How important is the write-up of a PhD thesis for an academic career?

How important is your written PhD thesis for an academic job search, assuming the results are already written in papers? Do search committees ever read your thesis in addition to your papers? My PhD advisor said that the written thesis is not important and I can write whatever I want as long as it's not about Star Wars.

How many species have existed on earth?

I found a paper estimating the number of species currently living on earth. Now I'm wondering If anybody tried to estimate the number of species that have lived on earth. I'm familiar with problems of "species concepts". But I'm sure, there is at least a number of all known fossils.

EDIT: In contrast to the question How many organisms have ever lived on Earth? I'm asking for species and not for individuals. The answer to my question can be used to ansewer the queston for the number of organisms. But still, The questions is different.

evolution - Alternatives to fittest-win and Moran processes as simple mathematical models of selection

When modeling selective sweeps as a micro-building block in models of macroevolution (not to be confused with misuses of this in creationist arguments), I use the fittest-win model of selection as a first approximation, or Moran process model when I want a more reasonable approximation.

In the fittest win model the probability for a mutant of fitness r to invade a host population of fitness 1 is 100% if r > 1 and 0 otherwise. In the Moran process model, the mutant of fitness r invades with probability $\frac{1 - r^{-1}}{1 - r^{-n}}$ for a finite population. Alternative in the limit as n goes to infinite, a mutant with r > 1 invades with probability $1 - \frac{1}{r}$ and 0 otherwise.

In general I am interested in simple models of selection of a single (or small concentration of) mutant invading an asexual host population of fitness 1 (with fitness constant and independent of frequency). Are there other common mathematical models for selection of this type?

publications - How common is it to get one very positive and one very negative review?

In the past year I have, on three separate projects submitted to three different venues (both conferences and journals), received incredibly mixed reviews. In each case there have been two reviewers, one with a very positive review and one with a very negative review, and the editor has decided to reject the paper without soliciting a third reviewer. They all follow this general pattern:

One reviewer: This is useful, interesting work.

• "well-written, informative, to the point...quite helpful"

The other reviewer: I don't see the point of this work.

• "To be quite honest, I am not sure what the purpose of such an article is."

I have two questions.

1. How common is this? It this just me or does this happen a lot? If the former, what can I do to help avoid it? All of these papers have included a discussion of the impacts/applications of my results and tied them to the existing literature. If this is pretty common, though, and it's just the luck of the draw then I'll keep plugging away and submitting.


2. How should I incorporate this feedback? While any rejection is frustrating, usually it comes with the silver lining of suggestions to improve the project. But what on earth do I do when the feedback is simultaneously "this is a good/interesting project that I find helpful" and "this project is useless"? I don't want to just throw out these projects, especially since I think at least some other scholars find them helpful/interesting.

At this point I'm confused and disheartened and would really welcome feedback, especially from other scholars with the same experience.

Thanks!

Is getting a second masters frowned upon?

I recently read on stack overflow that getting two PhDs just shows that you're unfocused and you don't know what you want to do. However, I'm at a small school with a 5 year Computer Engineering bachelors/masters program I feel like I should take advantage of, but I'd also like to go on to do another part time grad degree in the same field or Computer Science at a larger, better established school, while I work.

If I went to a larger school like University of Illnois or MIT or similar, will having a masters and going back for another be frowned upon, or is this a non-issue?

Answer

I don't think it is going to help your career much, so I would only recommend to do it if you enjoy the classes.

• 
  

  I have never seen a job asking for two Masters. If any employer would be impressed by two Masters, it would be because they are in different disciplines. (e.g., a Masters in CS and a Masters in Finance might look good if you are trying to get a particular position at a financial company)

  
  


• 
  

  Two CS Masters is redundant. The only time I have seen this is when a PhD program gives a MS en route to a PhD and the student already had a MS.

  
  


• 
  

  Industry is going to value experience over multiple Masters

  
  

If you do just enjoy the classes, you might think about a different field that still interests you and is relevant to your day job (e.g., HCI or math).

Or you may just want to look into a PhD program :)

EDIT: According to the responses to this very similar qeustion, Can a masters student apply for a second masters in the same field at another university?, it appears that a lot of schools may not even accept a Masters student that already has a Masters in the same field.

How to deal with dramatic drop in grade due to strict attendance policy

I'm currently taking a required class where attendance is counted at 15% of the grade. The policy is that if a student misses more than 2 lectures, they lose all 15% of those points. The class itself takes place 5 days a week, and attendance is taken daily and uniformly. I currently hold a 91% in this class, but I missed my third class today and I'm trying to decide how to proceed from here. I feel like all of the time and effort I've put into the class has been totally discounted for a reason that has nothing to do with my knowledge of the course material.

Am I wrong to feel as though this is an unfair mark? On one hand, I knew that this policy existed and the consequences for missing 3 classes. On the other hand, dropping a grade from an A to a C for such a small reason feels absolutely unacceptable to me. How should I approach this situation to help repair my grade?

zoology - Why is it that cats can jump so high for their size, compared with humans?

My cat is about 1' high at the shoulder, and I am a little over 6', but my cat can easily jump onto something as high as I am. That is 6x it's height. If a cat can do this, then Why can't I jump up onto my barn roof? That is a little less than 36' up. I have a hard time jumping onto even a 4' platform. Now if my cat had trouble jumping onto an 8" platform, I would think that pathetic. Do cats have muscles 20x stronger than humans, for their mass? Is it just their skeleton providing leverage?

Answer

Cats have different body structure than human beings. Its body-kinetics are quite different from us. Yes, muscles are quite strong, but this not the only reason. To know in-depth about the reasons behind the cats’ extreme jumping abilities, you can just refer this online article - "The Glory of the Cat – adidarwinian" at http://adidarwinian.com/the-glory-of-the-cat Along with the flexible spine, strong muscles, flexible joints, they have a peculiar trait known as righting reflex. The same article has information on this peculiar trait. Due to the righting reflex instinct, cats can even survive falls from the high rise buildings.

genomics - Is DNA sequencing coverage a function of sample purity?

How is coverage affected by the purity of a sample? And can coverage for a sample be affected by other things, like the library preparation or manner in which the sample was stored?

How to pitch a research idea to a professor as an undergraduate?

I have an idea which I'd like to work on with a professor at my university. In my initial email would it be arrogant to ask if he's interested in working with me on this particular topic (he's published some papers on closely related topics), or should I just say that I'm interested in generally doing research with him? I really do want to work on this particular idea but also don't want to come across as trying to tell him what to do.

publications - Is it okay to include a simplified and easy version of a result already proved?

I am preparing to write an article. For that, I got an easier proof of the already published result. My result is very simple to prove. Is it ethical to include this result in my article after citing the other author's work that we are improving their result? Kindly help. Thanks a lot.

Answer

Yes.

New proofs are always good and of scientific value, and may be of significant use and interest in their own right. In some cases they are even worthy of a paper of their own. As an example, just recently on MathOverflow I saw Zhi-Wei sun mention that a result of his currently has 6 proofs from 6 different papers and sets of authors (including his own and himself).

application - Should I waive my right to view my recommendation letters?

Most graduate applications provide a choice for applicants to view their recommendation letters at a later date. There is a mention of some US mandate alongside.

• Is it a better option to forgo this choice in the application? Will the recommending professor feel more secure then?


• What is the procedure for the applicant to see his/her recommendation letters? Does the university readily show them when asked?


• How ethical is it for the student to ask for the same, especially, for example, after being rejected from a program?

Answer

The secret to getting a good letter from someone is making sure they're going to write you a good letter before you have them write one. You should never need to look at a letter someone wrote for you, as you should basically know what they're going to write without ever having looked at it. In most cases, if someone doesn't feel comfortable writing a 100% positive letter about you, they'll let you know when you ask them and recommend you get someone else to write the letter.

With that in mind, it is definitely better to forgo this choice, for the reason you suggested... people will likely feel more comfortable to write freely and honestly when they know you won't read it. Regarding the procedure, I'm not familiar with the mandate, but if it is a US mandate, then they'll probably show it to you after a lot of waiting. It is definitely uncommon for someone to ask to see a letter written about them, and it likely would be looked down upon.

phd - Contacting a Professor about a possible Ph.D.

During my Masters I wrote and published a series of three research papers, which I presented at 3 different international conferences.

After my last presentation/talk at the 3rd conference, a Dean from an Australian university approached me and after talking for some time he gave me his business card and told me to send him an email if I'm interested in attending a Ph.D. programm at his university.

Now (4-5 months later): I will start my master's thesis in the summer and after talking to a lot of people (friends, parents, etc) I decided to contact him and ask about specifics. Turns out, I don't even know what to ask. (I havent sent the email yet btw).

• 
  

  In my eMail I start off with how we met (so he might remember me?) and then go on to say that he mentioned the possibility of the Ph.D. program at his university and gave me his business card.

  
  


• 
  

  I then mention that I will presumably finish my studies Nov/Dec 2018. (so he knows a possible timeframe)

  
  

I would like to ask him questions about the possible research fields, finance possibilities, etc - but our conversation was so short back then, I'm guessing I can't just ambush him like this.

So what can I write between mentioning that I will finish my studies and writing

• "I am looking forward to hearing from you, Best Regards,xxx"

Also: What would be something a professor might want to know about me (should I include my CV already?), and what questions show that I am interested, without ambushing him completely? Should I write an "apology-sentence" that I am contacting him 4 months later and not in the following weeks?

Any suggestions are welcome! Thanks in advance!

PS: I am from Germany and currently also study at a German University.

Answer

I formulated my mail as a "letter of motivation" - Just in the same way you would write an application in Germany. You could start with something like

"Thank you for the nice discussion about the open PhD position in your research group at the XYZ conference in October 2017..."

Then, you should mention that you had a very close look to his/her research and that this perfectly fits your interests because of "this" and "that".

In any case I would already attach the CV with all certificates and required documents.

journals - Former PhD supervisor faked results and submitted a corrigendum two years after publication

During my PhD studies, I published a journal article (one of total four) in a prestigious journal of my field. I gave my codes to my PhD supervisor, but he messed up things in the lab and lost it (I also didn’t care and lost, for I am pursuing different directions).

Two years after publication, my PhD advisor wanted to commercialize my PhD work and wanted me to develop the codes again without willing to credit me for my efforts. I found his emails harassing, malicious and blackmailing and stopped responding him by directing his emails to spam folder.

Out of desperation, he himself developed some codes and submitted a corrigendum in which he clearly tried to push an agenda to suit his commercialization efforts (I know what I am talking, believe me on this). This included falsifying earlier findings just because he didn’t understand my work and cannot implement it and thus, presented an alternate algorithm which clearly is inferior. From my experience with that algorithm, I know from his description of implementation in the corrigendum that the results he presented are clearly made-up. My PhD advisor has basically faked results in a corrigendum to suit his commercialization efforts.

What are my options ?

1. 
   

   Can I convey it to the journal ? (I have already conveyed to the journal that this corrigendum is submitted without my approval.)

   
   


2. 
   

   Can I offer my ex advisor to re-implement but giving me the due credit? What should I do?

   
   

bioinformatics - Good poly-A filtering rules or tools

I am aligning a large number of ESTs. It seems poly-A tails show in many different ways. In addition to occurring at the very end, they can be flanked by the cloning sequence one one end, or have mismatches/errors. What is a good rule or available tools that will handle the usual cases?

A few examples of the non-trivial cases I found, with their Genbank Accs:

>EE409337
... AAAAAAAAAAAAAAAAAAAAAAAAAGGAAAAAAAAAAAAAAAAAAAAAAAAAAAACCTTGTC
>EE409340
... TTTCTACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACTTGTC

>EE409361
... TTGTTAAACTGAAAAAAAAAAAAAAAAAAAAAAAAAAAACCATGTCGGC
TTACTGAATTGAA
>EE420306
.... AAAAAAAGTTATGTTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAGGGAAAAAAA
AAAAAAAAAAAAAAAAA

Cross-posted on SeqAnswers,Biostars.

dna - Why are the genomes of Humans 99.5% the same?

Human's DNA sequence is said to be roughly 99.5% equal. As far as I understand, this means that if I walked up to you and compared our DNA, the sequence of base pairs would be 99.5% the same.

My question is: Why is there only 0.5% variation in our DNA? I can think of two reasons:

1. 
   

   For some reason, the other 99.5% (roughly) is locked in place. These sections, if changed, either result in us not being 'human', or simply get some sort of genetic disease and so aren't very good mutations.

   
   


2. 
   

   There hasn't been enough time. I remember hearing that all humans have a common ancestor some long time ago. If that's the case, perhaps over time only about 0.5% of our DNA has had time to randomly mutate, and if we wait a really really really long time, more and more of our DNA will mutate, and we will become 'less like each other'.

   
   

Or am I completely misunderstanding the situation? I didn't take biology in high school so answers should be simple please.

Answer

In a genome that is 3 billion base pairs, a difference of 0.5% works out to a difference of 15 million bases. When a single base change can change the amino acid sequence of a protein, that can add up to a huge amount of diversity, which is what we see over the nearly 8 billion humans on the planet, and the 99.5% sameness is why we are linked together so closely as a species.

How can the lack of diversity be explained?

Nothing in Biology Makes Sense Except in the Light of Evolution.

The above quote was made by the evolutionary biologist Theodosius Dobzhansky. What this basically means is that you need to take a look at your question from the perspective of evolution and natural selection.

The first thing you need to note is that there is evidence to suggest that modern humans went through a population bottleneck. What that means is that at a certain point in our history, there were very few individual members of our species alive and this can account for the "lack" of diversity that we see in our genome. The number that is quoted is as low as 10,000 individuals left alive after the supereruption of the Toba volcano about 75 thousand years ago.

That means that there were very few mating pairs left, and that significantly reduced the genetic diversity of our species. This is known as Founder Effect.

Founder effects

A founder effect occurs when a new colony is started by a few members of the original population. This small population size means that the colony may have:

• reduced genetic variation from the original population.


• a non-random sample of the genes in the original population.

So if we use an average of 20 to 25 years per human generation, we are only looking at about 3,000 to 4,000 generations since there were maybe only a few thousand breeding pairs of humans. Contrast that with bacteria which can go through three to four thousand generations in less than a week, and you can begin to get a feel for why there is so much sequence homology (sameness) in the human genome. See Bottlenecks and founder effects at UC Berkley's Understanding Evolution site for more information.

You also should understand that any changes that are deleterious will be under strong selective pressure. This may not mean that the organism may not survive to reproduce, in may just mean that on average, they may be less successful; fewer offspring that have fewer offspring in comparison to the rest of the population. At some point that lineage may go extinct, either because the change makes it very difficult to survive, or the offspring make less desirable mates and eventually don't get the opportunity to reproduce.

Any changes that disrupt a vital gene will likely be fatal and will lead to spontaneous abortion or if the mutation was sustained in a sperm, then the inability of that sperm to survive to fertilize an egg, so the sperm that was heavily mutated may just never make it to the egg. The average number of sperm in a single human ejaculation is about 250 million. And yet only a single sperm makes it to fertilize the egg, and that is assuming that a fertilization event takes place. There is an incredible amount of selection that goes on in the act of procreation, even before we get to development.

Why the 99.5% to 0.5% figure might be misrepresentative of the population as a whole.

Another thing that you will want to think about is how the 0.5% to 99.5% number was arrived at. The referenced in the question links to a Wikipedia article Human Genetic Variation. The reference provided for this was from a New York Times article about J. Craig Venter, In the Genome Race, the Sequel Is Personal - Wade, Nicholas. September 4, 2007. The quote that is references in Wikipedia is:

Biologists had estimated that two individuals would be identical in 99.9 percent of their DNA, but the true figure now emerges as much less, around 99.5 percent, Dr. Scherer said.

The 0.5% figure is provided as a quote from Stephen W. Scherer, who was a coauthor of this paper, The Diploid Genome Sequence of an Individual Human, Levy, et.al. PLoS Biology; September 4, 2007. DOI: 10.1371/journal.pbio.0050254. From that paper the following quote is found:

Inclusion of insertion and deletion genetic variation into our estimates of interchromosomal difference reveals that only 99.5% similarity exists between the two chromosomal copies of an individual and that genetic variation between two individuals is as much as five times higher than previously estimated.
^{- The Diploid Genome Sequence of an Individual Human, Levy, et.al. PLoS Biology; September 4, 2007.
DOI: 10.1371/journal.pbio.0050254}

So at the very least, the statement was made in a peer reviewed article. However there are some problems with this.

The first is the method of the paper. It looks at a single human genome, that of Dr. Venter, and is used to draw the conclusion of 0.5% difference between any two individuals. And the comparison is made based on the analysis of differences between Dr. Venter's maternal chromosomes and paternal chromosomes. Let's look at what the problems might be here:

• It is a huge leap of statistical faith to assume that a single genome is representative of the nearly 8 billion genomes out there.


• Dr. Venter's genealogy is English on both parental lineages. We have to remember that there was another population bottleneck in middle ages Europe caused by outbreaks of cholera and the Black Death. This fact may imply that Dr. Venter's lineages are genetically close and that if his lineage were more diverse, say Indigenous Oceanian and English, they may have found a much higher percent difference between maternal and paternal chromosomes.

The donor's three-generation pedigree is shown in Figure 1A. The donor has three siblings and one biological son, his father died at age 59 of sudden cardiac arrest. There are documented cases of family members with chronic disease including hypertension and ovarian and skin cancer. According to the genealogical record, the donor's ancestors can be traced back to 1821 (paternal) and the 1700s (maternal) in England. Genotyping and cluster analysis of 750 unique SNP loci discovered through this project support that the donor is indeed 99.5% similar to individuals of European descent (Figure 1B), consistent with self-reporting.
<sup>- The Diploid Genome Sequence of an Individual Human, Levy, et.al. PLoS Biology; September 4, 2007.

DOI: 10.1371/journal.pbio.0050254</sup>

• Dr. Venter is male. The Y-chromosome was problematic to sequence, and you cannot really do a comparison between it and the X-chromosome. How would the genome of a woman compare?

The Y chromosome is 59% covered by the one-to-one mapping due to difficulties when producing comparison between repeat rich chromosomes. In addition, the Y chromosome is more poorly covered because of the difficulties in assembling complex regions with sequencing depth of coverage only half that of the autosomal portion of the genome. The X chromosome coverage with HuRef scaffolds is at 95.2%, which is typical of the coverage level of autosomes (mean 98.3% using runs). However it is clear that the X chromosome has more gaps, as evidenced by the coverage with matches (89.4%) compared with the mean coverage of autosomes using matches (97.1%). The overall effects of lower sequence coverage on chromosomes X and Y are clearly evident as a sharp increase in number of gaps per unit length and shorter scaffolds compared to the autosomes (Figure 3). Similarity between the sex chromosomes is another source of assembly and mapping difficulties. For example, there is a 1.5-Mb scaffold that maps equally well to identical regions of the X and Y chromosomes and therefore cannot be uniquely mapped to either (see Materials and Methods and Figure 3). From our one-to-one mapping data, we are also able to detect the enrichment of large segmental duplications 10 on Chromosomes 9, 16, and 22, resulting in reduced coverage based on difficulties in assembly and mapping (Table S3).
^{- The Diploid Genome Sequence of an Individual Human, Levy, et.al. PLoS Biology; September 4, 2007.
DOI: 10.1371/journal.pbio.0050254}

There is another thing that you need to remember and that is the history of the Human Genome Project. Dr. Venter developed a new method of sequencing and became a commercial competitor to the International Human Genome Sequencing Consortium project. While the International Human Genome Sequencing Consortium project beat out Dr. Venter's enterprise(8), it's approach, to use an amalgamation of the DNA of many donors, some of whom had their DNA included and some who did not, to preserve anonymity, Dr. Venter circumvented this by performing the sequencing on his own DNA. When his team was beat out by the International Human Genome Sequencing Consortium, he doubled-down, invested more time and effort and came up with the sequence put forth in this paper, which had a higher degree of resolution than previous efforts. The paper is making an argument for the value of their technique over the techniques being used by the International Human Genome Sequencing Consortium and is trying to make a claim of the superiority of their method. The data being presented is likely factual, but because of this history you have to look at the paper, the methods, and the motives behind it.

It is only 15.5 years since we had a full draft of a Human Genome Project produced by the International Human Genome Sequencing Consortium. In order to sequence that genome samples were taken from a few hundred individuals. Small stretches of the DNA were sequenced and then all of those pieces were put together in computer. That means that there was a lot of averaging that happened. So by default, the most prevalent base in the population of volunteers at every position was chosen. That means that that should be representative for the rest of the population as well.

When we make statements about comparisons in datasets as large as the human genome, more often than not we are looking at known, small subsets of the genome, and we are extrapolating by statistical methods based on that fact. One thing you learn as you read science papers, and not just science news articles, is that you always need to look at their materials and methods to determine how they arrived at their data and headline numbers. It is often quoted that we have only a 1.5% difference between Humans and Chimpanzees, however when you look at those papers the comparisons were done only on areas of the genomes that lined up well. That isn't to say that there isn't a remarkable degree of similarity between us and our nearest living evolutionary relative, it is just that there is more to the story than the headline.

Also, we don't have that many full genomes sequenced to compare to one another, as a percentage of the 8 billion people alive today. While we have representations from most a vast majority of the ethnic groups identified, we may be missing families with novel lineages.

Another thing that you need to think about is that many of the areas in the human genome are repeats and structural elements that do not encode for genes of affect gene expression. Things like telomeres, which protect the ends of chromosomes, and centromeres which are the attachment points on chromosomes that make sure that the are distributed properly into newly divided cells. These elements tend to stay the same because the proteins that bind to them require that sequence specificity in order to function properly, so those are regions were almost every ones DNA will be the same, and not just between humans. These elements often are very similar in most vertebrates.

We also need to consider structural RNAs. These molecules have functions within the cell that require that there sequences be highly conserved (unchanged). Ribosomal RNAs, Transfer RNAs, Small Nuclear RNAs all rely on their specific sequence to fold properly in order to perform their task in the cell. A single base change can change the folding of these elements and as a result they will loose their function, which means those cells won't be able to produce proteins properly which means that the cells will die. If this is happening in germline cells, then they are not going to be involved in fertilization so any mutations there will be passed on.

I could go on and on, but the take away is that it isn't surprising that there is very little sequence diversity on a percentage bases within the human species, but there are many caveats to that fact as well.

Edit: Significant edits to add relevant, referenced information to back up answer.

repository - ePrint Archive for PhD Dissertation in the Social Sciences

I understand there are a number of specialised ePrint archives or repositories where scholarly works could be posted for wider dissemination (for example, arXiv).

I am wondering if there is a preferred one for PhD dissertations in the social sciences?

Answer

You can publish an eprint of your dissertation in Researchgate.net.

coursework - Is it acceptable practice to list solitary courses on an academic CV?

I took some solitary graduate-level courses as a non-degree student at some US schools and plan to take further modules in England. These courses relate to my other degrees and certificates, but are from more elite institutions and provide more advanced, specialized training not easily found elsewhere. Is it acceptable practice to list solitary courses on an academic CV? What section and in what format might this appear in?

Answer

Acceptable? Sure. Useful? Probably not.

If you're applying to graduate programs, then listing these courses would be appropriate. On the other hand (at least for US schools), you need to submit official transcripts for those courses anyway. Also, if you expect those courses to play a significant role in your admission, you need to make that case in your application statement.

If you're applying to an academic position that is primarily teaching, then listing the courses might be appropriate to show that you have at least taken courses on the topics you intend to teach. But if you expect those courses to play a significant role in your hiring, you need to make that case in your application statements.

If you're applying to an academic position that is primarily research (including most postdocs and tenure-track faculty positions), there's no point in listing what courses you've taken. With rare exceptions, your research record (as listed in your CV, described in your research statement, and judged in your letters) is essentially the only thing that matters for such positions. Teaching experience might play a role, but classes that you've merely taken won't. If you think specific courses significantly strengthen your case—making you one of those rare exceptions—you need to to make that case in your application statements.

citations - Do I need to cite an artwork? How would I do it? Is permission needed?

In my academic paper, I have well over 100 figures, and would like to use an artwork I found online in one of my figures - it is not published in any book, it is just something they made and posted online. I would be using 1/6th of the author's artwork figure, and it would be so heavily modified it would barely be recognizable. The modified artwork would take up 1/40th the space of 1 such diagram (out of 100+) and used once only, it is a minor element of my figure.

(1) Do I need to cite the artwork in this case?

(2) Can you give any guideline on when an artwork citation is needed?

(3) Am I required to get permission from the author, or is it a courtesy to the author only?

(4) How would one cite an artwork in their dissertation?

Answer

Simply contact artwork's author (since the artwork wasn't published, the author is copyright holder, otherwise it usually would be the publisher), requesting permission to adapt the artwork. I suggest sending the author planned version, so that any potential issues can be assessed and addressed.

(1) I'd say Yes. The citation is usually located below or above the figure in the following form:

(Adapted from “The DeLone and McLean model of information systems success: A ten-year update.”, by DeLone and McLean, 2003, Journal of Management Information Systems, 19(4), p. 24. Copyright 2003 by M.E. Sharpe, Inc. Adapted with permission.).

(2) Since artwork is someone's intellectual property artifact, protected by copyright, it is usually (for an exception, see fair use in the next point) required to cite the artwork (as any other such artifact) to properly credit its authors. The format of citation depends on the publication style you're using (my example above is based on APA Style).

(3) You're required to get permission, unless you want to risk by using the fair use legal doctrine.

(4) If the artwork is part of a figure, see example above; otherwise, other relevant standard citation guidelines for visual elements apply, based on the publication style you use.

publications - What advantages and disadvantages should I consider in deciding whether to publish my academic book traditionally or self-publish?

I am an amateur mathematician. I am writing a research monograph in the field of abstract mathematics (general topology, specifically).

Should I publish it traditionally or self-publish?

There are many benefits of self-publishing (e.g with Lulu) an academic work:

1. No need to tremble awaiting my book to be rejected by a peer review. No responses like "first publish in articles, only then make a book". I am in full control what I want to publish.


2. I don't pay the publisher 80-90% of my revenue. (This also may make AdWords marketing of my book profitable and thus I can do a rather huge advertisement of my book myself using AdWords. I suspect, this may over-perform traditional publishers in the number of sales.)



3. I am in a full control of my book. No forced need to change something, if an editor's opinion differs from my own.


4. No need to convert it to LaTeX, I can use my preferred software such as TeXmacs.


5. The book goes into Amazon and other distribution channels anyway.

I can pay a professional scientific editor to edit my book for paid, as a kind of business investment.

Peer review is intended to choose which books are published and which are not. I can do fine without peer review, allowing the buyers of my book to decide for themselves.

Well, a potential buyer may prefer books published by a big publisher, but it (in my opinion) can be well replaced with big red letters "Edited and checked for errors by professor XXX."

Drawbacks which I know:

1. It may not be as good for my academic carrier as traditional academic publishing. (It does not matter for me anyway, as I am not a professional academic.)



2. Not sure if my book goes into university libraries (please comment on this issue).

I've pointed many benefits of self-publishing. What are drawbacks (except of pointed by me)?

---

And one more specific question: Is the number of books sold if using a traditional publisher, likely to greatly overperform the number of books sold if self-publishing? If yes, why?

Answer

Should I publish it traditionally or self-publish?

Why do you want to publish at all? You answered

I write the book to store down my research results and to spread my new knowledge. To make money is not the main aim, but it would be nice.

Given that: the answer is that you should certainly not self-publish your work. You can store your results and spread knowledge by having the material freely available on the internet, as I believe is already the case. The arxiv is one nice place to put work, but it is not the only one: you could put in on github or any number of other repositories. You can just put it on your own website and make sure that google indexes it. That means that billions of people can access it at any time.

Let me be clear with you: you are not going to make money self-publishing works of mathematics that you have not been able to publish traditionally. It is exceedingly rare for any mathematical text beyond the undergraduate level to make a profit that is worth the time taken to write it. (Maybe a few of Serge Lang's books qualify; probably not.) If you go self-publishing rather than traditional publishing, you will lose money, and what you're paying for is the vanity of being a published author.

The bar for interest by the mathematical community is much lower than the bar for the type of public interest needed to generate any real sales. The thought that you have "My ideas are too bold for the mathematical community, so I need to take matters into my own hands; they don't know the value of my work as well as I do" is not only crankish but actually specifically damaging to you: it makes you ideal prey for predators of various kinds. You told us in a previous question that you literally fell prey to a diploma mill and thereby lost money. The same mindset that you have now is going to cost you more money in the future.

I'm sorry to tell you this, but this has been going on for several years now, so I feel I should be plain: no one in the world has found your work to be of significant mathematical value. This means that, with probability slightly less than one, that your work does not have significant mathematical value. But in the unlikely event that your work does have value, you're not doing what is necessary in order to show it. Mathematical research is not about simply writing down structures that generalize other structures and proving results about them. You have to solve old problems or pose new ones that are of interest to the community. Bold statements of superiority would be a positive thing if they are specific and factual: for your work to be "superior", it should solve at least one problem that others have posed. If you've done that, please explain yourself properly and then your work can be published in the mathematical mainstream. If you haven't: please start to be honest with yourself about the value of your work. Your livelihood is at stake.

phd - Reading (& understanding) a lot of papers is hard. How to deal with it?

I am a student doing my Masters (in Computer Science). I am much interested in Ph.D and I know to do Ph.D I really need to read and understand a lot of papers. (I also know that its not all about reading papers, but doing something new and useful) but I find difficult to understand papers, especially mathematical. There are lots of things (like bloom filters, k-means algorithms, and a lot lot much more terminologies) which we, normally, don't encounter (except if you are a Ph.D or doing one) but are really crucial to understand papers.

I am not very good at understanding such stuff (atleast quickly, if given time I can but it takes time). Are there people like me who have done/are doing a Ph.D and had the same problem? If yes, how do you overcome it?

Answer

The good news is that you have a good 4-6 years of time to learn how to process that sort of material, and you aren't expected to be able to do it immediately. A professor once told me (about physics papers, but it translates into mathematical and CS papers fairly well) that eventually you start to read the math-heavy parts a bit like music -- you see familiar patterns, and you get the general idea without having to dig deep into the details.

Additionally, you'll find that the more classes you take, and the more reading you do really does prepare you for that next paper and that next step. You'll find that as you start specializing on a particular topic, most of the papers in your topic will become easier to read, simply because you have the experience and have gained the knowledge about the particulars over time. Furthermore, you'll start coming up with your own ideas in the subject, and this just happens to be the goal of graduate school!

There are lots of things (like bloom filters, k-means algorithms, and a lot lot much more terminologies) which we, normally, don't encounter...but are really crucial to understand papers.

The beauty is that you will start encountering them more, and you'll start understanding them more and more as you continue your education.

To answer your particular question,

Are there people like me who have done/are doing a Ph.D and had the same problem?

I still have difficulty getting through math-heavy papers (in CS), but I either re-read sections closely until I figure it out, or I ask someone to help, or I simply move on and hope that the rest of the paper fills in the details. I don't expect to understand everything technical that I read, but it becomes easier over time to get what you need out of a particular paper even if you don't get each and every detail.

publications - Which authority dictates/regulates that in computer science a journal paper cannot be presented in a conference?

I was taught that conference papers in computer science count as publications. Therefore, a journal paper cannot be presented in a conference because of plagiarism reasons, and vice versa.

I confirmed this information:

The weird part for me is understanding which authority (IEEE?, ACM?) regulates this? Is there any document that support this? It seem that this policy in CS emerged from the community (bottom-up; see for example this) – sort of like hand shaking or bowing in Japan – and is therefore self-regulated by people.

Related to this question (EDIT: I will ask them separatedly later as suggested in the comments but I feel I need to clarify certain issues I seem to be confused with):

1. 
   

   I have had multiple arguments with colleagues of other fields that disagree with me in that conferences papers/presentations don't count as publications (I am in a multidisciplinary field). I feel I tend to loss these argumentations because it is one CS student against the rest. In a way, it would be easier if I could refer people to some authority.

   
   


2. 
   

   If I simply don’t want to follow the rule for conferences that apparently don't count papers as publications, what are the real consequences apart from the social lynching? To be clear, the work is done but not published - just somehow presented in a conference (*). Is there any way to confirm that a conference or proceeding is formally registered as an (or to an) editorial/publisher?

   
   


3. 
   
   

   Is there any other way of presenting published results in a conference as, for example, simply abstracts (*)?

   
   

(*) In some areas people just present abstracts, and depending on the area, the conference accepts almost everything. The main goal of this seems to be networking - presenting the work and having the opportunity to interact with people that assist to your presentation (if any).

Answer

There is no central authority that regulates anything. Each journal and each conference have their own policies about such things. In any case, it is not in general true that in computer science "a journal paper cannot be presented in a conference because of plagiarism reasons, and viceversa". My answer to another question explains more about the difference between conference and journal publications and how they interact with each other (the answer is not area-specific, but it was informed by my specific knowledge of computer science publication conventions).

As for your other questions, they are a bit vague but I'll try to answer them:

I have had multiple arguments with colleagues of other fields that disagree with me (I am in a multidisciplinary field). I feel I tend to lose these argumentations; and basically nobody really believes me because I would need a bunch of people in my field as proof.

If I understand correctly what it is that you are claiming in your arguments with your colleagues, it sounds like they may be in the right. However, it's a bit unclear what your position is precisely, so perhaps you should try to clarify that.

If I simply don’t want to follow the rule, what are the real consequences apart from the social lynching. In a multidisciplinary field we are already kind of being punished when we hear that conference papers don’t count as publications. Is there any way to confirm that a conference or proceeding is formally registered as an (or to an) editorial/publisher?

Again, I'm not sure what rule you are referring to. As I said above, there is no centrally regulated system of rules. Each journal or conference will have their own publication policies which you should comply with. These are not "rules" in the sense that disobeying them will get you arrested, but not complying with these policies will quickly get your papers rejected and/or get you labelled as a dishonest or unethical researcher. If you are after an academic career, it is completely counterproductive to do this, and if you don't want an academic career, I don't really understand what would be your goal in trying to work around the publication conventions in such a way.

Is there any other way of presenting published results in a conference as, for example, simply abstracts?

Again, I disagree with your premise (at least in the generality in which it is stated) that one cannot present published results in a conference. I'm in math rather than CS, but I have done precisely that many times (Edit: to clarify: in math, conferences usually don't publish proceedings, so "presenting" does not equate to a publication). Even in many CS conferences, you could do that by taking care to first submit an extended abstract version of your paper to the conference, presenting it there, and following that up with a more detailed paper which you will submit to a journal. The order does matter, as the answer I linked to above discusses, but that's the logical order of doing it anyway, so I don't really understand what the source of your frustration is. If you add more details to your question I'll be happy to discuss them.

---

Edit: Here are some more thoughts addressing the very helpful clarification comments you left below my answer.

1. 
   

   I sympathize with your money issues, but honestly you are mixing two completely unrelated things here. The fact of the matter is, publishing in a journal first and then in a conference is less logical and rather defeats the entire purpose of the system of dual conference-journal publications (and, to be clear, I rather dislike this system myself and think it has some serious flaws, but it does have a certain logic to it, which you are trying to work against because of the unrelated money issues).

   
   

   What I think would make sense for you to do is to determine what is the optimal way to publish your research from a scientific point of view, ignoring the funding issues, and then go to your advisor and/or department, explain the problem to them and ask them to help you achieve that goal. If they are running an honest graduate program, it is their responsibility to provide grad students with the resources they need to succeed in their work. So, I think that problem ought to take care of itself if you go about things in a mature way instead of trying to work around the system, flawed though it might be, and ignore well-established conventions in your field.

   
   


2. 
   

   As for "conference papers don't count as publications", that statement simply does not have a well-defined truth value, and in fact, I think asking questions like whether a conference papers "counts" or does not "count" as a "publication" (whatever that is) is misguided and unhelpful. Here's what in my opinion is a more helpful way of thinking about this topic: a conference paper is precisely what it is, nothing more or less - it is a form of publication that has certain characteristics in terms of the rigor with which it was evaluated, the level of certainty that it is correct, etc. When you are evaluated by others in connection with job applications, promotions, etc., it is important that they understand the context for your achievements so that they can reach an informed opinion about how good your work is. When working in a multidisciplinary field, you are correct that there can be a risk that the people evaluating you are not sufficiently informed about the conventions in some of the fields you are working on to have that context. I agree that this can be frustrating and worrying, but I think there is only one correct way to address this concern, and that is to provide that context in an honest, clear, concise and readable way in your CV and other documents (research statement, publication list). If your department is unfamiliar with CS conference proceedings papers and how much they "count" for, explain to them what such papers are about; e.g., have two sections in your publication lists, one for journal publications and another for conference publication, and include a small footnote to explain the distinction.

   
   

   On the other hand, do not be tempted to try to game the system in any way, by, for example, withholding that context, trying to pass off a conference paper as a journal paper, ignoring editorial policies of a journal or conference you submit to, or any other means that can be viewed as dishonest or unethical. That will only lead to trouble.

   
   

To summarize, I understand from your comments that you have some legitimate concerns about funding travel to conferences and about having your work be evaluated by people who do not understand publication conventions in CS, but it seems to me that you are contemplating some rather ill-advised means for addressing those concerns. Academia is not perfect and one often encounters such less than ideal situations in almost every discipline, but I find that a little bit of creative thinking, maturity and honesty will almost always overcome them.

molecular biology - Photosystem 1 and 2; P680/P700; Chlorophyll a/b

I am getting slightly confused about how the above relate to each other. My current understanding is that P680 and P700 refer to the primary pigment reaction centres in Photosystems 2 and 1 respectively, with the numbers giving the peak wavelength of absorption. Now I initially thought that one of these primary pigment reaction centres must be composed of chlorophyll a and the other of chlorophyll b, hence the slightly differning absorption wavelengths. Instead, here it seems to suggest that the primary pigment reaction centre is always chlorophyll a. Most sources I have looked at do not specify what forms the primary pigment reaction centre (the Wikipedia article on photosynthetic reaction centre, for example, does not state for the general case of for photosystem 2; however it does mention that photosystem 1 has a special pair of chlorophyll a molecules at the centre).

So my specific questions are:

• Is the primary pigment reaction centre in both photosystem 1 and 2 (i.e. P700 and P680) a pair of chlorophyll a molecules?


• If so, what is chlorophyll b? Is it simply an accessory pigment?


• Finally, if it is the case that the primary pigment reaction centre is chlorophyll a in both cases, how can it be that it absorbs at a different wavelength in the two photosystems if it is the same molecule?

Answer

Regarding your questions #1 ("Is the primary pigment reaction centre in both photosystems a pair of chlorophyll a molecules?") and #3 ("How can it be that it absorbs at a different wavelength in the two photosystems if it is the same molecule?"):

Both reaction centers in Photosystem I and Photosystem II contain only chlorophyll a. According to Lodish (Molecular Cell Biology):

As in the bacterial reaction center, at the center of each chloroplast photosystem is a pair of specialized reactioncenter chlorophyll a molecules, which are capable of undergoing light-driven electron transfer. The chlorophylls in the two reaction centers differ in their light-absorption maxima because of differences in their protein environment. For this reason, the reaction-center chlorophylls are often denoted P680 (PSII) and P700 (PSI). (emphases mine)

Regarding your question #2 ("If so, what is chlorophyll b? Is it simply an accessory pigment?"):

Chlorophyll b has a different molecular structure (and, therefore, a different absorption spectrum) and it's less abundant in the chloroplast than chlorophyll a. Here is an image depicting their molecular structures and absorption spectra:

_{(a) Chlorophyll a, (b) chlorophyll b, and (c) β-carotene are hydrophobic organic pigments found in the thylakoid membrane. Chlorophyll a and b, which are identical except for the part indicated in the red box, are responsible for the green color of leaves. β-carotene is responsible for the orange color in carrots. Each pigment has (d) a unique absorbance spectrum. Source: "OpenStax College, The Light-Dependent Reactions of Photosynthesis. October 16, 2013."}

Both chlorophyll a and b are present in the antenna complex. Still according to Lodish:

As in photosynthetic bacteria, each reaction center has an associated antenna that consists of a group of light-harvesting complexes (LHCs); the LHCs associated with PSII and PSI contain different proteins.

However, most of chlorophyll b is associated to PSII antenna complex, not PSI, which is one of the main differences between PSII and PSI.

Source: Lodish, H. (2000). Molecular cell biology. 4th ed. New York: W.H. Freeman.

ethics - I didn't acknowledge someone who helped with my thesis, is there anything I can or should do now?

I received help with some aspects of my PhD thesis from a tutor (proofreading and graphics). Of the help I received, some mathematical notation they provided made it into my thesis.

However, I did not acknowledge the tutor in the PhD thesis for this help (since received).

Is there anything I could (or should) do to rectify this?

career path - How successful would one be in switching fields from PhD in computational biology/neuroscience to postdoc in computer science?

How successful would someone be who completed his PhD in something such as computational biology or neuroscience but wanted to pursue post-doctoral training and beyond in computer science?

I say computer science because, presumably, dissertation work in computational X involves programming and a working knowledge of data structures and algorithms.

Answer

I believe that career changes and "reinventions" are a regular part of modern careers in highly specialized fields. Very few people will be able to work in a single domain for their entire careers, and the ability to move laterally between "adjacent" fields will be a critical skill enabling one to have greater chances and opportunities for success.

Now, that said, your chances of success in any particular job hunt will depend to some extent on how "enlightened" your future boss (or hiring staff) are: some will actively seek out anyone with the appropriate skill set and enthusiasm for the work, while others will be more focused on people who have the "direct" skills they need, assuming such people will require less training to be able to carry out their work. Neither of these positions is "better"; they just happen to coexist.

graduate admissions - Do I have to submit transcripts from school I transferred out of for grad application?

Every grad school requires to submit transcripts from all undergrad and grad instatutions applicant attended including studying abroad.

Personally I am confused with one case. I entered first University just after the high school, but a year after I dropped it and entered another University (a branch of a well-known University that had been opened that very year). The main reason was that the latter University had a program with more advanced and fundamental courses in math and CS and with a researh component as a part of curriculum, and it generally better fit my interests and desires (another reasons were e.g. better professors, better ranking).

I feel that this episode of my life is worth mentioning in my SoP (I preferred to waste a year because I wanted to dedicate my life to science and therefore get better training for this goal). However I'm not sure if I had to get transcripts from that first University even if I just studied there for a year and wasn't satisfied with it's level of education.

Can anyone answer if I am obligated to get and submit this document?

Answer

If a graduate school requires transcripts from all your undergraduate institutions, then I would understand that to include the university you attended for just a year. Under the circumstances you describe, the content of that transcript should not have much effect on the admission decision (or on fellowship offers), but omitting it seems risky because it could get your application rejected (or ignored) on a technicality.

job search - Should I simultaneously apply for multiple jobs in different ranks at the same university?

Say this year the university A advertises one postdoc and one tenure-track position. If I prefer the tenure track position, but am not sure that I can get it, what should I choose between the following two options?

Option A: Apply for both postdoc and tenure-track positions.

Option B: Apply for tenure-track position only, hoping that even if I don't get it, the university will consider offering me the postdoc position.

I thought that Option A is safer, but some of my friends say the opposite. They think that if you apply for both positions, then even if you are good for the tenure-track position, the university will tend to offer you only the postdoc position, the lowest rank that you asked for.

Do you have any insight on this?

For more information: the job market I am referring to is the US'.

What if we have other situations: postdoc/lecturer, lecturer/tenure-track, or postdoc/lecturer/tenure-track?

Answer

My experience is in mathematics in the US. My personal experience is that people will not read anything especially deep into applying for both jobs. Everybody understands that the market is tough, and basically expects everybody to apply to every opening. I've seen instances where a person was considered both for a postdoc and TT position at the same university, and this was not seen as an issue at all (there was much more strategizing around the question of whether they would come for a postdoc).

In the vast majority of cases (without, say, a severe geographical constraint), I think if you consider TT and postdoc at the same place as both reasonable options for you and plausible possibilities, you're probably kidding yourself on one score or another. Generally if you'd even be seriously looked at for a TT job at University X, then when the postdoc committee looks at your file, they'll say "We could hire this person for a TT job. There's no way that a postdoc at University X is the best job they'll get." and they probably won't offer you the position. But unless you feel confident about which way it is, I don't see any problem with applying to both.

EDIT: One thing I'll add, which is mathematics specific: if you're applying MathJobs, the visual difference between applications for the different jobs is negligible. There is a column where you can see what positions the applicant applied for, but it's not very noticeable. So, it's quite possible the committee for one job won't even notice you applied for the other (I have seen this happen).

publications - Is it a bad idea to submit a paper merely to elicit reviewers' comments?

Some days ago I was talking with a friend of mine, who is currently a post-doc at the illustrious Italian Institute of Technology (IIT) working on humanoid robotics.

He was quite disgruntled because he recently spent a lot of time testing his latest discoveries and writing a scientific paper to submit to an important artificial intelligence conference, but on the day of the deadline, his supervisor asked him not to submit the paper. Indeed, his supervisor felt the experiments were not good enough, or the results were not excellent.

Anyway, he did not want him to submit the paper, and so he did not do it.

We discussed about it and we both stated that, even if the paper and the discoveries were not excellent, they should have sent the paper anyway. The eventual rejection maybe would have come later, by the reviewers, together with the important review notes. This way, they would have probably got a paper rejection, but they would have been able to treasure the reviewers' review notes. Instead, with his supervisor initial rejection, they won't get anything except their opinions.

So we thought that his supervisor had a bad idea.

My question is: why did his supervisor suggest him not to submit the paper? Why did he not think about the possibility of getting at least the reviewers' comments?

Is a paper rejection so grave a fact? Is it so dishonorable to get a paper rejection?

Ethics: Is it ethical for a professor to conduct research using a student's ideas without giving them credit?

I pointed a professor (my major advisor) to a resource (a data set), in an email exchange during the beginning of the semester, he published a paper based on this data set several months later, however I had no idea he was working on the project. He did not notify or mention to me about using the data set.

The email that I sent to him earlier when I pointed out the resource had no reply back, however it did indicate in his response that he did not know about the existence of this data set.

When I had a brief (15 minute) meeting with him, he denied that the data set was my idea and said that it was his research colleagues who he got the data set from. I must mention that this data set is freely available and open to the public (online).

My questions are: Is this professor's behavior ethical? and Would I be able to bring this as a complaint to a higher person in the department (since I have email evidence that he did not have knowledge of this data set prior to my informing him).

My final question to you all is whether I should stay with this person as a major advisor because I am having trust issues with sharing my ideas. The only problem is that anyone else I might choose as my advisor would result in me completely changing my area of research. Thank you.

Edit: Responding to the commenters, when I met with him in person, I he mentioned a paper which he authored, and when I asked for the citation he refused to give it to me saying, "I'll think about it". While my gut feeling is that I should change advisors, the other people in the department are not involved in my area of interest, and the other person who is conducting research in this field refused to be my advisor. What would you do in this situation?

Edit: Thank you for everyone's responses. Perhaps this was just a misunderstanding on my part.

phd - How to approach experts to get feedback on a paper

I'm a PhD student in pure maths at a university in Europe. For reasons that I won't go into, my research interests do not coincide with my supervisor's ones. This means that, although she gives me good general advice, she can't give me more "technical" feedback on my work. I've now written a complete first draft of my first paper, and I'd like to get some external feedback before thinking of submitting it to a journal. My question is:

What is the best way to approach the experts in my field (for whom I am a complete stranger) to politely ask if they can read my paper and give some feedback on it?

Emailing, of course, would be the preferred means of communication, so suggestions on how to structure a potential email to send to the experts are very welcomed.

Answer

What is the best way to approach the experts in my field (for whom I am a complete stranger) to politely ask if they can read my paper and give some feedback on it?

For a student who is not very senior -- let's say "very senior" means they already have a draft of their thesis -- I think that (probably: as usual on this site, a literal universal quantifier will get me in trouble) the best way to do this is with your advisor as an intermediary.

Don't misunderstand: you ask whether it is frowned upon for you to directly contact experts and ask for feedback and the answer is a resounding no: you can contact whomever you wish, and they may or may not respond. However, they are much more likely to respond -- and to respond more deeply and usefully -- to someone that they already know, at least by reputation, especially if that person is at roughly their level of seniority (and, yes, even more if that person is more senior).

When I was a PhD student, I didn't have the best luck "cold-contacting" people. I remember in particular trying to contact one guy who was a former student of my advisor and whose thesis I was reading. He was a professor in New York but he didn't have a webpage. I left a longish, awkwardish phone message for him at one point and never heard back from him. (Did he even get the message? Who knows??) I emailed a famous French mathematician and did hear back from him....four months later, which is like forever when you're in your 20s. I was so clueless back then: if I had been serious about it, I would have gone through my advisor, and they would have responded. Well, of course I knew that intellectually, but still somehow decided that it would be better if I did it on my own. (There were a lot of things that I did and didn't do as a graduate student that were directly motivated both by a desire for independence -- good -- and a lack of confidence -- bad -- intertwined in such a complicated way that it is hard for me to pull them apart even now.) It's not that people don't want to be helpful. It's that their time is at such a premium that they have to prioritize helping people that they already know.

If your advisor cannot direct you to those who have the research expertise you need, then I would say that she is not really your advisor and you need to find someone else who can fulfill that role.

Anyway:

1) As others have suggested, if you have completed drafts of papers -- even if not in as polished a form as you would want in order to submit to a journal -- then putting them on the arxiv is a great idea. You'll get some small (in most cases) positive (in my experience) number of "cold emails" just from them, and these can be priceless: in my case, more than once I got connected with the one other person on the planet who really deeply understood and cared about what I was doing.

2) A lot of times you will still send an email. It's just that your advisor will have greased the wheels for you by ensuring the recipient's, um, receptivity in advance. Let me give a little advice on that:

• Introduce yourself politely but don't make a big deal out of it.

You don't need to be overly obsequious or solicitous about their personal life and such. Something like "Dear Professor X, Hello there. I am a student at University A working on Subject B. Though we have not corresponded before, I think you know my advisor, Professor Y. She encouraged me to contact you about my work on C." That's plenty of introduction; you could get away with less.

• Try to write an initial email that the recipient can and will read completely as soon as they open it.

Thus you want it to be quite short, but not so short that it doesn't say anything.

• 
  

  Don't describe your work at length in the email. Instead, include files (of a reasonable length) and/or links to files or webpages. (If you have a webpage, you should put a link to it somewhere in your email!)

  
  


• 
  

  Make a clear request. Better: ask a math question.

  
  

If you include a 30 page paper and say "I'd be grateful for any comments you have": well, that's the sort of thing that I do to my good friends, and when I run into them the following year they politely apologize for not having finished it. Mathematicians like questions and -- here's a little psychological secret -- seem to regard a question mark as being much more compulsory of some sort of answer than most other people. (I am always amazed at how I can have a phone conversation or an email exchange with some non-academic type, ask a question, and their response completely ignores the fact that I asked them anything. To my eyes that is some kind of Jedi mind trick.) If you want to know whether X is true, ask them directly and right away whether X is true.

In fact, if you're not clear enough about what you want, it could go wrong in the other direction: some samaritan savant could reply with several typed pages that answer your question all too well and leave you without a thesis problem. (This is another good reason for getting help from your advisor.)

journals - Publication- rejection with advising to resubmit

I have received a decision letter from a Q1 journal with following remarks:

Reviewers' comments on your work have now been received. You will see that they are advising against publication of your work. Therefore I must reject it.

However, you may submit in the future better revision after resolving all these drawbacks mentioned by the reviewers, and as new revision

While a reviewer has mentioned "major revision", is this decision advising for resubmit after revising the paper? Does this mean "Reject and resubmit"?

research process - Increase chance of reply when e-mailing an eminent researcher?

I found this question, but it does not exactly match what I would like to ask. In my case, it's almost surely appropriate to send the e-mail (since my adviser suggested it), I'm just wandering as to what is the best way to formulate such an e-mail.

The situation

The situation is that there is this bigshot researcher in my field, who designed an experimental framework that is very widely used (which I want to use now). In the paper describing the framework (not so recent, ~2005), he compares 5 (then) state-of-the-art methods, and those 5 are still used as comparison references. The problem is that, even though implementations for the reference methods are provided, I can not find the parameters used to initialize the method.

It is stated in the paper that the parameters suggested by original authors of the methods are used, but, after weeks of digging through the framework paper, papers introducing the method for the first time, and even trying to guess the parameters so they match the ones used, I still can not get the ones used. Since I want to test the method with slight modifications and not just use it as reference, I can not re-use the implementation provided but instead need to run my implementation with parameters I can not find, and introduce modifications to that.

In short

So, to summarize and generalize: After a few weeks of looking for it, I can not find some parameters used in a (seminal framework) work published in 2005. These parameters are not needed to reproduce the work, but are important in extending it. My adviser suggested e-mailing the author of the paper (who is a well known in the community), but since he is so well know and I'm a lowly PhD student I feel kind of uncomfortable sending this e-mail.

The question

I do understand that this is probably the best (and possibly only) approach to getting the information I need, even if it is not very probable that it will work. With that (and my fear of bigshot academics) in mind, my questions are:

• How to best write such an email? Besides the basics (be polite and concise) I don't know where to even start.


• Do you have any advice on how to increase the chances of getting a reply? Maybe including my adviser in the CC of the e-mail would be a good idea, indicating my relation to a more established academic?

How does the human liver regrow?

I understand that there would have to be a portion of liver present to regrow from, so how much liver would the minimum to be able to regrow?

By what mechanism does regrowth occur?

Answer

At least 25% of the original liver seems to be the minimum for regrowth.

The initial regrowth is due to proliferation of hepatocytes: they exit G0 and enter mitosis. The ECM dissolves and is remodeled; the cholangiocytes and SECs also divide.

If you want to read more, you can visit the Google books link above, and the preview lets you read several pages on liver regeneration in rodents. (If it doesn't work, try changing the URL to your current location: books.google.com is US, books.google.ca is Canada, etc.)

citations - How should I cite a website URL?

I am currently writing a report and I have been compiling a list of references (from IEEE mostly) and I also have a number of websites.

My question is, what is the best way to note a website URL? Would it be to reference and cite a URL, would it be adding a footnote? An example would be a reference to google.com. Would it be the correct to just create a footnote?

I've started to just add a footnote each time a website is mentioned (using LaTeX) so for example if a javascript plugin is mentioned then a footnote would be added to the website URL. How would be best to do this as it would not suffice as a reference as it is just noting a website for further reading. I do not have time to waste be writing the whole report to then have to go back through and edit the document hence my question.

Answer

I suppose the easiest way would be to use the \newcommand command in LaTeX.

Put something like this before your \begin{document}:

\newcommand{\jquerynote}{\footnote{\url{http://jquery.com}}~}

Use it as follows.

We used JQuery\jquerynote to build the user interface.

If you want to change the reference to a citation or another format, you can replace the contents of the \newcommand

As far as to "What is the best way to cite a website URL?" the answer generally is that there isn't a standard. Personally, I use web sites as a citation if it contributes some kind of important intellectual argument to the paper. If I use web sites as a footnote, it's because it has to do with some kind of tool I used and is there simply to inform the user that I used Tool XYZ.

Using your example, if I said in my paper, "We used the Google search engine to identify evidence of bias in search engine results" I'd probably put that as a footnote, whereas if I said, "Company web sites from Google, Microsoft, and Apple about employment all state that having fun at work is important" may be citations.

(I should finally note that this is a personal convention rather than anything spelled out in a styleguide, but maybe it helps you?).

publications - Publishing and Self-Archiving

Recently I had a paper accepted by a major journal in discrete mathematics. Now the paper is going through the final stages of publication. The publisher sent me a link in which I have to specify the access policy for the paper. I can choose to either pay a fee (which I won't), and make my paper publicly available from the publisher website, or I can choose to self-archive, and then make my paper publicly available after a period of 24 months of embargo. More precisely, the text for the self-archiving is the following:

I wish to self-archive my accepted author manucript , which is my draft version of the article and which may include any author-incorporated changes from the peer review process. I can post this author manuscript on my institutional or subject-orientated repository immediately for internal use and make it publicly available after a journal specific embargo period has expired.

The problem is that I have already posted the revised version of my paper at arxiv much before receiving this access form from the publisher. So I have some questions concerning this paragraph.

1. The paragraph says that I can post the manuscript at a subject-oriented repository immediately for internal use. As mentioned before I already posted it to arxiv, which I think can be considered as a subject-oriented repository. Is that allowed? What do they mean by internal use?


2. What do they mean about making the manuscript publicly available after the embargo? I have a link at my homepage pointing to the arxiv page. Is this considered to be publicly available?


3. What is the difference between posting it to a repository and making it public?


4. Can I get in trouble if they find the link to the paper at my homepage?

Answer

The text you quote is from Elsevier, and their policy on hosting articles says that "arXiv and RePEc can update a preprint immediately with the accepted manuscript and a DOI link to the formal publication" (while the embargo period applies only to other organizations), so you haven't violated the agreement in updating the arXiv posting. You can add the DOI via the arXiv's journal reference feature once it is available.

research process - Is it ethical to use another university's journal subscription if yours doesn't have access?

As a graduate student, sometimes I really could use access to journals or databases of tables that for some reason my university doesn't subscribe to. I have friends at other Universities that do subscribe to these journals and it would be very helpful to have the data. Is it acceptable to ask them to retrieve the data? I don't really want to start this if it's going to run me afoul of the rules.

Answer

Is it against the law? Probably.

It it scientific misconduct? A breach of ethics? Hardly.

It is acceptable? It's your decision to make based on risk analysis. If you don't do it on a large scale (i.e. someone supplying many people with papers), it's probably okay. It is common practice.

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Also, be aware that many journal articles can now be found either in pre-print or post-print form online (though this depends widely on your field), either on institutional repositories or on the authors' webpages. If you're merely missing access every once in a while, you can also nicely ask the corresponding author.

phd - How to build healthy working relationships with my male colleagues as a young-ish, attractive-ish woman?

I'm a PhD candidate from Asia currently visiting a prestigious university in Europe. Recently I've noticed quite some "strange" behaviours of male "colleagues" around me (by "colleagues", I don't mean that we work on the same projects or from the same office. They are just people who work at or visit this place: faculty members, PhDs, or research staff).

For example, these gentlemen seem to be giving me a bit of extra attention: following me to the pantry; "appearing" several times at the same time at the place that I'd show up; or even try to wait for me when I leave. (Please don't suggest that I might be overreacting - I am quite confident that I'm not exaggerating here.)

Honestly, I am more annoyed than flattered. I want to focus on my research and want to be able to have healthy, normal, constructive working relationships with these people. I don't want any extra attention other than that I am a dedicated and capable researcher, and a nice person in general. However, because of these strange behaviours, I have to try to distance myself from some of them who I have had some friendly exchanges before. I've become a bit cold and unapproachable to them - I guess I am trying to say that I am not interested in anything romantic, and I don't want any attention in that matter. I guess some people might say, well, just tell them openly that you are not interested. I simply am not able to do that: first, they don't say anything or do anything that would allow me to bring up this topic; second, some of them might not even really want to pursue a relationship (they are married, or too young/too old for me anyway), but just kind of show some sort of admiration I guess.

However, I also feel very uncomfortable about that. I am by nature a nice and friendly person. I really feel bad about being cold and unfriendly to other people. Also, I want to have a circle of contacts that I can talk with about my research and their research, and get feedback and/or inspiration from that. I am not sure how I am able to have that type of positive working relationships in this kind of situation.

To clarify a few things...

1. 
   

   These male colleagues are decent, respectable, and in some cases, brilliant and achieved people. There is no inappropriate advance from them or anything creepy in this (or it would be rather easy to handle the situation). It is just the continued, affectionate attention that is making me uncomfortable.

   
   


2. 
   

   I am not sure this is associated with my newness or novelty. I have been here for eight months now and I did not notice this kind of attention at the beginning. Instead, I noticed the association with me slowly building up myself professionally here. I'd assume these male colleagues are slightly more refined than the general public and would look a bit further than a pretty face for a pretty mind (not that I am suggesting I am any or both of these). If this is true, then I would assume this issue would not go away as time goes by, but might hang around or even intensify as I become more established as a capable researcher. In that case I would have to find a solution for myself in the long term.

   
   


3. 
   

   After second thought, I guess I wouldn't be able to take the "dressing down" advice. I like to dress in a classy and elegant way and that makes me feel good (it is like I enjoy making my room clean and nice and that makes me feel good). I don't see anything wrong with it and don't want to punish myself with other people's reactions to me. In fact, I have become more convinced that the solution to this type of issue is not to make women less feminine/attractive. There should be other solutions where we can be ourselves and still be comfortable around male colleagues. I don't know what those solutions are though.

   
   

Please give me some advice on how to handle a situation like this.

graduate admissions - Should I send a 60 percentile Math GRE score to Applied Math PhD Program?

I didn't do well on math GRE(700, 60 percentile) and I have no time to retake the test. I am applying for applied math phd programs(some examples include Rice CAAM, Upenn ACMS, JHU's Department of Applied Mathematics & Statistics or my dream school Stanford ICME), and almost all of these programs do not require GRE subject but they recommend me to send.

I know that this score will definitely hurt me a lot if I am applying for pure math programs, but someone said that applied math is different. So I wonder if my score will have seriously negative effect? Should I send the score to those programms?

Thank you, I appreciate any advice!

phd - Is it a good idea for a nonnative English speaker to have native speakers help make the English in statement of purpose perfect?

I am applying to doctoral programs in the US.

Since I am not an English native speaker, I am wondering if it is okay to have native speakers help make my English perfect in my statement of purpose?

I ask so because I am concerned with that, since the committee definitely knows that I am not a native speaker in English, my perfect English in statement of purpose could lead them to suspect. By "suspect" I mean the argument: If this person's writing is this good, then this person's TOEFL scores must be almost perfect.

Answer

It's definitely a good idea (in fact anyone in your situation should do so), I have seen plenty of people around me in my graduate school who had done so. There even exist professional services specialized for this task (it's a pretty big business in some countries).

Regarding your concern that the jury might think that you have been "cheating", forget about it:

• by providing a flawless statement of purpose despite being non-native, you are showing the jury a lot of motivation;


• if the statement of purpose was used to assess your true level of English, they wouldn't ask for TOEFL/IELTS;


• when writing research articles later on, you will still often have a native speaker around to answer questions.

thesis - How to reconnect a relationship with a professor

Today

I'm currently in my final MSc year, and I have finished working for my thesis. I am under supervision of professor X, which I find myself at ease and actually enjoy what I do. My field is Chemical Engineering.

Background

Before starting my thesis, during the "thesis choice" period, I was contacted by professor Y, which I was in very good relations (we did some external projects before the thesis, with good results). One of the major aspects of working with Y was the possibility to go abroad, as he sent out his students quite often for thesis work. The drawback was the lack of direct supervision. Professor X on the other hand contacted me, but he was not in favour of the abroad experience, since he only works as a direct supervisor with thesis students.

Issue (first mistake)

I had two initial proposals from both professors. At first Y's proposal was way more interesting than X. I got a week to confirm Y, but after the third day, Y's initial proposal was changed (in a uninteresting project).

I thus contacted X, and after a week arranged for a thesis meeting. X's offer was also changed, but now very being intriguing, and Y remaining proposals were not as interesting as X. I said yes to prof. X and went personally to Y's office to tell my decision.

When I entered Y's office (without notice, as MSc students - per Y rule - are free to pass by his office freely), he welcomed me with a project that "was sure I would love", and there were also external profs and industry reps (for which I had not been notified) and quickly explained to me the thesis, all taking like I was in from the start. This "meeting" with me was not programmed, as I expected only Y being in his office.

Right after this meeting I made a big mistake. From all that was said in the meeting, and the confusion that was created, I said (verbally) yes to Y.

Issue's Aftermath (second mistake)

I continued working with X, and received NO news or advices or any message from Y. My suspect is that Y's project came to nothing, but seeing that no messages came from Y, I made the second mistake as I continued working with X not alerting Y. I know that a single e-mail could have resolved the issue, but since that period was also characterized by a grave family issue, that e-mail was never sent.

Question

As the months passed and considering my today situation, and (fortunately) all the personal issues have subsided, what could be the best course of action of regaining contact with Y? After all, he did nothing wrong to me and I know I made some terrible mistakes, I want to apologize such to not truncate our 4 year relationship.

Answer

I think you have gotten yourself into a pretty deep mess if it is really as bad as you suggest and not just a sense you have of the situation. But, the only way to proceed is to go visit the professor in person and steel yourself for whatever occurs. I'd make an appointment first, to give the other person a chance to think about their own response.

You may well owe an apology, so prepare to give it. But, as long as the prof isn't a monster, it may well turn out better than you fear. But it may also take a while to completely dispel any bad feelings if they exist so a single meeting may not turn things around like flipping a switch. But a face to face meeting will give both of you a sense whether a continued professional relationship is possible and desirable.

It may be the professor was disappointed when you left, but also possible that he/she is so busy generally that it didn't register too much.

The past is what it is and can't be changed. The future is up you you. But expect that the transition may be uncomfortable.

What do search committees really read in a CV during initial screening for a faculty position?

Faculty positions are very competitive, and each advertisement should roughly receive hundreds of applications.

I think search committees cannot spend more than 1 min reading each CV during the initial screening (correct me if I'm wrong).

CVs are usually 10-20 pages documented in different formats, and it is not easy to capture potentials of a person in 1 min.

Owing to the fact that not all committee members are fully familiar with the journals in which applicant has published, his/her research impact, his/her universities of education, or the importance of his unusual achievements.

Then, how does a search committee shortlist the candidates during the initial screening? What do they quickly look for in a CV to keep the candidate?

NOTE: My assumption for 1 min for each CV was based on a simple math. If a job ad receives 400 applications, each member should spend almost 7 hours to review only CVs (not looking at other documents). If my assumption was somehow wrong, please forgive me. Your answer can clarify the issue anyway.