ethics - While teaching how should I give justice equally to both female and male students?

I am 27 years old unmarried male teacher. I have been a teacher (lecturer) for the last 6 months in an Engineering institution. My students are 4 to 5 years younger than me.

The problem is that while teaching I have soft corner towards female students. I don't understand whether it is due to opposite gender attraction or due to female students asking more doubts than male students. I help female students more than male students. I know that it is against moral ethics of teacher's profession. But I couldn't change my attitude. Now, I think that male students might have noticed this and they may make complaints against me to the principal.

So what changes can I make? While teaching how should I give justice equally to both female and male students equally? Or should I quit teaching?

Answer

Normally, the problem is the other way round.

For instance, one phenomenon is that I often found with male students is that they override/overrule/overtalk female ones. If that happens more than sporadically, I interrupt them and tell them to let the other student speak out (of course this cuts both ways). I mention this as a concrete example for a trigger/action based approach that works well to reduce imbalance. With this, I get good participation from the whole group.

You talk about "soft spots". Beware, this signals danger. Your student's gender should be strictly taboo for how you deal with them. It is absolutely essential that all your students feel equally respected. Is it that you give more time to females? Then actively allocate more time to males. Is it that you encourage females more? Balance this by introducing some competitive element (such as voting on responses, competitive problem solving); male students tend to like that (of course, I am generalising, it needs playing by ear). Intersperse your presentations with adventurous anecdotes of topic-relevant scientists.

Generally: make a point of addressing more of the neglected students. BTW, this does not only hold for gender, but also for preference by activity or ability. Activate less able, or less active students. If you do that well, you earned your badge as teacher.

Under no circumstance treat your teaching as a dating opportunity. It is not. Getting a jealous girlfriend might be an idea to help getting things under control - if you cannot do it yourself, it may be the way to delegate that job to her (and I am not yet entirely sure whether I am joking here).

Acceptance into graduate math programs

I have been hearing different views about my likelihood of getting accepted into a math graduate program.

Which of the following factors contribute most to the acceptance of a non-math undergraduate into a math graduate program (please order them)?

1. GPA


2. Recommendation letters


3. Publishing math papers

---

Since I am an engineering student I only registered basic math courses (such as calculus, linear algebra, etc.). However, I studied a lot of other more advanced courses by myself. My GPA is about 3.5. A lot of people have told me that I need to raise my GPA in order to get accepted into a decent math graduate program and this is worrying me.

Courses that I self-studied: Undergraduate abstract algebra, real analysis (with an introduction to measure theory), first 4 chapters of Munkres' Topology, elementary number theory, graph theory

Courses that I am self studying: Hungerford's abstract algebra, algebraic topology

Courses that I plan to study: algebraic geometry, algebraic number theory, complex analysis.

I also managed to finish 2 math papers. So the question is:

Where do I stand now?

Answer

Since you are an engineering major who took only the standard math courses, I infer that your overall GPA is driven by your engineering coursework. I don't think that graduate admissions will learn much from your grades in engineering, good or bad. The GPA of 3.5 is not that bad in engineering, especially if (as it seems) your heart was not really in it.

Self-studying is great, but the knowledge acquired from it needs to be evaluated by someone. Acing GRE Math would send a signal that you indeed learned something. If during your studies you kept in touch with math professors in your school, and they know enough about you to write an informed letter full of specifics, that would be even better.

The opinions on undergraduate papers in math are divided: e.g., not everyone considers them a good way to spend time as an undergraduate. I would not expect the admission committees to seriously read papers sent with an application, though they will glance at them.

So, my order is: letters, GRE math, papers, GPA.

citations - Should I cite author names as they appear in the journal or as I know them to be complete?

Since I've been using Mendeley to manage and extract metadata from my PDFs, I've come to notice that authors are sometimes denoted with all their initials and sometimes with just one. I assume this has to do with different journal's rules on denoting author's names. However, this makes a mess in my author list in Mendeley, as the same person may be known under two or even more names (e.g.: "Last, F."; "Last, First"; "Last, First M,"; "Last, First Middle").

If, for completeness' and tidyness' sake, I edit the author fields to always have the most complete name of the author available to me regardless the journal the author published in, I inevitably will change the way I cite them. For example, an article from a certain journal only uses the first initial:

Last, F. Article Title, Journal name, x:y (YYYY), pp. xxx-xxx

After I have "updated" my authors, it is possible my citation includes also the second initial, i.e.:

Last, F.M., Article Title, Journal name, x:y (YYYY), pp. xxx-xxx

So my question is: am I incorrectly citing the article when I include more complete information about the author's name than is given by the journal article itself?

Answer

I can see your problem but I am afraid you will have to live with the mess. The reason is that a publication must be referenced exactly the way it is published. The exception is that it is permissible to abbreviate first names to initials to adhere to the standard of the publication in which you intend to publish. It is, however, not allowed to remove middle names (initials) if they are part of the original publication, nor to add initials if they were not part of the original. I know many authors who have published under one and two initials randomly, but there is not much one can do about it.

Now, if you do it in your reference program, there is nothing wrong with that, but you need to make sure your changes do not migrate into published work that you write.

Just an example, Uniform Requirements for Manuscripts Submitted to Biomedical Journals: Manuscript Preparation and Submission: Preparing a Manuscript for Submission to a Biomedical Journal states:

Some but not all journals check the accuracy of all reference citations; thus, citation errors sometimes appear in the published version of articles. To minimize such errors, references should be verified using either an electronic bibliographic source, such as PubMed or print copies from original sources. [The text then goes on to discuss retracted articles.]

publications - Is there a general way to find or get notified of relevant conferences and meetings in your field?

Here's the problem: I don't know what are the relevant conferences and meetings for me to potentially attend/present in. Every conference I've been so far has been passed down to me by a much older professor who knows it by experience.

I feel like this is an important topic, and yet all the tools I tried to use to find conferences (such as allconferences and conferecealerts) fail to find me relevant things.

Is there a method to reliably find relevant for you conferences worldwide? Ideally it would be good to get notified when a new relevant conference is announced.

I know there are some websites (such as arxiv-sanity and google Scholar) that suggest papers for you to read based on previously loaded papers, so I wouldn't be surprised if there was some similar tool where you put some conferences with a few keywords and it spits out suggestions.

Cheers

physiology - Can the body of any organism on Earth live without impairment both in vacuum, and within Earth's atmosphere?

I know from reading that a human in vacuum needs a space-suit to survive.

Is the body of any organism on Earth capable of living equally in vacuum, and on/below Earth's surface within the atmosphere?

Answer

Remarkably, Tardigrades are multi-cellular animals which can survive the vacuum of space.

publications - Is it appropriate (as a PhD student) to email other researchers asking about some details in their papers?

It has happened on several occasion now, that I read a paper, understand 95% of it, but there are some niggling details which I simply don't get. I ask around, I ask my advisor, and nobody is able to help (either because they don't get it themselves or they are too busy, which is completely understandable).

I have often felt like simply writing to the author of the paper, asking clarifying questions. But these are all busy people, currently on the job market, interviewing everywhere. And another thing is they also know my (rather famous) advisor pretty well.

Would it be weird to write to them? If so, should I mention my advisor at all? I don't want to put my advisor in an awkward situation, at the same time I don't want to seem like I'm hiding some information.

I am just not comfortable asking such a stupid question to my advisor, hence asking here. Thanks so much!

Answer

As a professor, I've received many emails from graduate students at other institutions over the years asking me questions about my research. Not once has any of the following thoughts ever crossed my mind following such an email:

1. 
   

   This student is doing something "inappropriate" by contacting me at my publicly listed email address.

   
   


2. 
   
   

   This student is "stupid" or is asking a "stupid question".

   
   


3. 
   

   Oh, this student mentioned their famous advisor. Their ignorance reflects poorly on their advisor. I will make sure to complain to the advisor the next time I see them.

   
   


4. 
   

   Oh, this student didn't mention their advisor. Something's fishy here. I need to know who their advisor is, and preferably know it's someone famous who can help me in my career, before I dignify their email with a reply.

   
   


5. 
   

   Etc etc, i.e. any other bad thought that suggests the student has crossed some invisible line separating lowlifes like them from (supposedly) important, powerful people like me.

   
   
   

Instead, here is a sampling of ways I actually react when I receive such an email:

1. 
   

   Oh, how nice. Someone at [name of cool university] is thinking about [name of my paper]!

   
   


2. 
   

   Oh, how nice. A student of [name of famous advisor I am friends with] is thinking about [name of my paper]!

   
   



3. 
   

   Oh, how nice. This student pointed out a weak point in the presentation of one of my proofs. I hadn't thought of the question that way, it's quite interesting! Seems like a smart student, would be nice to meet them some day.

   
   


4. 
   

   Hmm, I'm kind of busy with lots of other things so this email stresses me out a bit. Oh well, I'll find time to reply to it some time in the next few days. In the meantime, how nice that someone is taking an interest in my paper and has interesting things to ask/say about it.

   
   

As you can see from these two lists, basically the whole premise assumed in your question about the mindset of a professor receiving an email of the type you are thinking of sending is deeply misguided. Professors (the vast majority of them at least) are simply nothing like the scary, classist, pretentious, easily offended, thin-skinned people that a lot of students and other people seem to think they are. They are busy, yes, but the main thing that makes them so busy is that they are passionate about their work and usually cannot pass on an opportunity to discuss it with someone, regardless of their academic rank. So, good luck sending your emails! I'm sure you will be pleasantly surprised by the replies you get. :-)

phd - How to select a dissertation committee member wisely?

I'm currently developing my dissertation proposal, and am in the process of choosing my committee members. I have heard that one should carefully choose their committee members, since they ultimately judge if and when your PhD work is done. As far as I can tell, a committee member should at least have some expertise in my research topic. I'm sure there's more to it than that, but I want to know what other qualities should I look out for? What qualities in a committee member should I avoid? I imagine these other qualities are subtle and difficult to judge at first. Nonetheless, how do I know if they are a good fit for the success of my PhD?

astrobiology - Can life subsist on anything else but water?

Inspired by an answer to a previous question.

It's hypothesized that extraterrestrial life could be based on silicon rather than carbon as its main structural element.

Are there similar theories about an alternative "life solvent" rather than water?

human biology - Why do we have no enzyme to digest cellulose?

As we know, cellulose is the most abundant polysaccharide in nature. Why don't we have an enzyme to digest cellulose?

genetics - Genotypes in diploid/haploid cells under mitotic/meotic cell divisions

I am new to genetics , and am stuck with the following question at hand:

If $2$ cells with genotypes $(A/a)$ and $(A/a,B/b)$ undergo mitotic and meotic cell divisions respectively, what will be the genotypes/gene compositions in the resultant diploid and haploid cells with respect to the above mentioned alleles?

Can someone help me how to proceed?

Answer

Though broad, here I provide a summary in graphical way.

Mitosis:

.

---

MEIOSIS: 2 successive steps : Meiosis-1 and meiosis-2

Meiosis-1

---

Meiosis-2

---

So lets see what happens with cells given at question.

1. Cell with genotype Aa

(monohybrid or one-point cross-experiments; that means we are looking to gene-pair at 1 loci; not looking to any other genes):

1. A. Mitosis:

Possible genotypes of their offsprings: All Aa.

1. B. Meiosis:

gametes will show 2-possibilities ; A, a.

---

2. Cell with genotype AaBb

(dihybrid or 2-point cross-experiments; that means we are looking on genes of 2 loci; not to any other cells):

2.A. Mitosis:

all offsprings AaBb.

2.B. Meiosis:

If given condition says the loci for A (or a) and B (or b) are on same chromosome (linked genes) and no crossing-over is there;

then We will get only 2 types of gamete AB and ab.

If crossing over(s) take place between the 2 loci; then we'll get 4 types of gamete AB, Ab, aB, ab; but their ocurring frequency will deviate from Mendel's independent assortment.

If the 2 loci are not-linked; i.e. they are located in distinct chromosome; then also we'll get 4 types of gametes AB, Ab, aB, ab; but they will follow Mendel's independent assortment pattern.

Reference:

1. 
   

   Concepts of Genetics, 8th Edition (EBook) By William Klug, Michael Cummings, Charlotte Spencer / Pearson; chapter 2 (mitosis and meiosis)

   
   


2. 
   

   The science of Genetics, 6th edition, by George Burns and Paul Bottino, Macmillan.

   
   


3. 
   
   

   Genetics/ P.K. Gupta/ Rastogi Publication Meerut

   
   

graduate school - In teaching, what are the advantages of using slides over doing board work?

At my university, most lecturers and professors use slides in teaching. This is true for most engineering, mathematics and science courses. I am more comfortable with doing the board work and then sharing my hand-written lecture notes with the students. From my personal experience, I feel that the latter is a better way of teaching.

So, what are the advantages of using slides? Why do you use slides?

Secondly, does the answer to the above question change if you were teaching graduate students?

molecular genetics - Criteria for the numbering of human chromosomes

What were the criteria devised for the numbering convention employed in human chromosomes? When was it fixed?

Correct me if I am wrong; it appears that chromosome pairs 1 to 22 were originally ordered in terms of perceived structural size, which ended up fitting neatly with the quantity of base pairs (but not with the quantity of genes).

The sex chromosomes in turn were arbitrarily assigned as "pair 23".

Is this sound?

Thanks in advance.

Answer

Why do you think it was "fixed?" Here's a nice review of the history of human cytogenetics, which included not only the original image from 1956 but points out a report which comments on the standardization of chromosome number. The autosomes were indeed numbered by length, and the sex chromosomes are traditionally put at the end as they are "numbered" 23 but clearly function quite differently. Gene content was decades away from being known at the time, and honestly isn't even known now. It's also just as arbitrary; simple size is easy enough and makes for rather nice pictures.

ethics - How to deal with cheating when university policy is ineffective?

I am co-teaching a relatively large class with two other colleagues in a big university. Each semester, most students are amazing, trustworthy, and well-behaved and it is a pleasure to work with my students. But there is a very small group of students each semester who cheat and I don't know how to deal with them.

The university has a detailed, strict, and elaborate policy for dealing with cheating. We send students suspected of cheating to a special committee where they decide if the student actually did anything wrong. The committee demands a copious amount of evidence before it convicts any student, yet at the same time, the university policy is so restrictive that we cannot collect evidence. For example, we are not allowed to do anything that indicates or suggest a student may have cheated. We are not allowed to mark their papers, move them during exams, or even talk to them. This means that most students get away with cheating if they are sent to the committee. Students who have copied identical answers from a neighbor over and over in quizzes got away with it in the committee. This process is so pointless that the course coordinator does not report most of the cases to the committee anymore.

I don't mind that a few students get away with cheating but the universities' restrictive policy shuts all the doors to any further discussion with the students. I am not looking for ways to punish my students. I want them to understand why cheating is unfair to other students and, hence, unacceptable. I want them to understand integrity and honesty are far more valuable traits than getting good grades in college.

Any suggestion on how I can communicate these ideas and their importance to my students?

---

Edit:

I am sorry for not being clear. My question is not about how to prevent cheating. It is bout how to have a conversation with cheaters.

We do what we can to prevent cheating. We randomly seat students, make two copies of the exams, assign a good portion the final grade to labs, and use various other techniques. This question is about reaching to the cheaters and having a discussion with them.

graduate school - Are Identical Make-up Exams Fair?

I recently took an exam, and our professor told us that we should submit our question sheets since 2 other students in our class are going to take a make-up exam. We were also told that we were not allowed to talk about our exam while the other 2 are around. I presume this means that their exams are going to be identical to ours (For the sake of argument, let us assume that this is the case, and it is not in fact a strategy or something of our professor).

Our class is on weekdays (MWF for 1 section and TTh for another), but we had our exam on Saturday afternoon. Since we all have class on Saturday morning, it is okay to have an exam on Saturday afternoon since we would already be on campus. Apparently those doing the make-up exam have conflicts with their plans for Saturday afternoon which the professor accepts.

Essentially, we can't tell them the contents of the exam. Our professor claims that this is so as to not compromise the integrity of the exam.

So here's my first question:

Is it fair to the students taking the exam earlier that the make-up exams are identical to the original?

We are grad students of mathematical finance.

Expansion:

It seems to me that the fact that it is too easy for the two others to find out the exam questions should be reason enough for our professor to give a different and possibly even harder exam and that doing otherwise is in itself compromising the integrity of the exam.

If it's not compromising the integrity of the exam, why not just have the same exam every year and collect the question sheet from students (which, cmiiw, actually doesn't really do anything since we can just copy the questions on a bond paper and bring the bond paper home)?

See possibly related question.

Second question:

I seem to recall that department policy is that make-up exams are "generally" (exact word in undergrad syllabuses but not in our grad syllabuses which makes no mention of such) more difficult. If the answer to the first question above is yes, then does it follow that the "generally" should be removed?

P.S. I truly cannot imagine how difficult it must be to a mathematician: research, teaching, consultation, conferences, etc. Thus, I am aware that it is no easy task for a teacher to just come up with a make-up exam, but nevertheless for the sake of maintaining the integrity (maintain is not compromise?) of exams, I believe this should be done.

neuroscience - How do neurons receive the ions needed for creating electrical pulses?

I really wonder how ions are transported into the brain and the neurons for creating electrical potentials - how do ions get from our digestive system to the neurons? Or are the ions just freely released into the brain like hormones? Or are they transmitted during neural signalling somehow (via neurotransmitters maybe)?

Answer

Short answer

The sodium-potassium pump in the epithelial cells lining the brain capillaries pumps Na⁺ and K⁺ into the brain.

Background
The blood-brain-barrier is formed by the endothelial cells lining the capillaries in the brain. Not many compounds can pass this lining, especially not when they are hydrophilic, such as charged metal ions. However, as you rightfully state, somehow these metal ions, and especially Na⁺ and K⁺ need to get access to the brain because they are crucial for membrane potentials and action potentials, and hence for neuronal survival and function. And indeed they can, albeit the exchange between blood plasma and brain is slow compared with other tissues.

Intravenously administered K⁺, for example, exchanges with muscle K⁺ in 1 hr, but K⁺ exchange in brain is only half completed in 24 to 36 hr. Na⁺ exchange is somewhat faster, with half-exchange into brain occurring in 3 to 8 hr. Despite its relatively slow entry into the brain, Na⁺ exchange across the blood—brain barrier appears to occur by mediated transport. This occurs, in part, through brain capillary Na⁺,K⁺-ATPase (the sodium-potassium pump). The Na⁺,K⁺-ATPase in the brain also may mediate removal of interstitial fluid K⁺ from the brain and thereby aid in brain K⁺ homeostasis.

<sub>Reference
- Laterra et al. In: Siegel et al. eds. Basic Neurochemistry: Molecular, Cellular and Medical Aspects. 6^th ed. Philadelphia: Lippincott-Raven; 1999</sub>

conference - Flying with a poster tube as a hand luggage

I am flying to a conference, in which I am presenting a poster.

In principle there might be a problem, as the poster tube:

• is a second piece of hand luggage,


• it is longer than the limit allows.

However, it seems that it works (once I tried with no problem, my colleagues usually have no problem).

Does it happen that one is not allowed to take a poster tube in the hand luggage?

If so, how to avoid this problem? (Advice, tips and tricks are welcome.)

If the question is place-specific, I'm interested mostly in EU.

On agreeing on length of PhD program in advance and three year studies

I know people say in Europe (say in Computer Science) a PhD normally takes three to four years. My concern is: is there no way to know the number of years in advance? Is it not something I can "agree" with the supervisors before hand how long it will take? Exactly? Not approximately, rather exactly. In other words are three year long phd programs common?

job search - Who to address on the cover letter?

In the cover letter of an application to an academic job, should we write

Dear Search Committee Members,

or

Dear Professor A, Chair of the Search Committee Members,

or

Dear Professor A, Chair of the department

or what else?

In case we don't know who the chair of the Search Committee is, should we write the department to ask?

Answer

I address all cover letters, letters of rec, etc. "Dear Committee Members:" Don't waste your time addressing it to an individual. The only thing you can achieve by doing that is embarrassing yourself and giving the search committee the chance to have a good laugh at your expense. If you do it correctly, it doesn't actually achieve anything; why give yourself one more thing to stress about?

job search - Gaps between PhD and employment?

What is the longest gap of unemployment that will likely not affect your chance of getting an academic position (post-doc or faculty)?

For example if you graduate from your PhD in December or January but most post-doctoral/faculty positions in your field don't start until May-Sept, is a partial year's worth of unemployment looked down upon in future job applications? If not, what is the longest gap that won't look so negative while applying to future jobs?

Answer

I am not sure how you are using the term unemployed. Clearly someone with a paid academic position (e.g., adjunct teaching or lab tech) would not be considered unemployed. I am not sure if you consider an unpaid lab tech or a paid burger flipper as being employed. To me the real issue is being out of the field.

If you cannot get a relevant paid position and but can afford to be without income for a few months, then a year gap, and probably longer, isn't problematic. In fact many labs will hire unpaid researchers. In this case you could continue to conduct new research, publish, apply for grants, and gain new contacts. You could likely stay in an unpaid position as long as you could afford it without any affects on future job prospects. If you cannot get an unpaid research position then it really depends on how long you can milk publications from your past research and produce new research without any affiliation to a research group.

If you cannot get a relevant paid position and cannot afford to be without income for a few months you can sometimes find paid work in a related field. Working as a paid lab tech (e.g., washing test tubes) or adjunct teaching. These types of jobs won't help you publish more or get grants and in fact take time away from publishing, research, and getting grants. That said they can provide a limited set of new skills and cotnacts so are probably sustainable for a year or so.

In the absence of getting even a peripherally related job taking an unrelated job (e.g., burger flipper) even for a short period (i.e., months) gap can be problematic. Not only will it slow down publishing, research, and grants it may make you less flexible about being able to take up a new related position (e.g., how much notice would you have to give). You are also not building new skills or contacts.

A lot of the impact will depend on how important publication speed is in your field. If a few month delay in publishing will result in you being scooped, any gap is probably bad. Similarly the ability to do research without any resources will help you weather a gap. Similarly, if your field has new instigator grants with a clock that starts ticking upon graduation then gaps are bad.

supervision - How can a researcher in his early career attract good PhD students?

As stated by the title, I want to know what a researcher in his early career, i.e., having not had any graduated PhD student yet, can do to attract good candidates. The reason I am asking this question is because PhD applicants usually look for supervisors who have many successful PhD students.

publications - Why does a copy editor count the number of characters on a line?

I got my paper back with remarks of the copy editor. One annotation counts the number of characters in a line. I have been told to ignore it, but I am still interested to know what it is for.

On the bottom of the page, the copy editor wrote: "73 × 39 × 27 → 25p.". 73 is the number of characters, 27 is the number of pages of my manuscript. 39 is the number of lines per page minus 1. It seems to be a calculation for the final number of pages (judging from the "p.") but I don't see how that figure would be calculated by multiplying these values.

I am using a template provided by the journal.

Answer

73 x 39 x 27 would give an estimate of the total number of characters in your manuscript. They presumably have some standard estimate for the number of characters that fit on one page in the final format, and they've divided by that number (not shown) to get 25 pages.

I can't think of a good reason to subtract 1 from the number of lines per page (unless one line is obviously a header or something) so I'd wonder if they just miscounted.

defense - What title do you hold after you've defended but before you graduate?

Two friends successfully defended their dissertations yesterday, and many people have congratulated them, calling them Doctor so-and-so. I explained to my wife that they actually don't have that title until the graduation ceremony, that it's similar to a President-elect, who isn't called the President until they are sworn in. So, what title does a doctoral candidate take after they've defended but before they graduate?

Answer

There isn't a formal, universally accepted title here. The general standard has been to call them "Doctor" since everything else is in principle a formality.

The only other note that I'd make is that it's not commencement that makes the student in question a doctor, but rather conferral of the degree by the university. Some universities may confer degrees multiple times per year, but only have one commencement ceremony.

So, I would not include "Ph.D." next to my name, but in the education of my CV, I'd write "Ph.D. (to be conferred Month Year)," as that is entirely accurate representation of the state of affairs.

phd - How to tell a faculty member that I don't need him on my thesis committee anymore?

Out of five needed members for my doctoral thesis committee, four are fixed. For the fifth member, I approached Mr.A. He has no real connection to my research or topic but I contacted him because he was just as good a fit as anybody else in the department to be the fifth member. I have never worked with him or taken any classes but we did talk a lot in the first few years where he would just ask about my progress by the copy machine, etc. We don't even have a "rapport". The relationship is absolutely neutral, nothing positive/friendly, and nothing negative. I asked him to be on my committee and he said yes. I said I'll get back to you with dates, etc. He is a senior tenured professor.

Then about a month later, I was looking at the CV of some of the new hired (junior) faculty in the department Mr.B (this is his first year) and I see that we have a collaborator in common. Mr.B has published multiple papers with him and Mr.B is working with the same code and the code managing team that we are working with. He is definitely a good person to have on my committee. I finally see Mr.B after a few more months (because of busy schedule/travel/etc.) and he agrees to be on my committee.

The question is, how can I tell Mr.A, as tactfully as possible, after about four months of being quiet that he is basically rejected from my committee because I didn't know about Mr.B but now that I know, Mr.B is a much better match than he is? That I don't need him but I do appreciate his offer? I don't want to antagonize Mr.A or burn any bridges. Should this be in email or in person? Should I explain or just keep it terse? Should I keep it vague that I don't need him and thanks for his time? Or should I tell him about Mr.B and why he is a better match?

FYI, this was before anything official/paperwork was done so there is no problem with that.

Answer

I think you're making a bigger deal about this than necessary. You enlisted Professor A to serve on your committee because you needed a fifth man, not because of any close research connection. More recently, but still before signing any paperwork, you found Professor B, who does have a close research connection.

Just tell Professor A that! Problem solved. You don't have to dither about how to present this information: send it in an email or send it in person. The information of the previous paragraph is sufficient: you don't need to dwell on your connection with Professor A as much as you did in your question. (But by the way: asking about your progress at the copy machine is what I would call "friendly". At least he knows who you are and something about your progress in the program, and he cares enough to ask about it sometimes. That puts him ahead of the curve in many academic departments at many universities.)

What you do not seem to realize is that if Professor A has no close connection with your work, it is overwhelmingly likely that he was being friendly indeed by volunteering to serve on your committee anyway, and he'll be equally happy or, more probably, a little happier not to serve. Since he is a senior tenured professor he has lots of stuff to do. Serving as the fifth man on a student's committee is not nearly such a prestige job that his layoff needs to be sugarcoated. He'll understand, and he'll be especially happy that someone with more relevant expertise will be taking his place.

hematology - Does a blood transfusion cure disease?

Does transferring blood between two people also transfer all the white blood cells?

Why can't AIDS victims with low t-cell count just get blood transfusions till they have more t-cells? Why can't someone who's over a cold give blood to someone with a cold to cure them? I know this is silly, but I really want to know why this won't work.

Answer

Not really no. Most blood transfusions we think about are red blood cells or platelets, which don't have the immune function you're asking for. That's a good thing. Usually, if there are white blood cells in the transfused blood, the host's immune system will recognize them as foreign and destroy them. Remember, your cells all look like foreign invaders to my cells; blood transfusions of red blood cells are carefully matched to limit negative reactions. There is also a process called transfusion-associated graft versus host disease in which the donor white blood cells will attack the host cells; this mainly occurs in immune-compromised individuals, but GvHD is definitely something to avoid. Blood transfusions are usually filtered and irradiated to remove, among other things, white blood cells.

That being said, people are beginning to use white blood cells as treatment. A new therapy being studied heavily for all sorts of diseases, from cancer to HIV, is to take the hosts own white blood cells and grow them up in the lab to select for the strongest and most effective cells. The researchers then wipe out the individual's immune system and give them a dose of their own, super-powered white blood cells, hoping that works.

Sometimes it kind of does. They've also been trying a new system, similar to what you propose, using bone marrow. They had a huge success with an HIV-positive individual now referred to as "the Berlin patient." They gave him a marrow transfusion which would produce HIV-immune white blood cells and replaced his immune system. He was and is effectively cured of HIV/AIDS.

publications - How to find all of the responses to a published research paper?

While searching through various journals with my library's on-line journal search tools, I have occasionally found short articles which are simply comments on other published papers. These short articles might have various kinds of comments, but generally describe why the first paper's research or theories are flawed. In addition, sometimes I have found replies from the original author of the first paper, responding to these comments, for e.g., to clarify the meaning or perhaps to give further support to their original arguments.

• Do such exchanges generally only occur within the same journal, i.e. the responses are published in the same journal, or can these occur across journals?


• Are there any special tools to assist with locating all of these "replies"?

Answer

First, it may depend on your field, but at least in mine (physics and chemistry), it is rare for papers to generate comments or replies, and really extraordinary for a paper to be followed by multiple comments. (The editor usually lets the original authors reply to the comment, however.)

Some publishers provide links to the comments and replies on the webpage for the original paper. Otherwise, you can locate those comments using the following criteria:

• they are published in the same journal, or in a preprint server (like arxiv)


• their title includes “comment on” or “reply to” (or other such publisher-dependent prefix that you need to identify)

Finally, you should get the list of all newer papers citing the original paper, and check them out. If you're investigating a paper in depth, you’ll do that anyway :)

Reviewing a revision, after the original review did not reach the authors

A couple of months back, I reviewed a manuscript and recommended a Major Revision. Ten days ago, I received the revision for review, with a note from the editor asking me to expedite, since the review process had already taken a while (not due to me).

However, from both the initial decision letter by the editor and the authors' response, I see that my initial review did not reach the authors (I checked: my review is in the system). The other review, which did reach them, mostly raised points orthogonal to mine, so if I were to review the revision again, I would likely reiterate my original points.

I immediately notified the editor and expressed that I would be happy to re-review, but would appreciate a confirmation that this review would then actually reach the authors. No response. A week later, I wrote again. No response. That was three days ago.

To be honest, I am a little miffed. Not so much that my initial review, which I did spend a considerable amount of time on, was not forwarded - stuff happens. More that I am not getting a response to what to me appears a straightforward question. After having been asked specifically to move quickly on this.

At the moment, I am vacillating between either doing the review ASAP or waiting for any kind of response from the editor first, but this second option seems passive-aggressive to me. Additional info: I know the editor, we meet regularly at conferences. I know that since he has been appointed dean, he is drowning in work.

Questions:

• Has this happened to anyone else? How did you react?


• Am I overreacting? Should I just review and stop whining?

Answer

I cannot say whether the situation is due to sloppiness or due to some technical issue but it seems odd and something that should not happen. I gather that you were in an electronic review system of some sort and then the review should automatically be forwarded. In a journal not working with an electronic system, something like this is more likely to occur but should be a one off mistake in any case. Problems like these, if they recur regularly, will likely sink the journal reputation in the end. you probably have some sense of the standings of the journal.

The lack of response may not mean much and I would not over-interpret it. It is of course not a positive reflection of the journal.

Anyway, I would recommend you to basically re-use your earlier review. Look through it after reading the paper and authors comments to see if anything can be removed. If you catch anything new that needs corrections, of course, add it. You have done the work once and unless the paper is completely rewritten with significant changes to discussion and conclusions, your comments still stand. You can only reiterate your verdict of Major Revisions, which should lead to a third round. I think, under the circumstances that would b fair, unless the authors fully comply with your suggestions, in which case the editors can use his/her discretion (depending on a second reviewers response of course).

So bottom line: your initial review needs to reach the authors but with corrections for whatever has been changed. Unless you receive some explanation for what has happened from the editor, you have to draw your own conclusions about the quality of the journal and particularly the editorship. Try to form a well-founded opinion, whether you think the journal is worth your attention in the future. One mistake is reason for caution, but not reason for judging.

independent researcher - How to get an advisor for my amateur research?

I'm about to embark on a research project in complex systems on my own spare time. It seems like the idea I have is a good one. However, it would be better, for obvious reasons, to have an experienced person guide me. What are the chances that a university professor would agree to guide me while I try and churn this out? (Obviously, I want it to be as professional as possible).

If I don't get anyone on board, what are my chances of publishing, or at least getting a pat on the back from admissions committees when I apply for graduate school? Do they appreciate this kind of thing?

entomology - Bee (?) identification

I live in Michigan. I just saw a bee that I think I've seen before, but only this time was I so struck by its uniqueness and - for lack of a better word - scariness.

I'll describe it. It was maybe an inch and a half long. Maybe bigger, maybe smaller (I'll admit that I was hurrying to get away from it). It looked like a queen bee, but longer and slightly thinner. However it had wings that were very profoundly orangish-red. Like burnt orange maybe.

I haven't been able to find any matching pictures online. It is theoretically possible that it was covered in pollen, and I am incorrect about what I think I saw, but assuming it wasn't (as I do believe this isn't the first time I've seen this guy or one of his friends), does anyone have any clues as to what this could be?

EDIT: PHOTOS

After considerable patience. I was able to capture some photos of this guy. One of these photos is post-processed a little to emphasize the color.

A couple things about these photos.

1. They were extremely difficult to take because the bee never stops moving. I don't know if this behavior is useful for identification, but he is always in the same place (in front of one house), and he flys back and forth between a small crack in the sidewalk (a nest?), and between 5 and 10 feet away. He moves like a dragonfly (that's the best way I can think to describe it), and he doesn't stop - he'll seem like he is going to land, and then flies off. This morning was an exception.


2. These photos do not fully capture the depth and vividness of the redness of his wings, nor do they adequately convey just how large he is.

Answer

Nice pictures! From the back pattern, size, and antennae shape, I'd say this is very likely a Cicada Killer wasp (Sphecius speciosus), cf., for instance, this picture taken at a similar angle to yours.

There are many good resources online about Cicada Killers, including this page from the MSU Extension Office, and the Wikipedia entry Sphecius speciosus.

It would be interesting to see if you could find the distinctive burrow (photo / video) of your resident wasp!

Can I submit the results of a poster to another conference as a full paper?

If I presented a poster at a conference that contained the results of some research, can I then write a paper using those same results and submit it to another conference as a full paper?

Answer

This depends on the customs of the field and the venue. I will answer based upon my experience from an HCI-related subfield of CS:

Conferences usually have some requirement of novelty for published works. Therefore, if a paper associated with the poster already appeared in some proceedings of the first conference, you might not fulfil this requirement. First, however, some different cases might apply:

• If the poster was not "formally published" (i.e. did not appear as a (short) paper in any kind of proceedings), you should be good to go.


• If the poster was supposed to be "formally published", but the conference organizers never got around to setting up the proceedings of the poster session, you're in a bit of an inconvenient situation. Your work is not published in a way that it can be cited (well, it can, but it doesn't look as verifiable as other papers and is not archived by any publisher), but it has been presented. You may want to contact the conference organizers in this case whether publishing your work again is ok, or else you may want to wrap your work in something larger (i.e. present something new, but reiterate the points from the poster as a part of the exposition).

Even if your poster was published in some kind of proceedings, there may be some options:

• Posters are often allowed to present work in progress. If your poster (and the connected paper) was presented in a way to present work in progress, your new conference paper might indeed present the final state of whatever you devised. This can essentially match the content of your poster, but provide more details (see also below).


• Even if the poster presented final results, the term "results" seems to be seen in a very wide sense at least in my fields, possibly in others. A full conference paper provides much more space than a poster paper, and on the poster, you probably presented different (more visual) things than you would in text. As such, you can shift the focus of your conference paper compared to the poster; where the poster focused on the results, the conference paper might discuss the methods used to obtain the results in depth, including design decisions, citations of similar experiments, a verification of the reliability of your experiments, etc. This kind of description can be useful for the community and subsequent works, and as such should provide enough new content, despite being based upon the same material as the poster.

editors - How to create an editorial board for a new journal

I want to start a new scientific journal. After doing all he initial work about setting up a journal now I want to know how will I be able to create an editorial board?

professors - How can PhD student repair relationship with supervisor after PhD student engages in independent research without supervisor?

When I had just started my PhD in Computer Science in Korea, a Physics PhD student in the EU proposed a collaboration. He and I wrote one paper for a conference. I learned last week that the paper was accepted. He is first author. I am second author.

I did not tell my professor about this project even though he was my supervisor then. I mentioned it to my professor recently. He became very angry. He asked me to remove my name from the paper. He said that all my work represents his lab and my university. I shouldn't conduct other work.

My professor's points

• 
  

  The collaboration should be done between supervisors. (My professor's background and interest do not fit with my coauthor.)

  
  


• 
  

  Another issue is none of us can present the paper at that time, asking someone for authorship is acceptable for this situation?

  
  

My question

How can I mend things with my professor and continue to collaborate with my coauthor?

Answer

It's reasonable for your professor to want some input as to how you spend your time, and it's customary for students to keep their advisors informed about other things they are working on. You have perhaps committed a slight breach of etiquette by not telling him about this project earlier.

However, in my view, it is deeply inappropriate for him to ask you to take your name off the paper. He is your advisor but he doesn't own your life. You have done the work and as an academic it is your right to publish it. An interaction like this would have me thinking about looking for a new advisor, quick.

If the professor has technical concerns about the quality of the paper itself and thinks that it is not ready to appear in the scientific/academic record, then he should discuss this with you, and you should share those concerns with your coauthor and come to a decision on their merits. But I feel it's not appropriate for your professor's reputation to be part of that conversation - just decide whether the paper is good and publishable or not.

Your second question is unrelated but I'll address it here anyway. Do not add another person as author (your advisor or anyone else) just so they can present it at the conference. In order to be an author, a person must have made a significant intellectual contribution to the work, and it's unethical to "gift" authorship for any other reason.

In many cases, conferences allow a paper to be presented by someone other than an author. So if you know someone who is attending the conference and willing to present your paper, they may be able to do it without you unethically making them an author. But if the conference really requires one of the authors to attend and neither of you can, then I suppose all you can do is withdraw your paper and resubmit to a conference which you can attend.

ethics - How to get rid of unwanted and annoying co-author?

I'm currently a 2nd year PhD student from a computational field. I'm going to submit my first paper about a new optimization algorithm. I've been working intensively on the problem for the last 2 years and finally managed to get the results I've been longing for so badly. Besides the professor, I'm also supervised by another postdoc whom I respect a lot. Although the two didn't contribute to the ideas I present in the paper, they helped me a lot to understand the field and prepare the paper. So, they obviously deserve to be coauthors.

However, there is one man in my lab who is really ruining my mood and indirectly prevent me from concentrating on writing my paper. He is a postdoc, 15 years my senior, and has been with the lab for ages (he has a permanent position). Just for the record, he hasn't published any first or last author paper since 7 years. We are assigned by the professor to the same subgroup meeting. We use the subgroup meeting to report our individual scientific progress.

About a year ago, he came to my desk I said that I should include his name in the work I was working on because A (the professor) said so. I was quite surprised to hear that because he had nothing to do with my project besides sitting in the same meeting. Nevertheless, I agreed because I just simply didn't care about who should be on the coauthor list. I didn't submit the paper that year because the results were still very unsatisfactory.

Since then, the postdoc constantly asked me to do many things for the project, which I thought didn't make any sense. I simply told him that he should brought up his request during the meeting when the professor is there. And every single time the response of my professor was something like "Why would you want to do that?" and his answer was "Because I'm interested in". I wish my professor whould have said "Then do it yourself".

My professor goes abroad quite often. So, most of the time the subgroup meetings took place without him. About 6 months ago I came up with an idea which I thought very promising and I presented it in the meeting, without the professor. The postdoc basically told me that I need to stop wasting time on my ideas and listen to his suggestions instead if I want to finish my PhD. I felt very offended and spent days and nights coding my idea. 2 months later, I got the best results that I could ever ask for. I presented the results in front of my professor and others. Everyone was happy except one man.

Today, when I was trying to finish the paper then he came in. He asked me to do yet another ridiculous analysis. I told him that I cannot see why this analysis could make the paper better. Besides, this is already the final stage and everything has been discussed thorougly with the "real" coauthors. He answered me "This might not go into the paper but I'm interested in knowing it. I'm the author and I'm allowed to make request". My reaction was something like a silent WTF and he immediately corrected the word "author" to coauthor. I tried my best to not ask him the question "What did you contribute to the paper?"

The professor is currently away for 3 weeks. I want to submit the paper as soon as possible but this man made me crazy. He would talk to me all day long until I do want he wants. I don't want to write to my professor to complain about him. But I'm afraid that he will use his coauthorship to keep bothering me.

What should I do? Thanks for reading the long story!

------------------- UPDATE ABOUT THE SITUATION ---------------------------------

First of all, THANK YOU ALL FOR THE COMMENTS AND ANSWERS!

Today, the man came to me again! After 1 hour of "discussing", I just gave up and spent the whole day explaining to him how he could do the analysis he wanted himself. It would be much faster if I do it myself because I wrote all the code but he just insisted on doing it himself to "not bother" me.

Before I gave up, I told him that the professor knew about what he wanted to do (he mentioned it during our lab meeting 4 weeks ago). My professor has read the draft version of my manuscript and made comments. And I haven't heard any word from him that I should do the analysis the postdoc suggested. We already have all the experimental results we need and the manuscript is now almost finished. I told the postdoc that if he want to do the analysis then let discuss it together when the professor is back or if he think that it is urgent he can write to the professor. He refused.

I understand that he probably wants to contribute something. He told me that I need to explain why I designed my algorithm that way, using experimental data. In the manuscript, I did explain the rationale behind it and in the result part I compared my method with others (including the current best one) using 120 real datasets of all kind. We already reach the page limit of the journal. The rationale behind the design of my algorithm is quite obvious and he totally agrees on that. But still, he said that I need to show it with the data. He told me to change the way my algorithm works and compare the modified version with the original one. I don't understand why he want to put everything in the paper, not to mention that it is so obvious and doesn't make the paper better at all.

Lesson learned for the next project!

biochemistry - Does DNA react in all of the ways most other acids do?

As I understand it from my basic chemistry, there are some fundamental reactions that exist between any acid and other substances for example acid-base reactions that form a salt, and the existence of a state of equilibrium in water.

Do these reactions and equilibria occur to DNA (or, for that matter, RNA), which has only ever been described to me as an 'acid', and does this affect the processes DNA goes through, like replication and transcription?

Answer

It may seem counterintuitive that deoxyribonucleic acid has nitrogenous bases. Nonetheless, nucleic acids (thus including RNA) were called that way because the phosphate backbone (linked by phosphodiester groups) is a derivative of phosphoric acid.

Phosphoric acid

Image Source

Phosphodiester group

Image Source

Note that the only difference between these two groups is that in the case of the phosphodiester, two O-H bonds are replaced by O-C bonds. This make the last remaining hydrogen atom quite acidic (can quickly be identified by how the conjugate base exhibits resonance). In fact, it is so acidic that at physiological pH, the phosphodiester group is deprotonated, giving that nucleotide a negative charge. This property is does have a profound effect on DNA's structure and "behavior" in a cell, and is often exploited in genetics, such as in gel electrophoresis.

An interesting fact is that this acidity of the phosphodiester group actually competes with the basicity of the nitrogenous bases. However, since most often DNA is double-stranded, individuals bases will hydrogen-bond with its partner to make base pairs, which stabilizes and thus reduces this basicity.

TLDR: Although different acids of different molecular composition can act in very different ways, the overall acid-base chemistry is seen in nucleic acids.

species identification - Can an organism exist as a single cell but come together as multi-cellular during certain times?

I am trying to remember a particular segment from a BBC special, about a single celled species. However, at certain times all the individual cells came together to form a structure, not unlike a mushroom, to scatter something like spores into the wind. Afterward, the individual cells separated and continued on as individuals.

Am I remembering this incorrectly? Is this even possible?

Answer

Welcome to Biology StackExchange.

Am I remembering this incorrectly?

No, you're remembering it correctly.

I think you're talking about slime molds. You'll find more information on the wiki page

Is this the video you saw? These images are pretty cool.

Is this even possible?

Yes (given that it exists). There is no way to correctly answer this question as it really is an open-ended question. But here are a few words that may push you writing further posts.

Just a few words on the evolution of altruism

The main interest behind this life-cycle is that not all individuals reproduce. Some individuals form the stalk while others go through meiosis (see below on the life-cycle).

How unfair does it seem to those who form the stalk! Why would those individuals forming the stalk spend energy to help other individuals to reproduce?

Kin selection

Let's think about us, vertebrates, "real multicellular" organisms. The cell that is in your eye is never going to reproduce. Although it is spending all its energy into helping your ovules/spermatozoids to fuse. Why would this cell in the eye make such an effort? The genes in the spermatozoids/ovules are essentially the same as those in the "eye cell". Therefore, by helping your spermatozoids/ovules the eye cell is actually contributing to spreading copies of the genes that it is carrying. This is referred to as kin selection.

Slime molds and altruism

Now, the story is not exactly the same for the slime molds. The cells in the stalk can be quite different from those that are undergoing meiosis. Altruism can exist in a variety of different mechanisms and it would take several books to go over the literature about the evolution of altruism. Without knowing the literature specific to the slime molds reproduction, I just want to notice that the cell in the stalk will die anyway, whether or not it spend energy helping other cells reproducing. There is, therefore, no fitness cost into construction a stalk. Little population structure (causing higher relatedness within deme than among demes) could be enough to allow this behaviour to evolve.

Just a paper (that I haven't read) on the subject

Hudson et al. 2002

Genetics of the fruiting body

Interestingly, similar genes are being used in Dictyostelium discoideum (slime mold) to create this fruiting body than what is used in multicellular eukaryotes (ref.). Thanks to @Tim Cutts for this info.

botany - Do immature fruits perform photosynthesis?

Most immature fruits are green: peppers, pine cones, plums, lots of them. I want to know if the green is from chlorophyll in the cells. Do the fruit cells perform photosynthesis? When you cover a green stem or leaf, it will turn pale and stretch. That is because the stems have little need for chlorophyll in the dark, which is why they are pale. They stretch because the auxins in the stems are not destroyed by the photons, and the stems stretch out and topple over. If a green fruit is covered, will it turn pale and stretch like that?

Answer

The green pigment is indeed chlorophyll, and the fruits do perform photosynthesis. It's not just "fruiting" plants that do this either. Some shading experiments i saw estimated that up to 30% of the sugars assimilated into the barley ears (basically the grain) can come from photosynthesis occurring in those organs.

career path - Pursuing a Second Master's Degree(Part Time) : pros and cons

I am currently working in a manufacturing company as a software developer and have just completed my masters in control and automation in 2011 with my bachelors in "Electrical and Electronics". My main reason for doing my first masters is to change to my domain from IT where I was working as a programmer for 1.5 yrs. Now I am thinking of doing a second master's degree in mechatronics, because I am short of some knowledge in the electrical and automation field which I think is must for me to become an expert in the factory automation field.

Even though I feel it will be helpful for my personal career and reputation. I find some doubts whether a person having a double degree is welcomed in the job market or not. Also Frankly, In my opinion, I used to think that who are having many degrees as people who run away from real-world jobs and are not as competent as those who have years of experience. Another thing is I also want to do MBA after 5 or 6 years. So, can someone tell me what are the pros and cons of having multiple degrees?

defense - What makes someone deserving of a Ph.D.?

Few days back while attending a thesis defense, one Professor was asking the defender why does he think, he deserves the degree. I was wondering since then, is there really any general answer for that? or the answer should be given describing my own work and then emphasis them how it is important for research field?

I asked the question here to know your opinion about it and to list down what could be the possible answers to this question.

united kingdom - Postdoc salary negotiation (UK)

I am interested in taking up a postdoctoral position in a UK institution. The appointment details write:

Appointment will be on a Fixed Term Contract for 3 years and with a starting salary in the range of £29,517 to £42,187 p.a. inclusive dependent on postdoctoral experience. It is anticipated that the starting salary will be in the range from £29,517 to £33,740 p.a. inclusive.

I just started a family and I will need ~£36,000 p.a. to break even when calculating living costs in UK (London). Is it reasonable to negotiate for a ~£36,000 p.a. salary? (I know it is somewhat on the high side but not insane by UK standards.) It is reasonable to apply in such a position and explain that I will expect an substantial increase (~10%) in my salary within my first year of employment if I start around the £32-33,000 mark?

I do not want to waste my time or theirs on this matter but clearly my cover letter is not a place to put this concern forward. I also think ill of the idea of e-mailing a potential hiring manager/team lead with queries about a salary raise right off the bat.

The USA-based post-doctoral appointment I currently hold pays ~£40,000 p.a. I do not mean to sound like a money-grubber; I am genuinely interested in the position and I think I will be a great fit for that team but I do not want to endure a ~20% pay-cut.

Answer

You have the same issue that many people do.

The cost of living in London (rent or buying a home) is often double what it is outside of London, yet salaries are about the same in London as elsewhere in the UK.

It is common for professionals (e.g. computer programmers) in their 30s to not be able to afford more than a small room in a shared house if they choose to live in London. Expecting to support a family on any “normal” single salary in London is unreasonable.

If you are willing to spend 2hr each way commuting, then you can get a lot cheaper housing, but your train ticket will often be over £5K a year. But why have a family if you are commuting so much…?

thesis - What to do when your student is convinced that he will be the next Einstein?

As an adviser, I have found it to be a detrimental motive for a student to focus solely on surpassing Einstein in achievement, for many reasons. One student in particular has busied himself with the deconstruction of relativity and strives to break it down and replace it with a much better system. Not only that, he's attempting to construct a theory of quantum gravity and the refutation of string theory, among many other ridiculous sounding tasks.

The student told me earlier that "Einstein's physics will soon come to an end." when I asked him about his work on his thesis. Then when I saw his thesis, it was complete gibberish, wrong in many aspects. I tried to tell him this but he simply wouldn't listen and told me "You do not understand anything."

He then went to looking for a different adviser but failed, since nobody wanted to work with a man who wants to "surpass" Einstein. When he was rejected by everybody, he came back to me and we were on equal terms again. But now, he's trying to write another thesis. And he told me AGAIN that "It'll be something that will break string theory."

Every student that does physics today at least has a feeling, however slight it may be, to be the next Einstein, to have a revolutionary impact on science, but it's quite saddening that only 1 out of 900,000 people would actually do so. And for this student of mine, I know for sure that he'll soon fall into a well and never get out of it again.

This situation can be likened to a very similar situation in mathematics, as if your proof of a famous conjecture turns out to be wrong, say good-bye to your reputation forever.

I must mention that I do not want to drive him away completely from this. If the student indeed finds a "real" problem in fundamental physics, then let him work further on it. But this must not be the only thing that he should work on, which he is doing with the most robust motivation.

A big problem is that the student has a highly peculiar personality and is introverted; if you tell him something, he has a distaste for authority and considers himself to be the "smartest" and superior than all of everybody he knows, including me. He says that "People in physics today lack imagination" and things of this sort.

I am rather confused. What should I do? Should I try to leave him, or should I tell him in some way to quit doing this and focus on something more plausible and if he doesn't do this then I should do something else?

phd - How to overcome "No Research Experience" in CS Ph.D applications

I am a 4th year computer engineering undergraduate student who will apply for Ph.D. programs this winter/spring, for the next fall semester. I have decided to become an academic 2 years ago, and head of department said "keep your gpa high and you will be fine". Well, I have increased my gpa, from 2.5 to 3.5 but now I see that I need research experience to be admitted to good programs. ( I can't afford masters program)

I thought I didn't need a research experience, yet while I was thinking that, I see that undergraduate students all over the world were doing research. I admit I was naive to think so but I was guided that way. So few months ago I am trying to learn about admission process and I see many people over the internet with tons of research experience and even papers waiting to be published, or already published. And the most important part of SOP is research experience.

And guess what? There is no lab at my university. And not a single instructor that does research in the field I want. It is a very small department (5 full time assistant professors).

So obviously, I cannot get into a top or very good program with these conditions, and they have every right to decline me. But I believe it is my right to get into a good valid program that matches my interests. I shouldn't take the whole responsiblity of non existent opportunities that other students had in other universities.

I would like to know, from experienced people, about what I should do to get into a Ph.D. program without direct proof of research capabilities. No lab work, no research, nada. Just reading many papers in the field I am interested in for last few months, and high motivation.

Or is it a point where I should say "That's life and never fair" and have plan B and plan C?

Thank you

Answer

If you need research experience for a program, then you need research experience and there's not much you can do about it besides gaining that experience. Even if you did gain entry into such a program, you will lack the research skills of your peers. You'll be starting off on the back foot.

A PhD is a long-term commitment to poorly paid slave labour. What if you find out you don't even like research, 1 year in? I would strongly advise the "try before you buy" approach. Get a Master's degree or a postgraduate diploma, that has a reasonable research component.

A good PhD program will want you to prove that you have the commitment and research skills to pull it off. Once you can do that, you have a good chance for admission. If research experience is a requirement, then you can't just shrug it off.

masters - Is it plagiarism to hire a freelance programmer for an assignment but change a lot of it before you submit it?

I took freelancer tutor help for a Python programming coursework during my MS but did not submit the exact code he gave, I refracted it and changed a lot of it. Is it considered plagiarism?

I am asking this question to clear the self-guilt and to know more about code plagiarism.

publications - Is asking an author I'm reviewing to cite me a conflict of interest?

I'm reviewing a paper whose work is quite related to some of my early PhD work, that was about 2 years ago. I have a paper published in a Journal that proved that method A had good solutions for the problem X.

Now I'm asked to review a paper that does a variation on method A, although they never cite my paper at all, is not exactly the same, but I think there should be a reference, if not because it is my paper, but because by the time I did the survey no one else had used that method.

Now, that said, is it a breach of interest to ask the authors to cite my work, or at least read it?

Answer

If I were you, I would ask myself the following question:

is it better for the paper to be aware of my work?

I believe this is the main question you need to ask. If you see your work is relevant to the problem and can enhance the paper content, then you have to point to it. If you see your work as a complement of the paper just reference it in the review.

publications - Is publishing on arXiv early a good idea?

I have a lot of unfinished manuscripts in the field of communications engineering and computer science on my computer, and I'm wondering whether it is a good idea to publish them on arXiv before the articles are finished and submitted to a journal or a conference.

One benefit of publishing on arXiv is that it helps to establish that I'm the earliest inventor of something. But I suspect this is a double-edged sword. What happens if I post something to arXiv, somebody else builds on the work and adds more material and publishes it in a journal (perhaps citing my pre-print) before I have a chance of publishing my article in a journal? Does a typical journal accept papers that were novel when posted to arXiv but are not novel anymore? Let's assume that I have an intention of publishing the papers in a journal within a couple of years at most, not within a decade or two.

Another benefit of publishing in arXiv I can see is that many publishers allow one to update previously published material on arXiv with the accepted author manuscript immediately, but do not allow uploading the accepted author manuscript to arXiv if not published prior to submission to a journal within an embargo period. So, by uploading the material to arXiv early I could effectively remove the embargo period.

One potential drawback of pre-publication in arXiv is that theoretically some journals or conferences could consider the material non-novel which could eliminate the chances of publishing in such a journal or a conference. Are there any noteworthy journals that have a policy of not permitting material that has a preprint on arXiv?

I can see the following options:

1. Submit preprints to arXiv as early as possible, i.e. when the work is so complete that it might be interesting to others; when accepted, update with the accepted author manuscript.


2. Submit preprints to arXiv a couple of weeks or a month before submitting the paper to a journal or a conference; when accepted, update with the accepted author manuscript. This would eliminate the risk of somebody building a better work on top of my work and quickly publishing it.


3. Submit preprint to arXiv after publication in a journal. This might in some cases mean I have to wait for an embargo period of a year or so.

Which of these options is the best?

mathematics - How can an undergraduate be recognized for work done on a paper, with a fellow PhD student and a professor?

I am an undergraduate student, and recently I was introduced a PhD student in my university's math department.

In a brief interaction with him, he mentioned that he was doing work in Differential Topology, an area which I happen to be self-studying at the moment. I asked him about his research problem, and mentioned what I was self-studying, and he offered me an opportunity to work with his PhD advisor (a former professor of mine), and himself, and stated that they were looking to publish a paper in mid 2018, and I could possibly be listed as a co-author.

He has yet to run the idea past my former professor, but he has stated that my former professor would be all on board with the idea. My former professor likely does not know or remember me, we only had one brief interaction during a class on Discrete Mathematics (coincidentally the interaction was about Differential Topology and some other Differential Geometric stuff, because he saw me reading a book on it before class commenced).

However, my university has no official undergraduate research program, so everything (i.e. any research conducted) will likely be done on an informal basis. My main question is this, how can I protect the work that I do on a project like this? What measures can I take to ensure that whatever work I do is credited, if the paper containing my work is published?

Firstly it should be noted, that regardless of whether or not my work will be recognized on the paper (if any contributions to the paper are made by my part) I still intend to take this opportunity and work with the PhD student and my former professor, mainly as it will be a good learning experience for me on how to properly do research, the possibility of being listed as a co-author is just an added bonus.

Also I'm well aware, that it's probable that I may not make any contribution at all, however I am asking this question in the event that I do contribute some work towards the paper.

If it's of any importance, I have a good relationship, and am somewhat well known by other faculty members (Topologists) in my universities' math department, as they have previously allowed me attend lectures for their courses which are only reserved for students in years above me.

Answer

What measures can I take to ensure that whatever work I do is credited, if the paper containing my work is published?

Unlike other answers, I'll mention that it is not unheard of for higher-ups to fail to credit more junior collaborators. So while you have no reason to believe this will happen in your case, some relatively-benign protective measure may be in order.

I would suggest one (or more) of the following:

• Using some relevant on-line collaboration tool - such as a git/mercurial repository for paper drafts, or a Dropbox/Box.com/OwnCloud shared folder through which you exchange files - preferably one which they cannot delete on their own.


• A bit of "wordsmithing" in some of your email exchanges with them so that whoever reads the email exchange understands that either some of the work is assigned to you, or some of the results were obtained by you. Things like doing a bit of planning or roadmapping over email typically achieve this effect without sounding off.



• Engineering one or more occasions in which you and one of the other two are discussing your joint work in the presence of a third party with closer/better relations to you than to them.

The first two you could probably do regardless of wanting to protect yourself; the third one involves at most a bit of bragging, which is understandable for an undergrad and can be minimized.

Each of these reduces the degree of plausible deniability in a theoretical argument about credit, and even more importantly, discourages the very inclination your senior collaborators may have to ignore your contribution.

---

A side-note: There could be three scenarios here regarding the extent of your contribution to such work.

1. Sufficient to merit co-authorship


2. Sufficient to merit a "crediting mention" ("The authors wish to thank Ms. Jane Smith for useful comments regarding frobnicating the bar").


3. Less sufficient

... and with you being an undergrad it will be hard for you to tell the difference between these three. So if you feel you're being under-credited, consult other people first, discretely, for their opinion on this.

Good luck and I hope you don't need any of this advice!

teaching - Understanding an abnormal grade distribution

I have three years of experience teaching as part of a team (many teachers, some with more experience, agreeing on a syllabus and preparing the tests together), but this year is the first time I am fully in charge of some courses.

After grading the mid-term exam for one of my class, I noticed I had a weird grade distribution:

(If this is useful, there are 24 grades, the set of grades is { 1.2, 1.4, 1.4, 1.9, 2.0, 2.3, 2.6, 2.6, 3.4, 4.2, 4.2, 4.3, 4.6, 4.6, 4.8, 4.8, 4.9, 5.3, 6.0, 6.2, 6.4, 7.1, 7.8, 7.8 }, the average is 4.25 and the standard deviation is 2.01.)

I have looked carefully at all my previous tests, and I can confirm I have never seen a curve like this before.

In my short experience, I have heard, read of reflected that a distribution with two curves would probably either mean that a) a large subgroup of students cheated or b) as a teacher I am mostly addressing the best students and letting the others down.

But this looks like there are actually three curves, and I am wondering which characteristic of my teaching or my students could explain that.

Besides, if someone is aware of any scholarly work on this subject, that would be lovely. I couldn't find anything myself.

Answer

There are several possible factors here: given the relatively small number of points available, lumping can skew how grades are distributed, particularly if they're also awarded in whole number increments. (That is, there's not enough refinement in the model to separate things out.)

Another issue is that the sample size is relatively small; twenty-four students is not a particularly large sample size—your standard deviation here is two points out of 10! Also, you should try plotting the data according to half-integer bins (0.5 to 1.5, 1.5 to 2.5, etc.); you'll end up with a very different distribution.

So, basically, I wouldn't try to draw any definitive conclusions from such a plot or distribution.

graduate admissions - Unconscious bias toward recommendation letters written by men?

This is an attempt to rescue a strongly down-voted question.

Are there any studies investigating possible unconscious gender bias in evaluating recommendation letters? Specifically, is there any published evidence that recommendation letters with female authors are (or are not) less effective than recommendation letters with male authors? Studies considering letters for graduate admission, faculty hiring, or promotion and tenure are all relevant.

Let me emphasize that I am not asking about intentional sexism, which I assume is sufficiently rare to be insignificant, but rather unconscious bias. I am also not asking for anecdotes, but pointers to actual published literature.

Similar studies have revealed significant gender disparity in several related academic contexts, including recommendation letters for male vs. female applicants. Other examples include:

publications - Is it bad to ask the editor about the status of a submission on seeing that referees' reports were submitted a week ago?

This question is about inquiring regarding paper status.

I had submitted a paper, and recently I just discovered that the manuscript tracking system shows that the editorial committee has received the referee's report. But, this status has remained for over a week and I still have not heard from the editor handling my paper.

Should I then email the editor as a reminder? Would this act instead be taken as urging?

Answer

Once reviewers reports have been returned, the editor has to assess the reviews in light of the paper and provide the author with indications on how to proceed. Exactly how this come through will differ between fields and editors. The main point, however, is that a certain amount of work is usually needed to process the reviews before passing the manuscript with comments back to the author. Since editors also handle, sometimes, quite large volumes of papers in parallel, your manuscript will be placed in a queue and the editor will likely take each manuscript in order. In addition, many, if not most, editors do their editing in parallel to ordinary faculty jobs which may at times further limit their available time. It is thus reasonable that this process may take several weeks. In "my" journal we as editors have three weeks for this process before being reminded by the electronic submission system that the manuscript is "due". We often make this deadline, but not always depending n workload.

So, one week is definitely too short a time to expect a response. Three weeks seems to be reasonable in my field but I would maybe allow even additional time to pass. It is probably good to talk to your peers who may have experience with the particular journal and also your field to get feedback on what is considered reasonable.

Added to clarify a comment: it is never "bad" to contact anyone, but it is only fair to allow a a "reasonable" (in the sense of the field and specific journal) amount of time to pass since the early contact will not likely yield anything productive. What, on the other hand, is bad is rather the attitude with which some contacts are made. Insights into appropriate time frames will help to keep communications as fruitful as possible.

mitosis - How are different types of cells created from zygote?

In the process of mitosis that starts from zygote, how do different cells appear? What happens that some cells become one type and some another?

For example, is there a cell that divides into a blood cell and a skin cell?

thesis - Can I use text from my dissertation in a manuscript?

There has been general discussion of whether one can use a published work in their dissertation, with the consensus being 'of course'! The first two chapters of my thesis will be published works. I'm interested in the reverse now; I intend to write the third chapter of my thesis as a draft of sorts for a publication. Now I'm wondering whether including text and figures from my dissertation in a [future] manuscript constitutes 'self-plagarism'.

A fellow graduate student advised me that it's only 'self-plagarism' if I formally copyright my thesis, however, I'm skeptical of that being the important distinction.

Answer

In the context of a university, self-plagiarism (or auto-plagiarism, as it tends to be known) generally only refers to submitting the same work for two or more different credit-bearing assignments within the institution, or submitting work which has been awarded credits at another institution.

There's generally no restriction on using work submitted for a university degree in a publication, unless the university specifically expresses its ownership of that work (which sometimes happens if the work was involved in a commercial or collaborative project).

You can get into trouble for publishing the same work in more than one publication, but because the contract you sign with the publishers will specifically prohibit you from doing this (or will specifically allow it) this is not plagiarism as much as it is fraud. Even then, providing they know in advance, most publishers will allow authors to include chapters in monographs that are based around previously published articles, providing the initial copyright holder gives their consent (which in academic work they usually will, as long as the original publication is cited).

publishability - Is developing a cheaper method ever considered to be originality in academic research?

Say, in a particular field of science, method A or equipment B are the standard. Now I have invented method X or equipment Y which cost much less than A or B.

What are the necessary conditions, if any, that allow X and Y to be published as a journal paper?

(This question of course is loaded with my own assumption that originality in an academic research does not include cheaper price. I have long held this assumption from a simple fact that I have never encountered such thing as being cheaper being described in any background/introduction section in any journal articles I've read.)

zoology - Bug Identification: Tiny Bugs in Fairport NY

We have been finding a ton of these tiny bugs (pin head size or smaller) outside on our patios, outdoor tables, on the grill, etc.

What are they and how do we get rid of them?

graduate admissions - How to address being interested in two areas in statement of purpose

I am applying to graduate school in US. I am wondering how I can write statement of purpose If I am interested in both signal processing and communication system. Should I talk about why I am interested in both and talk about researches and projects I have done in both areas and my future research in both fields since I like both equally?. However I was thinking this is too much and is going to pass the word limit for statement of purpose. I am looking for some advice about this. Any advice will be greatly appreciated.