statement, you can provide some background on the adversities that you have faced and how you overcame them. If you have significant financial hardships that you are battling through, for example, then a diversity statement would probably be the place to talk about that and hope that someone would care enough to have it positively impact your admission decision.

Whether the "diversity statement approach" will work or not depends on (among other things) your particular situation (e.g., how inadequate is your preparation for grad school due to graduating early relative to others in similar situations?) and the number of available slots the school has for cases such as yours. I still think this approach is too risky to count on, and I would, again, encourage you to look for other ways to stay in your undergraduate program for the "normal" amount of time so that you may reap the many benefits of doing so.

masters - How to ask an university for application selection result before accepting an offer from another university?

I have an offer from one university and still awaiting results from others.

How to approach other universities and ask them about my application status so that I receive my selection / rejection before the deadline of accepting the offer? Is it rude to inform the universities that I have an offer from another university and will be accepting if the results are not announced before the deadline?

All the universities are in the same region.

Answer

Like everybody else is saying: Just Ask.

And do it sooner rather later. Telling a university that you have an offer already will signal that other schools' further along in the process think you're great.

And anyway, you have absolutely nothing to lose by asking. If they want you, they're not going to think it's annoying and will be afraid that will lose you to your other offer. If they don't want you, asking can't hurt. If they are on the fence, a signal that you're admittable will only help.

etiquette - How to acknowledge unhelpful conversations

In an acknowledgments section to a mathematical paper, one conventionally says the paper has benefited from "helpful conversations" with so-and-so that clarified matters in some way, started one's wheels in motion toward an idea, and so on.

It happens fairly frequently, though, that I email or otherwise approach a colleague I suspect may have some insight, only to have an unhelpful conversation. By this I mean that although the exchange is well-informed and pleasant, through no fault of the other party I am unable to gain anything from it mathematically and it has no bearing on what I ultimately publish.

In these situations, my correspondents have made the generous donation of their time, so I feel they ought to be thanked, but on the other hand the paper has not actually benefited. How should I acknowledge their contribution?

Answer

I agree with Anonymous Mathematician: There are lots of non-obvious ways to contribute to a paper, and it never hurts to be generous. But if they really did not contribute to the paper, then there is nothing to acknowledge in the paper.

If you really feel you owe them thanks for something that isn't a contribution to the paper, just call and thank them.

publications - Is it better to publish a few papers in one journal, or one paper each in several (equally good) journals?

Suppose there are several journals with the same impact factor. Is it better to submit my papers to one of them or each time I finished a manuscript it is better to submit to an equally good journal that I have not published in yet.

I am early in my career and I already published two papers in the same journal and I am going to finish my third paper, which potentially can be published in the same journal as my previous two papers.

citations - How to review a paper that relies heavily on references to unpublished work?

I am currently doing a (blind) review of a paper for a Journal in the engineering field. The manuscript seems okay so far but relies to a large extent on a unpublished paper, cited as Miller et al. forthcoming. That publication was not submitted along with the manuscript. The author seems to be involved in that publication, but is not co-authoring it. Since no journal or publisher is given, I am assuming that the manuscript is under preparation and to be submitted to a Journal.

Furthermore, there is no summary of the central data and results e. g. in the supporting information. That makes it hard to follow some of the assumptions and conclusions.

1. How should I proceed?


2. And does this in principle justify a rejection of the paper?

journals - Manuscript status changed from "Reviews completed" to "Editor assigned"

I have been confused with the present status of my manuscript whose status follows the following timeline:

1. Manuscript initially submitted through Editorial Manager (Springer): 25 Jan 2017



2. Under Review: 27 Feb 2017 till 9 Jun 2017


3. Reviews completed: 10 Jun 2017 till 22 Jun 2017


4. Editor assigned: 22 Jun 2017

The journal is in the field of Computer Science and Computational Mechanics (Applied Computer Science).

My inferences from the above strange timeline:

1. The reviews have been completed and the system administrator or the journal manager assigned the editor (who is assumed to be associated with it earlier) to take care of the review reports and make a call.


2. The number of review reports is not sufficient. It would be re-reviewed and handled by another editor.


3. It is a software issue or a bug.

I have the following questions:

• Whether is my inference correct?


• As one can see, it has been 6 months already. Is it too early to send a gentle reminder to the editor-in-chief to look after my manuscript?


• Is such a timeline of manuscript 'strange' at all? (Although it is difficult to answer this unless the editorial manager software is understood properly.)

Related posts and questions:

Which is a better choice in case of a graduate admission?

Which is a better choice in case of a PhD application and why:

1. Submitting a transcript which indicates an incomplete study (50/120 credits completed) and 5 dropped (not failed) courses.

vs.

2. Concealing an incomplete study.

??

If #1 is a Hobson's choice, how can I explain that to satisfy the admission committe?

career path - How do I gain back my faith in my PhD degree?

I am 3 years into a PhD program at a top North American university in STEM. My daily routine includes working on my research and preparing for courses I am assisting. In general, I would say that there is always work to keep me motivated. I have a good relationship with my supervisor. However, I don't feel valued by my department.

Recently an undergrad in one of my class had a chat with me about deciding on pursuing grad school. He asked me about my research and the courses that I took. I felt that he wasn't very impressed, as he was more industry-oriented and failed to see how real analysis can help anyone.

He then asked me couple things which left me even more self-conscious

1. I wish to go to graduate school, but I also fear that I will miss out opportunities to make hundreds of thousands of dollar per year working in industry. I also wish to be financially independent and have an early retirement. Can doing a PhD for five years offer this reality?

I had really no answer to this question, as I am in constant doubts myself over the rising opportunity cost of doing a PhD. There is a part of me that beckons me to leave academia immediately. It tells me that I could do so much better, be more free only if I had made the choice after I graduated with my Bachelors. Only if I knew how little I would be paid compared to my peers.

2. Programming and software development are highly valued skills in industry. Almost all jobs nowadays requires some form of it. Do you think your degree has prepared you to be competent in these areas?

I cannot say yes to this question either. I do use programming every now and then, but I am in no way comparable to a person who works solely in this field. It does seem that programming skill seems to be the only skill that employers value, a litmus or IQ test for a world of graduate students with questionable credentials. Even newly minted PhDs are directly sent to software developments, albeit more specialized. No, a graduate degree has not prepared me to be a competent coder, the one skill that would make transition from academia to industry so much more smoother.

3. Do you believe in the theory and methodology you are developing? How do you know that your model can be used by actual people, like the products people develop in industry?

I cannot answer this question either. All the techniques, theories I developed seemed to only produce more techniques and theories. None of which I can see or use to directly benefit anyone. That is not to say they are bad for publishing paper. In fact I feel that they might be too good for this narrow purpose, and I have lost sight in what excited me about research in the first place: the potential to have real-life impact on real actual people. No, I do not believe in my own research, or that of anyone else who are working in my department, aside from the few people who are doing it along with industry.

4. What do you do when you are not working on your research?

I paused for a second. I don't know what I am doing besides research and teaching assistance duties. While my peers on instagram or facebook are traveling all around the world, visiting new places, I am bound to my institution. I cannot leave it for there is always more work. It is like a full-time job except that it is from 9 in the morning to 9 in the evening, occupying weekends, holidays, and all the moments I could have spent with my loved ones. Have I made the wrong decision?

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This conversation compounded on a few more I had in the past few weeks with fellow graduate students after the semester started to wind down. Each of them displayed pessimism over the rising cost of living, and missed opportunities. Yet they still have faith in their (however abstract) research, which I feel like act as more of a distraction than anything else.

I wonder if this is the start of a long descent towards regretting my PhD all together. I am really starting to feel that a PhD is a punishment towards my lack of conviction in my studies, or me being unable to develop a passion for something. "If only I was solely interested in anti-jamming self-packing oscillators! maybe I could have been working for the oscillator company and making bank! How do these people get interested in this esoteric thing?"

Am I even better than an undergrad student in any way?

Every day I wake up telling myself that the grass only looks greener on the other side, and I can't really tell if I could have been happier in industry. But there is always the lingering thought of what could have been.

Has anyone ever had these thoughts at some stage of their PhD career?

Is there any way to renew my faith in my PhD degree?

Answer

Oh man, where does one begin...

I am half-way in to my second postdoc at what I consider to be the best research facility in Northern Europe in my field. So take my advice as such, although where you work does not say so much about you, as one might think.

How do I gain back my faith in my PhD degree?

Short answer: you don't, as long as you are in status quo. If something changes by an act of serendipity, maybe you do..

Longer answer: you might regain some faith, by reframing your reference point. In other words, change your expectations and your feelings might change as well.

Regarding the questions the student asked you:

1. If optimizing your overall income is a primary concern, don't bother with a PhD. Yes, there are cases where having a phd might pay off by making a high-paid job available, but cumulative work experience, raises as well as the confidence and training you get on job will likely end up as a bigger plus.

... wish to be financially independent and have an early retirement. Can doing a PhD for five years offer this reality?

There is certainly no reason to panic if financial independency is what you are striving towards, though. I have been financially independent from my family/loans the entirety of my graduate studies, and even managed to save enough money to get a mortgage loan to buy myself an apartment (small but more than decent) while I was a PhD student.

That might be more of a statement of which country you live in (e.g. Sweden vs USA) or which city you want to do pursue graduate studies (e.g. San Francisco vs San Diego). The point is that you do make a living, you are not an undergrad anymore.

Don't even get started with pension subject, that stuff is too complicated. Practically unless you are making a stupendous salary or some wicked investment decisions there is no guaranteed early and relaxed retirement. As populations get older on average, and indirectly their costs to the society increase, the pension systems will have to undergo a significant restructuring, and I for one am expecting that to create some very heated debates and go down not so easily.

Bottomline: Do a PhD if the subject interests you deeply, or if you think you will be gaining a skill that is highly valued in industry. I am working with bioinformatics, and if I want to get a job in this field, without a PhD you are not really respected. I have some friends that have done PhDs in economics, which were highly valued and allowed them to land jobs they would have otherwise. That may not translate to every field however.

2. Doing a PhD is not an education that prepares you for a profession. It's an academic degree not a professional one. You need to keep that in mind. Actually, write it on a post-it, put on your mirror at home and repeat it to yourself everyday. Twice, if you can, in the morning and evening when you brush your teeth...

It's so easy to lose track of that insight. Doing a PhD is education to become an academic, to think critically, to be able to read and teach (to some degree at least). You will get to be a better critique of others' work and your own. You will get training on reading and writing. You will most likely face the boundaries of your intellectual capabilities. But no it does not directly imply you will be better at a job, unless that job is specifically related to the things I mentioned above.

Do you think your degree has prepared you to be competent in these areas?

No, a graduate degree has not prepared me to be a competent coder, the one skill that would make transition from academia to industry so much more smoother.

No, it shouldn't either. That's why there are certificate programs, and bootcamps, Coursera and Khan Academy, and software carpentry etc etc.

However, did you stop to consider that doing a PhD might have you working on an actual problem, to which you get to design a novel algorithm to solve that problem, or to improve the solution? Or maybe a new protocol for networking/encryption etc? Having some specialized experience might make you an indispensable profile for a company looking for expertise in that field. But no by default, graduate studies do not make you a better professional.

3. Re: relevance

How do you know that your model can be used by actual people, like the products people develop in industry?

In most cases, you don't! At least not for sure... You can look at citations of your papers, although even that can be misleading as people cite other papers for many different reasons. I actually asked a question somewhat related to this a while back...

In some, rare, cases you might end up doing something that changes the landscape of the field; like writing a software that becomes the de facto gold standard for a particular type of analysis. You might come up with a technique or a protocol that is used by others. Or you might even stumble on some key result, by sheer luck.

More likely, you will provide incremental additions of knowledge into an ocean, most of which will go unnoticed, at least initially. If that bothers you, that is OK. It bothers me too, and I do consider my position in academia as well. But that should not cause you any despair. It only shows that you want to be proud of your work and get the acknowledgement you deserve. Unfortunately we don't always get what we want.

4. Re:Comparing yourself to the others especially on social media

While my peers on instagram or facebook are traveling all around the world, visiting new places...

Stop! Social media is literally designed to create that feeling. At the end of the day, you never know who goes home to cry about their day, no matter how amazing their Instagram photos may look, or how much "fun" they are having wherever they may be.

For many people their life online, or at least they portray their life online, has become their identity. There are many people who have analyzed this in great detail. I especially like this article (go ahead and listen to the talk in its entirety). Also read about online influencers (here's a starting point).

Edit: As @FrankHopkins pointed out in the comments, doing a PhD might actually take you to many exciting places for conferences or courses. I have been to a number of really cool places, most of which I would either not bother traveling on my own or would be able to afford at the time :)

---

Overall my answer(s) might appear very dystopian. But I would rather say realistic, and in any case, they are based on my experience.

I'd like to wrap it up on a positive tone, with hopefully concrete steps to help you find your way around, because ultimately, nobody can tell you if you have taken the right decision.

Here are some concrete steps I can suggest for you to feel a bit better:

• 
  

  Get a mentor! Someone at least 10 years your senior and ideally someone who has a life story that resembles your own. Of course finding a good match might be tricky but check whether or not there is a mentorship program provided by your university/faculty/student council etc.

  
  

  Listen to that person's story, but make sure you don't fall into tutor-student relationship. How did s/he take the critical decisions in his/her life? What was valuable to them at that time, and how did that turn out later? How does the person define success?

  
  


• 
  
  

  Speaking of success, try to think real hard about what you define success to be. It's great to make lots of money, or have an h-index in the 100s but it's really not the whole picture. You might end up working yourself to the bone and still not be happy/successful enough. As a rule of thumb, I'd recommend avoiding taking anything quantifiable as a measure of success because anything that goes to n also goes to n+1.

  
  


• 
  

  Don't let others dictate your mindset, whether they are your peers or seniors. There is a lot of "fake it 'till you make it" out there.

  
  


• 
  

  Try to see where you make/made a difference. That could be helping a peer solve their problem, going to a meeting instead of your boss so that he can go take his/her sick kid from daycare. That could be helping a student in a lab, or writing to a fellow academic on the other side of the world, to help him/her sort out the mess that is a life in academia. ;)

  
  

Hope it helps!