paper submission - Editor of manuscript assigned after reviews were completed

Recently, I submitted a paper to a journal. The paper was reviewed and the reviewers asked for some changes. I revised the paper and sent it again. The paper was reviewed again and after a few months the status was shown as "reviews completed". But the status was again changed to "editor assigned". Could you please explain to me what does this imply?

publications - Which ACM copyright license to use?

ACM now offers authors of published papers a choice of two copyright licenses: the "traditional" ACM Copyright Transfer Agreement or the ACM Publishing License.

How should I choose between these two licenses? What are the advantages and disadvantages to the authors of each license?

I care a lot about maximizing the ability of others to read the paper (e.g., maximizing my ability to make my paper available on my web page, institutional repository, etc.); are there any relevant differences between the two licenses that affects this consideration? Are there any other important differences between the licenses that authors might care about?

Answer

First off, please note that IANAL.

That said, the Copyright Transfer Agreement is what ACM used to be doing to everyone: when you publish with the ACM, you transfer your copyright to them, and thus lose ownership of your creative work. The ACM has been receiving criticism for this as the Open Access movement has gained momentum.

The Publishing License seems to be their response to this criticism: with the Publishing license, you retain copyright yourself, and instead grant ACM a specified list of rights:

1. An exclusive, worldwide, royalty-free, perpetual, irrevocable, transferable and sublicenseable license to publish, reproduce and distribute the work in any way they feel like — including to hand these right on to other parties.


2. A non-exclusive permission to publish, reproduce and distribute any software, artistic images and auxiliary materials.


3. These rights “infects” any minor revisions (derivative work with less than 25% new substantive material).

I don't actually know what the exact implications here will be — the conditions are restrictive, but the copyright remains with the author.

botany - How to correctly and accurately identify a few species of trees from their leaves?

I want to identify a tree from one of the 12 species listed based on observing their branch and leaves. Is there quick and neat way to do it?

Red Oak, White Oak, Red Maple, Striped Maple, Tulip Poplar, Black Cherry, White Pine, Virginia Pine, Dogwood, Hickory Species, Sourwood and Cucumber Magnolia.

Thank you!

peer review - Should I list people who are in competition with me as reviewers to exclude for "conflict of interest"?

I am submitting a a paper to a top conference and I need to determine the reviewers with conflicts of interests.

There is a big competition in having papers accepted at this conference, among people working in this area. Also, it is very likely that my paper goes to people who are in the same area for judgement. Particularly, some of these people are not very honest and they blindly reject other people's works, in order to publish their own papers. To myself, it has been proven the dishonesty of them.

Is it OK to put these people in my list of reviewers to exclude because of conflicts of interests? There are other researchers who can judge the quality of my paper honestly, because I am not putting everybody on that list. But is it right to do so?

Answer

In my experience, when a conference asks authors to identify reviewers that are conflicted, they want you to identify reviewers who fall into certain categories of people who should not review your work because they have a relationship with you personally that could bias their review. For example: your advisor, your colleagues, your current collaborators, your family members, etc. They are not asking you to list reviewers who you consider to be your competition.

For example, the instructions for POPL 2017 say:

As an author, you should list PC and ERC members (and any others, since others may be asked for outside reviewers) which you believe have a conflict with you. While particular criteria for making this determination may vary, please apply the following guidelines, identifying a potential reviewer Bob as conflicted if

• Bob was your co-author or collaborator at some point within the last 2 years


• Bob is an advisor or advisee of yours


• Bob is a family member


• Bob has a non-trivial financial stake in your work (e.g., invested in your startup company)

Also please identify institutions with which you are affiliated; all employees or affiliates of these institutions will also be considered conflicted.

If a possible reviewer does not meet the above criteria, please do not identify him/her as conflicted. Doing so could be viewed as an attempt to prevent a qualified, but possibly skeptical reviewer from reviewing your paper. If you nevertheless believe that a reviewer who does not meet the above criteria is conflicted, you may identify the person and send a note to the PC Chair.

ethics - If someone conducts unethical research unbeknownst to anybody, but produces positive results, what would happen to the research once discovered?

I was just wondering about this specific scenario.

Say someone was researching nature vs. nurture, but his experiments involved keeping babies in a controlled environment for the first 10 years of their life. His research is secret and he has ways to smuggle children for his research (don't ask how).

After 15 years, he publishes a paper and confirms that there is a set amount of characteristics that can be transferred via genes.

What would become of the researcher and his research? Will the researcher be jailed, but the research results recognized?

---

This question is about unethical research in general, not just ones involving human subjects.

P.S. No babies were harmed in the making of this post

Answer

Unfortunately, history has already forced this question upon us, and the answers are not entirely clear. The Nazis inflicted widespread and breathtakingly horrifying human medical experiments on their victims during the Holocaust. These yielded quite a bit of medical data, that some want to unearth and apply today.

This has ignited quite a bit of debate on the ethics of using this most obviously and supremely unethical research. The science may be dubious as well, given the circumstances under which it was performed. An excellent discussion of the dilemma may be found in the article "The Ethics Of Using Medical Data From Nazi Experiments" by Baruch Cohen. In essence, Cohen argues that in certain extreme cases it may be possible to use the data, but only when accompanied by strong condemnation of the methods and only when it concerns information that is both otherwise impossible to obtain and of life-saving importance.

Nazi medicine is an extreme case, but unfortunately by no means isolated, and the judgement of history and science on these studies contains less uniform condemnation than we might like. The modern consensus, however, seems to be that except in very unusual circumstances, unethical studies should not be rewarded in any way by recognition.

graduate admissions - Can a PhD student write a letter of recommendation for coauthor/collaborator?

My good friend and I coauthored a paper that was accepted at a major research conference. He works in industry and has now decided to apply for PhD programs. He asked that I write him a letter of recommendation because I am most familiar with his academic strengths and research work. I've been working on research level problems with him for the past 3 years.

Question: Can I write him a letter of recommendation even though I am only a PhD student?

ethics - Do I need to wait for a journal to "consent" to paper withdrawal before submitting elsewhere?

I have a question about submission elsewhere and journal's "consent" of paper withdrawing.

Recently I have withdrawn a paper of mine from a journal, which I want to submit elsewhere. Since I knew that the journal had received my email (by read receipt device) on withdrawing the paper and since I am just in the stage of being notified that the paper has been accepted for publication, the problem is: In order to submit the paper elsewhere, do I have to wait for the journal to consent to the withdrawal?

I am looking for some ethical advice.

Answer

I'd recommend waiting a week or two to see whether you get a response to your withdrawal. At this stage it can't be urgent to resubmit immediately, and having their reply would guarantee that they are aware that you have withdrawn the paper. (By contrast, I don't think an e-mail read receipt means much. For all you know, an administrative assistant opened the e-mail and then mistakenly deleted it without realizing what it said.) I wouldn't go so far as to say you are required to wait for a response, but better safe than sorry.

I think you've got a much bigger issue to worry about, though, and that's why you withdrew the paper after acceptance. At least in mathematics, withdrawing an accepted paper is extremely unusual. To a first approximation, it typically means there's something seriously wrong with either the paper or the journal. You can certainly do it, but given the effort that has gone into handling and refereeing the paper, you will cause offense if you don't have a very good reason.

If you inadvertently submitted the paper to a junk or predatory journal, then you don't need to worry about causing offense. (Offending the editors of predatory journals is not a bad thing.) In that case, withdrawing the paper is certainly the right decision.

If you dreadfully screwed up in your choice of journal, for example by submitting a brilliant breakthrough to a respectable but not impressive journal without realizing how good the paper was, then you should apologize profusely for wasting everyone's time. Hopefully they'll understand that it was a genuine mistake on your part, and they'll sympathize with the awkward position you are in and give their blessing to resubmitting elsewhere.

If the paper is seriously flawed, then that's a respectable reason to withdraw it. You might look bad for having submitted it, but then again, the referee didn't find the mistake either. But this isn't a compelling reason to submit elsewhere soon: if you don't check whether the original journal is willing to publish the revised paper, then it looks like the changes were just an excuse to withdraw the paper.

Under normal circumstances, it will cause offense if people think you are withdrawing an accepted paper just to try your luck at a more prestigious journal. In particular, this is a dangerous impression to leave if you ever hope to submit to this journal again. As an editor, I would certainly not be happy to see a new submission from an author who had previously withdrawn an accepted paper without a compelling excuse.

All this gives you another reason to move slowly and wait for a reply. If you have a good reason for withdrawal, then it's worth making sure you have communicated it clearly. In any case, you are doing something rather unusual and serious, and it's best not to give the impression you are treating it lightly or casually.

How to find out the first name of a professor whose home page lists only first initial?

This is probably a soft question. I am interested in complex analysis, and I want to ask the first name of this person, S. Ponnusamy, whose name I wish to mention in a paper.

What is the best way to go about asking such stuff?

What effects (if any) do audited undergraduate courses have on graduate admissions?

I'm an engineering undergraduate, and my university doesn't require me to take any math courses past the standard calculus sequence and differential equations. The field I am interested in entering in grad school is slightly math-intensive, to the point that it requires more math than what I have taken. At this time, I have two years left to graduate, and I'll be taking about 17-18 hours each semester until then, so it would be very difficult me to tack on an extra math course. I was considering simply officially auditing one, so that it appears on my transcript and so that I at least have some exposure to the subject.

My question is: will this have any positive benefits while I'm applying to graduate school? Or would the admissions committee assume that I didn't learn as much as someone who actually took the course, and take it with a grain of salt that I know the material?

On a related note: what about if the course I audited was on directly in my major? Would that be beneficial (if it were, say, a graduate-level course)?

Answer

My question is: will this have any positive benefits while I'm applying to graduate school?

I think you are asking whether it will make your application more competitive. Answer: not much. At many/most universities, anyone can audit any course at any time, and it doesn't certify anything more than that they showed up for class -- in some cases not even that. I had an auditor in a course this semester who showed up for the first half of the lectures and not for the second half. My response: ok. It shows up in my records -- so presumably also hers -- that she audited the course. I am not asked to assign a grade of any kind.

Or would the admissions committee assume that I didn't learn as much as someone who actually took the course, and take it with a grain of salt that I know the material?

They would probably not assume anything at all. They would certainly not regard this as being evidence that you learned the material: getting a poor grade in a course certainly does not demonstrate learning of the material, and auditing shows less than that.

Of course you can learn things by auditing a course. But you can also learn by outside reading and in other ways. However most students at this level learn more by actually taking a course, and of course if you do well in the course then that knowledge gets certified (to an extent) and can be used advantageously in your graduate application.

Story check: you say that you have two years left of undergraduate study and can't find time to officially take one course that you think will be beneficial to your intended graduate study. This professor who read graduate applications for several years finds that hard to believe. In two years you should be able to work in the time to take one extra course, e.g. by (i) taking courses over the summer or (ii) getting excused from one course in a sequence, say by taking an exam which shows your competence. This is something to talk to your undergraduate advisor about.

physics - Can a theoretical physicist win a Nobel Prize anymore?

The background: The big news in the science world this week is that, on Thursday, it will be officially announced that LIGO has detected gravitational waves. Some people have even started talking about a Nobel Prize. I agree that this is a momentous accomplishment and these people deserve all the nerd glory the world has to offer; that said, I feel that, in a fair world, this Nobel Prize should be shared between LIGO and (posthumously) Albert Einstein. After all, he is the one that came up with the theory of physics that predicts things like gravitational waves.

The observation: Nobel Prizes can't be awarded to deceased individuals; the Nobel Committee doesn't award Prizes for theoretical work before its predictions are experimentally confirmed; and theoretical physics is churning out ideas that can't be directly tested with today's technology and resources. Put these factors together, and I have this uneasy feeling that Englert and Higgs might have been the last theorists to receive a Nobel Prize. It really looks like Stephen Hawking and Ed Witten, which are widely recognized as among the best theoretical physicists ever, will never get one. For practical purposes, the Nobel Prize in Physics has become the Nobel Prize in Engineering Physics.

The question: are there any theoretical physicists that are young enough, their work groundbreaking enough, and the testing technology sufficiently within our current reach, that a Nobel Prize could reasonably be awarded to them?

career path - progressing from high school teaching into academia

I have been a high school teacher for coming on 14 years, in 8 schools, in 2 countries. While teaching still is enjoyable, I feel with the near completion of my PhD (in physics), that I am ready for a new challenge in academia.

I have no illusions though, it will be challenging to even get into academia. I know I also have to be published (have 3 peer reviewed papers published).

How should the skills developed in high school teaching be touted to be relevant for academic postions?

Answer

If you are near completing your PhD, then I assume you also have some papers coming out soon. If not, then your dissertation will probably be worth 3 papers, so I wouldn't worry too much about that part.

Conveying information to an audience with varied skills and backgrounds is always a valuable thing in academia. Whether in written manuscripts or conference presentations, this is usually the problem to be solved. My advisor was fond of constructing lectures, no matter the audience, as if they were to be given to college freshmen. I'd say a lot of freshmen are not too different from high school students.

A successful PhD defense signifies that you have the ability to do novel work in your field, but your teaching skills will enable you to tell others about it.

interview - Tattoos in the Workplace

I'm an undergraduate mathematics student finishing my degree. I plan to go to grad school, and ultimately aspire to become a professor. I really like tattoos, but I'm hesitant to get one because it could affect my future job.

Of course, if I did get one, it would be discrete and innocent. What I really want is the axioms from ZFC wrapped around my upper arm.

I'm very interested in hearing people's thoughts on tattoos in the workplace, particularly from people who work in mathematics. Do you think it is acceptable? How would you judge someone based on their tattoos? Do any of you have tattoos? What are your experiences?

graduate admissions - How to judge the reputation of a potential advisor or research group for good quality research for PhD?

I am planning my PhD and am applying to various labs and professors.

I am getting positive responses, but I am having trouble making a decision as to which lab to go for. How can I judge the quality of research of a group? What parameters shall be kept in mind while making a decision? I usually look for relevant research interests.

students - How should a university deal with outsourced essay writing?

My campus is full of flyers, typically attached to lightposts and so, advertising to write essays for money. There's plenty of such services offered on the internet as well. Presumably, many students make use of such service.

Clearly, it is unwise for students to make use of such services, and I suppose it violates regulations. How can a university deal with the issue of ghostwriting? That means: how to identify probable cases of ghostwriting; how to proof that ghostwriting took place; and how to sanction it? It seems considerably harder to tackle than plagiarism.

bibliometrics - Construct a network of citations

I had the thought that I should run a computation on my document to see things like: How many times I cite each source, how many times I cite each author etc. Then I thought that isn't enough. What if I cite A_foo, B_foo and C_foo, but both A_foo and B_foo cite C_foo. That is worth knowing. A graph of citations between the texts that I am citing will revel interesting information. For example nodes with out any parent, will generally indicate new and original ideas. While they may draw on other things, those things are distant enough from my work that I am not citing them. Nodes that have no links to any others, show that I am bringing in an idea from another subfield, perhaps.

This graph should be computable, I know google scholar maintains a list of almost everything I've cited, and for each thing lists who has cited them.

Has this been experimented with? Are there existing tools for the job? If there isn't I might mess around with some python and put something together.

My references are all in bibtex.

I would like to construct a graph of the citations.

evolution - Fossils of intermediate stages?

If Humans are evolve from Monkeys, there must be stages in the evolution process, when it was 1% human and 99% monkey, 2% human and 98% monkey and so on. This is because evolution was a very slow process that occurred in a span of thousands of years. So we expect there must be fossils of this intermediate stages under earth. These intermediate-stage fossils must be many times in no. as compared to 100% human or 100% monkey.

But why do we do not discover these intermediate fossils?

teaching - What to do with teachers who think their subject is "extra special" and gives students too heavy a load?

I've had my fair share of teachers who give so much more load than the previous teachers of the same subject. A whole extra project, much more papers, or exercises, etc.

The bigger problem is that there comes a time where in a single semester, several of the teachers think this way, and MOST of them give an extra project/exercise EACH, on top of the current curriculum projects.

This strains the students too much.

How should a student approach these types of situations?

citations - Include article in bibliography I didn't cite

Say I gained knowledge from a review article. However, I don't cite that review article. I do cite articles cited by that review article, but not the review itself.

Should I still include that review in my bibliography?

molecular genetics - Gene and Protein isoform

What is the relationship between term "Gene isoform" and "Protein isoform"?

Say a gene can make 3 isoforms, will it produce only (maximum) 3 isoform protein?

Whether to include a middle initial in author name on academic publications?

When a person is starting their academic career and submitting their first paper, they need to give some consideration to what their official academic name should be. Consistency across publications is an important principle. A common consideration is whether to include a middle initial in academic publications. Thus, I was interested in what general advice you would give to a PhD student or early career researcher deciding whether to include their middle initial in their author name on publications.

A few possible principles:

• Always include a middle initial because it reduces the chance that your name will be the same as another academic (including cases where only initials are shown in references), or because it looks more distinguished.


• Only include a middle initial if your name is common, because there is a simplicity in just having a first and last name that is desirable where possible.

So, in summary:

• What general advice would you give to PhD students and early career researchers about whether to include a middle initial in their publication author name?


• Would you give different advice depending on the name (e.g., John K. Smith compared to Ambrosia K. Hooperdinkel)?

Note that this is different to some related questions about (a) whether you can add a middle initial to previous publications (b) the importance of name consistency, (c) how to cite papers with inconsistent initials.

How many people are required to maintain genetic diversity?

Imagine humans were to colonize a distant planet and it was a single one-way trip. How many people would they need to bring?

Obviously 2 is the minimum, but that would result in a lot of inbreeding.

So what number is the minimum number of people you can have in an isolated community and still maintain a healthy diversity?

Answer

Actually it is a very important question for laboratory animals (and, I imagine, endangered species) and was calculated to be 25 couples.

With any number of animals (including humans), there is always some inbreeding happening, but you can reduce it with the number of breeding pairs and careful pairing. When you get to 25 pairs (50 animals) and have complete control over pairing, you can sustain the genetic diversity practically infinitely (especially if you take into account spontaneous mutations).

Of course, such control over who can have children with who (plus whether one is at all allowed to procreate and what will be the sex of their children!) would be questionable morally, so in case of populating a distant planet, we would need a larger group, to provide for sexual preferences, fertility problems etc.

Some information on laboratory outbred stocks.

genetics - Do transcription factors bind to both strands of DNA?

Do transcription factors (or generally proteins) bind to only single strand of DNA or both strands? Since it can have non covalent bonds to both strands in theory. I would like to know the mechanism. Any reference books, papers or links will be helpful.

Answer

The short summary is that typical TFs bind and read both strands together, as a basepair sequence. Some proteins instead recognise a site on the helix by its shape and flexibility. ssDNA-binding proteins obviously bind one strand but they do this in a non-specific manner. RNA-binding proteins recognise the sequence on a single strand by inserting intercalating planar residues between bases! All of this binding is non-covalent.

Transcription factors recognise sites in dsDNA, with DNA-binding domains. The rest of the protein might surround (partially, to varying degree) the negative outer surface of the dsDNA double helix with positively-charged surface, in order to hold it on to DNA as it scans (perhaps) along its length.

DNA-binding domains: major groove

The following domains are found in many transcription factors, and they all recognise both strands. More correctly, they recognise basepairs and their orientation. The first 5 pages of this lecture slideshow demonstrate that the chemical groups on the side of basepairs, accessible in the major groove, allow proteins to distinguish A:T, T:A, C:G & G:C by the order of hydrogen-bond donors, acceptors, and a methyl group.

Hence, TFs recognise a sequence of basepairs - oriented such that one strand is (e.g.) pTpCpApG, and the complementary strand is pCpTpGpA; and the bulk of the protein may 'sit' on one strand or the other - or a nearby gene may locally define one strand or the other as the coding strand but this does not mean that this one strand is read.

These are common domains that all recognise basepairs in the major groove by interactions with residues on a probing aplha-helix.

TATA-binding protein: minor groove

TATA-binding protein (TBP) is a different, interesting case. It binds the 'TATA-box' via the minor groove, where the exposed chemical groups only distinguish [A/T] from [C/G], but not their orientation. This means that the sequences on each strand cannot be easily read from the minor groove. TBP instead recognises the shape and flexibility of the double-helix at the TATA-box, 'grips' it by the minor groove and bends the DNA, which aids the melting of the strands to the transcription 'bubble'.

The TATA-box sequence is usually pTpApTpApApA on the coding strand upstream of the transcriptional start. This is the convention when giving the sequence of a TF-binding site, but you couldn't say that TBP actually reads TATAAA - it doesn't!

Here is another, similar set of lecture slides.

Even better, here is the same material covered in a popular textbook.

industry - Does it make sense to get a PhD if a person does not want to be in academia and prefers to stay in business?

I am working in a highly technical field (quantitative finance/ statistical analysis) for a private company with a Master of Science degree in economics.

Does it make sense to get a PhD (in quantitative finance, math, statistics) if I do not want to be in academia and prefer to stay in business.

What I expect from PhD:

1. Structure and deepen my knowledge in the relevant fields through high quality classes (where I sit and listen and learn and do homework to make sure that I have learned).



2. Get the ability to read any scientific article in the related fields and without much pain understand 90% of it to the very last detail (and implement ideas from the article in my work).


3. Possibly acquire certain thinking and problem solving culture (so vague... and I guess after my Master I have a fair part of it already(?))

Also important:

1. PhD was never mentioned as a prerequisite for a promotion or a salary increase.


2. My colleges who have PhD are not visibly advantaged by the company (do not know about the rest of the industry, but the company being a big player is representative of it).


3. I enjoy learning new stuff on my own (not a problem to spend many nights with a math book), but hate the status of a student (little money, slave of professors and their peculiar exam requirements).

So should I go for a PhD or rather a specialized Master, or develop myself through separate university courses of my choice and professional programs + self-study?

Any pieces of advice from people used to be in my situation?

Answer

Ultimately no one else can make this decision for you. At best we can give our biased (after all many of us here will have taken the PhD/academic route) opinions.

First of all doing a PhD for financial or career reasons is not, in general, a good idea. Yes we all know the story of google, but Larry Page and Sergey Brin didn't go into the PhD planning to make it big and it was their passion that produced google. A PhD is a long and sometimes painful process taken on because the individual gets a buzz from the challenge, the field and a desire to push it forward. There will be weeks if not months when nothing is working or making sense. I think it was Boot and Randall, after having developed the high-power magnetron for radar at Birmingham university and giving the allies a much needed early warning system, who attributed their success to something akin to "the one day in which all the equipment in the lab happen to work". Tongue and cheek and modesty no doubt, but it serves as a good antidote to research life - very few things, codes included, work first time! Its the burning passion that keeps you going time and time again until you get results.

Second, a PhD is not taught (Not sure where your from but the USA and some European PhD's do have a taught masters in the first year, but this is not the norm in Europe). Classes to a large extent are not an efficient use of time, they serve to give a broader overview of the field but will certainly not be anywhere near enough to get you through a PhD. If its being taught in a class its not research! And its certainly not going to be a novel idea for your thesis. At the end of the PhD you should be the world expert on the niche area of your field, there are no (or few) textbooks on the subject - because you have written them yet!

When reading papers, even the most experienced academics, are unlikely to understand everything first read, the specific technique maybe, the unique application? probably not. As a research you don’t want to waste time absorbing every little detail, just the bits relevant to your research. You simply don’t have time.

Research does teach you a certain set of skills, first is how to deal with failure and keep going - Persistence. Project management (3 year long project after all) skills and of course critical thinking and problem solving skills, particularly in the technical areas.

Now, none of what I said should be taken as trying to put you off but rather help you make an informed decision. You could possibly look at a research masters, known as an MRes? This may be the best of both worlds. Good luck with whatever you choose to do and remember you don't need PhD's or degrees to continue learning, someone above mentioned online course and these open access avenues are a great way to expand your knowledge.

funding - How does "buying out" of teaching work?

Several times I have met young visiting faculty members who got "bought out" of teaching. This means that some senior professor opened their grant treasure chest and pays money so their younger co-worker needs to teach one course per semester less than usual.

How does that actually work? On the department side, they probably need manpower to offer courses to their students. Does somebody else do the job then (for the money) or what is the background with those buy-outs? Can people buy out themselves? Who can do such things and what are the official and unofficial issues with such a procedure?

graduate admissions - What would be the possible consequence of concealing an incomplete degree?

I attended a 2y MSc mixed mode (Coursework+Thesis) program which is incomplete as of today. I have completed two semesters and still 2 more semesters to go.

I have dropped 3rd semester and never attended the 4th one. Coz,

1. I ran out of money.


2. I didn't like the program as it contained too much coursework. A whole load of coursework unrelated to my area of research interest was hindering my effort towards getting into research. Suppose, I am interested in Machine Learning. But, I have to study Economics and so on.

Now, I found that I, actually, can apply to Ph.D. programs without completing an MSc program (there are a lot of universities which accept Ph.D. students without MSc). I have good GRE score, so the chance of getting into a Ph.D. program is very high. But, I am worried that my previous incomplete MSc program will discredit my CV and statement of purpose as the dropped semester would be considered as failed courses.

Would it be a crime to not to disclose the incomplete MSc program? What would be the possible consequence of concealing an incomplete degree?

Answer

I wrote about this here.

Short answer: yes, it is considered dishonest, and the possible consequences are severe. You could be dismissed from your new program, or, if it's discovered after you finish, have your degree revoked. The likelihood of this actually happening is hard to evaluate, but those sorts of sanctions will certainly be "on the books" and available if the school decides to enforce them.

You'll be much better off if you submit the transcript and explain in your application why you decided to drop.

teaching - Device for writing a lecture with a stylus for video lecture recording

I would like to start recording mathematics lectures for students to watch on their own time.
I need to find a device that allows me to write out the lecture with a stylus and import it to a computer.
I suppose I could buy an iPad or something close to it. But, that would be a bit of money. I am looking at a Wacom Bamboo Splash. The problem here is that the writing area seems very small (the class is a math class).

• What is a good device for writing out lectures to a computer?


• Is there a device that makes this work best and is not hundreds of dollars?

Answer

If your department has a document camera, especially a newer model, then you could use that. I currently use a document camera for my regular lectures. I write on the paper under the camera, the camera sends it to the computer and the computer sends it to a projector, where it gets projected onto the big screen in the lecture hall. This way I can look at my class the class the entire time and I do not have to worry about whether students in the back can read the writing on the whiteboard in front.

The document camera I use can also be set up to display the images it captures on the computer. Then, with video capture software, (CamStudio is an example of one with a free option), you could record a video as you write.

If your department does not have a document camera, you can set up something similar with a webcam, which would be cheaper to buy but produces lower video quality. Set it to look down on the paper. You write your lecture, and the computer records it. Alternatively, your institution may have an instructional technology office that could loan you a document camera (or may even have a more advanced set up).

genetics - Why are female clones more often produced

As a student of biology when ever I come by artificial cloning, I always find examples of females being cloned - Dolly the sheep, CopyCat, Daisy, etc. The only male I could see was Fibro mouse and a few more. What is the reason behind this? Is the male genome more difficult to be cloned? I am specifically looking for genetic reasons or other complications.

Answer

They aren't, anymore. It was a fair guess at the time, but first I think we should define what cloning in this context mean.

Our own cloning tag says:

The process in nature or in the lab by which a new organism is created that is genetically identical to its predecessor.

For animals - I'm going to use Dolly as an example since you do as well - when we say "cloning" we usually mean somatic cell nuclear transfer. This image from Wikipedia sums up the process:

Basically, you take the nucleus of your to-be-cloned animal and put it inside the egg cell from another animal. Dolly was not produced by one animal but by two - a donor and and a surrogate. She was made using mammary tissue (another good image here) from the donor, which is important to note.

Dolly was the only one out of 277 egg cells that made it. This is a hard technique, and we still don't understand a lot of it. With even less information at the time, some prevailing ideas were:

• Maybe there's something special about reproductive-based tissue


• Maybe there's something special about female tissues

Even when using a different technique (e.g. Cumulina), early cloning attempts hedged their bets with those same tissues. That's why Fibro, the first male cloned (from tail), was a big deal - he showed that any tissue could be used, and that reproductive or female tissue wasn't inherently special. You still need an egg and a surrogate, but if you can get the nucleus right it's just as doable.

phd - Details an applicant should include/exclude in an introductory letter to a prospective grad school adviser?

I'm applying for graduate school (PhD in computer science), and I'm considering writing to faculty whose research areas match with what I intend to pursue, to understand:

1. Whether they'd be looking for new students at all in the coming year?


2. If they did, would they be potentially interested in my profile (I know no-one would guarantee an acceptance without me going through the process of application), but it would help to know if they would not be interested at all in me - which would leave me free apply to other schools in which I get a neutral/positive response.

Keeping the above in mind, what would be the best way to introduce myself in the first mail?

• What should be the salutation - I know "Respected Sir" sounds archaic, but was wondering if "Dear Professor X" sounded too informal or not!


• Do I state my credentials (details of where I did my undergrads/masters) first, or do I state my purpose in writing to him/her?


• How to mention my background concisely, without giving too much details, while at the same time not "underselling" myself as a potential grad student?


• I want to give a link to my resume/profile hosted on my website - should I embed the hyperlink, or is it better to write the link in plain text?


• How do I end such a letter - the obvious ones (such as "see you soon" or "till we meet again") being not quite suitable in this case)?

I'm basically afraid of saying too much (causing vexation) or too little (resulting in no response to my missive). I understand that the faculty are accustomed to seeing their inbox flooded with such mails each year, few of which ever get a positive response - which may not always be due to lack of an interesting profile, but the manner in which the mail is worded (Many professors have explicitly mentioned on their websites that they would not respond to generic "Do you have funding" type of queries no matter what the credentials of the student are!).

Though my interest is specific to CS, I believe it would apply to other fields as well. Also, I would be interested in the opinions of both present faculty members (who have to sort through such mails), and past applicants to grad-school (who have the experience of successfully writing to their advisers before applying)...

Answer

I have a list of things you should do from my seniors (Some might disagree):

1. Try not to over-sell yourself. There is a fine line between stating facts about yourself and boasting. Stay on the former side.


2. Try not to mention things and leave them abruptly or incompletely. For e.g., Don't say "I was involved with a project in the University of X where we studied Cancer Treatment." (Thats it). What did you do? Where did it lead? What is the status now? Thats the crux of the information and sadly, that is left out.


3. Have an interesting question or comment in the mail. Merely stating that you read a paper or attended his talk is not enough. Billions of other students will be stating the same. What made you like it? Why was it relevant to you? Side note: Surprisingly, many professors who I mailed have been interested on how I stumbled on his paper.


4. Never ask direct questions that the professor wouldn't like answering (At least in the first mail). Asking him about his funding status isn't the best idea in the first mail. This is true for many reasons: For one, most profs wouldn't like telling you such details without you proving you are worth it (Why would they?). Secondly, your intentions are getting obfuscated. Are you really interested in the professor ( & his research) or his money? If his research was interesting but he couldn't fund you for X years, would you still go?


5. If this wasn't obvious, don't mass mail/mail merge.


6. Be honest about what you say. This includes no exaggeration.



7. Make it short. No one likes reading a billion lines to find out who you are.


8. Emphasize your work and what differentiates you from the rest rather than your grades and scores. Grades and scores (GRE/AGRE) are bonuses (or deal breakers) but they are secondary.

publications - Open versus Blind reviewing process

A question I have been wondering for a while is if there exists an actual proof that a blind reviewing process (i.e. where the reviewers are anonymous, and the reviews not published) is better than an open one (i.e. where the reviewers are not anonymous and/or the reviews are published along with the accepted papers).

Basically, whenever I question the fact that having a blind reviewing process does not guarantee any quality (which, somehow, usually coincides with receiving a poor review for a paper ...), I'm told that anonymity is crucial for the reviewing process. But is there any proof of that? I don't believe there exists any perfect system, but I'm just not sure why does the blind (or even double-blind) one is considered as the best (or the "least worst").

Answer

The 2008 study entitled Peer Review in Scholarly Journals - Perspective of the Scholarly Community: An International Study aimed "to measure the attitudes and behaviour of the academic community with regard to peer review." Some quotes from the summary:

Double-blind review was preferred. Although the normal experience of researchers in most fields was of single-blind review, when asked which was their preferred option, there was a preference for double-blind review, with 56% selecting this, followed by 25% for single-blind, 13% for open and 5% for post-publication review. Open peer review was an active discouragement for many reviewers, with 49% saying that disclosing their name to the author would make them less likely to review.

and

Double-blind review was seen as the most effective. Double-blind review had the most respondents (71%) who perceived it to be effective, followed (in declining order) by single-blind (52%), post-publication (37%) and open peer review (27%).

A 2008 article in Nature (and a correction) discusses the above study but the article is about double-blind review versus single-blind review, and not about blind review versus open review.

How do you prepare for a meeting with a potential masters thesis advisor?

I want to do a thesis masters with a specific teacher in the field of Antennas. I am supposed to meet with him to discuss about this in 2 weeks. I am undergraduate in electrical engineering graduating this May.

How can I prepare for this meeting?What to expect?

I guess I should bring my CV and transcript. Maybe personal projects.

ethics - What should I do if my master's advisor used a figure from my thesis in a publication without citation or acknowledgment?

A year ago, I finished my Master's degree and ended 6 months of working for an incredibly manipulative and demanding supervisor. We started working on a publication of my Master's results, which is awaiting final approval (post-corrections) at the journal we submitted to.

Last week, I read a paper this supervisor had published recently, which had a figure taken directly from my Master's dissertation. Our in-press article wasn't cited, and I wasn't co-author, referenced, or even mentioned in the acknowledgements. No direct reference was given for the figure, but the text surrounding it made it sound as if it had come from another article by my supervisor from last year.

It seems pretty clear to me that this is plaigarism - we worked on this project together, certainly, but the final product was a result of my work and their guidance.

My problem is, I don't know how to deal with it. We are currently co-authoring a paper, so I don't want to cause a rupture. I also plan to continue working in this field, and would like to avoid having a senior researcher and previous supervisor to be angry. At the same time, I don't want them to get away with using my work, and taking all the credit for it.

I will certainly tell them that I feel uncomfortable with how they used my work, but realistically, what can I expect/hope to happen here?

UPDATE - the figure in question is an overview of a simulation model I created, so is pretty much the core part of my Master's work.

zoology - Are there any known examples of animals with air-conditioner type cooling?

Sweating is often poor at cooling, particularly on humans and animals with a lot of hair or fur because it collects on clothes and other coverings, trapping heat in while promoting the growth of potentially pathogenic bacteria. Additionally, sweating leaks out important electrolytes and water.

With that in mind, are there any known examples of animals that mimic an air conditioner's heat pump? In particular, consider a special channel where blood (or even better: a specialized cooling fluid) is pressurized (almost similar to inflammation) and pumped through a fin, then depressurized on the way out.

genetics - The human has 46 double chromosomes or simple chromosomes?

What I mean: does the human cell have 46 of these:

or 46 of these:

Thank you in advance.

Answer

Your first picture shows a chromosome that has been (1) condensed and (2) undergone DNA replication. During G1 interphase (normal cell activity; not dividing), your chromosomes actually do not look like either of the pictures. They look more like a mass of noodles (called chromatin; look at the image provided below); it is only during prophase (step 1 of mitosis, where the cell undergoes division) that the chromosomes condense into the form you have depicted in picture 1. Now, in G1 interphase, you only have single chromosomes. You have 46 of these, which can be grouped into 23 pairs—23 from your father, and 23 from your mother. Remember they aren’t condensed during this stage.

I have also included a diagram of the cell cycle:

In S interphase, DNA undergoes replication, and each of the 46 chromosomes create a double. This double sticks to the original chromosome at a point called the centromere. So long as the two “chromosomes” are conjoined at the centromere, the two “chromosomes” are considered as one chromosome, consisting of two sister chromatids (each like the “single chromosomes” you had previously). Again, in S interphase, chromosomes are not condensed, and look more like noodles than either one of your pictures.

During prophase, the chromosomes look like picture 1. Picture 2 depicts a sister chromatid during prophase (and metaphase), which is considered a chromosome after anaphase (when the two sister chromatids are separated from their centromere). Remember that when the chromatids are not conjoined at the centromere, they are considered each as their own chromosome.

Thus, the human body always has 46 chromosomes. They are “double chromosomes,” as you call them, during S phase of interphase to the beginning of anaphase of mitosis. They are “single chromosomes” from anaphase of mitosis to the beginning of S phase of interphase. As most cells spend the most time in G1 interphase (normal activity), you can say that most of the time their chromosomes exist as single chromosomes. Again, note that most of the time they don’t look like your pictures, except for the times that I mentioned above.

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EDIT: To answer the question in your comment:

If during interphase the DNA is not yet condensed and looks like a mass of noodles, then how can we know that there are 46 chromosomes (single ones in this case)?

During interphase, it is indeed difficult to tell how many chromosomes there are. It is only when they condense that they become visible to the eye and can be observed through a microscope. Chromatin, in its noncondensed form, is considered as euchromatin—that is, true (noodly) chromatin. When it is condensed, it can be referred to as heterochromatin. We can only count the number of chromosomes when they are in heterochromatin form; euchromatin is invisible to us. If we align all the chromosomes present, we will get something called a karyotype. Look below.

(You can see each chromosome in each of the 23 pairs are “double chromosomes.” These chromosomes were likely documented during prophase. Some karyotypes show "single chromosomes," most likely taken during anaphase or early telophase.)

In any case, double or single, we can observe that there are 46 chromosomes at all times. If we see "double chromosomes," we would find 46 chromosomes. If we see “single chromosomes,” we would still find 46 chromosomes. In both cases, we would find 46 centromeres, and ergo, 46 chromosomes.

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References

I don't want to kill any more mice, but my advisor insists that I must in order to get my PhD

When my supervisor pitched the PhD to me, it was all about analyzing "big data". I had BSc/MSc experience in wet-lab biology (mainly culturing cells), however I wanted to branch out into Bioinformatics since I am, and always have been, fairly good at programming in C, and data analysis in general.

I chose this particular PhD because the idea was we take a particular tissue from a mouse, run all kinds of different assays on the same pool of cells, and then create an analysis that would essentially get more information out of the data than any 1 assay alone could tell us, by integrating the data together in clever ways. That was the plan anyway.

What actually happened was that the protocol to get this tissue out of the mouse had yet to be developed, and without the tissue there would be no sequencing, and without sequencing there would be no data. So for the first year I had to roll up my sleeves (figuratively), and learn how to kill a mouse quickly and painlessly, to cut out and purify that 1 tissue I needed for sequencing. Again, in reality, this wasn't so simple. Although you don't/didn't need a licence in Germany/Europe to just kill a healthy mouse and take out some tissue (only to kill it in stressful ways, or if it's a mouse with a special phenotype), I feel you should still ideally be taught. Unfortunately, although other PhDs/Postdocs in my lab work with mice, I couldn't get anyone to teach me at the time, so the whole experience was pretty traumatic. I started off by filling up cages with CO2 (completely) and then putting the mice in, rather than what I now know you should do, which is to slowly increase the CO2. This will forever haunt me. I later learned to do cervical dislocation, which is better for everyone.

However, after I was able to sacrifice and extract the tissue I needed, I started getting asked to do more and more frankly grotesque experiments. Draining all the blood from a semi-conscious mouse. Implantation of electrodes. Cold room experiments. I can think of several more, but it's not really suitable for here. Of course this was all legal and above board - and important science that needed to be done - however I just cannot personally continue doing this sort of work. It all makes me feel slightly sick, and more importantly, I hate myself for doing it. What started off as probably 20-40 mice for the data I needed, is probably now at 500-600. Maybe more. I stopped counting.

But the reality I face now is that there are still 2 more years to my PhD to go, and I really don't/can't continue this for another 24 months. I have explained the situation to my PI, but he tells me quite bluntly - "this is what you are required to do as part of your PhD". On one occasion he said if I didn't do it, that's OK, but "you won't have enough data for your PhD defense."

That is total nonsense of course. I've already published and the data analysis - which I am now spending most of my time doing - has gone great. I'll be publishing some of the tools pretty soon too. The problem is that if I stop killing mice, my boss is going to really make things miserable for me for the next two years - and the end result of that might even be I'm asked to stop working on the PhD. I don't know exactly how or through what mechanism I would get kicked off the PhD, but my boss/PI is obviously a lot more senior than me and he's paying me every month (which he reminds me of, every month), and we both know if I don't kill the mice, some one else is going to have to.

What should I do?

EDIT: Out of respect for the German PhD system, I should point out that my supervisor isn't German - and I'm confident that another supervisor would have handled the issue very differently. Whilst I'm not confident it is an isolated case, I don't think in this scenario there was anything the Institute (or affiliated University) could have done better/differently.

Honestly, the take home message for me is that I wish I had asked this question sooner, had received all of the kind and encouraging words earlier, and then maybe I would have had the courage to do the right thing before it grew into something more difficult. Thank you all so much!

Answer

tonysdg asked in a comment

Can you talk to the department head? Or even better, a university ombudsperson (aka a neutral 3rd party who can discuss your options with you)?

and you replied

I don't know - I'm studying in Germany and I can't speak German.

While it might be a good idea to learn German, you most probably don't have to know German to contact your university's ombudsperson.

Universities tend to be very international environments, and English being the predominant language in middle and western European international research, the ombudsperson is likely to know English and maybe even some other foreign languages. If they don't (or if they don't know English well enough), they can probably get hold of a trustworthy interpreter/translator.

More importantly, I absolutely cannot do anything that results in my PhD coming to an end. If my supervisor gets in trouble, it hurts both of us.

Similar to medical practitioners, priests and attorneys an organization's official ombudspersons are usually required to grant confidentiality to all who come to them for seeking advice or for filing complaints. They might be trained in de-escalating hairy situations of power abuse by superiors in scenarios of dependency like yours. Usually, they will not take any action that you didn't agree to, unless they are required by law to do so (which isn't the case often) or when the situation requires escalation to stop severe harm (e.g., if others are in danger by someone's action).

The exact rules might differ from organization to organization, but it is neither rude nor is there any shame in asking the ombudsperson what rules apply to their role before even deciding whether to confide in them. So if you don't make public that you're going to see the ombudsperson, doing so should pose near-zero threat to you and your PhD project.

Having said that, I will definitely look into it

Please do. Even if your university does not have an official ombudsman or ombudswoman, there might be unofficially assigned persons of trust in the institutes fulfilling a similar role and playing by similar rules. (If there are, again, ask what the rules are before proceeding.)

Your university's website probably has more information on this. If it's a larger university (and by the type of research you do, it probably is) the website and that information is likely available in both, German and English.

You can also ask your head of department, head of institute, the university's headmaster or any other of your boss's bosses, who the ombudsperson responsible for you is. If you ask them, you can (and probably should) do so without mentioning that (and why) you want to see the ombudsperson.

I did a web search myself and found there is an official German organization called "Ombudsman für die Wissenschaft" (ombudsman for science), appointed by the renowned association DFG (Deutsche Forschungsgemeinschaft e.V.). The organization's website seems to be entirely in German, but they do have an English inquiry form for reporting conflicts and suspected violations of "good science" rules / suspected scientific misconduct.

They seem to be more focused on "good science" rules and scientific misconduct investigations than on conflicts, but according to their own examples in these presentation slides, they do consider "Inadäquate Doktorandenbetreuung" (inadequate / unsatisfactory support / supervision of PhD students) a violation of those "good science" rules, not just plagiarism, made up data, skewed results etc.

They also publish a "Liste der Ombudspersonen an deutschen Hochschulen und Forschungseinrichtungen" (list of ombudspersons at German universities and research facilities). I'm not sure how up-to-date that list is, but the people on it are probably still around. If they aren't active ombudspersons any more, they can probably tell you who's in charge of their chair nowadays.

Whether you confide in a local ombudsperson at your university or send an inquiry to the "Ombudsman für die Wissenschaft" organization is up to you. The DFS's white paper that lead to founding "Ombudsman für die Wissenschaft" is explicit about this:

Hochschul- oder Institutsangehörige werden ihre Probleme in der Regel bevorzugt einer örtlich erreichbaren Instanz mit Kenntnis der lokalen Verhältnisse vortragen wollen. Sie sollen dazu aber selbstverständlich nicht verpflichtet sein, wenn sie es vorziehen, sich unmittelbar an den [...] überregionalen „Ombudsman“ zu wenden.

(My translation: University and institute members will usually prefer to bring their issues forward to a locally available entity with knowledge about the local circumstances. Of course, they shall not be required to do so if they prefer to address the [...] supraregional ombudsman directly.)

publications - Should I correct a successfully completed Master's dissertation before publishing online?

I successfully completed my Master's dissertation a while back and I've decided I would like to publish it online to help others and probably print a copy for myself to up on the bookshelf. The dissertation was good but it wasn't perfect. Other than the usual typos, there were a few minor mistakes with how I presented the data which my professor pointed out. Should I correct these things before publishing or is that not the done thing?

faculty application - Is it useful to add excerpts from teaching evaluations in a teaching statement?

Is it useful to add excerpts from teaching evaluations in a teaching statement included in a faculty application?

A fair amount of teaching statements seem to contain some, but since excerpts are typically cherry picked I wonder whether the admission committee cares about them.

genetics - How is the exogenous DNA protected from degradation during bacterial transformation?

During transformation, a bacterium can take up DNA from its environment. A small fraction of bacterial species are known to be naturally competent, meaning that they can engage in this sort of horizontal gene transfer in their natural environments.

As I understand it, naturally competent bacteria carry genes that encode the machinery necessary to facilitate the transport of this DNA across the membrane and into the cell. The exogenous DNA binds to a receptor located on the surface of competent cells, gets fragmented into small pieces, and then one strand is degraded while the other strand is transported across the membrane into the cytoplasm with the aid of a DNA translocase enzyme. Ultimately, assuming a sufficient degree of homology, it incorporates into the host genome via recombination.

During this process, however, the DNA has to be protected from degradative nucleases. I remember reading something about a transformation-specific DNA binding protein that coats the entire length of the DNA strand and prevents degradation. Is it the same translocase enzyme that facilitates movement across the membrane that is responsible for this? Or is there another protein involved?

And then, regardless of which protein is responsible in the case of natural competence, how does that protein get expressed and activated in the case of artificial competence? When we induce competence in the laboratory through one of various methods (e.g., electroporation), the DNA is essentially forced into the cell through openings in the membrane, so no transferase protein is needed. What signals the bacterium, then, to express the protective binding protein? What keeps the exogenous DNA from being readily degraded by endogenous nucleases? Whatever signals induced the expression of this protein in the case of natural competence would seem to be absent when competence is induced artificially, and it doesn't make any sense that the bacterium would constitutively express such a protein.

When citing a journal paper, should I use the online publication year or the print publication year?

I want to cite a paper which was published online (Open Access) in 2012 and later published in a printed journal issue in 2013. Which publication year should be used in the citation?

citations - How to react to your work being cited incorrectly or in a misleading way?

This morning when I opened my email I was very excited to find a Google Scholar update telling me of two new citations from two different sets of authors each to a different paper of mine. As usual, I immediately checked the papers to find out if the authors were praising or criticising my work (or perhaps they found a mistake in one of my papers!). To my surprise, in one case the authors wrote a misleading statement which resulted from stretching quite a lot some of my conclusions. In the other case, the authors simply made an incorrect claim (details below for the curious). It's not the first time this happens to me - I even got one citation completely out of context once. How to react to this kind of situation?

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Details for the curious:

1. 
   
   

   In the first case, the authors cite a paper of mine where I compare two different methods to calculate elastic properties of materials. My main conclusion is that one of the methods converges much faster than the other one with the size of the basis set - in other words, it's computationally much cheaper. For calculations with usual basis sets the first method is much more accurate than the second one, with disagreements between the two in the order of 10% or even 20%. They claim that I show that both methods agree within a 1% of each other, which is misleading at best, because for the second method to agree within 1% of the first one one needs to do a very expensive calculation. That is one of the main points of the paper and it got completely overlooked by the authors.

   
   


2. 
   

   In the second case, the citation is plainly wrong. The authors cite my paper as an experimental work on InGaN semiconductors while it actually is purely computational.

   
   

Do any schools offer teaching or research assistantships via distance education?

I would like to complete an MRes or PhD, but do not live in an area with any schools. I would rather not relocate. I see that many schools offer paid MRes or PhD programs entirely via distance. Do schools sometimes also offer teaching or research assistantships via distance as well?

copyright - Can images with a "noncommercial use only" licence be used in teaching and academic presentations?

Can I use images with a "noncommercial use only" license (such as CC-BY-NC) in my slides, both for teaching and conference talks?

Answer

I'd bet it's probably fine, but there's no way to get a definitive answer without asking the copyright holder (this is one of the weaknesses with the noncommercial Creative Commons licenses). The Creative Commons definition of commercial use is use that is "primarily intended for or directed towards commercial advantage or monetary compensation". Most teaching and conference talks seem pretty clearly noncommercial to me by this standard. But what if someone argues that you're only doing that teaching to earn money? Does the mere fact that you are using this material to help you do your paid job transform it into commercial use, or can you argue that in fact your use was not motivated primarily by earning money? What if you're getting paid an honorarium to give a talk - does that make it even more of a commercial activity? You could end up in all sorts of debates about what the "primary intentions" are, with many borderline cases, and there's no objective way to resolve the disagreement.

The Creative Commons organization does not attempt to settle these issues, but does note that "not all educational uses are necessarily NonCommercial uses, so your use of an NC license may preclude use of your work in some educational contexts". There seems to be no official guidance as to what this is intended to cover. Maybe it is limited to cases such as selling teaching materials, or maybe it is much broader.

In practice, I imagine most people using a noncommercial license would not object to these uses. There is a study of what users have in mind when choosing such a license, which doesn't directly address your issues but may shed light on them. However, it's worth noting that people have in fact had nontrivial disputes over what constitutes noncommercial use, with at least one court decision that disagrees with what I would have predicted.

I can't really imagine anyone would sue you over ordinary teaching or conference talks. The worst plausible scenario is probably offending the copyright holder (and being asked to remove the image), not getting sued. That could be a risk worth taking if you believe that these uses should be considered noncommercial.

Of course I'm not a lawyer or an expert in Creative Commons licenses, and I don't know the real risks, so you should take this whole answer with a grain of salt.

human biology - Why do sneezes come in pairs or more?

I very rarely sneeze just once, usually there's two coming in a row, and I've noticed the same thing in other people and even in animals. Is there any reason for this?

Answer

The very simple answer is that the causal factor or trigger hasn't disappeared after the first sneeze. Sneezing is a reflex, partially autonomous, to clear the nasal cavity of particles that don't belong there. As long as the trigger is not removed, the reflex is repeated.

This is also one of the reasons that allergies that cause sneezing, such as hay fever, continue as long as the factor causing the allergy is present.

note taking - What are the pros and cons of laptops in a classroom?

I simply could not pay attention in a lecture if I brought in a laptop. I always take notes by hand, especially since that's supposed to be better for learning.

A professor of mine stated that laptops are distracting to other students and moved them all to the left part of the lecture hall.

I'm curious, what are the pros and cons of using laptops in a lecture, from both a note taking and teaching perspective?

I would like to teach someday and I can see myself banning laptops (I also hate the typing noise but that's just me).

Answer

I think due to increasing lecture sizes, and in complex or technical courses, having something like a tablet or laptop is considerably useful!

There's something to be said of classroom etiquette, however, in that not everyone is equally courteous. Some big no-no's for most of my lecturers were:

(1) No recording via the built-in camera, especially without permission, and no holding things up and taking photos. People learn in different ways, but we have to standardize the classroom somewhat, because not everyone can idly sit by and concentrate while 10-20 people are holding up their tablets, taking flash photos, or doing something otherwise weird/distracting to copy lecture notes.

(2) If you have the slides up on your personal device, make sure it's the only thing you have up unless otherwise specified. No one wants to see someone elses Youtube, Facebook, etc. during the lecture.

Beyond that it is distracting to hear the tapping of many keyboards vigorously trying to take notes all-at-once. I think that these people do themselves a disservice by taking word processor notes, however, and that to a great extent hand-writing the notes even if you have a personal device helps to enrich you in the material. My personal method was laptop set to slides, write notes on paper. But again, not everyone learns the same way. At that, for some complex courses I constantly search terms I didn't understand or concepts I might have forgotten about so I don't get utterly lost in the process. To me this decreases the amount of hand-raising and review questions.

I think that having some ground rules, and a little talk about common courtesy in the beginning of the term is good. It's penalty enough for some people to get called out for being discourteous in front of the class, so a ban? Perhaps not. And like I said in the beginning, lecture sizes are up there and not everyone has choice hearing/vision, so laptops/tablets help supplement those people who can't see the presentation or can't hear the lecturer.

peer review - Is reviewing papers mandatory?

I am baffled by this question. Elsevier boycott aside, is one supposed to review a paper every time he/she is asked? And somebody will be upset if he/she declines the request to review? Or is this only maths thing?

Reviewing paper is unpaid, while it takes a lot of time and effort (at least for me). As such, I expect someone in editorial board to be thankful if one accepts to review a paper, and move on if his/her request for reviewing is declined.

To be angry with a (junior) researcher for not reviewing a paper is unacceptable behaviour for me. We are not slave.

Note: Until now, I am happy every time I am asked to review a paper.

Answer

No, reviewing is not mandatory, it's just good community service.

When I'm soliciting reviews, as an editor or program chair, I would actually much rather have people who don't want to review simply decline to review. It does mean that I have to search for more reviewers, but it's much preferable to getting low-quality reviews or no review at all.

Moreover, there is always a limit to the amount of service that one should be expected to do. If you're reviewing a good amount of papers (see discussion in this question about how much is enough), you should feel free to triage. Just be polite when you decline: even with things you don't want to deal with, it's usually better to simply say "I don't have time right now" (true enough) than to offend a person by completing the sentence with something like "... for your crappy journal" or "... for this horribly tedious-looking paper."

Of course, there is always the possibility of encountering an ego-centric jerk on a power-trip, but life is too short to spend all of fearing that you might encounter such.

etiquette - Is it appropriate to drop by another university's professor's lecture to talk about research afterwards?

There is a professor at a university different from the one I study in, who I like to do some research with. I emailed her and did not receive any answer even after sending a follow-up email (a week after the first email). I knew her class schedule, but not her office hours. I thought about going to where the class meets to talk to her after her lecture (introduce myself, try to remind her of the email and express my interest in working with her over and ask her to read my CV that I emailed to her, or arrange some time to meet me and discuss about possible opportunities) .

Since I am not a student at the institution where she works and given the nature of my inquiry and the fact that she didn't answer my emails, I thought this might not be appropriate. I wanted to ask your opinion on whether you think there is a way for me to go and talk to her without it being inappropriate. (I thought about emailing the TA of the class and asking about the office hours of the professor, but I doubt if that's any better.)

Answer

Appropriate should even be, effective less.

You stated you knew her class schedule, so if she is free after the lesson you may have success to speak with or, better, to ask her when she can dedicate you some minutes.
It can be appropriate if you will be polite, clear, specific and concise.

E.g. I need 5-10 minutes to speak about xxx. I read those papers of yours (a,b), I find interesting yyy and I would like to work on it maybe in the zzz development. I'm currently student/phd/whatever in the ttt university. Is there any way to arrive to work on this subject with your group? What can I do?

There are, by the way, other ways in which you can contact her.

Secretary of the group or of the department. Each professor belong to group(s) and/or department(s). Find which, and call the secretary. (Again concise). Ask how to contact that professor.

Conference or Talk. If you have the time and the occasion it may be more effective if you find an open event in which to meet, e.g. if she takes part on a conference, or she has a talk accessible for you. In those occasions people is usually more open, and has already reserved time to speak.

Professor of your university of the same field. If you can access to some professor actually enrolled in your university in the same field of the one you want to contact, you may ask him/her information about that professor and how to contact. If they personally know each other, you can ask to be introduced too, or at least to send her a mail.

Her Office. Knock the door and ask when she has some time to speak with you about xxx...

ps> She may have some time to dedicate to students... you may try to go in that time, but you will be after the needs of her students.

graduate school - MS student in CS meeting advisor for the first time in person (USA). What should I wear? (male)

I am meeting him in his office on campus. I am a master's student in computer science. I figured that suit and tie would be too formal as it isn't really an interview since I already have the position. If I were just regularly attending grad classes, I may wear T-shirt, shorts and flipflops (during the summer/fall) and jeans, polo, light jacket, sneakers during the cooler months. Should I wear khakis, dress shoes, and a nice button down shirt? Ties? Yes or no? I want to make a good first impression but not have it look like I'm trying too hard.

In addition, he invited a few other grad students to his house for a cookout next weekend. What should I wear to that? I'm guessing more on the casual side but should I go in shorts/t-shirt or jeans/polo?

Answer

I've never even visited any universities in that part of the country, but I think your comfortable shorts/T-shirt should be perfect for a cookout in any part of the country. For the first impression, make sure you choose something comfortable. I think dress shoes would probably be overkill. However, a short-sleeved button shirt (i.e. tailored shirt with a collar) would be a nice touch. Do you have some sort of sports shoes? That would be a happy medium between dress shoes and flip flops. If not, I'd go with the dress shoes.

If you ask what food to take to the cookout, I'll chime in on that one too.

graduate school - Emails being ignored by University

I am a graduate student in the U.S., specifically California although I am not sure it matters.

After three months in the American university system I am almost convinced there is an organizational level plot to ignore my emails, or people's emails in general. From Health Centre personnel to personal advisors it seems no one manages to answer an email.

Over the course of four weeks I emailed this employee at the Student Health Centre, not once, not twice, but four times. Each time I would receive an automated response "We are very busy bla bla bla will reply in 48 hours", and each time I patiently waited a week without response...After a month I decided that the only way to get an answer to my question was to corner said employee in their office and ask them!

Later during the quarter, I attempt to get in touch with my advisor. I get an half baked reply to my first email (it seems they couldn't be bothered reading past the halfway mark), and then nothing to my several other emails. (Just to be clear, I am not spamming anyone. We are talking about one email per week at most) As it turns out, said advisor went on sabbatical leave between my first and second email - and didn't bother to inform anyone or set up automated email responses...

Even later during the quarter, I get a new advisor. I email said advisor asking to set up an appointment since they need to sign one of my forms. As you can imagine...nothing, no reply, nada. Send another email a week later....nothing, tumbleweeds in my inbox.

Over the four years of my undergraduate degree, I think only one of my emails did not receive a reply. Given that my undergraduate was in the U.K., is there something about the American system that makes people not reply to their emails?

I am aware that most graduate lecturers have outside jobs, but it seems even in person some staff have little to no clue as to what their task is, they are slow in getting back to you, and are not helpful in general.

I was just wondering if the issues I am encountering are related specifically to my university of if it is an American issue?

Thanks!

Answer

Is there something about the American system that makes people not reply to their emails?

I've spent my education and career in the American system (including California) and haven't had any particular problems with people being unresponsive to emails. This is probably specific to your institution and/or the individuals involved.

That said, in your academic life you will certainly encounter more people who don't respond to your emails, so you need to be comfortable with other forms of communication, and to have strategies to handle such cases:

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  Call by telephone

  
  


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  Visit in person

  
  


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  Talk to an administrative assistant

  
  


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  Find another person who can help with your issue

  
  
  


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  Escalate to a superior

  
  


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  Ask a colleague if there is a particular reason why the person might be unreachable (e.g. sabbatical, leave of absence, vacation, has quit, medical problem, is dead, etc)

  
  

And as mentioned above by Anyon, it is also an important skill to write emails that minimize the effort needed for the recipient to read, comprehend, and respond. This also will improve your chances of a useful response.

research process - Following literature - What is a good configurable publication notifier?

I would like to keep up to date with public literature in my research field. All relevant publications are of too big a volume to follow and so the problem invites some automatic mechanism of filtering and notification.

Do you know of any good mechanism (desktop\online application etc.) that could be configured to alert on new publications according to specific criteria?

Three criteria that I would think would be very useful in such a mechanism are :

• Follow by researcher name - I would like to know of any new publication Prof. X was involved with.



• Configurable citation filter - I would like to know of any new publication which cites any of Prof. X papers or a specific one.


• And\Or\Not keywords - I would like to know of any new publication that has both keywords A and (B or C).

Do you know of such existing app? Any recommendation to such (or similar) applied functionality would be greatly appreciated.

Thanks!

Answer

Your institution (for example its Harman Science Library) and many others have the database product Web of Knowledge. Precisely the alert criteria that you described, and more, are available through that product.

The selection of journals covered in its flagship collection, Web of Science, is curated with the goal to cover all of, and more than, the core literature of all scholarly fields, naturally without attempting to cover all journals in existence. Alerts in Web of Knowledge can also simultaneously search up to a dozen other collections including Medline, depending on your institution's subscription. You can see the collections in the subscription that is available to you by choosing the "Select a Database" tab. You can browse and search the journal lists for the various collections.

genetics - How to turn teosinte into corn?

If I want to turn teosinte into corn, using ancient methods like the Native Americans did, then how much time it takes, and what do I have to do?

For the sake of the question, let's assume that time is not a problem for me. Say I live 10,000 years. But of course, I prefer to have maximum efficiency. If I can get the result in 3,000 years, that's better than 5,000 years.

Answer

Initially I didn't like this question very much, but I changed my mind when I realized that there is actually ongoing research to do exactly what you propose in order to study just how long it takes to get maize from teosinte.

John Doebley at the University of Wisconsin-Madison has a project ongoing to breed 30 generations of teosinte to be more "corn-like" on a single parameter, the length of the lateral branches.

The first challenge is to find a strain that isn't already contaminated by modern maize - that isn't completely possible, but he selected a strain that has minimal hybridization. You would have to do the same.

Second, you have to plant someplace isolated to further prevent hybridization. Dr. Doebley has a plot in Hawaii for this purpose.

Note that even though this scientist is only selecting over 30 generations, he doesn't anticipate that much of a change (i.e., he doesn't expect to have anything like corn when he is finished), and he is only selecting on a single parameter and furthermore, this parameter was chosen specifically for being easy to score, showing a lot of variation in the existing population, and influenced by a known single gene. Many more generations would be expected to get a product like modern corn. And even domesticated corn has changed significantly over thousands of years of agriculture.

For this answer, I simply reference the project site that I linked above, but in case that link goes dead, here is some literature that the project cited directly:

Beadle, G. W., 1977 The origin of Zea mays, pp. 615-635 in Origins of Agriculture, edited by C. E. Reed. Mouton, The Hague.

Beadle, G. W., 1978 Teosinte and the origin of maize, pp. 113-128 in Maize Breeding and Genetics, edited by D. B. Walden. John Wiley & Sons, New York, NY.

Doebley, J., A. Stec and C. Gustus, 1995 teosinte branched1 and the origin of maize: evidence for epistasis and the evolution of dominance. Genetics 141: 333-346.

Doebley, J., A. Stec and L. Hubbard, 1997 The evolution of apical dominance in maize. Nature 386: 485-488.

Doebley, J. F., A. Stec, J. Wendel and M. Edwards, 1990 Genetic and morphological analysis of a maize-teosinte F2 population: implications for the origin of maize. Proc. Natl. Acad. Sci. 87: 9888-9892.

Iltis, H., 1987 Maize evolution and agricultural origins, pp. 195-213 in Grass systematics and evolution, edited by T. Soderstrom, K. Hilu, C. Campbell, and M. Barkworth. Smithsonian Inst. Press, Washington, D. C.

Wang, R.-L., A. Stec, J. Hey, L. Lukens and J. Doebley, 1999 The limits of selection during maize domestication. Nature 398: 236-239.

Wilkes, H. G., 1967 Teosinte: the closest relative of maize. The Bussey Institute, Harvard University, Cambridge.

Wilkes, H. G., 1977 Hybridization of maize and teosinte in Mexico and Guatemala and the improvement of maize. Econ. Bot. 31: 254-293.

arachnology - Identification of a small flat bug

So for the last few days I have been noticing these small bugs in my bathroom -- they don't appear frequently, and I see them once or twice a month. The characteristics and behavior I observed are as follows :

• They RARELY move around.


• They are extremely flat, like totally flat


• Some are small, some are big (but still the overall size is small)

Below are the pictures :

I cropped this picture since the original size was 5mbs and the limit was only 2. If anyone wants the original image I can inbox them .

Appreciate any help or suggestion with this :)

EDIT 2 I am adding another image for greater clarity , hope this helps

Edit 3

Location: Karachi Pakistan.

Size: 0.2-0.4 cm

As for nearby animal populations: No not much, just the usual street cats.

For a few months these bugs were gone until recently they have started to appear in the bathroom, like I see them 2-3x a month just sitting still for hours and hours.

Answer

Definitely an arachnid and mite (subclass Acari), and very likely a member of the order Parasitiformes, of which there are more than 100,000 species!!

Your specimen brings to mind the family Argasidae (the "soft ticks" -- so called because they lack a hard scutum).

Specifically, your specimen reminds me of Argas reflexus, the pigeon tick. (which has been found to be an increasing pest and human concern in urban settings).

^{Credit: Milan Kudlička}

Based on the size of your specimen, I would guess you're looking at a non-adult stage.

However, this is just a guess, and I will try to explore other species in this general group to see if I can come up with a better-supported guess.

(By the way: any pigeons living nearby??)