graduate admissions - Does one need a master's in math before taking a PhD in pure math?

I finished bachelor's in mathematical finance and am nearly finished with master's in mathematical finance (I am already done with thesis), and I plan to pursue a PhD not in mathematical finance but in pure mathematics particularly stochastic analysis.

Is getting into a PhD in pure mathematics possible without a master's in pure mathematics? If so, how can I best prepare for it what difficulties may I encounter?

I have two concerns in particular:

1. I feel I do not have enough training in mathematical research. In undergraduate studies, we did not have many mathematical research projects. Some of our projects included researching on particular topics involving applications of mathematics we learned (since we were an applied mathematics course) and problem sets, but I don't know for how much they count towards mathematical research experience. We had some statistics and finance projects, but obviously they don't count.

We did not have a thesis in undergraduate studies, and most of our theses in master's did not involve much pure mathematics (which in mathematical finance would be stochastic analysis since as far as I know no other non-statistical math is used in mathematical finance). I have a hunch none of us this batch or in the batches before us ever had to research in mathematics for our/their theses.

2. I do not have much exposure to other kinds of mathematics. One of my coursemates helped me realize that one of my reasons of choosing stochastic analysis is our limited exposure to other math. I was aware of this but did not think this was a problem.

As far as I know, MS Math programs require Complex Analysis, Real Analysis, Linear Algebra, Abstract Algebra and then some electives and thesis. I don't think the lack of classes is a problem as I guess I can take those during the PhD program. To me, it seems my concern is the lack of a mathematical thesis.

So, is my limited exposure to other math a problem?

Our math classes besides Calculus I, II, III, Linear Algebra and Elementary Probability are:

1. 
   

   1 class of each: ODE, PDE, Discrete Mathematics, Numerical Analysis/Scientific Computing, Elementary Real Analysis (the one with Riemann-Stieltjes), Advanced Real Analysis (the one with Lebesgue), Advanced Probability (the one with Measure Theory)

   
   


2. 
   

   4 Statistics classes. (As I like to put it, "More statistics than I'll ever use in my life.")

   
   


3. 
   
   

   NO Complex Analysis, Abstract Algebra, Topology, Graph Theory or Number Theory (though the last 2 are in our discrete mathematics, they weren't taught in our discrete mathematics classes).

   
   


4. 
   

   2 Stochastic Calculus classes

   
   

This comment says I should be "be comfortable with mathematical proof in a variety of areas"

Answer

It depends on the country.

In the US, it is frequent that students go from undergrad right into their PhD. While there, some do get a Master's, but as a side effect of coursework for the Ph.D. Though, I myself did get a Master's first.

I believe it is more common in Europe to get a Master's first due to the shortened Ph.D. process there.

bioinformatics - How much Open Access Data is there in genetics?

Type of data of interest

I would like to consider

• Genetics data (SNP, microsatelites, whole genome sequencing, RFLP, ...)


• Genetic - phenotype data (disease-related data, QTL, etc...)


• Sequence annotation and function


• Transcriptomic data

I would like to include data on any living thing (including data from fossils) and not only human data. To avoid issues of semantic I would leave out epigenetic data.

Question

How much (in bytes) of such data is available in Open Access online?

Difficulties

I realize getting to such estimate might be hard and the estimate may be very inaccurate. Also, the format used for storing these data will definitely affect the relationship between information content and storage usage. But if someone can give just a rough order of magnitude, a vague intuition, it would already help. Is it a few terabytes or a few petabyte or even more?

I would welcome as well a detail of how you got to this estimate. I am particularly interested in what fraction of it is human data (if you happen to get to such fine detail).

united states - What are the perks of being a tenured professor at U.S. universities, besides having academic freedom?

For instance, one of my professors went to Princeton (for his undergrad math degree) for free, because his parents are tenured faculty at Princeton. Is such a benefit available to tenured faculty at most U.S. universities? This is assuming that a tenured professor's children are qualified to be admitted to the school.

Besides having academic freedom, what are some other, lesser-known, considerable perks of being in academia as a tenured professor as opposed to being tenure track?

(Main motivation for the question is to follow up on a previous question in which the OP asked about the stresses of academic life, specifically, in mathematics research.)

Answer

Universities offer all sort of "benefits" to its employees. Some of these "benefits" do not have a monetary value (e.g., flexible work schedule). The benefits available to faculty are often different from the cleaning staff. Further there are differences in benefits between tenured/tenure track and adjunct faculty. I can only think of three benefits, that have a monetary value, for which there are differences between tenure track and tenured faculty

Sabbatical: Some universities do not permit pretenure sabbaticals. It is often hard to differentiate if sabbatical eligibility is tied to tenure or time in service. Brown University provides different sabbatical benefits pre and post tenure.

Housing Assistance: Some universities provide housing assistance (discounted homes, mortgage assistance, loans, etc). Portions of the housing assistance program at Columbia requires tenure.

Parking: Some universities provide parking passes. Carroll College provides reserved spaces for tenured faculty while other faculty and staff simply get a parking pass.

In terms of perks that do not have a monetary value, this varies widely by department. Tenured faculty often get to be chair of the department (which may or may not be a perk). Departments may also give tenured faculty priority in terms of teaching schedule, departmental and university service requirements, office space, and lab space. The sabbatical system, internal funding, and administrative support may be skewed in their favor also.

advisor - Is it OK to start a PhD with a side project still running from your master's?

I just finished my master's and I am about to start my PhD studies. As I am very used to do many independent projects during my bachelor's and master's, I am willing to continue a side project on a fairly related topic. Actually, this is project is on a topic completely related to my potential PhD project and even during my job interview my supervisor said it is a plus for me to have experience with these kind of projects.

I have been working on this project from second year of my master's and I worked only about 3-4 hours per week on that, so I guess I can manage to keep it as a side project. The thing is it still needs some work to lead to some acceptable results, but I'm sure it will pay off, if I can make it. Yet, learning about the methods used in the project are really helpful for my PhD project as well. The problem comes where most professors want concentration from their students and this might not be Ok with working with another researchers. Besides, my collaboration in the side project seems not to be very efficient since it is a side project for my collaborators as well.

The question is should I discuss this with my professor even if I want to dedicate some of my free time to that? Should I risk my relationship with him in the early stages of my PhD studies (in case he is not Ok with that?)? Do I look like some trouble maker if I ask him about this? Do you think I should continue this project or just simply drop it and concentrate on my PhD project?

Answer

Let me answer in two parts:

1. With the right advisor, projects undertaken on your own initiative will be valued rather than seen as a problem.


2. You definitely need to talk to your advisor now to make sure you're with the right advisor.

Expanding on this a bit... one of the hardest things for many people to learn in a Ph.D. program is how to organize and initiate their own research portfolio. You show signs of doing this right from the start, so as long as you are willing to accept feedback and guidance, this is potentially a really good thing.

Whether it is a good fit for your advisor, however, depends on what your advisor's needs are at their current stage in their career. Some professors really need their students to be focusing on particular problems that the professor currently wants or needs to tackle. Others are able to give their students more freedom to wander intellectually. This is partly based on career stage (pre-tenure professors are likely to demand more focus), and partly on personality (a control freak or an empire-builder will not be mellowed by tenure; a highly confident professor may give much free rein even before tenure).

So: talk with your advisor about your desires and plans. If your advisor is receptive to the idea, great: now you can sort out how to balance things and make sure you aren't neglecting any responsibilities or making strategic mistakes. If your advisor is not receptive, you need a different advisor.

physics - How do I get physicists to listen to something that they do not want to hear? (Not a duplicate)

My words are coherent and intelligible. My arguments are valid and sound. It is nonsense to accuse me of being a crackpot simply because you do not wish to hear what I have to say. Please remove the duplicate tag on this post?

I have discovered a mistaken assumption that was made three centuries ago and has somehow been overlooked since then. It is a principle that was initially and remains to this day "proven" by a perceptual error. If we put the demonstrations and examples to the test of measurement, it is clear that the principle is mistaken. It has deep rooted effects on almost every aspect of science.

It is actually a very simple problem which makes my task more difficult because I face the argument that the theoretical physics papers I have produced are too short to be of importance. This is nonsense. Bear in mind that there is no restriction on the minimum length of a physics paper and I have discovered that the more material that is available to a person who is determined not to accept something, the more hooks there are available for a confirmation bias to manifest. I have discovered through my attempts that brevity is key to overcoming confirmation bias. There is good reason that there is no restriction on the minimum length of a physics paper. Unfortunately, I have not yet discovered the key to overcoming the cognitive dissonance that confirmation bias quickly evolves into.

My papers have been rejected without peer review more than a hundred times despite having had them professionally edited to ensure that they are properly formatted and error free.

I am censored on every science forum upon which I have tried to post anything related to this in most cases before any discussion has taken place. This post itself is being marked as a duplicate with nonsensical reasoning.

It is bad science to reject a submission without even addressing the presented argument. It is bad science to reject a logical proof without showing that the premisses are false or the deduction flawed. It is bad science to base your beliefs on tradition and ignore and censor any information which might conflict with them. It is bad science to immediately accuse someone of crackpotism the moment they say something which threatens your beliefs. It is bad science to drown someone out with ad-hominem, ridicule and mockery in order to prevent that anyone else might hear what he has to say lest they be open to correct thinking.

This is a very important issue and I am not prepared to give up on it because people would prefer not to hear it.

Once the denial is overcome, this will resolve many of the anomalies that are floating around in the world of physics. Not only that, but many of the worlds greatest minds are wasting time on problems that are a result of this mistaken assumption and once they realise that, their attention can be applied to issues that are realistic instead and this might result in progress the likes of which we have not seen in many years.

It is extremely important.

How do I get my arguments properly addressed?

evolution - Book recommendations for evolutionary models

I was recently working on getting a statistical model of a DNA sequence. To do this I found that understanding evolution quantitatively seems to be quite important. I would really appreciate any book recommendations on the basics of evolution.

I come from an Electrical Engineering background and have a limited knowledge of evolution and biology.

Answer

You either want a introductory book in evolutionary biology or a book that offers mathematical models of evolutionary processes.

In my first class of evolutionary biology I had this textbook: Futuyama, Evolution I think it gives a good start to the field and offers a good overview of the difference subfields.

If you think you already know enough about the concepts selection, genetic drift, molecular evolution, etc… and you want a book that provides mathematical formulations of evolution, then you might want to have a look into the field of population genetics. On this post you'll find some book-recommendations

If you are particularly interested into molecular evolution, I'd suggest: Yang, Computational molecular evolution

Maybe you are particularly interested into the statistical methodology used in DNA annotation or in phylogeny. Then…. I don't know! It's not quite my field!

publications - Preserving ownership of authorship in the period after leaving a position and before journal submission

Background: I am currently working on a paper as a first author with 3 other members. My tenure with the research institute ends on the end of this month and I have no intention to continue any working relationship due to the very complex political environment and "back-scratching" among upper management in this research institute I am in, plus my observations of other ethical issues.

However, I intend to submit this paper to a journal after the end of my tenure. This journal has an associated conference that has deadline submission on the 15th July 2018. For this particular conference, an acceptances of a paper for this conference would enable a direct proceeding to its associated journal. I have a valid concern aimed at the senior research fellow (No PhD), whom I report to and who is also the last author of this paper, due to strong corroborated anecdotes (credit stealing included) from multiple employees. As far as facts is concerned, he comes from industry after 20 years, without a PhD, and sorely lacks technical skills in my observation. This further cements my concern and I am aware that there exists a possibility that my concerns may be misguided.

Measures taken:

1) I have created an official email confirming the roles, responsibilities and order of authorship of each team member involved in this project. The email has been acknowledged by each individual team member including aforementioned senior research fellow/ programme director (without a PhD). His role is to review to review the draft before my submission (possible and probably potential red flag?). He has not acknowledged nor mentioned anything in his reply about getting back to me with changes to the draft.

2) I intend to submit my paper to an open journal arXiv before submitting any draft to this senior research fellow.

3) 2) is followed by a submission of a draft to senior research fellow with a co-correspondence to the integrity office, worded in a diplomatic manner.

Are these three steps sufficient? What more should I be aware of?

Edit: The email also serves as a centralised communication where any work done by must submitted to that email.

Answer

In the world of patent, researchers establish priority in the following way. They keep a bound notebook (no loose-leaf) so that pages can't be added between other pages. Whenever they have a good idea for which they want to establish priority they make a dated complete note of the idea. They then get a colleague to date and sign their note. At some companies most employees always have this patent book with them so they can record ideas as they occur.

Then, if another person somewhere tries to patent the idea, they can present the patent book as evidence of prior art. The other person in this case may be completely unknown to you, but for patent, priority is pretty much the whole game.

You can do something like this yourself, if you are unsure. It needn't be confrontational to your co workers. Make a signed and dated (paper) copy of each version of the paper that you work on and have a non-involved but trusted colleague sign and date it. You can even leave them with a signed and dated copy so that you each have one.

The existence of these copies protects you a bit from being excluded. But in the absence of a problem, they are just private notes and so non-confrontational.

For your future, you are likely better off with cordial relations with your co-authors. It may even turn out that they are proud of their association with you.

peer review - How to handle plagiarism on method that does not affect outcome results when reviewing a paper?

I was reviewing a paper related to my field (computational fluid dynamics) a while ago and, while reading a part of the methodology section where the numerical scheme and the equations were explained, I had a weird sense of déjà-vu. Regretfully, I found out that the author had plagiarized about three to four paragraph from a paper published two years ago. What was even crazier is that the author had plagiarized me, since the paragraph he had copied were from a paper I actually had previously published, thus explaining the feeling of déjà-vu.

I obviously noted that in my review and in my message to the editor, but I did not reject the paper directly. I acted this way since it was in the methodology section and related to mathematical formulas and really did not affect the outcome of the result. Was I in the wrong? Should such small plagiarism warrant instant rejection or is it sufficient to point them out and let the editor deal with that?

Answer

There is no such thing as unimportant plagiarism. And three to four stolen paragraphs is not small.

You did the right thing to report it to the editor. But I also would have rejected the paper. There is no place in academia for academic misconduct. It certainly shouldn't be published.

research process - Is it feasible to take an unsure PhD topic?

I was working towards converting to a PhD but was unsure of what research I would do. Suddenly an idea striked my mind and I discussed it with my advisor. He doesn't have much experience in that exact field but has been in the area for around 6 months.

He said that he thinks that idea is feasible but doesn't know what would be the approach, and not sure whether the results would be positive in terms of PhD because there several parallel domains. Moreover, literature doesn't have much details on that exact topic. And my literature survey (pretty limited though) has only enhanced my confusion. Probably because my idea deals with application of a recent class of techniques to optimize a problem.

Is it worth to convert to a PhD with such an idea ?

Answer

This is exactly how most of the really great PhD students I've seen have all started. Working on a problem with unknowns is a process called "research."

Clearly, you are going to have to find some collaborators with more experience in the field than your advisor, but that's part of the process as well. Hopefully, your advisor can assist with networking / introductions / etc. The support of your advisor will be critical (as it is for all PhD students).

The trick is to make sure you have a backup plan and a way to convert to it if necessary. Don't spend three years mucking around if you're not making progress. But, spending 6 months investigating if there is something there -- that's well worth it.

publications - Doubt regarding authorship

One of the master's student is working on a research problem. I am a PhD student. I have an idea which I proposed to my advisor on the same problem. Now he wants me and the masters student to work on that idea and publish a paper. Would I be treated as a first author in that paper or would I be a second author?

human biology - Has a beneficial mutation ever been documented?

I am trying to find a case/study where scientists documented a mutation in an animal or human that was to the benefit of the host.

The closest thing I have been able to find is sickle cell anemia (SCA) helping to fight malaria. However, the life expectancy for people with SCA is 40 – 60 years, and in 1973 it was only 14 years (source). I am looking for another case, preferably one that is not life-threatening.

Are there any other cases where a beneficial mutation — one where the good outweighs the bad — was documented?

By beneficial I simply mean that it helps or protects the host in some way, while not causing substantial harm. As in my example of SCA it can benefit the host if the host lives in an area with malaria. However, it is also life threatening and reduces the life expectancy of the host.

If — for example — SCA would only cause pain and not be life-threatening, then it would (in my opinion) be a beneficial mutation. While not purely beneficial, it would still increase the life expectancy of people living in an area with a high occurrence of malaria.

Answer

Lactase persistence

This is a somewhat unusual example but has been well studied, and would seem to satisfy the criteria of the question. Let me start by quoting the Wikipedia entry for those unfamiliar with the phenomenon:

Lactase persistence is the continued activity of the enzyme lactase in adulthood. Since lactase’s only function is the digestion of lactose in milk, in most mammal species, the activity of the enzyme is dramatically reduced after weaning.[1] In some human populations, though, lactase persistence has recently evolved[2] as an adaptation to the consumption of nonhuman milk and dairy products beyond infancy.

Studies on the geographical distribution of lactase persistence (e.g. AJHG (2014) vol 94, pp. 496–510) show that lactase persistence is associated with cultures which practice pastoralism (specifically herding bovines), supporting the hypothesis that the trait evolved because of the benefit it conveyed to such populations in allowing them to use bovine (or caprine or ovine) milk to survive in adulthood.

There is no doubt that lactase persistence is a heritable — i.e. genetic — trait, as can be seen from consulting the OMIH (Online Mendelian Inheritance in Man) entry. This has extensive documentation, including description of the base changes associated with the trait:

Enattah et al. (2002) found a complete association between biochemically verified lactase nonpersistence in Finnish families and a C/T(-13910) polymorphism of the MCM6 gene (601806.0001) roughly 14 kb upstream from the lactase gene locus (LCT; 603202), located on 2q21. It was the C allele that associated with hypolactasia.

The molecular mechanism of lactase nonpersistence (the putative original human condition) — affected by mutation at this position — is still not completely clear. Recent work suggests:

Epigenetically controlled regulatory elements accounted for the differences in lactase mRNA levels among individuals, intestinal cell types and species.

Finally, I refer to the evidence for the Wikipedia statement that “lactase persistence has recently evolved[2]”. This is a paper by Bersaglieri et al. in The American Journal of Human Genetics (Am. J. Hum. Genet. 74:1111–1120, 2004). I am not a population geneticist, so I shall reproduce the relevant section of their summary unedited:

In northern European–derived populations, two alleles that are tightly associated with lactase persistence (Enattah et al. 2002) uniquely mark a common (∼77%) haplotype that extends largely undisrupted for 11 Mb. We provide two new lines of genetic evidence that this long, common haplotype arose rapidly due to recent selection: (1) by use of the traditional F_ST measure and a novel test based on p_excess, we demonstrate large frequency differences among populations for the persistence-associated markers and for flanking markers throughout the haplotype, and (2) we show that the haplotype is unusually long, given its high frequency—a hallmark of recent selection. We estimate that strong selection occurred within the past 5,000–10,000 years, consistent with an advantage to lactase persistence in the setting of dairy farming; the signals of selection we observe are among the strongest yet seen for any gene in the genome.

genetics - How are oranges in the US or anywhere made seedless?

How are oranges in the US or anywhere made seedless? Please explain the broad principles and not the technicalities.

Answer

Oranges and other fruits are generally not actively made seedless. Rather, seeds may fail to develop due to either lack of fertilization (pollination) or a natural tendency. The natural production of unfertilized and thus seedless fruit is called Parthenocarpy.

To quote the Scientific American article (3) mentioned by Oreotrephes:

Fruit development normally begins when one or more egg cells in the ovular compartment of the flower are fertilized by sperm nuclei from pollen. In some plants, however, fruit develops without fertilization, a phenomenon known as parthenocarpy. Parthenocarpic fruit has advantages over seeded fruit: longer shelf life and greater consumer appeal.

The most frequent reasons for lack of seed development are pollination failure, or nonfunctional eggs or sperm. In many plants, self-incompatibility genes limit successful fertilization to cross-pollination between genetically different male and female parents. This property is exploited by citrus farmers who grow seedless fruits, such as navel oranges and clementines. Because these cultivars are self-incompatible, they fail to set seed when they are planted in orchards of identical plants (clones). These plants have a high frequency of parthenocarpy, however, so they still produce fruit.

Parthenocarpic varieties may arise from a lack of pollinators. From the Wikipedia page on Parthenocarpy:

Plants moved from one area of the world to another may not always be accompanied by their pollinating partner and the lack of pollinators has spurred human cultivation of parthenocarpic varieties. Some parthenocarpic varieties have been developed as genetically modified organisms.

To preserve the seedless trait, parthenocarpic trees can be propagated by grafting. It is possible that more kinds of seedless fruits will be engineered in the future (3):

Plant biologists have learned that if the plant hormone auxin is produced early in ovule development, parthenocarpic fruit can grow on plants that do not usually exhibit this property. Thus, genetic engineering will most likely give consumers parthenocarpic fruit in many other species in the near future.

publications - Importance of Undergraduate Research

How important is it for an undergraduate student majoring in Physics and Mathematics (or any other science) to have experience in research (e.g., have a peer reviewed paper to his name most probably in collaboration with a professor) at the undergraduate level, keeping in mind that he will be applying for a master's or other postgraduate degree?

Answer

If you want admission to the very best PhD programs in the US, prior formal research experience is very important, if not necessary. Admissions committees are primarily looking for evidence of research potential. The best possible evidence for "I'll be a good researcher someday" is "Look, I'm already a good researcher." So having formal peer-reviewed publications is better than having publishable but unpublished results, which is better than having research experience but no publishable results, which is better than having no research experience. If you're applying to the top PhD programs, you will be competing with applicants (yes, plural) who have peer-reviewed publications (yes, plural).

How to check citations and references match in a manually prepared document with APA author (year) citations?

I like to use bibliographic software (e.g., Endnote, BibTex, etc.) to manage my references. However, sometimes I am working on an existing article that has been written with APA citations and references written manually. For example, I might be working with a collaborator who has written the first draft or I'm adapting a student thesis for journal publication. As a result, citations get added and deleted, and there are reference errors: (1) citations present with no reference; reference needs to be added (2) references present with not citation; reference needs to be deleted.

So, a common task when such documents are being finalised is to go through the document and pull out all the citations and check them against the reference list and fix any errors. This is generally a frustrating task, because (1) unless you are careful errors can be made, and (2) if the document is edited further, the document may need to be rechecked.

Question

• What is an efficient strategy for identifying citations without references and references without citations in a document with author (year) style citations (e.g., APA, Harvard)?


• Are there any automated tools that perform this checking?

biochemistry - Why is thymine rather than uracil used in DNA?

What is the advantage gained by the substitution of thymine for uracil in DNA? I have read previously that it is due to thymine being "better protected" and therefore more suited to the storage role of DNA, which seems fine in theory, but why does the addition of a simple methyl group make the base more well protected?

Answer

One major problem with using uracil as a base is that cytosine can be deaminated, which converts it into uracil. This is not a rare reaction; it happens around 100 times per cell, per day. This is no major problem when using thymine, as the cell can easily recognize that the uracil doesn't belong there and can repair it by substituting it by a cytosine again.

There is an enzyme, uracil DNA glycosylase, that does exactly that; it excises uracil bases from double-stranded DNA. It can safely do that as uracil is not supposed to be present in the DNA and has to be the result of a base modification.

Now, if we would use uracil in DNA it would not be so easy to decide how to repair that error. It would prevent the usage of this important repair pathway.

The inability to repair such damage doesn't matter for RNA as the mRNA is comparatively short-lived and any potential errors don't lead to any lasting damage. It matters a lot for DNA as the errors are continued through every replication. Now, this explains why there is an advantage to using thymine in DNA, it doesn't explain why RNA uses uracil. I'd guess it just evolved that way and there was no significant drawback that could be selected against, but there might be a better reason (more difficult biosynthesis of thymine, maybe?).

You'll find a bit more information on that in "Molecular Biology of the Cell" from Bruce Alberts et al. in the chapter about DNA repair (from page 267 on in the 4th edition).

ethics - Wondering Wether to tell the Truth to another PhD program that I have resigned from the first one

As you may know, I have resigned from a PhD program after spending year although working hard and I have discussed that before here in the platform. Now, all the positions I had applied for was rejected once they know I Have resigned from another group which is fairly known in our field. Now, I am now in short contract in isolated country in Europe and having contract month by month and today I get a very low salary, they take exploited my situation I had which they already know, and they try to make benefit of me to do all the work they want.

Now, I have another opportunity and I am afraid, to tell the truth, that I was a PhD student, I can tell them that I was a research graduate student, is that ethical. Really I do think that telling the truth no one will believe me and I think it leaves a bad impression or a suspicion although I am trying to be positive and mentioning we didn't have the same research interest, this doesn't work in all interviews although they are interested, but afraid from my previous experience. My question: How I should answer about my experience at ex-group and how I can call it in a way that didn't leave a bad impression?.

paper submission - What are the reasons for journals to have a policy against publishing material available as a preprint?

As it can be appreciated from this list of journals with varying preprint policies, certain journals consider a preprint to be "prior publication". In other fields like Chemistry, there is a strong policy against preprints.

I'm curious about those reasons, if there are other reasons, and if they hold weight.

publications - what do you do if your PhD advisor publishes a solo paper on your topic?

I was working with my advisor on a research topic for six months and we had some results. The important idea was his, but the initial idea was mine and we worked on it together. Now my advisor has published the results without my name in the authors. The paper is in an important conference.

What do I do ? Is this normal ? Should I talk to my advisor about how I get my name in a paper ? How do I approach that topic ?

I'm his only PhD student and he has joined the department recently.

Edit : The paper was written by my advisor but we derived the results together, although his contribution was more important. He included my name in acknowledgements. Should I risk upsetting my relationship with my advisor over this ?

Answer

You asked,

Is this normal?

The answer is no, it's not normal. If two people work on some research together, the "normal" thing is for them to write the paper on it together, and for both to be authors on the paper.

It's possible that you seriously overestimated your contribution to the work and don't actually deserve authorship. Even in this case, it's clear you were involved in the research and it's not normal for your advisor to go ahead and publish it without discussing it with you first.

(When I publish work that involves students whose small contributions do not warrant authorship, I always discuss it with them first. I explain why I don't think they can be an author, give them a chance to state any disagreement, and also tell them what additional work they could do in order to merit authorship.)

However, the latter (your contributions did not merit authorship, and your advisor failed to discuss this with you) is somewhat more forgivable than the former (your contributions did merit authorship and your advisor published without you anyways). (You do say your advisor is new, and probably inexperienced in advising.)

To answer

What do I do?

You should talk to your advisor. This is the only way to really understand which case you are dealing with.

You can bring this up in a non-combative way without upsetting your advisor; for example, you can ask "What do I need to do in order to deserve authorship on future papers?" This gives your advisor an opening to discuss why he thinks you didn't deserve authorship on the conference paper, and for you to respectfully state your perception of the situation.

There may still be a chance for you to get some credit for this work, if you come to agree with his point of view that you didn't do enough to deserve authorship on the conference paper. For example, once you and your advisor have come to an agreement on what it takes to get authorship, you can propose that the two of you work together on an extended version of his conference paper for a journal - on which you will be an author :)

Unfortunately, it's also possible that after this conversation you believe you did deserve authorship, and that your advisor published your joint work without you for no valid reason (i.e., committed misconduct). In this case, the best advice I can give you is to start looking for another advisor.

Finally, the lesson for the future is: talk to your collaborators about authorship early and often.

sensation - Do ants feel acceleration?

The organ we have to provide us with current acceleration information is quite complicated. Because an ant queen didn't seem to notice when I picked up the bottle she was in, I have a suspicion that ants don't really care about acceleration and therefore can't tell where it's up and where it's down.

Am I right? If not, how do they sense acceleration?

Answer

According to Clinical Neurophysiology of the Vestibular System By Robert William Baloh, Vicente Honrubia, page 8, the vestibular system (animals' "accelerometer") is as old as 600 million years and is present in invertebrates.

I assume (without a precise source) that this is especially important for flying insects (after all, accelerometers were engineered for flying machines in the first place!) and that the ant didn't respond because the acceleration to which you submitted it was not deemed harmful.

phd - Ethicality of continuing my Ph.D. with intentions of leaving

I am currently in my first year at a funded Ph.D. program. I have a graduate teaching assistantship in the form of teaching three introductory biology labs (1 credit per) plus the other responsibilities of being an instructor. I also have a six credit (tuition waiver) course load and a stipend.

Prior to coming to this program, I declined an offer from another funded program. It was due to financial reasons such as making a big move to the city and whatnot. I was a fresh undergraduate out of college and I was not ready for that move. I am in the position to make this move now and the offer is much better than my current program.

I have many different quarrels with this current program. There is a lack of structure and much of what I expected at a Ph.D. level course/program was not met. I dislike the current field I am in and I don’t believe I would be happy doing this for the next 4 years. I did not have intentions of leaving prior to starting here, but as I mentioned things here are not as what I expected. Through discussion with the head of the department I declined, I was able to get my declined admission deferred to next fall. In February, I will hear if I receive funding again.

Now my issue is that I am currently in a lab rotation with my prospective advisor and I have not told anyone that I will be leaving. I am afraid that if I tell anyone that I plan to leave after the year, I will be looked down upon and it would affect my courses for the year. I want to withdraw from the lab rotation because the program I will be going to does not have any use for such a course. However, I am worried that if I tell my advisor why I am withdrawing, it will impact me negatively. In the off chance I do not receive funding, I will most likely be staying in this program and if they know I wanted to leave and didn’t because of funding, I fear I will be looked down upon.

1. How unethical is it to continue this year and finish up without mentioning any of my intentions to leave the program for another?


2. If I do withdraw from the lab rotation, should I mention why I am doing so or just mention that I was not expecting the course work to be so intense (which is true due to my teaching taking up so much time, I am behind).



3. How unethical is it to use my 6 credit tuition waiver to take courses in the spring that would hopefully transfer to my other program?

My contract runs 9 months so I can’t just leave.

publications - How to efficiently proofread my own mathematical paper?

The main purpose of this question is to collect some advices to efficiently proofread my own mathematical paper (when there are two authors or more, it is easier since one is supposed to read what the others write). When we write mathematics, there are a lot of not so minor mistakes we can make:

• We omit to introduce a notation.


• Non-uniform notations.


• A sum should stop at n+1, not at n but the last term is not important.


• Etc...

Of course, we would like to limit the number of such mistakes in order to save the reader's (and referee's) time.

• 
  

  One possibility is to wait a long period of time in order to "forget" and read what is written, and not what we have in mind. Although "hurry for publishing" is very bad, we cannot always wait a lot of time (thesis defense, applying for post-doc/permanent position) and we would like to make the process fast.

  
  


• 
  

  An other possibility is to send a draft of the paper to a colleague. But he may be busy and not read too much into details. Anyway, when we are alone to write a paper, we would like to send to the colleague a document without too much typos and mistakes mentioned in the beginning of the question.

  
  

Answer

A general technique, applicable not only to mathematical papers, is to list common mistakes, such as the one you noted. Then, you do a revision of your paper for each item on the list: reading only to look at uniformity, reading only to look if you introduce all notations, etc.

I've picked up this tip in the following book and it has worked well so far.

The book also suggest to reduce the familiarity with your text, so you might be able to read it as a "new" reader and thus find mistakes or parts that are not clear. You could do that by putting away the manuscript for a few days/weeks, printing it, changing the font, etc.

application - Monitoring PhD positions in CS

Are there any ways of getting to know about new PhD positions in CS other then just looking trough university/research groups web sites? Maybe people from different branches can name some specialized mailing-lists where PhD positions announcements are quite usual. I am particularly looking out for computer systems, mainly dealing with cache problems, scheduling problems, multicore architectures, etc.

Here are a couple of websites that I found:

I would appreciate any help. Thanks!

Answer

If you know the field you want to study and have read some good papers, contact the authors and ask them what mailing lists are good for their field.

You might also state your motivation: they are generally good at knowing who has funding and may even be looking!

grading - How do you judge an Indian CGPA score?

Let's start with background: I'm European, don't know much about undergrad educational systems, and especially grading, outside my own area. So, I receive a CV from an Indian undergrad with the following section:

             

Now, I have no idea whether the scores displayed here are dismal, average, good or excellent. Wikipedia doesn't know what CGPA is, except in Nepal (and the student in case was not educated in Nepal), so I turn to you, Academia Stack Exchange, to help me solve this riddle!

Answer

Two factors can be used to get a broad idea about an Indian engineering student - one is the college and the second is the CGPA.

College:

The Indian Institute of Science and Indian institutes of technology are top technical institutions in the country. Of late, multiple IITs have been set up, leading to (arguably) diminishing quality. The original seven IITs boast of excellent faculty in most departments and are understood to be better than the newer ones.

Besides, there are regional colleges like National Institutes of Technology and Anna University and BITS which are also among the top engineering colleges in the country.

Grading System:

Most of the above colleges use the CGPA system for grading. Students are awarded grades ranging from S (=10) to D (=6) in various courses that they enroll over a period of 4 years. In a course, the top performers could expect an S, the students who have scored 80%-90% could score an A and so on. Obviously, the exact grades depend on the instructor and the overall performance. A student that scores S in all his courses over 4 years ends up with the perfect CGPA of 10.0. A 9-10 CGPA indicates mostly excellent track record and so on.

It should be clear that the CV in the question reflects a mediocre score in a top college.

publications - Subscribe to cross-listings on arXiv

I'm interested in subscribing to cross-listings on the arXiv; similar to their regular e-mail alerts, but with the caveat that I'm interested in papers cross-listed on both quant-ph and cond-mat. The majority of papers relevant to my research seem to be cross listed between those two one way or another.

I haven't found any way to do it through the arXiv subscription system; does a third party service exist? Is there a better way to zero in on these intersectional areas? Barring the existence of such a method, I may try to create my own; is there a stable API worth using?

Edit: Found the API, must have missed it earlier

ethics - How should I communicate that I do not hold the views expressed in a paper I wrote

I am writing a paper for a class that requires me to write from a perspective I disagree with. To an external observer it may not be clear that I am not allowed to disagree with the premise of the prompt.

I disagree with it to such a degree that I would like to add something at the beginning or end of the paper that expresses my dissent in case my work or record is made public for some reason. It would be professionally and personally embarrassing to have the work become public.

Is there a way to do this professionally? Is there a way to do this without offending my professor?

Answer

I would precede my paper by a strong explanatory note disassociating myself from the views expressed in the paper, in boldface and surrounded by a big black frame. For extra clarity and safety, I would then quote verbatim the assignment that the project is fulfilling, before starting the actual paper. E.g.:

Confessions of a cannibal
Final project for Philosophy 101

[your name]

Explanatory note: the views in the essay below are written in the context of a final project assignment for the course Philosophy 101. They are fictional and do not represent the author's actual views on cannibalism or on any other subject.

Project assignment: "Write a 4000-word essay written from the point of view of a cannibal living in New York City in the year 1987. Discuss the narrator's views and opinions on cannibalism and other topics of interest."

[body of the essay]

I should note that you say "To an external observer it may not be clear that I am not allowed to disagree with the premise of the prompt." It's not clear to me if you mean that you are not allowed to include an explanatory note of this type, or even to quote the assignment text. If that's what you meant, I'd have to say that forbidding you from including such explanatory text would in my opinion be tantamount to requiring you to actually pretend to be a cannibal (or other such person with unsavory views), which would be a highly unethical requirement. In the face of such a restriction, I would frankly refuse to hand in such an assignment, and take the matter up with the instructor and/or higher university authorities.

emotional responses - How to deal with fear of failure as a PhD student?

I am working on a mathematical topic that is basically my own concoction. I have days where even the simplest thing takes ages to do and I realize that's because, deep down, I am terrified that things might not work out. This is in different way: I am scared my topic might not be novel enough, appreciated etc. ; I am also scared that checking parts of proofs will reveal catastrophic mistakes.

I rationally realize that this is part of the game and I do my best to take mistakes I find as good news that my work is improving, but at times I am just paralyzed and unable to do things.

I am also bothered by the presence of colleagues in my office, afraid they might judge my work (and at the same time going to a hidden place in the library helps a little but is also very annoying and uncomfortable).

I am sure this must be, to a different degree, experienced by many PhD students.

What are some strategies to fight fear as you work?

Note that I realize there really is a deeper confidence issue and I am already seeking help for that. I'd be happy to hear considerations on the possibility of therapy or counseling and how it worked for you as well as day to day tips and strategies.

Answer

To some degree or another, the feelings you describe are common in graduate students (and other people). Here are some comments from around the Internet, for example:

FEAR !!

I self diagnosed this of myself just this week to explain my behaviour for the last 6 months . I called it boredom, annoying , painful etc but actully I am afraid to progress because someone might say”not good enough”. I am engaged in a systematic review and all I have to do now is read (albeit systematically) but simle right ?

I just applied for some funding and as I drew out my timeline for the project I thought “will I or can I actually do this”? The answer of course is I can but if my will is left up to me I am fearful I’ll self destruct !!!! There I go again fearing!!

(Marese kelly on Thesis Whisperer)

I just can't do it. I've spent the last month rewriting the first paragraph over and over. Yet, it is still not good enough. When I sit in front of my computer I usually feel paralyzed with fear. This might sound bizarre, but it is true. Yesterday I felt more courage than the average day. I worked on my thesis for hours. Yet, at the end of the day, I was still in the first paragraph. I didn't used to be like this. Believe it or not I was an outstanding student. Now I don't even dare to discuss science with my colleagues, I might say something stupid.

(jesuisperdu on reddit)

I have sweated in the fear of failure, and all I can say is that this fear continues even after you have passed the doctorate. In fact, that’s when the fear of failure can be worst! Because now you have to take your research and creative work out of the sheltered workshop of the academy and impress not just a couple of examiners, your supervisor and an academic panel, but people who will put down money (hopefully) into your ideas and research.

(On 100 days to the doctorate & beyond)

Many of the fears described by you and the people I quoted above, are about how you may be perceived by others. One thing that people with this kind of fear sometimes find helpful is to identify when they are feeling fear of being judged, then remind themselves about the realistic standards by which people in their position are judged. In your particular situation:

• Nobody* expects you or others in your position to never say or write something that is mistaken or uninformed.


• Nobody* expects you or others in your position to have a thesis topic that revolutionizes the field, to win a Nobel prize for your thesis.


• Nobody* expects you or others in your position to constantly dazzle with your brilliance.


• Nobody* expects you or others in your position to win every award you are put up for, to rack up hundreds of citations on your published work, to get the highest possible scores on student evaluations of your teaching... you see where I'm going with this.

You may also find some of the material in this Perspectives on Perfectionism series helpful. (Even if your fears are not exactly perfectionism, they are similar in many ways and similar strategies may help you.) In particular, the exercises in Challenging my Perfectionistic Thinking (such as the "Thought Diaries") and Adjusting Unhelpful Rules & Assumptions (especially worksheet on Page 8) may be useful.

---

* Nobody reasonably expects this. There may be some people with unreasonable expectations, but it's really not worth concerning yourself with what they think :)

etiquette - My paper's content is slightly changed from the abstract I have submitted to a conference, can I edit the accepted abstract on my poster?

I'm fairly early on in my PhD research. A few months ago I submitted an abstract to a conference, which was accepted. The conference is coming up soon, and my research has taken a slight turn away from my accepted abstract (still same field, collaborators, etc...--just asking slightly different questions and taking a slightly different approach).

My question is, am I obligated to put the program-accepted abstract on my poster? If I am, should I try to tie my poster content as closely to that accepted abstract as possible? Or can I present poster content that would've been more appropriate for a different abstract?

Or can I use a different abstract on my poster, and thus tie the content more closely to what my current research path is?

What about keeping the original abstract in its entirely, but appending it?

EDIT: I'm in the field of astrobiology (probably most similar to the fields of geology or astronomy if I had to relate it to a more conventional field)

funding - Is it appropriate to mention one's religion in an academic CV?

I recently moved to a Nordic country in an academic position. For my first grant application, I collaborated with other researchers at the university. As I was submitting the proposal along with the CVs, I noticed that two of the researchers had mentioned their religion. I have never seen this in academia, at least in South-east Asia where I spent majority of my work life.

Here are other details that I think are relevant:

• Our research domain is engineering, not humanities or social sciences.


• Both researchers are Muslim.


• The funding agency is a private one that favors industrial collaborations.

My questions:

• Is it appropriate to mention one's religion in an academic CV?


• Does mentioning one's religion help in grant proposals or academic positions? I think in a fair world it shouldn't.


• Do western countries, especially European, favor candidates who are Muslim?

funding - What are CNRS research units and how are they staffed

The Centre national de la recherche scientifique (CNRS) is the major funding body in France. With nearly 32,000 staff members it is bigger than the US NIH and US NSF combined, yet only has a 1/10 of the budget.

Both CNRS and NIH have multiple institutes (although the NIH institutes are all health related and CNRS covers a range of science). The CNRS then has 952 mixed research units, 32 proper research units, 135 service units, as well as 36 international units while the NIH has a large number of intramural labs.

What are these different research units and how are they staffed (full time researchers or academics with other teaching duties)? Is it at all like NIH intramural labs or MRC centres?

Answer

Wikipedia is your friend. Read the CNRS wikipage, and look at CNRS official website.

CNRS is the largest public pure research organization in France, with a staff exceeding 31000 persons, located in many geographical areas in France; many CNRS teams share office buildings with e.g. some French universities; several French research teams (UMR) have mixed staff, some funded by a University, and some other funded by CNRS, perhaps even working in the same office room on similar research. Getting employed by CNRS is really very hard, and there is a lot of competition. BTW, CNRS researchers are not very well paid, and most of them are not only very competent, but generally passionate about their research. They are not (contractually) tenured members of some University, even if most of them do teach a few courses somewhere (in addition of their researcher work), either at some University or at some Grande Ecole.

It's supposedly some unknown research center somewhere in Europe

CNRS is the largest basic research agency in Europe (mostly funded by the French public State budget). It is French (even if of course it gets some research grants from outside, e.g. from French ANR or European Commission's H2020...)

CNRS researchers are working in all kind of science and research (e.g. biology, history, computer science, physics, sociology, paleontology, chemistry, mathematics, etc etc etc ....). Most of them have at least a PhD (doctorat d'université), usually even their HdR (habilitation à diriger des recherches). Even if CNRS researchers are French civil servants, they are not all French citizens (even if most of them are).

There are some other public (French state owned) organizations in France doing research, e.g. INRIA, INRA, CEA, INSERM, (and dozen of other smaller research institutions) etc... Unlike CNRS, these other organizations are usually dedicated to some specific science or technological domain, and usually work on applied research.

Online material on the cnrs isn't helpful at all

Why do you say that? The Overview page of CNRS website is quite informative (and looks quite objective to my French citizen eyes)! And the CNRS wikipage gives a complementary look.

French economy is not used to fund research (in the sense that private corporations in France spend much less money in funding research, notably in public labs, than their counterpart in the USA or even in Germany). So the funding of French research works differently from North American country (and is lower, in terms of percentage of GDP).

BTW, I don't understand well what the NSF exactly is in the USA. My perception is that it mixes the role of CNRS and of ANR in France.

reading - Is there a place in academia for someone who compulsively solves every problem on their own?

To be honest, I'm not entirely sure how I'm still in grad school.

I've been researching under one professor's wing for two years now, ostensibly shooting for a PhD (note: no topic yet), and I have accomplished nothing except write a lot of code, fill a bunch of notebooks with theorems and scratchwork, and whine a lot.

Insofar as I can surmise, my precise set of skills is good for one thing and one thing only: Solving problems that have already been solved... but only from scratch, my way. And I'm too stubborn to know when to give up.

For homeworks I go in completely unprepared and take them like a puzzle, and somehow, this usually doesn't work out too poorly (note, I am a physics student, so these homeworks are of the mathy, proofy, yet still occassionally handwavey kind). I hack and hack away at a problem unassisted for hours to days with no progress until I finally make a crack in the wall and can see the light shining through. Then I beat it eight ways to Sunday, making my solution simpler and simpler until I am satisfied that every step has both a clean form and a clear motivation. My test-taking strategy is similarly devoid of preparation, and also fortuitously manages to work out well.

As far as I can tell, my strategy works in these cases only because homeworks and tests are problems which are hand-crafted to be surmountable. In these cases, my stubbornness alone is enough to pull me through eventually. It was enough, in fact, to pull me all the way through primary and secondary school and to my Bachelor's.

But obviously, grad school isn't about homeworks and tests.

---

For one, I can't read academic papers in my field. Or rather, every academic paper I try to read goes one of two ways:

• If it is a very abstract and theoretical paper, then I can't read it because I'll get too easily excited; I'll get to maybe the second page of definitions and axioms before my head is flooded with ideas and I absolutely need to pull out my notebook and begin trying to gain an intuition for them. (This seldom goes anywhere and I usually just end up tiring myself out after several hours of hacking on some theorem orthogonal to the paper)


• If it's an experimental paper, I can't read it because it means nothing to me. There are no ideas I can synthesize from "we did X using Y and found Z." My mind races about other things as I'm reading and I can't shut it up! In the end, I don't remember a word I read.

And as far as it concerns me, computational papers and applied theory might as well be experimental, because ultimately there's a point where everything goes into a black box and the result pops out. This is a shame, because I know that these computations can expose new and interesting emergent properties of the theory; but sometimes it's just too difficult finding the ladder down from my ivory tower.

---

My research is going about as well as one would expect for somebody who can't read any papers!

For any problem I've ever worked on for research, I've always begun with trying to solve the aspects that stand out to me; enumerating the set of solutions to some nasty-looking equation, or devising an algorithm to compute something which is faster than the obvious brute force strategy. Months fly by and I either fail, or I successfully, unwittingly, and needlessly derive my own formalism of e.g. the theory behind HNF matrices and unimodular matrices after several strokes of dumb luck.

In all cases, papers already existed which solved these problems. I just couldn't bear the thought of having to seek them out and read them!

---

I've discussed various aspects of my struggles with my parents and a number of faculty (including, of course my research advisor) and everyone I've talked to has advised me to continue. I gathered from these discussions that feelings of inadequacy are rather par for the norm in grad school, and that evidently my classwork has impressed a portion of the faculty who still appear to have confidence that I can succeed... But unfortunately, as far as I can see, I am a one-trick pony.

Is there really any place in academia for somebody who is incapable of recognizing and building upon the existing work of others?

ethics - I used external help for my masters thesis coding work

Hi I wrote my masters thesis and it got A grade. I wrote 20,000 words on my own but I took help for the coding portion. Ideas were mine but he helped me putting them into action - discussing solutiouns, helped in debugging , helped in finding code from internet etc .Have I plagirised in any form ?

publications - Ways to get free and legal access to research papers as a researcher

I’ve discovered that website like ResearchGate offer the possibility to ask the paper editor to provide his paper for free. Many are collaborating.

Are there any other ways for researchers to obtain free access to papers?

Answer

I always use the following methods to get many inaccessible papers.

1. Open Google Scholar.


2. Search the title of the paper.


3. Click see all versions (you can see many places where the same paper is available)


4. Check one by one whether they are downloadable

Another method, I always use when I really need an inaccessible paper, is just to write an e-mail to the corresponding author to send that paper. My experience is that I have always received the paper in a return email.

publications - Citing full names of authors

Different journals have different standards regarding author names - some mention only the first name (i.e. "William Webb"), some mention also an initial of the middle name ("William A. Webb"), some mention only initials ("W. A. Webb"), etc.

So, when I copy BibTeX records of papers to my bibliography manager, the names are copied in different styles, and also appear in different styles in my bibliographic listing.

My question is: is this a problem? Should I go over all my bibliography, each time I write a paper, and make sure all names have the same format?

Answer

Let me cite Donald Knuth (from this webpage):

Do you know any of these people?

[...] I try to make the indexes to my books as complete as possible, or at least to give the illusion of completeness. Therefore I have adopted a policy of listing full names of everyone who is cited. For example, the index to Volume 1 of The Art of Computer Programming says "Hoare, Charles Antony Richard" and "Jordan, Marie Ennemond Camille" instead of just "Hoare, C. A. R." and "Jordan, Camille."

I also think that a database with complete names is the way to go. The more complete the names are, the less ambiguous (consider all the different "A. Smith's", "X. Zhang's" or "H. Kim's"…).

human biology - Where do the 31 spinal nerves start/meet?

Which part of the brain is the first place (from top to bottom) where all 31 pairs of spinal nerves (on each side) meet? Or if they all start at one place - where is that?

Nominally, the beginning of the spinal cord is the medulla oblongata, but perhaps the spinal nerves or some sort of "root" of every nerve start at the Thalamus?

Answer

They don’t meet.

Some framework:

• Spinal nerves contain motor, sensory, and autonomic fibers. Each of these have different pathways.


• Spinal nerves don’t go to the brain. Rather, they synapse in the spinal cord with other neurons which in turn go to the brain (sometimes requiring one more synapse).


• In the case of motor neurons, we talk about upper and lower motor neurons. In the sensory system, we talk about first order and second order neurons. Explanation below.

Regarding sensory (afferent) neurons:

• Touch and limb position sense are mediated by the dorsal column-medial lemniscus system. The first order (primary sensory) neurons from the spinal nerves, synapse on a second order neuron in the dorsal column in the medulla. There it decussates (i.e. courses to the contralateral side) and ascends via the medial lemniscus to the thalamus. There it synapses with a third neuron that courses via the internal capsule to the primary somatic sensory cortex.


• Pain, itch, and temperature sense are mediated by the anterolateral system. These first order (primary sensory) neurons synapse at the spinal level they enter. The second order neuron decussates at that level and courses rostrally via the anterolateral column, ending up in the thalamus. There it synapses with a third neuron that courses via the internal capsule to the primary somatic sensory cortex.

Conclusion: It takes three neurons (inclusive) to get from the spinal nerve to the primary sensory cortex in the postcentral gyrus of the parietal lobe.

Regarding motor (efferent) neurons:

• Limb muscles are innervated by circuits beginning in the primary motor cortex. These upper motor neurons descend to the medulla, decussate here, and continue caudally via the lateral corticospinal tract. At the level of the spinal nerve, they synapse with neurons in the lateral ventral horn. These are the lower motor neurons that become the spinal nerve.


• Axial/girdle muscles are innervated by circuits that also begin in the primary motor cortex. These upper motor neurons synapse in the midbrain, descend, and decussate at the appropriate spinal level. They synapse there with the lower motor neurons that exit the spinal cord and end up in the muscles.

Conclusion: It takes two neurons (inclusive) to get from the primary motor cortex in the pre-central gyrus of the frontal lobe to a spinal nerve.

In the cortex, these circuits also don’t all come together. They are actually quite diffusely organized across the sensory and motor cortices. Here is a representation of the sensory cortex.* It is a schematic of the post-central gyrus with pictures to indicate where the signals from various body parts end up. The motor cortex is similar. (Google homunculus if interested.)

In addition the pathways described for cognitive perception and control, there are others that help with sub-conscious control of movement (e.g. those involving the cerebellum and basal ganglia), sub-cortical perception of pain signals (e.g. amygdala), and even spinal reflex arcs that never reach the brain. Not all circuits that begin or end in the spinal nerves are destined for or originate from the cortex

This is already considerably over-simplified, and the autonomic system is more complex yet and is not confined to spinal nerves, so I won’t detail it. These signals originate in and feed back to an entirely different area of the brain (mostly hypothalamus). Similar to the motor and sensory systems, at least one synapse is required to connect the brain to the peripheral nerve.

Conclusion: they don’t meet.

---

^{Reference: Martin, John. Neuroanatomy: Text and Atlas. McGraw-Hill Medical; 3 edition (March 27, 2003)
*The source of this image is: http://www.mindtrippingshow.com/mind-trip-of-the-week-17-how-do-we-feel-the-world}

bibliometrics - Is there documentation on how long it takes before publications are indexed by Scopus and Web of Science?

The two major bibliographic databases - Scopus and Web of Science\Web of Knowledge - have one very badly-documented limitation; their update lag. While the majority of papers are added quickly, it can take several months for individual papers to be added.

As an example, I ran a search in Web of Science looking for all papers published by my institute in 2014. In November 2015, it reported 290 papers. In January 2016, 293. In February, 305.

In other words, a few percent of the papers took a year or more to be added to the database, which startled me - I was expecting a lag of perhaps three months. Some of these delayed entries are from relatively obscure journals (specialist Australian publications) or book series, and it seems reasonable that these might take longer, but most are from mainstream titles - one is even from Philosophical Transactions of the Royal Society, as established a journal as it's possible to get.

Scopus is comparable. In November 2015, it reported 340 2014 papers, 356 2013 ones and 351 2012. Running an identical search three months on brings us to 341, 367 (!), and 353 respectively - so a few papers are still being added up to three years after publication. (Unfortunately, Scopus doesn't expose the date items added to the database, so it's not possible to identify which ones were added most recently - it's possible that some were due to journals being added to Scopus for the first time along with their back-issues.)

This is, of course, something of a headache for producing stats. But more practically, it could be a real problem for disseminating science - something being unintentionally missed or delayed from one of the big indexing services can make it much less discoverable and much less likely to be read, built upon, or cited, especially in that important first year.

So, the core question: does anyone know of documentation (or research) into how substantial these delays are; how they're distributed; and whether they're getting better or worse?

(I've spent some hours searching for this but to no avail. I'm wondering if I may just be looking in all the wrong places.)

publications - "With editor" status for 2 months: is it normal?

I'm a bit worried because one of my papers have been more than 2 months "with editor" status. It's a science journal (field: drug residue, food), from a famous editorial and impact factor 3.3. I'm used to 48h desk reject and I was wondering about the options of being so long with this status 1) very busy editor 2) my paper was forgotten 3) there is a mistake on the website

Oh, normally we have the option to send an e-mail to the assigned editor, but in this case there is only "view your submission".

Edit:

At the end it took 2 months but... We are under review!

Answer

Times vary a lot between journals and, I believe, disciplines. Two months seems like a relatively long period to me but not unheard of. Out of your three reasons I would not opt for 2 or three depending, of course on the form for submitting manuscripts. If it is digital I am sure 2 and 3 would not be high on the list, if it is manual, by post or e-mail, then the likelihood is higher.

I think a busy editor is one possibility. It is not clear from your question if this is "with the editor" after submission or "with the editor" after review. If we consider the former, the most likely reason, in my experience, is that it has proven hard for the editor to get reviewers to accept to review. This occasionally happens to me and I can say that it has no clear relationship to the possible quality of the paper. In the case of the former (after review), the busy editor becomes a more likely candidate since the editor should study the reviews, decide on the faith of the paper, and possibly provide guidelines for your revisions.

If you have any indication, from for example peers, what typical handling periods are in the journal where you submitted your manuscript, you should definitely contact the journal to ask about the status of your submission. Such requests are commonplace (too common in fact) so try to assess if the two months is long or normal in the case of this particular journal before contact.

paper submission - How can co-authors check the status of a submitted manuscript in Elsevier Editorial System?

I know that after submitting a paper through Elsevier Editorial System, the corresponding author can check the status of the submitted paper online. But how about co-authors? Can the corresponding author give a permission to the co-authors to enable them to check the status of the paper as well? If yes, how that can be done?

Answer

The answer is No, he/she cannot cannot give any permission to the co-authors after submission to EES and before acceptance, as mentioned here:

I am a co-author on the paper, I would like to be able to see the status of the manuscript. I have the manuscript number and I am registered on the journal website.

After submission, you can only see the status of a submitted paper via the corresponding author's EES homepage. You will not be able to search for this submission via your own author's EES homepage.

So just the corresponding author can check the status before acceptance. But after acceptance, co-author can track the status as well:

After acceptance, the article is recorded in our tracking system, you can use the production reference number along with the Corresponding Author's name to track your paper status and add your paper to your personal homepage on http://www.elsevier.com/trackarticle.

citations - Citing old or new papers of same work?

Often researchers publish their work incrementally. Abstractly speaking, let's say, in 2010 the researcher publishes version 1.0 of his algorithm/system/framework. Two years later, he publishes an improved version 2.0 of the same algorithm/system/framework.

If I want to cite his work, should I

a) cite his oldest work (advantage: typically, older works have more citations),

b) cite his newest work (advantage: my readers will be directed to the most uptodate version of the author's work), or

c) cite both?

Answer

You might cite both by saying "Idea X, originally developed in [1] and extended in [2], shows that ..."

classification - How many species can have the same scientific name?

For my science homework, a question came up asking how many species can have the same scientific name. I'm pretty sure that each species has a different scientific name, but just to be sure...

microscopy - Dataset of microscopic images before and after staining?

I am looking for a freely distributed dataset of microscopic images. I am hoping to find a dataset that would feature histological images before and after staining (e.g. H&E or some other standard one, preferably). I have been searching through various databases, but I cannot find a proper set. I hope the sample size to be at least about 100. Suggestions?

evolution - Do animals exist with an uneven total number of digits?

I recently finished reading Contact by Carl Sagan. In the book they talk about a pattern in the transcendental number like pi or e, and comment that it is found in base 10 or however many fingers the race has to count with.

When in the end they find a pattern in pi it is in base 11, which I found a strange choice since I can't think of an animal that has an uneven total number of fingers, and I would think that most evolution would result in a somewhat symmetrical design.

Do any animal exist that has an uneven total number of fingers or equal lim, excluding polydactyly and oligodactyly?

Answer

Your conclusion relies on the supposition that all beings must count using their finger tips (or the most paralogous, "finger-like" limb). In fact, even within humans this is not necessarily true: the Yuki native people of California count in base 8 by counting the spaces between their fingers; meanwhile the Oksapmin people of Papua New Guinea count in base 27 (an odd number!) via counting a range of different body parts. One can easily imagine counting in base 20 by counting on fingers and toes. Heck, the Sumerians used base 60. And here's a scheme for counting in base 16 on your fingers.

So, it's entirely plausible to count in base 11, even when assuming morphological symmetry. The beings just need to settle on precisely which 11 parts of their anatomy to count.

As for your actual question, I am unaware of any species with an uneven total number of fingers and I would be surprised if we found one, based on an argument of developmental symmetry and overall (coarse-grained) evolutionarily conserved development plans within major clades of extant animals.

masters - How many hours a day on Mathematics as a successful student?

My motivation to ask this question actually comes from here, receiving negative reactions for 12 hours a day or even 7 hours spending time on Mathematics.

A person usually spends 4.5 years to accomplish a BSc plus a MSc coursework. Books that I found to study in pages (BSc+MSc) approx. are:

• Calculus (760)


• Algebra (450+940)


• Topology (510+540)


• Analytical Geo (210)


• Real Analysis (610+520)


• ODE (440)


• Complex Analysis (480+350)


• Differential Geo (510+420)


• Logic (260)


• Number Theory (480)



• PDE (320)


• Total: 7800 pages.

Supposing spending 30 min per page of studying and 2 hours per page of exercises, so it takes (4/5)×7800×0.5+(1/5)×7800×2 = 6240 hours = 5.5 hours a day in 4.5 years (excl. Sat+Sun) for a student.

The problem is:

1- I think that a Mathematics student has to learn more than I have listed, for example other subjects in Mathematics.

2- a Mathematics student has to spend on other than studying texts, like attending classes, other courses (e.g. computer) as well.

How a typical university student in Mathematics spends a few hours in average on studying and knows a lot Mathematics and is able to start research, which I am not capable of? It's a paradox, or maybe I am not smart as other?

Thank you.

PS I am not officially a uni student yet, but I had to spend 12 h/d on average to study the mentioned books which I am pretty sure are less than what a uni student covers in their studies.

cv - Difference between contributed and invited talk

I am a second-year PhD student.

Through a grant I was able to organize a scientific visit for myself to another university. The aim of this visit was just to talk and discuss with some of the staff there about their research.

Prior to my arrival, my host notified me that they frequently hold internal seminars/colloquia etc. and would I like to give a talk. I obviously accepted this offer.

My question is, when listing this talk on my CV, should I list it as contributed, invited, or just a 'Talk'?

I only ask as typically I think of the term 'invited talks' for more senior, established academics and it was I who petitioned my host in the first instance for a visit.

Any input welcome. Thanks

masters - Ethical GPA rounding

I am applying for a master's program in the US and am not sure how I should present my GPA ethically when discussing it. I have an undergrad total GPA of 3.394 and when asked to put in my undergrad GPA it only gives room for 2 digits and nothing more. EX: 3.0. Can I round up my GPA since it's so close to 3.4, or would this be unethical and I should round down to 3.3?

To make this as general as possible: How should one round their GPA when only 2 digits are accepted, and they're less than .05 away from the next digit?

Answer

There are widely accepted standard rounding rules: any number greater than or equal to 3.35 should be rounded up to 3.4. There is no reason to expect that an application would want non-conventional rules for rounding GPAs.

tenure track - Advice for On-Campus Interview?

I have an on-campus interview next month. Being my first time to make an on-campus interview, I have no experience on how to properly do that. I was asked to give a teaching demonstration for 30~45 minutes. The university is focused on teaching and they have only a master program (no PhD ). I am planning to present my research work as "a teaching demonstration". Is that okay?

Answer

If you want to mention your research at all, consider the following plan. The think you really want to avoid is being overly pedantic and going over the head of the likely audience. Pitch the talk at undergraduates.

In such a talk, you don't want to try to impress people with your brilliance. It is more important to stress that you are inspiring. Save brilliance for the later session in the faculty lounge with Sherry instant coffee.

You don't give your field, but your profile suggests it might be mathematics or similar.

In the talk, rather than going through details of the research, you can talk about what it is that got you started on it. Make it relevant to some undergraduate course, if possible. How does this connect to, say, elementary topology, or even Calculus. In some math fields this is easy. You don't have to draw all the connections, but just give a hint that what they are now studying has extensions and that those are "interesting."

Talk about the main result just a bit, but mention why it is important. If possible, talk about what future explorations might look like.

Your goal is to show insights into the field, whether math or not, and not details.

But the main idea is to leave the typical fairly good undergraduate with the idea that "I can do that, too."

If you can make it interactive, all the better. If you can ask questions, for example, you can get them engaged. Leading questions, actually.

And even if you skip talking about your research altogether, do the above things in your talk.

mathematics - Are Doctor of Arts (D.A.) degrees in math taken seriously?

Morris Kline's Why The Professor Can't Teach mentions many problems in current mathematical education in university. The author said the Doctor of Arts (D.A.) in Mathematics was created to solve these problems. But I noticed that there are only three universities that have this degree in the U.S. (even in the world). They are

1. Carnegie Mellon University,


2. University of Illinois at Chicago and


3. Idaho State University.

I even heard an associate professor in CMU said they want to halt this degree. So my question is, has the D.A. degree in math been taken seriously?