thesis - Revocation of Master Degree

I didn't give the dimensions of the machine that I designed in my master thesis. My supervisor said that you don't need to give dimensions and said that they are useless for a thesis: you don't make a design as an engineer, you are doing research. So I didn't share the dimensions. And I have dimension-related findings/figures in my thesis. I mean, if you change dimensions, half of the graphs/results need to be revised. But now, I learned that some people say that it makes your thesis misrepresent. Is it the case for my thesis?

On the other hand, I spent three long years for this thesis and I never plagiarised. I asked every question to my supervisor. But today because of this situation I'm very stressed. I didn't want to a mistake but because of my supervisor's reckless situation I don't know if it will cause my thesis to be revoked :(

You can imagine that; in 80% of my study I have 2 data sets: one of them subject data the other one is my design. So, you can't change the subject data I mean they are constant numbers and also I give reference to that data. But my design's dimensions can be changed and if you change them all my figures are changed because the structure is changed. Can you make a comment on this situation please?

publications - What is the explicit meaning of “corresponding author”?

Problem

This question was triggered by the comments on this discussion, but comments and answers on these questions confirm the existence of conflicting ideas.

There seem to be two prevalent interpretations of the word corresponding author:

1. 
   

   The corresponding author is the one who corresponds the (unpublished) paper to the journal, i.e., who performs the technical process of submitting the paper, is available for requests on the review and publishing processes, and so on.

   
   


2. 
   

   The corresponding author is the one who corresponds on the (published) paper with anybody who likes to do so, e.g., because they found an error or like some clarification.

   
   

What I found out so far

Until today, I was only aware of the first interpretation, which was confirmed by my experience: For all papers I submitted, I automatically became the corresponding author and cannot remember that I could choose one of my co-authors for this role. Some of these journals do not even indicate a corresponding author to the reader. Also, there already is a way to indicate that an author is available for questions on the paper (interpretation 2): stating the e-mail address.

On the other hand, other journals do indicate corresponding authorship, which makes little sense for interpretation 1. Also, the value put into this role by some funding agencies for its implied meaning makes more sense for interpretation 2 (not that I completely agree with it).

Looking for some guidelines from publishers covering multiple fields, I found the following instructions on denoting the corresponding author from Elsevier¹, which kind-of covers both interpretations:

Clearly indicate who will handle correspondence at all stages of refereeing and publication, also post-publication.

While there are other questions on this site touching this issue, they focus on consequences of the interpretation, such as how to assign corresponding authorship, the implications of corresponding authorship, or whom to address with a request.

Actual question

What is the explicit meaning of the word corresponding author? Interpretation 1 or 2 as listed above, both, something else, or is this an extreme example of academia’s inhomogeneity and the answer depends on the field or publisher? Please answer only if you have more to offer than personal experience and individual journal guidelines. In particular, please address the possibility of a varying meaning.

---

^{¹ which is separate for each journal, but seems to be identical in content for many journals}

Answer

IEEE distinguishes between contact author and corresponding author:

Contact Author: This is the person who is contacted in regards to the submission during the peer-review and production processes.

Corresponding Author: This is the person who is listed as the author to be contacted in the printed publication.

PLoS states two types of corresponding authors:

Please note that the corresponding author for the online submission process can be different from the corresponding author of your published manuscript.

Copernicus uses the terms contact author and corresponding author:

From submission to publication, the authors of a manuscript are formally represented by the registered contact author(s). After publication, the authors of a manuscript are formally represented by the corresponding author(s) specified in the published paper.

Personally, I've seen this differentiation several times. Sometimes the corresponding author is simply a role in the journal system that the submitting author/person can assign to one of the authors during the submission process. The corresponding author might also change during the process.

Conclusion:

Some publishers make a difference between the author corresponding with the journal (submitting/contact author) and the author corresponding with potential readers of the article (corresponding author). Some publishers don't. It's absolutely inhomogeneous and seems also to vary by journal not only by publisher. And it varies over time.

---

Side note:

And yes, these publishers are indexed in SCOPUS and Web of Science (Science Citation Index, Thomson Reuters Master Journal List).

Search for the publishers in SCOPUS (select checkbox "publisher") or the Thomson Reuters Master Journal List (TRMJL). The latter includes all journals indexed in Web of Science. Unfortunately, the search in TRMJL is only based on journals and not on publishers. Search for "plos" to see PLOS journals, "ieee" for IEEE journals and e.g. "geoscientific" to see two Copernicus journals. See also IEEE indexing agreements, Visibility of PLoS and Copernicus metrics.

publications - Literature review and authorship

Let's say a research assistant has provided help on conducting a literature review and that some of the references are eventually used in a published paper. Would the research assistant normally get some kind of acknowledgment or authorship if they did not contribute any written material?

Answer

I think you should definitely mention the research assistant in your acknowledgements, but not as an author. For such questions, I generally refer to the Vancouver Protocol, a widely used standard to determine appropriate authorship (search "Vancouver authorship" on the Web and you'll see that it is fairly well known):

The ICMJE recommends that authorship be based on the following 4 criteria:

• Substantial contributions to the conception or design of the work; or the acquisition, analysis, or interpretation of data for the work; AND


• Drafting the work or revising it critically for important intellectual content; AND


• Final approval of the version to be published; AND


• Agreement to be accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved.

Furthermore,

Contributors who meet fewer than all 4 of the above criteria for authorship should not be listed as authors, but they should be acknowledged.

So, according to these principles, the research assistant is not a coauthor, but ought to be acknowledged.

Also, please note that coauthorship is often considered an ethical issue (that is, it is considered unethical to include someone who does not merit authorship, or to exclude someone who does), whereas it is more of a professional courtesy to acknowledge someone's contributions (that is, it is nice and collegial to acknowledge someone, but it is not considered unethical not to do so).

graduate school - What are the options for fellowships for international grad students in USA?

I'm looking for fellowships that an international grad student can apply for, to support him/her while working towards a Ph.D. (additional to whatever funding that may be available as TA). So far, I've been able to identify the following:

The main criteria for selecting award winners are: l) excellent academic records, 2) genuine financial need, 3) admission to a reputable institution of higher learning and 4) thoughtful and coherent educational and career plans. Candidates are also evaluated on their extra-curricular interests and achievements, potential to achieve their goals and likelihood to succeed in a foreign academic environment. Applicants are expected to have some years of work experience in their field of interest.

It would be great if I could get to know of similar fellowships that an incoming student can apply to, before starting grad school.

Answer

The Smithsonian offers fellowships for international grad students, specifically a ten-week summer internship for pre-dissertation grad students and 3-12 months of funding for post-dissertation grad students. Also, you get to work at the Smithsonian.

Can one or two emoticons be used in a PhD Thesis?

I have a very dumb :-) question:

Are emoticons (if rarely placed - one or two times) in a PhD thesis considered unorthodox?

I have an introduction where I give an apt example and appended some small footnote where I make fun of the author (that's me) and I was so laughing when writing this I almost liked to put a smiley at the end of the footnote.

The reader of this question should note, that the thesis is already enough serious such that a smiley might be surely a relieve for the reader maybe :-)?

What is the general thought about this?

Update: After all these enlightening, entertaining and thoroughly funny thoughts, I decided to go with a humorous footnote but of course without a smiley. :-P

Answer

I highly value humor and love to entertain whenever I can. In formal writing, I would encourage you to go ahead and write something that you think would be funny. Then reread it. Then reread it again. Read it aloud. Read it silently. Read it again tomorrow while you edit it. And read it again. And again. And again. Imagine reading it out loud to the people with the least sense of humor you know. Imagine reading it to a person with a furrowed brow, in a bad mood, who is trying to find anything they can to rip apart what you have laid down, to find a reason to cast it aside as useless junk.

Then read it 10 more times, as any good writer must inevitably do. Now imagine reading it again in 10 years (if you are lucky and what you've done turns out to be of use).

Personally, I have found that after the 20+ time I've read something, it isn't even funny to me anymore - and I think I'm hilarious! But even the best jokes I've ever told never landed 100% of time, or to 100% of the audience - and in formal writing I don't even know who the audience is - they might speak my language as a 2nd (or 3rd or 4th) language.

Being stubborn, I like to write humor into anything I make. But after the 20th read through I realize it just isn't funny any more, even to me - and if that's how a reader would feel who doesn't get or appreciate the joke, it just isn't worth it any more to me to include it. I'm basically writing a technical instruction manual, and there's a reason those things aren't really funny - you are supposed to read them and refer back to them repeatedly, and jokes get old fast.

If I really like a joke, I'll save it for when I can make it in person, in a talk or in a presentation, when I can personally hear the laughs (or gauge the room and know to skip it entirely). Or I'll be funny on a website like this so I can wallow in a mass of glorious unicorn points.

But in formal writing like a thesis or important research paper? Well, you decide after you've read it for the 30th time if it is still worth inclusion, or if that emoticon makes you smile - or if you want to poke it in its tiny little semi-colon eye.

brain - What really is color and how do we perceive it?

How do our brains actually transform the information that the cones in our eyes receive into the different colors that we can see and imagine?

Answer

Despite its simplicity, this question demands a so complex answer that we can start by saying:

We still don't know.

Because you are talking about the colour as a sensation, as something that I feel and that I (literally) see. And here is the problem: as such, the "colour" is not a physical reality.

Some people may disagree here, but colour is not a physical property of any material. Light is a physical property. The wavelength, the energy, the frequency of light are all physical properties. Even the crazy quantum nature of the photon with its restless existence is a physical property. But not colour. Colours are creations of my mind, my nervous system, my idiosyncratic consciousness.

For instance, It's simply impossible to know if the red that I see in my mind is the same red that you see in your mind. The fact that we both call it "red" or the fact that we both agree that the colour of the blood is the same colour of the wine doesn't help at all: this is a problem of qualia:

http://plato.stanford.edu/entries/qualia/

https://en.wikipedia.org/wiki/Qualia

And the same goes for all other conscious experiences derived from the exteroceptors, such as "taste" and "sound". What I feel is particular and nothing can guarantee that another person feels the same, even if the stimuli are the same and the nervous impulse to the CNS are the same.

To finish, I'd like to propose a thought experiment, for you to understand the subjective nature of the colour:

We tend to imagine that the world is the way we see it (as primates, we value the vision very much). But we have only 3 different cones, giving us roughly 1 million (100$^3$) different colours. Reptiles, as the birds, have 4 different cones, and some of those reptiles, as pigeons, have 5 different cones, giving them the ability to "see" 10 billion colours (100$^5$). This is hypothetical, of course, to really perceive all these colours the animal needs a huge brain cortex, but let's suppose that they see (perceive) all these 10 billion colours.

Now try to imagine these 10 billion colours, you, who are an organism that only perceives 1 million colours. It's impossible. And it's impossible for a talking pigeon to explain to you how he/she sees the world, how all these 10 billion colours are, the same way that it's impossible for you to explain to an animal with achromatic vision what is green, purple, orange, cyan, magenta etc...

This is what we call qualia.

But, as someone that loves cognitive ethology and science in general, I don't think that this is something beyond the realm of sciences, something impossible to know... this is a problem that can be scientifically addressed and, with the ingenuity of the neuroscientists and other biologists, we can someday understand the "redness" nature of the red we see.

phd - What books, biographies or survival guides are helpful for women in engineering in academia?

Recently, I was giving a small informal talk in a local college. The audience comprised of engineers and my talk was based on current research in engineering. One of the girls asked about the position of women in academia. I answered that stating that academia was like just another field for women but now that I think of it, it might not be entirely true.

I thought that perhaps I could refer interested female student to resources explaining any gender specific aspects of academic life. I've read 2 books "Surviving your Stupid Stupid Decision" and "What you came for." Both were books to read before PhD to discuss common problems and their solutions presented as a preparatory handbook or survival guide. I am looking for something similar, but specifically addressing the aspect of gender in academia. I don't have a specific question in mind. A cursory Amazon search failed to yield any fruitful results.

I'd like to find resources applicable to female students:

1. Engineering in North America but maybe even Europe. These students showed some statistics of bias within academia.


2. Interested in joining faculty positions or industrial labs.

Are there books, biographies, or survival guides for women in academia?

How to become a journal editor?

Being an editor of a journal can be time-consuming, but has obvious benefits (especially if one enjoys reading and reviewing manuscripts). So I expect many academics have a desire to become an editor.

I have never seen an advertisement for a position on an editorial board, which leads me to believe that most positions are not filled this way.

How do most people become editors, and how might a person wishing to become an editor achieve this (without setting up a new journal)?

Answer

Open positions in journal editorial boards are frequently not advertised (though that happens). Instead, when a vacancy appears, the chief editor will typically look for people with the required expertise and ask them whether they would be willing to serve.

Often, editors will have different specialties. So an editor who is stepping down would need to be replaced in his specific area of expertise. Given that he is an expert and should have a good overview of his specific field, he will most likely be asked to suggest possible replacements.

Chief editors will usually be "elevated" from among the non-chief editors, since these already know the journal and its specifics.

---

So, how to go about to be invited as an editor? Two things:

• Build a reputation as an expert in a specific field. Submit good quality papers to the journal you are most interested in (and others), go to conferences etc.


• Build a reputation as dependable and articulate. Hand in reviews promptly, and write good reviews. Editors remember people who write good reviews.

Of course, this is not a guarantee of being asked for an editorship.

copyright - Am I allowed to share a final copy of my published paper privately?

Suppose I published a paper in a journal with no open-access policy, but with the usual constraints regarding copyright.

A researcher that I do not know in person has asked me for a copy of a this paper I coauthored. Am I allowed to share the final-version PDF file with him/her (by e-mail)? I mean, does it make any difference with sharing it publicly (which I do know I am not allowed to)?

If not, what would be a polite way to tell him/her so?

Answer

Am I allowed to share the final-version PDF file with him/her (by e-mail)?

From a (US) legal perspective, that depends entirely on the publishing agreement. Some journals do allow this; if so, it will be stated explicitly in the agreement. For example, the APS copyright transfer agreement includes the text

The author(s)...shall have the following rights (the “Author Rights”):

3. The right...to make copies of all or part of the Article, including the APS-prepared version without revision or modification, for the author(s)’ and/or the employer’s use for educational or research purposes.

Without something like this in the agreement, whether you're allowed to share the paper depends on whether it can legally be considered fair use. No copyright agreement can prohibit something which falls under fair use, but on the other hand you don't really know what falls under fair use until a court tells you. I'm not sure if there's any precedent on whether sharing copies of an article for private research use qualifies as fair.

I won't address this from a moral perspective since you asked whether it's allowed, but as some of the other answers show, it's possible to reach a different conclusion that way.

I mean, does it make any difference with sharing it publicly (which I do know I am not allowed to)?

Well, this also depends on the publishing agreement. By default, if the agreement doesn't say anything otherwise, there is no difference between sharing the article publicly and sharing it privately; both qualify as unauthorized distribution, and both are similarly illegal. But the publishing agreement may allow for some forms of public sharing. Going back to the APS agreement, it includes several clauses allowing various forms of public sharing (under "Authors' Rights"):

2. The nonexclusive right, after publication by APS, to give permission to third parties to republish print versions of the Article or a translation thereof, or excerpts therefrom, without obtaining permission from APS, provided the APS-prepared version is not used for this purpose, the Article is not republished in another journal, and the third party does not charge a fee. If the APS version is used, or the third party republishes in a publication or product charging a fee for use, permission from APS must be obtained.

3. The right to use all or part of the Article, including the APS-prepared version without revision or modification, on the author(s)’ web home page or employer’s website and to make copies of all or part of the Article, including the APS-prepared version without revision or modification, for the author(s)’ and/or the employer’s use for educational or research purposes.

4. The right to post and update the Article on free-access e-print servers as long as files prepared and/or formatted by APS or its vendors are not used for that purpose. Any such posting made or updated after acceptance of the Article for publication shall include a link to the online abstract in the APS journal or to the entry page of the journal. If the author wishes the APS-prepared version to be used for an online posting other than on the author(s)’ or employer’s website, APS permission is required; if permission is granted, APS will provide the Article as it was published in the journal, and use will be subject to APS terms and conditions.

So under this agreement, you (the author) can post the final journal version of the article on your own personal website, and you can post preprints (i.e. versions you prepared prior to submitting to the journal) on a site like arXiv or grant permission to third parties to distribute these versions.

human anatomy - Why do we have two of some organs, but not all?

We have two eyes, but we don't have two hearts. Why do humans have two of some organs, but not all?

Answer

Here is my overly succinct answer.

I doubt we will ever know this for sure. But, it basically comes down to ancestral bilateral symmetry in development; this defaults to two organs and is broadly symmetrical except where the organs are central. See this article for a more thorough answer regarding bilateral symmetry.

Further exceptions to symmetry occur where evolution pressured the body into not bothering to grow the second of an organ due to a waste of resources for the body, or functional advantages emerged from asymmetrical evolution. I always like the ears of an owl for an excellent example of two asymmetrical features that provided a discrete advantage when it comes to locating the source of a sound.

publications - Status of submitted article changes the date but status remain from 'With Editor' to 'With Editor'

I Submitted a paper 2 months ago, the current status is "With Editor" and the status date of the manuscript (from With Editor to With Editor!) has been changed twice. What does it mean ?

etiquette - As a student with questions about a paper, can I email the author myself or should I ask someone else to contact him?

I am reading a paper and have questions about the details of the procedure described. I have read other papers by the same team but they don't explain too much about that procedure anyway. I think it might be common, but my supervisor doesn't know it too.

I am stuck and I want to get out of it. As a student working on my master thesis, can I email the contact author for the manuscript cold out, or should I ask someone to contact him for me? I would ask my supervisor but I don't want it to imply that I'm avoid taking initiatives when I could do it on my own.

Answer

You can definitely contact a paper author. They might be of the 'it obviously follows' == after 5 pages of calculations kind, or the empiricist who published the 20 successful regressions or simulations out of 200, with 180 contradicting their result or being inconclusive; and in either case ignore your question. From personal experience though, it can even lead to breakthroughs: in my case, someone sent me his lecture notes which clarified something I was stuck with, and related to the submitted question. However, if your advisor knows the author, or simply is well-known in their field, do mention that you are their student, as it should increase good will on the author's part - after confirming with your advisor that they are cool with it. Showing that you are active, interested, and independent should also go down well with the advisor.

plant physiology - How is photosynthesis observed?

How is photosynthesis observed?

• 
  

  Say I have plants A and B, and I want to find how fast they are able to turn carbon dioxide into oxygen. How would I experiment this?

  
  


• 
  

  Say I have one plant A, which has two kinds of leafs B and C. I hypothesize the B-leafs produce oxygen faster than the C-leafs. What kind of experiment could I set up to test this?

  
  

biochemistry - Domains in cell membrane

How is movement of proteins and lipids between different domains of cell membrane prevented?

Why is the noncytosolic layer not able to do lateral movements between domains but cytosolic layer is able to do so?

Answer

There are various mechanisms through which membrane proteins can remain localized in the membrane. See the below figure from MBOTC (book):

                                               

(A) They can aggregate together so that their relative positions are constant.
(B) They can be anchored to the Extracellular Matrix
(C) They can be anchored to the cytoskeleton
(D) They can be anchored via cell-cell interactions (adherens junctions, hemidesmosomes etc)

(E) Not mentioned in the figure; mentioned in the comments. Lipid rafts are membrane regions which are composed of rigid lipids like cholesterol and sphingolipids. Lipid rafts are thicker than regular membrane and do not diffuse into the latter. Some proteins are specifically anchored to/incorporated into the lipid rafts (T-Cell receptor, IgE receptor) and their relative position with adjacent proteins (co-receptors) remains constant.

Why is the noncytosolic layer not able to do lateral movements between domains but cytosolic layer is able to do so?

Where did you read this. Both layers can do lateral movements; if proteins are specifically "anchored" to one side of the membrane then the concept of domain applies to that side only.

Are contributions to conference proceedings considered to be "archival" publications?

While technical papers are generally considered to be "non-archival" and journal papers "archival", I couldn't find a clear statement about papers that appear in conference proceedings. Does it matter in which for the proceedings are published, e.g. only online, on CD/USB drive, or printed with/without ISBN?

Answer

Unfortunately, the reason you can't find a clear statement on this issue is because there isn't one. The answer depends heavily on the field and the particular conference, and there isn't necessarily an absolute answer even in a specific case. It may depend on why you care:

1. 
   

   You may care yourself, because you want your paper to be carefully archived and made available in perpetuity. In that case, it depends on whether a long-lasting, trustworthy organization has committed to providing access forever (and whether they have archiving contingency plans in case they go out of business).

   
   


2. 
   

   You may need to make this distinction to assist in evaluating your CV. In that case, the evaluators probably care primarily whether the papers are carefully refereed and in their final form, but the only way to know for sure is to ask them what their criteria are.

   
   


3. 
   

   You may be wondering whether you can publish an updated version of your conference paper in a journal. This depends on the customs in your field, and it requires agreement from both the conference and the journal. The publishing agreement for the conference should specify what sorts of further publication are allowable (if it does not, then you should be sure to ask, since saying nothing suggests they do not expect any further publication at all), and the submission instructions for the journal may also address this issue. If your submission is a revision of a conference paper, you should always specify this fact clearly and give a precise reference somewhere on the first page and in the cover letter, to make sure nobody could accuse you of hiding the previous publication.

   
   
   

The answers to these questions can vary. For example, major theoretical CS conferences are archival in sense 1 (permanent archiving and availability) but not 2 or 3 (papers are not necessarily intended to be in their final form and definitive versions may be published elsewhere).

etiquette - Is it appropriate to send an email to a professor at the end of the semester thanking them for their teaching?

I'm aware of very similar questions previously asked - all with good answers. These usually pertain to following up with a professor after a recommendation. My question is specifically about sending a thank you letter to a professor at the end of a semester.

My current semester is ending in three weeks and it has been my favorite semester by far. My professors taught their material really well and I was engaged non stop from the beginning of the semester. Among my professors, some assigned great homework questions, or lectured really well, or were very accessible during office hours. Overall, I had a great learning experience this semester and I want to express my appreciation because I haven't had a semester like this in the three years I've attended school.

I understand it may seem silly to question what is just a polite and appreciative gesture (I think it's silly myself), but I'm a little intimidated about the impression it will leave on my professors. I want to avoid the stigma of "teachers pet." For this reason, I've considered writing anonymous notes, but that seems creepy.

Kind of a light dilemma but I'd like some input because after thinking about it for a while I think it's an interesting topic. Thank you!

Answer

In the academic culture I am familiar with, this is a perfectly appropriate and appreciated thing to do after grades have been released. (A letter at the end of the semester but before grades are finalized can look like an attempt to influence the grading process.)

I have received some emails like this, and I was very happy to receive them. They left me with the impression that the student is a mature, appreciative, and thoughtful person, not that he/she is somehow trying to be a "teacher's pet."

graduate school - Why doesn't academia incorporate spaced repetition in higher education?

There are many publications explaining advantages of spaced repetition. I found a summary of some of them here.

While a lot of studies show many advantages of spaced repetition, it is not formally applied to higher education. Why is that?

UPDATE 1: In order to clarify my question, I added a quote form this publication:

Furthermore, even after acknowledging the benefits of spacing, changing teaching practices proved to be enormously difficult. Delaney et al (2010) wrote: “Anecdotally, high school teachers and college professors seem to teach in a linear fashion without repetition and give three or four noncumulative exams.” (p. 130). Focusing on the math domain, where one might expect a very easy-to-review-and-to-space strategy, Rohrer (2009) points out that mathematics textbooks usually present topics in a non-spaced, non-mixed fashion. Even much earlier, Vash (1989) had written: “Education policy setters know perfectly well that [spaced practice] works better [than massed practice]. They don’t care. It isn’t tidy. It doesn’t let teachers teach a unit and dust off their hands quickly with a nice sense of ‘Well, that’s done.’” (p. 1547).

Rohrer, D. (2009). The effects of spacing and mixing practice problems. Journal for Research in Mathematics Education, 40, 4-17

Vash, C. L. (1989). “The spacing effect: A case study in the failure to apply the results of psychological research”. American Psychologist, 44, 1547 (a comment on Dempster’s article?)

By the way, I am not trying to defend this publication or the quote. I just want to figure out if people believe this is true. If yes, why policy makers do not formally incorporate spaced repetition in education systems.

UPDATE 2: I really appreciate your interest in answering my question. I think there are still some unclear points that I want to mention here:

Please read the article in my question. Then you'll see the difference between "active recall" in spaced repetition and being exposed to concepts by reading books or attending lectures in our education system. Here are a couple of quotes:

active recall is a far superior method of learning than simply passively being exposed to information. ... There are many studies to the effect that active recall is best. Here’s one recent study, “Retrieval Practice Produces More Learning than Elaborative Studying with Concept Mapping”, Karpicke 2011 (covered in Science Daily and the NYT) ... “Forget What You Know About Good Study Habits”. New York Times.

While "spiral learning" is basically the foundation of spacing, in addition spacing heavily relies on active recall. Furthermore, spacing takes advantage of chunking in designing flash cards.

Moreover, there are well-defined spacing algorithms, designed by famous psychologists like Dr. Leitner, that significantly improve the efficiency of learning. Please look at studies by Professor David Shanks and Dr. Rosalind Potts.

Finally, in response to those who think spacing only improves memorizing, please read about the results of Professor Bjork's many years of experiments, specifically "Kornell, N., Castel, A. D., Eich, T. S., & Bjork, R. A. (2010). “Spacing as the friend of both memory and induction in younger and older adults”. Psychology and Aging, 25, 498-503."

Now, do you believe schools should leave students on their own to discover efficient ways of learning, or do you believe it's better to incorporate these well-studied methodologies into the education system? As a student, I pay my school to provide me with motivation, pathways, and efficient ways of learning, rather than merely providing me with a competitive environment to prove myself for a better job in the future.

Let me clarify this: I love education, research, and even just being at school. However, I believe in considering all improvements that technology has provided for us in different aspects of our lives, and I believe our education system is too old. I believe we can apply well-studied theories of learning, knowledge, neuroscience, and psychology to our education system, through the use of technology, and really improve our education system. I am trying my best to play my small role in this regard. My main purpose of asking this question in this forum is to brainstorm with you to collaboratively and learn how to improve our education system.

Answer

In tertiary education, it is the responsibility of the students to pick appropriate learning methods. It is simply not the task of a university to incorporate spaced repetition or any other learning technique, because revising and repetition is something that students have to do on their own. Bluntly put, if students "exhibit [an] illusion", that's something students must fix, not the university.

What could be done at universities is inform students about techniques such as spaced repetition (and I am not convinced this isn't already happening one way or another).

As you say, some universities pay attention to assessments of education quality. Certainly, such assessments are not looked at for their own good, but because some other decisions are based upon them. For instance, funding for a university might be influenced by results from an assessment, but if the respective funder does not take into account retention of learning, there is no motivation to try and influence this aspect. Likewise, some kinds of assessments may be paid attention to by marketing and PR departments of a university, while they are of little to no interest to the actual teaching staff.

Then, if an aspect is not covered by any assessment the institution considers relevant, the decision will be made based upon what the teaching staff considers most beneficial (usually in an uncontrolled process, by each teaching staff member individually). And this can well mean to give students some more responsibility in order to help them evolve into autonomous professionals.

Now, if you ask why external assessments do not take into account retention a lot, that is quite a different question, and its answer has to do with a mixture of ignorance and convenience:

• Ignorance because the people who set goals for such assessments know little about the individual subject areas, and also design the assessments in a subject-agnostic way, as the (possibly unrealistic?) expectation is to also make very different subjects comparable. Depending on the assessment, it may also be a design goal to make the assessment results comprehensible without knowing anything about the subject.


• Convenience because "We do not know." or "We will see in X years." are too impractical answers, even though they might be accurate. The assessments are probably designed with the idea that once the assessment is over, there is a final and definitive result about the current state/quality of the university. This in turn favours a disregard of aspects that need to be measured over prolonged periods of time, such as retention long after an exam.

evolution - How did the huge dinosaurs cope with gravity and loads on bones, etc.?

It's very costly to be a huge animal. Your mass grows in cube when you scale up, but you still only have two/four legs to support the same weight. This increases the pressure that your body needs to cope with.(this is easy to see if you compare an ant with an elephant. The elephants legs are much thicker and strudier in comparison to it's body)

Looking at a T-rex for example, speciemns have been found that are believed to weight more than 9 tonnes, compared to an elephants 10 tonnes. T-rex has ofcorse has only two legs. The heaviest dionsaur is believed to have weight 80 tonnes. That is the weight of about 20 cars on each of their feet.

How could they support such massive weights?

Answer

Assuming that gravity was essentially the same (other answers to this question notwithstanding), very large dinosaurs were dealing with the same forces that they would today. There are two clades of dinosaurs in which gigantism evolved, Sauropoda (quadrupdeal sauropods) and Theropoda (including T. rex). Each "solved" the problem of large size in different (but also somewhat similar) ways.

The main reason why large size was not a problem was that, if posture changed to align the forces between the animal and the ground, the bones are compressed. Bone is very strong in compression.

Theropoda

Theropod essential operate as a see-saw, with a large muscular tail balancing a large head. As such, they did not likely use much active muscular force to balance. The analogy is a human standing. Just standing, you don't need much muscle force to balance.

Hutchinson and Garcia (2002) showed that, because of a lack of plausibly large leg musculature, T. rex could not run. For a range of postures, they estimated how much muscle would be required to balance the animal and found that running behavior was unlikely.

Hutchinson, J.R. and M. Garcia. 2002. Tyrannosaurus was not a fast runner. Nature 415:1018-1021.

Sauropoda

Sauropods show many similar adaptations as elephants, the largest extant land mammals. Their limbs were held upright (erect), which requires less energy for balance. Some sauropods had air-filled bones, which would also lighten the skeleton. Wilson and Carrano (1999) document the evolution of posture through sauropod evolution from a biomechanical perspective.

Wilson, J.A. and M.T. Carrano. 1999. Titanosaurs and the origin of “wide-gauge” trackways: a biomechanical and systematic perspective on sauropod locomotion. Paleobiology 25:252–267.

neuroscience - What is the function of nodes of Ranvier in axons?

In a neuroscience class I'm taking, it was explained that myelin covers axons in sections, the uncovered sections are called nodes of Ranvier, and signals propagate much faster in the covered sections.

But if it is faster for signals to propagate along myelinated regions of the axon, why doesn't the entire axon get covered by myelin? Wouldn't that make it faster?

Answer

Every signal rapidly fades out with distance if it is not amplified. So if the whole axon were covered with myelin, action potentials wouldn't reach their target. Each Ranvier node can be seen as an active signal repeater.

How to get people to reply to emails and what to make of a no response?

Most people in research probably have first-hand experience regarding how difficult it is to get some people to reply to emails, e.g. (but not limited to) some reputed professors. It is also difficult to establish how to interpret a lack of response, because the person can be just busy and miss your email (i.e. "save for later" then forget about it) or might be purposely ignoring the email. I find the lack of response particularly annoying when contacting a listed "corresponding author" about their paper.

I have experienced several extremes: professors who reply within hours (or even minutes!); professors who failed to produce any response at all; even once I sent a job query and didn't get a response until after 2-3 months later, when the professor apologized about forgetting to reply and said he was very interested in my application.

The latter case almost cost me a job (luckily I had already secured a position elsewhere), and as it turned out later I could have resolved the situation by sending the professor a reminder that he had not replied to my earlier email. But how could I have interpreted his lack of response as either forgetfulness or disinterest?

The situation is usually better with postdocs and graduate students, who tend to reply, and when they do their replies tend to come faster.

Hence, my questions are:

• How to improve the chances of getting a reply to one's email besides the obvious "be brief and to the point"


• How to interpret the lack of response


• When is it appropriate to send a reminder and tips to avoid annoying the recipient with it

Edit upon request:

The typical content of the emails I'm referring to would be regarding the work done by the email's recipient or at their lab (questions about papers published by them, for instance). Non-spam job applications or surveying possible collaboration could also be included here.

Answer

If you want to know why you get faster responses from grad students than professors, just take a look at this comparison of email volume when transitioning from student to professor. Afterward the load just continues to rise (the number of emails I get per month is now much greater than anything shown there).

Many researchers -- particularly faculty -- have an email address that is publicly listed on the internet. That means that anyone in the entire world can contact them about anything at any time. Some well-known researchers get a huge amount of email, and could not possibly respond to it all even if they did nothing else. Even a fairly ordinary mid-career professor with some research funds gets a pretty high volume of email from total strangers. I'm not referring to outright spam but to things like applications for student/postdoc/researcher positions; requests for research assistance, or inquiries about research collaborations and so forth. Replying to such email cannot trump essential duties like research, student advising, and teaching, so the time for it is limited.

Initial message

Given a queue of tasks (emails) that perhaps cannot ever be completed in the available time, one must prioritize. If you are emailing a complete stranger, your email is not likely to be at the top of the queue. The best way to make sure your email stands out is to

• Ensure that it does not look like a form letter. Currently, the only messages I don't reply to at all are those that look like the sender could have sent identical messages to everyone in my department (usually, they did).



• Show that you have done your homework. If you're applying for a job, do you have some research ideas that the professor would be interested in? What makes you especially qualified for the job? If you're looking for a collaboration, reference specific things in the contact's papers that are of interest to you.


• Along the same lines, don't email a stranger asking them to do (home)work for you (yes, it happens a lot) or requesting information that you could find for yourself on the internet.


• Be polite. Recognize that you are interrupting a complete stranger without having been invited to do so. You are not entitled to their time; you are requesting it.


• Write clearly and concisely. If it's a first contact and you want to ask questions, try to ask just one question.

Lost messages

It does happen that messages get lost, due to spam filters or by being buried under other newer messages. If you don't get a reply, there is no way to know whether the message was lost or just didn't make it to the top of the queue. If it was lost, a reminder may be appreciated by the recipient.

Reminders

Typically, I would wait at least a week before sending a reminder. I feel that a reminder to a total stranger after 2 days is not polite. In your reminder:

• Be extra polite.


• Do not blame the recipient. A good strategy is to say you are sending a follow-up in case your original message went to spam, or something similar.


• Remember that you have no idea what is going on in the professional or personal life of the recipient, and you are certainly in no position to judge their actions.

If you are corresponding with a collaborator, the above rules still apply. Last month, a friend and collaborator suddenly stopped replying to emails just when we had nearly completed a manuscript. I waited two weeks, then sent a message just asking if she was okay. In fact, it turned out that a major personal issue had arisen that -- among other things -- prevented her from doing any work during that time.

genetics - Why can't we breed watermelons without any remaining seeds in the flesh?

Watermelon is just starting to come in season in the northeastern U.S., and having a seedless watermelon is convenient. The only downside is, the "seedless" almost always still have the immature, sterile white seeds in them.

What is the mechanism for breeding these watermelons so that only these white seeds remain? What is the genotype that results? Could the genetics be modified so that there are virtually no seeds (short of any minor aberrations) left in the flesh of the fruit?

Answer

The seedless watermelons, like bananas, are a crop that are specifically bred to be trisomic (three copies of a chromosome). The consequence is the seeds are non-viable.

How long to wait after sending an email to a professor before I should assume that I will never receive response?

I have sent an email to a professor at a local university. The email asks for assistance with a fairly large science fair. I have done much of the work and the email was asking about how I could improve it. After 4 days I have not received a response yet.

Usually people check their email on a fairly regular basis (Once a day, usually) and so I am naturally worried about it.

Is it possible the professor has not read the email yet or should I email other professors?

Answer

It depends on how long you think it takes to answer your email!

If you are just asking a few simple questions (= request for information), you can politely email again the professor after one week. Make sure you make your email as simple to answer as possible (bullet points, yes/no questions).

If you are asking the professor to do something for you that goes beyond answering an email, it is more complicated. An absence of answer can often be interpreted as a 'no'.

Keeping track of bibliography references for an entire research group

This is a related question to my previous one about keeping advisees aware of literature.

Given the relatively large number of papers that are out there, it's inadvisable to force every student to start from ground zero in building up a reference library. To me, this suggests that there should be some centralized ways of keeping track of bibliography references.

The low-cost but high-maintenance route to me would be to have an SVN repository to which people can update their own personal bibliography files. Are there other more time-efficient routes to manage this process when:

• people have different computing platforms and workflows (Windows with Office, OS X with iWork, Linux with TeX, etc.)?


• working with collaborators at other institutes?



• it's important (according to university/workplace regulations) not to have data stored "in the cloud"?

Answer

I accomplish this using the groups feature of Mendeley. It works on all three major OS's, allows you to share bibliographies easily with both your group and external collaborators. It also allows something that I think is very important -- lots of bibliographies on particular topics within the realm of what my group does. See, for example

I should mention that Mendeley's web interface to bibliographies is awful. But the desktop interface is quite nice and (most importantly) can export Bibtex.

Mendeley does store your data in the cloud (if you consider a bibliography to be "your data").

Update: I stopped using Mendeley when it was bought by Elsevier. I haven't found a satisfactory replacement.

Is it right to use 'X is a new research topic of interest to our lab' to indicate that the lab has not done research on 'X'?

Is it right to use 'X is a new research topic of interest to our lab' to say that the lab has not done research on X before?

I want to convey:

1.The lab only focused on research topic 'Y'(e.g. proteins) in the past. In the future, 'Y' will still be the focus, even though 'X' will be the secondary focus.

2.The lab lacked established biological experimental conditions for conducting research on topic 'X' (e.g. miRNA) two years ago, since topic X belongs to different field. I was the first student to conduct research on topic X.

I am a student, not the PI. I want to describe the experimental conditions when I began the project in PS for PhD application. I started from scratch and encountered many difficulties.

(I hope my edits would make the problem more clear, thank you! )

Besides, Is there a more polite way to say 'our lab'? I mean the lab I belong to.

teaching - What are some good ways to keep students coming to lectures?

Having taught calculus for several semesters, I've noticed that the number of students attending lectures are gradually declining (especially for the 9am session). I would not be worried if they have learned the material by themselves so don't see the need of coming; However looking at their exam scores I concluded that a lot of them are not doing so well in the class when they miss lectures.

So what are some good ways to keep students coming to lectures?

ethics - Is a professor required to provide homework solutions?

For graduate school classes, if a professor writes his own homework questions and creates his own problem sets, is he required to provide solutions to the homework problems, after the homeworks have been turned in and graded by his teaching assistant(s)?

grades - How to measure entropy of exam results

In this answer to a quora question, the answerer mentions how the 'entropy' of a set of exam results can be used to measure how well the exam differentiates between students.

Should I be computing the entropy of my students' exam results? How do I do it? How should I interpret the entropy information?

Edit: How is entropy related to standard deviation?

Answer

Entropy measures how much information you learn on average about each student from the exam results. For example, imagine an exam on which everyone gets a perfect score. In that case, you would learn nothing, so the entropy is zero. If half the students get one score and half get another, then you learn one bit of information about each of them. If you want to assign meaningful grades on the usual U.S. scale, you'll need at least several bits of entropy, and the 3.5 or 4 bits mentioned in the quora answer sounds reasonable to me.

The idea behind the answer you link to is perfectly reasonable: if your exam results have low entropy, then that basically means they are clumped together on too few possible scores, and you don't have enough ability to distinguish between students. On the other hand, I don't see much point to actually computing a mathematical measure of entropy (e.g., Shannon entropy), except perhaps for fun if you enjoy that sort of thing. Instead, you can just look at the range of scores and judge how well they distinguish between students. Think about how you might assign grades, and you'll rapidly see whether you run into problems, without any need for mathematical computations.

Furthermore, doing it by entropy is a little subtle anyway. Strictly speaking, Shannon entropy pays no attention to the distance between scores, just to whether they are exactly equal. I.e., you can have high entropy if every student gets a slightly different score, even if the scores are all very near to each other and thus not useful for distinguishing students. The quora answer obliquely refers to that (in the discussion of bins), but still this means you can't just compute a single number without thinking.

So I'd view entropy more as a metaphor than a number most professors should compute.

career path - Are faculty positions more competitive than government research lab positions?

Whenever I've been in the audience of a faculty interview presentation, I left impressed but demoralised. It appears the bar of making it as far as the interview is very high indeed, and I don't know if I'll ever be able to reach a similar level. On the other hand, I know quite some people employed as researchers at national/supernational scientific research laboratories, or at research divisions of operational government institutes. I don't get the same impression there. It seems to me that people who obtain faculty positions are more outstanding than those who obtain scientist positions for governments.

Is my impression correct? Is it less competitive to get employed at research laboratories or government institute research divisions, than it is to get employed as faculty at a university? If yes, why is this so? At a university, faculty spend their time writing grants, teaching, doing administration, and hopefully still a little bit of science. At research labs, the exact division of work probably varies, but involves doing research, developing products, writing reports and papers, perhaps doing consultancy or other work. Unless one loves teaching (I suppose nobody loves grant writing), I'm not sure why a position at a university would be more desirable/competitive than one at a laboratory. Is my impression wrong, or am I missing something?

(I have this impression for at least Sweden, United Kingdom, United States, and Canada.)

graduate admissions - Does stating terminal degree as Master's (and not PhD) hamper my chances of getting selected in a grad school?

I'm applying to a grad school in the US for fall 2016. While filling the application, I stated my initial and terminal degree preferences as Master's only (and not PhD) as I want to work in the industry post MS. Will it hurt my chances of getting selected?

publications - In what tense (present/past) should papers be written?

That is, should it be present tense or past tense?

Should there be a difference between the abstract, main body and the conclusion?

Does the field of publication have any impact?

Answer

The rules of thumb are:

• Established facts are reported in the present tense (“The path of light follows Fermat's principle of least time”). However, you should use the past tense when you refer to previous work in the field (“Maxwell et al. demonstrated clearly in a laser cavity experiment that no mirror is perfect”).


• The experiments, simulations or calculations you performed are narrated in the past tense (“We dissolved the remaining solid in a 5:1 solution of acetone and benzonitrile, and heated to 200°C for three hours.”)


• Discussion of the data presented in the paper uses the present tense (“The results obtained, shown in Fig. 3, clearly emphasize that the cell colonies grew faster on pink toothbrushes than green ones. We attribute this to the color-sensitivity, or kawai factor.”)


• Mathematical proofs are written using the present tense, because going through the proof occurs at the time of reading (“From Eqn. 1, we derive the following system of inequalities”).

Overall, the choice of tenses is actually pretty logical.

neuroscience - How do firing patterns arise from the activity of many ion channels?

In his answer to another question, Bryan Krause says:

Ion channels don't exhibit any firing patterns: neurons exhibit firing patterns that depend on all the channels present [...].

I understand it this way: The observable and measureable firing pattern₁ of the neuron (created at the trigger zone) is the linear superposition of tiny "firing patterns₂" of all the (voltage-gated) ion channels at the trigger zone, which in turn depend on the probabilities of opening and closing which are the same for all ion channels of the same type and obey some Hodgkin–Huxley-like law. These probabilities correspond directly to the shape of firing pattern₁.

The rhythm with which each single sodium channel opens and closes ("firing pattern₂") doesn't have to mimick firing pattern₁ exactly, only roughly and probabilistically: the open-close-ticks must occur near to the spikes of firing pattern₁, but not exactly and not at every spike. And some complete outliers are allowed. The rest is superposition.

Seeing things this way, indiviudual ion channels do exhibit "firing patterns₂", but these may look quite different than firing pattern₁ (although not completely).

Is this kind of reasoning correct?

If so: Can the following conclusion be drawn: The time scale of a firing pattern₁ depends on the number of ion channels at the trigger zone? This might be seen when looking at the rise time of a single action potential: If there is only one sodium channel, rise time will be larger, if there are many, it will be smaller. Is this correlation strictly linear?

Answer

Typically the activities of the ion channels are not called firing patterns as in neuroscience we refer to "firing" when we mean the elicitation of action potentials (spikes) but yes: Whenever an AP was fired a sufficient amount of sodium channels had to be open and therefore I thing your reasoning is correct. In other terms what you are saying is that the effective channel conductances change during an action potential.

On your conclusion: In the regime of natural parameters the time scale of firing pattern 1 mostly depends on the time constants of the voltage gated ion channels and not so much on the absolute number of channels (especially if all the conductances would scale equally). In the world of Hodgin-Huxley like coupled- and nonlinear-dynamical systems the voltage does not scale strictly linear with increasing the participating max. conductances. The interplay of max. conductance and temporal gating dynamics resulting in the effective conductance itself depends on the voltage and there are nonlinearities. So the correlation between the number of channels and the AP rise time is not expected to be strictly linear.

See the figure for a little example: I tested my reasoning by increasing the max. conductance for the sodium channel of a simple HH model and checked the max. steepness of the voltage (normalized by peak voltage).

Hope that answers your question(s).

artificial life - Bootstrapping (symmetry breaking) in evolution

Many fascinating phenomena in nature show different behaviours on the micro and the macro level. Here I am especially referring to phenomena that are symmetric on the micro and asymmetric on the macro level. Let me give an examples from physics:

Arrow of time: Physical processes at the micro level are completely time-symmetric, if you reversed time, all laws would remain the same. Yet on a macro level they are not time-symmetric, we have an obvious direction (flow) of time.

It seems to me that we have a similar situation with evolution:

On the micro level it is really only about adaption (and not about improvement): You put some beings into an environment and they adapt, you change this environment and they adapt. No improvement, just blind "back and forth".

Yet looking at the whole tree of life on the macro level we have a different picture, we see all kinds of emergent phenomena:

• explosion in diversity


• emergence of complex interconnected ecosystems with completely new dynamics of their own


• true innovations in functionality (sensors, actuators, information processing etc.)


• and finally of course higher order functions like abstract intelligence (and even qualia)

To make the difference more concrete I will give a gedankenexperiment of two planet simulators. In both cases you accelerate time so that one hour translates into one billion years. Both simulators function differently in a subtle way but you don't know how. You throw some simple sims onto both planets and let the evolution simulation run. You don't switch your computer off and go to bed, the next morning you decelerate time and take a look:

• Planet 1: The simple sims quickly adapted to the environment as expected (but they stayed simple because evolution is not about improvement but about adaption).


• Planet 2: Some strange looking sims wish you a good morning and want to discuss the technicalities of the Riemann hypothesis with you.

My question
What are the minimal conditions that have to be met to get this kind of bootstrapping (symmetry breaking from micro to macro level) started. And what is going on at the core of this transition from micro to macro.

Edit
My specific point is about the symmetry breaking process in the sense of system dynamics. To give an example of a possible answer it could be something like Parrondo's paradox, a fascinating phenomenon from game theory where you combine two symmetric (losing) processes to get a (winning) asymmetric process. More can be found here: Parrondo's paradox.

Answer

I found a paper which gives four conditions that have to be met:

• Condition 1: A rule should be enforced that individuals must meet some minimal criterion (MC) before they can reproduce, and that criterion must be nontrivial


• Condition 2: The evolution of new individuals should create novel opportunities for satisfying the MC


• Condition 3: Decisions about how and where individuals interact with the world should be made by the individuals themselves


• Condition 4: The potential size and complexity of the individuals’ phenotypes should be (in principle) unbounded

Source: Soros, Stanley (2014): Identifying Necessary Conditions for Open-Ended Evolution through the Artificial Life World of Chromaria

Chromaria is "an experimental platform that allows the exploration of evolutionary theories in an intuitive and visually engaging way" from EPLEX, the Evolutionary Complexity Research Group at the University of Central Florida (UCF)

graduate admissions - What is a good length for the statement of purpose in a U.S. PhD application?

Certain schools give you specific details about their statement of purpose. For example a maximum of a certain number of words, double spaced, two pages maximum, etc. If a school does not provide any of the above-mentioned details, what would be a good lenght in terms of number of words to engage the admission committee? Is a single space statement of purpose too compressed, or is it acceptable?

I know that brevity and conciseness are important, but I find it hard to fit all the information they want in a one page. And I have to list relevant experiences, future goals, research interests, and which people I would like to work with in the department.

Answer

Depending on the program I would keep it between 1.5 to 2 pages. I framed mine to answer the following questions:

• Why am I applying to this school.


• What are my research interests.


• Previous academic accomplishments.


• Previous professional accomplishments.


• Personal story of triumph (optional, I talk about having to drop out of high school to support my family)


• What is your goal after graduation.

Addition:

I would also target schools that are pumping out the research that matches with your interests... this will help when you are stating why you are applying like:

A major factor in helping me choose Awesome University was Professor Awesome's research on being awesome. I feel that this aligns well with my research interests, and would make for a great fit between me and the department.

Also, if you talk about any abstract ideas be sure to elaborate on them to give a level of specificity. They want to see you be able to translate abstract ideas into specific thoughts.

publications - Verifying that cited results are still current before publishing

Assume you are knee-deep in a project, going through a series of papers that are seemingly relevant to your project. You found this ~10 year old paper, which looks very promising indeed. A lot of interesting results, good discussion, etc.

At this stage, I think it's obvious that you should check whether or not the results and conclusions in the paper are still valid by searching for any correspondence related to the article (e.g., pointing out that some claims do not hold, etc). However, I have yet to find anyone that digs into such information. You normally find a paper, read it, find more interesting papers through references and keep on digging in this manner until you have accumulated "enough" articles to form an educated opinion.

My questions are as follows:

• 
  

  Is this (or any other) type of quality assurance process, when it comes to cited literature, common practice?

  
  


• 
  

  Is there a way to streamline this process? PubMed does not seem to include all correspondence related to each article.

  
  
  

---

_{I should perhaps note that, if you are in biomedical sciences (especially related to complex diseases), about half of the publications turn out to be wrong or misleading after some years, and perhaps a quarter more are shown to be incomplete in its findings. I believe it's in the nature of biology, in contrast to more human defined sciences like mathematics or computer science. There are no formulas or calculations to check the integrity of the work published.}

journals - How to handle a paper by a reviewer who wants to be paid?

A reviewer declines to review a paper because he wants to be paid. Some time later, this reviewer submits a paper to the journal (or to another journal who's aware of what happened – very possible with today's editorial management systems). How should the journal handle this?

Possible options:

1. Pretend we didn't notice and review as normal.


2. Write him an email to tell him we're aware of it, but are reviewing the paper anyway because we're a magnanimous journal.


3. Charge him a submission fee which we then use to pay the reviewers for that paper only.



4. Charge him a submission fee which we then use to pay the reviewers for that paper only, plus some extras which we use to pay the editor.


5. Desk reject because "our reviewers are on strike because they're not paid so we can't find reviewers for your paper".

I'm concerned taking retributive action will come across as petty and / or lead to a lose–lose situation. However, not taking retributive action doesn't feel right either – if the reviewer is not willing to review unless paid, then it's hard to expect other people to review (or handle) his paper unless paid either.

If it matters, only the first part really happened: The reviewer used the "decline to review" button with a reason that went something like: “Sorry, I don't review unless I'm paid. Feel free to contact me again to discuss rates”. Still, this decline reason is logged in the EMS, so it can happen in the future.

Answer

The editors of a journal should be professional at all times. Like in any part of life, in academia there will also from time to time be annoying individuals. Don't get down to their level.

Your point 5. would be simply acting out of vengeance. Regarding points 3. & 4. – is a fee a regular thing for this journal? Because if not, it would be a vengeful misconduct. If there is a fee, is it usually used to pay the reviewers? If yes, why wasn't this author paid for his review? If not, why are you considering an exception? This won't be a one-time incident: if you write again to those reviewers, they will want to be paid again, because you set a precedent. If they tell colleagues they were paid, you will be short of reviewers because everyone will want to be paid and will refuse to review otherwise.

Point 1. is the only right thing to do; if you want to be malicious, maybe also 2., but that's still a bit unprofessional to me.

In general, the author's and reviewer's role (even for the same person) should be separated. Being a reviewer is mostly voluntary, and it's just agreed/expected in the community to act as a reviewer from time to time. You cannot force anyone to do it. But you are obliged (as an editor of a publisher's journal) to consider for publication papers that you receive. Just get over this, and maybe consider avoiding working with this person as a reviewer or other such roles in the future. But don't dismiss him as an author. Don't be vengeful.

biochemistry - What is the name of the bond between phosphate and the sugar in a nucleotide?

I am slightly confused about what the name of the bond is between the phosphate and sugar within a nucleotide. All my research comes up with is a phosphodiester bond being the backbone of DNA. But within a single nucleotide, would we perhaps call it a phosphoester bond (all of my searches of phosphoester bond correct it to phosphodiester, so I don't think the term 'phosphoester' is in use...); or maybe it would be an O-glycosidic bond as it is a sugar molecule covalently bonded to another molecule via an O atom?

Answer

Phosophoester is a valid term. There are at least a 1000 peer-reviewed articles that use this term. IUPAC Goldbook defines nucleotides as:

Compounds formally obtained by esterification of the 3 or 5 hydroxy group of nucleosides with phosphoric acid. They are the monomers of nucleic acids and are formed from them by hydrolytic cleavage."

Phosphoester or phosphoric ester means an ester of phosphoric acid.

advisor - How should I take a potential PhD supervisor's age into account, when planning to follow PhD with habilitation?

I plan to apply for PhD in Finance/Statistics next semester, and hence searched for potential supervisors.

An issue I have is that many interesting candidates are above age 60, and in Germany Professors retire at 65, such that a subsequent post-doc/habilitation would most likely require a different supervisor after PhD. One Professor just started his position at age 40, but so he has not many notable publications and I am unsure whether he might change university soon (he just changed it from another 4 years position).

Could someone advise me on the importance of age for selecting a PhD supervisor in context of a long-term future academic career?

The time for PhD would be 4-5 years, and PostDoc/Habilitation/AssociateProf usually again 4-6 years, with goal of potentially becoming Full Professor in Finance/Statistics.

Answer

First: a few people commented that thinking about your postdoc/Habilitation before even starting your Ph.D. is premature. I disagree. I have seen too many people coast along during their Ph.D. time without ever knowing what they are going to do afterwards, and certainly not preparing for their post-Ph.D. time, whether in academia or in industry. So I would say you demonstrate good long-term thinking. Already thinking about your academic career will help you prepare to work out a research program, network (more on this below) etc.

Second: there is no problem whatsoever with changing advisors between the Ph.D. and the postdoc period. To the contrary! If you stay at the same place for almost ten years, you will need to explain why you never moved, never checked out other places to work, other approaches to research. Many, many (most?) people will switch advisors at least once, or possibly even do postdocs in two different places.

Incidentally, this is why I think it is a good thing you are already thinking about your long-term future now, because it is never too early to start meeting people at conferences with your future in mind. You may just meet someone at your first conference who you could collaborate with or spend your postdoc time with.

So I would definitely recommend that you consider the older potential advisor. He sounds like he could introduce you to lots of people, and you will likely not need to pack up and move somewhere else during your Ph.D. period, which seems possible with the younger professor and which could somewhat mess up your personal life.

Of course, these considerations are all not the highest priority. You should definitely keep other aspects in mind in choosing where to do your Ph.D., like the kind of project you would be doing for either of the two professors, or whether the two of you "click" on a personal level, or what financing there is, or lots of other things you should discuss with your potential advisor ahead of time.

Finally, there is no Habilitation in Germany any more. Nowadays, Germany has moved to a more American style in academic careers. You will do a Ph.D., then a postdoc, then usually a Juniorprofessur (roughly, assistant professorship - not tenured and limited to six years), then get your Ruf to a tenured position. It's quite possible to skip the Juniorprofessur, though.

graduate admissions - A good motivation letter

I am writing a Motivation letter to be used in applying for masters from German or Finland Universities. I have following points explained in my motivation letter:

• How I see this technical world


• Why I chose Computer Science in my under-gradute


• What I learned in under-gradute



• What are my interests


• Why I want to pursue Masters


• Why I chose their University

What could be the format of a good motivation letter?

What other points could be included to make it more explaining about myself? And how to arrange those points? How to connect a motivation letter to your CV?

Answer

Well, just typing "motivation letter" or "cover letter" into Google seems to spew up links to loads of hints, tips, and how-to-s, so I guess it's not so hard to find materials outside of here.

So, instead, I'll focus on the advice that was given to me last year when I had to write one, since it worked for me :)

An important thing to realize is that a cover letter is supposed to complement your resume, not duplicate the same information. Thus, your qualifications and achievements should mostly stay in the CV.

Also, you should focus mostly on the position you are applying for, what makes you want it and what makes you think you would be good for it, which means that "how I see this technical world" probably does not deserve much elaboration (one sentence should be okay in my opinion). You are trying to convince them that you are the One and show them what makes you different from the bulk of people applying. What makes you more suited, more likely to succeed, or a better fit than other applications they're considering. (I would guess it's easier for a Master studies application since they will be admitting more than one/a handful of students).

Finally, the structure that I used, and will probably use the next time I will have to write something like that, is dividing the letter in to three parts:

• you: here's where you'll put information on you. While you're not supposed to list all your achievements here, you should emphasize or elaborate on specific achievements, skills and motivations that make you especially suited for the position you're applying for


• 
  

  them: it is important to "prove" that you're not sending out generic application letters. You demonstrate that you're familiar with the work done in the university/lab/research group you are applying for.

  
  

  If you're applying as a PhD student to a lab/professor, you might want to mention a specific paper or project and write an intelligible sentence or two about that. If you're applying for a University, you might want to pick some specific of their programme that especially caught your eye.

  
  


• 
  

  you and them together: first section is about how awesome you are. The second, how awesome they are. Now (to conclude), you have to show why you thing you would be awesome with them. Why do you think you're a good fit, right there? This section is not only about what they can do for you, you also have to try and convince then of how they can benefit from you.

  
  
  

Finally, the letter should not be longer than one page. Somewhere, you can even find this as a hard limit on an application. In my experience, you should also not have more than 3 sections. I managed to put an introductory sentence and an finishing sentence just fine in the "sections" I mentioned. Also, your writing should be impeccable. If you can, get a native English speaker to check your language. Use a spell checker. Pay attention to details. Getting an address wrong, or a letter in a name, shows sloppiness. Maybe it does not consciously affect the decision, but it might on some level.

And the last advice I got, which I did follow, but you don't have to take it as a hard rule: avoid negative statements. It's supposed to give a better tone to your letter. So, instead of saying, e.g. "Unfortunately, I couldn't find and internship during my last summer", you should write something like "Having a free summer before my last year, it allowed me to spend more time reading upon the areas of my choosing". The positive statements should help you present the facts in a more positive light.

writing - Creating paper on software tool

In my master thesis I developed a software tool that improves a common workflow used in a certain industry. Currently, no such tool exists, and this workflow is conducted manually all around the globe. I am currently in the finalization phase of my thesis and my supervisor told me to write a paper on the tool and the worflow improvement.

Now here is my Problem:

• I have the tool and I can show that the workflow is performed better with it (our industry partner puts almost no limits on use cases, interviews, etc)


• I have no idea how properly package this into a paper (also, what to objectively measure to "proof" the improvement)

Could someone please point out a few "good" papers, where a software tool was created for a problem domain (where no such tool existed before) and evaluated so that I can learn from it's structure, the approach and the proper "packaging" of the entire paper?

publications - Why do editors sometimes accept a paper even if a reviewer recommends rejection?

For the last many days, I have a question in mind related with the editorial decision of accepting or rejecting the manuscript after peer-review:

Few days back I got a review report from a very reputed mathematics journal in which reviewer 1 had given some good points and suggestions to further improve the paper while reviewer 2 had given some points and rejected my manuscript. Although, its not tough to revise the paper as per the suggestions of reviewer 2. I would like to know why editor has given me chance to revise the manuscript while reviewer 2 has rejected it. I asked this question because in the past I had bad experience of rejection despite of getting acceptance from one of the reviewers.

Answer

It is up to the editor whether to accept or reject. The reviewers only make recommendations. Even if the reviewers give positive recommendations, the editor can decide to reject a paper.

If both reviewers give negative recommendations, it is much less likely for the editor to accept a paper. If there is a mix of opinions the editor has to make a judgment, subject to whatever internal procedures the journal has in place. It seems like, this time, the decision was favorable for you.

etiquette - How to politely and logically explain that I don't want to receive notification at my private social media account?

My department is becoming more and more annoying by posting everything in Facebook group, from exam results, seminar schedule, to private information about students ( telephone numbers, addresses, emails, etc.)

I don't know how to explain them that I care about safety of personal information and that privacy of my personal information are important to me, but please be aware that I don't want to sound pretentious. Is there any way to address this issue correctly?

publications - Can I ask the editor for rapid processing (rapid peer review) in the cover letter of my paper submission?

I'm a PhD student and I need to (almost desperately) squeeze in another paper for my dissertation in the next 6 months. Is it acceptable to explain my situation to the editor and ask to set a tighter deadline to the reviewers?

My field is health sciences and biostatistics.

publications - Is it acceptable to email the authors of a paper for the slides they used while presenting it in the conference?

I've noticed that while there's no alternative to going through the actual paper in detail, it often helps if I've gone through the presentation based on the paper, which the authors had used while publishing their papers. (Mostly because, the few presentations on TCS papers that I've seen have good geometric examples/illustrations which may have been instrumental in getting the intuition in the first place, but the brevity required by CS conferences mean very few of them make it to the published paper!)

While a few authors graciously maintain the links of such slides on their web-pages, most do not - and I haven't even seen a single CS conference maintaining such documents on their web-page!

So, I've the following questions:

1. Since I'm ultimately interested in understanding their work (and extending it if possible), is it considered OK to email the authors for the slides (if they still have it)?


2. If it is, do I have to justify/explain why I want the slides, or would just a polite request do (with minimal explanations on my part to keep the mail short!)?


3. Would making such a request more than once make the author feel offended, and/or make them think that someone who can't read papers at the highest level without "assistance" isn't exactly someone worth helping out?


4. If there are 2 authors listed, without any implications about who is the corresponding author, should I mail both of them at the same time (which may lead to both of thinking the other would be responding), or separately (which may lead to duplication of efforts!)?

I'm not sure what to tag this query with - feel free to re-tag/add more tags as you see fit!

thesis - What are your thoughts on epigraphs in theses?

I am wondering if there is a general consensus as to the suitability of epigraphs in a thesis, either a single one at the start of the document, or an appropriate quote to begin every chapter.

For example, at the start of a technical chapter describing some code, I could write

Beware of bugs in the above code; I have only proved it correct, not tried it. - Donald E. Knuth

I am lucky to have complete freedom over how I choose to typeset my thesis (Master's thesis in astronomy) and I like the idea of a thematic quote to begin a chapter. However, I am wary of seeming unprofessional or tacky so I am curious to get some more thoughts on the matter.

Manuscript status changed to editor assigned after under review, what could be the reason?

Recently I submitted minor revision to springer journal. For 3-4 days, the status of my manuscript status was showing to be Editor Assigned and after that status changed to Under Review. Now status of manuscript is changed to Editor Assigned again. What is meaning of this change ?

Answer

The first mission of the editor is to assign reviewers and take a decision depending on their return. Hence the first Editor Assigned to Under Review. The reason with it is now Editor Assigned can be due to several reasons. This depends a lot on the manuscript management system, and the editorial practices.

Either:

• The editor has already received the necessary reviews, and is taking a decision (perhaps taking another look at your paper)


• The editor has not received the necessary reviews.

The second case may be caused by different situations. Even with a "minor revision", it may happen that:

• not enough of the first round reviewers have responded. Some journals impose a minimum. So he is looking for another reviewer (or doing the review himself), as suggested by @Buzz


• the 2nd round raised more than minor concerns. Sometimes, after the first round, a reviewer notices sometimes more important, and can ask for a major revision (or a reject). So the editor may add another reviewer, to settle the case.

The latter happened to me once as a guest editor. ED1 said major, ED2 said minor. After round 2, ED1 said OK, ED2 said reject. A very painful situation for everybody.

I wish you are just in the editor decision frame.