funding - What are some good practices for applying to the NSF Graduate Research Fellowship Program?

1. Is it possible if I could get 4 letters of recommendation?


2. How far in advance should I notify those who are writing my letters?



3. Does activity on sites like Quora, Stack Exchange, and Reddit's AskScience (as well as a personal webpage/blog of one's research) count as public outreach?

Answer

I think it's helpful to understand how NSF graduate research fellowship applications are reviewed. [Caveat lector: This answer was written in 2012; the application requirements and the evaluation procedure have both changed significantly since then. I strongly recommending consulting someone who has been on the review panel more recently.]

Each application consists of the following components: a 2-page personal statement; a 2-page description of past research; a 2-page description of proposed future research, transcripts, and exactly three recommendation letters. If you attempt to send four, NSF simply refuses the fourth letter; on the other hand, if only two letters arrive by the deadline, your application is rejected without review.

All 10000+ applications are reviewed in a single three-day physical meeting. Applications are split into 30+ subject areas, each considered by a separate review panel. Each panel has 20-30 members and reviews 300-400 proposals. (All these figures are ballparky; panels vary in size depending on the number of applications.)

Before review, applications are divided into levels based on the applicants' time in graduate school: None (30%), less than a semester (30%), less than 12 months (30%), and more than 12 months (10%). All level-1 applications are reviewed together, then all level-2 applications, and so on. Expectations are significantly higher for more experienced applicants. The precise expectations obviously vary by discipline, but in computer science, pre-students need a credible research plan, early students need publishable results, and older students usually need multiple publications. The "more than 12 months" level is only for people with extenuating circumstances, like a significant change of field.

The 12-month limit counts time that applicants have actually been registered, not time since entering their first graduate program. So a student who started a PhD program in August 2011 and does not register for classes this summer will still be eligible in September 2012. If you want to apply in your second year, do not take classes your first summer.

Each review consists of a "letter grade" (excellent, very good, good, fair, or poor) and a narrative evaluation of "Intellectual Merit"; a letter grade and a narrative evaluation of "Broader Impact"; and an overall numerical score. The panelists use the numerical scores to cluster the applications into four categories: Yes (10%), Maybe (25%), Honorable Mention (5%), and No (60%). NSF uses the narrative evaluations to decide which Maybes get fellowships and which get honorable mentions.

Every proposal is reviewed twice, the proposals in the No pile are retired, and each of the remaining proposals is reviewed a third time. Thus, each reviewer reviews roughly 35-40 proposals. On average, each reviewer spends 20-30 minutes on each proposal. That's just enough time to read each of the documents once, make a snap judgement, and then assemble a narrative review from a pile of boilerplate sentences. It's brutal, especially because most applications are strong.

So anything you can do to make your reviewers' life easier will work to your advantage. Every component of your application should directly address each of the two main review criteria. In particular, all three statements and all three recommendation letters should include a paragraph describing intellectual merit, starting with the phrase Intellectual Merit in boldface type, and another paragraph describing broader impact, starting with the phrase Broader Impact in boldface type. Both paragraphs should say something specific, substantial, and credible.

For security/privacy reasons, the review panel does not have internet access; reviewers are not even permitted to use their own laptops. So if you use your StackExchange participation as an example of broader impact, be specific about how you participate; the panelists can't look up your answers or your reputation.

Another point to keep in mind is that reviewers are probably not experts in the applicant's chosen subdiscipline. An application by an aspiring astrophysicist studying planetary climatology (to make up a random example) might be reviewed by a high-energy astrophysicist, an expert in planetary formation, and a string theorist. Yes, your statements must include enough field-specific technical detail in your statements to be credible, but the overall goals and merits of your proposed research should be clear to a broader audience.

For fine details, it's always best to talk with faculty in your field who have experience with NSF fellowship winners, either as an advisor, a reference, or a panelist. (The most useful letters read "I have written reference letters for x NSF fellowship applicants, of which y were successful; I would rank this student among the top z of those fellowship winners.") It's also a good idea to talk with past fellowship winners in your (target) department; ask to read their applications and their reviews.

See also NSF's advice.

teaching - How to motivate students to debug their work independently

For the last few semesters, I have taught a graduate-level course (mixture of Master's and PhD students) that has a very substantial data analysis component in which every assignment involves analyzing data based on what was covered in the prior 1-2 week's worth of lectures. The prerequisite is my university's introductory statistics course, which teaches students basic statistics (t-tests, z-tests, linear regression, etc). We recommend a particular statistical language to use and provide coding suggestions in that language, but students are also free to use whatever they feel most comfortable using.

Increasingly, I am finding that students in the course rely on me to solve every coding error or problem they encounter, and in many cases, the top hit of a Google search for the error/problem suggests more or less what I would have as well. Some students are "repeat offenders" in that even when I show them how to use Google to look for debugging help, they still come to me with Google-able questions.

I want to be sympathetic to students who may not have much statistical computing experience beyond the introductory statistics course we teach, but at the same time, I feel that graduate-level students need to be able to solve these sorts of questions on their own. In my field, you cannot survive without knowing how to write code to analyze data, and part of that is knowing how to debug your code when inevitable errors/bugs arise.

Has anyone run into this sort of issue before, and what, if anything, helped?

ethics - Is it ethical for a lecturer to require students to purchase an online learning kit where kit is used for course assessments?

I am taking a course in a may-not-be-top-but-still-decent university located in North America. The course lecturer forces us to pay for an online learning kit from Pearson by adopting all the graded quizzes provided in that learning kit.

That is, if one refuses to pay for the learning kit, he or she will have no access to all the quizzes, which in total constitute 20% of the final grade of that course. Moreover, all the text completion questions are basically exactly the same sentences copied from the eBook. Therefore, if you simply pay for the learning kit (~$50), then you will have a hard time doing the quiz as compared of those who buy the combo including the eBook (~$90).

In summary, if

• you pay ~$90, during every quiz, simply do CTRL+F, you can always find the exact sentence in the eBook, and hence you can get nearly full marks.


• you pay ~$50, you can access the quizzes, but you may have to search somewhere else and spend more time on the quizzes.


• If you pay nothing, the 20% marks are gone.

I, as a victim who unwillingly paid $90, find it irritating and unethical, as I feel this is some sort of a coalition between the lecturer and the publisher. I understand that some lecturers do have recommended textbooks as well, but they are not mandatory! That is, if I can learn that course well by other books, I am free to do that. If I didn't buy the book and hence screwed the course up, that is my own responsibility. I cannot blame any one for that. But this lecturer's deed actually bans the students who do not pay for the learning kit from the quizzes.

Is this ethical? Wait, is it even legal? How may I fight for our rights as students on this issue?

Answer

I'll start with

How may I fight for our rights as students on this issue?

For one, politely express your displeasure to the professor.

Some professors aren't in tune with the cost of textbooks, and may not realize what a burden it is to shell out $90 for their course, when it's $90 that you can't recoup by selling back the text, or avoid by using the library's copy of the text.

They may even think they're doing you a favor by offering this "interactive" system, not realizing that you don't find it useful.

If the professor isn't interested in hearing what you have to say, you can further express your displeasure in the end-of-course evaluation (my university's specifically ask about the textbook) and possibly in a respectful letter (signed by your classmates) to the department chair.

Is this ethical? Wait, is it even legal?

As the other answers have pointed out, it's not universally considered unethical or illegal.

As unpleasant as the result is in this case, it probably would not be a good thing to set too many bureaucratic rules on what textbook or other educational resources a professor can assign. Given that the cost of tuition is usually many times higher than the textbook price, it is generally desirable for the professor to assign the textbook that will (in his/her opinion) offer you the best educational experience and therefore, the best return on your tuition investment.

Of course, students tend to appreciate when the professor can find a low-cost option that is also educationally sound. But that's generally considered a bonus, not a requirement.

In this case it sounds like the extra content doesn't contribute anything useful to the educational experience - in which case, you should let the professor know. (Again, politely and non-combatively.)

I also want to point out that requiring "bundled" course content that goes along with the textbook is closer to assigning a required software package (which, unlike textbooks, you can't buy used or re-sell) than assigning a textbook. I agree with you completely that it's substantially different than being asked to pay for a textbook.

For every class I've ever taken that required specialized (non-free) software, my university installed the software on my laptop for me for free (given that I was registered for the course in question). In most cases, instructors try to use free software or software that comes with a free student license, because they realize that a software purchase is different from a textbook purchase. Or they'll provide the software on lab computers that students can use during set hours.

Imagine if you had to buy a new non-refundable software package for almost every class you were enrolled in, including buying the same software multiple times for a sequence of intro classes on a subject.

Yeah, it's a waste of money, but your professors might not see that unless you point it out.

citations - Copy pasting sentences from abstracts of other papers for describing related work

This topic has already been described to some extent, e.g. here:

Is verbatim copying several paragraphs of text with citation considered plagiarism?

But I do no think that it has been completely discussed, especially in the context of related work and abstracts.

When I am writing the section about related work in my papers, I tend to describe the work of each other related researcher in a few sentences with my own words and referencing their papers. However, in a current paper that I am writing I have realised that the abstracts of more than a few papers that I want to mention are so well written and are so concise that I cannot do any better. Writing my description would be just a waste of time, and result in a less concise text.

So I am thinking about copy-pasting two or three sentences from the abstract of each referenced paper. And possibly adding, removing, or changing a word or two that may not be relevant in the context of the paper that I am writing, so it's not really a plain copy paste.

I have read that it may be a good idea to put quotes, but I find quotes, especially their immoderate use, as bad style.

Can I get in trouble for this? I would not go that far in considering anything of this as plagiarism, as the work is referenced and I am not taking credit for someone else's work.

Personally if one would do the same with my work, I would not be concerned at all, on the contrary, as long as not more than a few sentences are taken and the work is properly referenced, but you might have a different view.

Answer

So I am thinking about copy-pasting two or three sentences from the abstract of each referenced paper.

This seems absolutely appropriate, as long as you quote them correctly. Which brings us to:

I have read that it may be a good idea to put quotes, but I find quotes, especially their immoderate use, as bad style.

It is not only a good idea to do that, it is required. You need to make explicit that those are verbatim copies. The semantics of copying text from a paper and summarizing the key points yourself are different for a reader, and you need to make this difference explicit by demarking which parts you have taken in verbatim.

Can I get in trouble for this?

Yes.

I would not go that far in considering anything of this as plagiarism, as the work is referenced and I am not taking credit for someone else's work. Personally if one would do the same with my work, I would not be concerned at all, on the contrary, as long as not more than a few sentences are taken and the work is properly referenced, but you may have a different view.

This reminds me a bit of a few high-profile cases of plagiarisms that were going around lately in the german-speaking areas. Often, the excuses presented by the accused authors were similar ("hey, the text I copied wasn't really that important - it was just the introduction after all!", "I cited it anyway, I just did not make clear that the text is actually copied from there", etc.). These excuses never fly. Be rigorous with your handling of sources. Everything else is just playing with fire.

human biology - Is the 'fluttering feeling' when under stress neurological or physical?

I'm sure that everyone is familiar with the sensation commonly known as "butterflies in the stomach". It is commonly experienced during periods of anxiety or stress (e.g. before high stakes job interviews or roller coaster rides) and apparently (after my web research) often felt in new romances without an obvious cause of tension.

However, whilst my googling did turn up an inordinate amount of rubbish regarding love-sicknesnes, I have been unable to find even a suggestion as to a mechanism as to the physiology behind this feeling. Is it a sensation of physical change in the stomach (some sites vaguely mentioned the restriction of blood flow to critical organs but it was entirely unsupported) or is it neurological in nature?

Answer

If you want to find out about the the relationship of this response to romance in particular, there's a pretty comprehensive research paper called Love is more than just a kiss: a neurobiological perspective on love and affection[1] which reviews a lot of the work done in this area. This is pretty good as it discusses all the different stages including breakup.

Essentially, there seems to be a lot factors at play which elicits various responses through different stages of love.

In terms of anxiety and stress, initially, there's a large increase in levels of cortisol[2] and a marked drop in serotonin. Depletion of serotonin is found in many psychiatric conditions such as depression, anxiety and panic disorder. There's even been evidence that these levels at early stages of love are similar to those suffering with OCD. Obviously, the 'symptoms' of early love are quite similar to these conditions so it's hypothesised that this, at least in part contributes to those feelings.[1]. It was found that these levels are back to normal in 12-24 months.

The elevated levels of cortisol contribute to the feelings of stress but this hormone has also been shown to promote attachment.[2].

There are also changes in activity of the amygdala. Responsible for regulating a lot of emotions such as fear and sexual drive, the amygdala can activate autonomic nervous system responses through the mechanisms which Kevin described.

There are a bunch of other things at play here including dopamine, oxytocin, vasopressin, nerve growth factor (NGF), testosterone, increased activity in the hypothalamic-pituitary-axis (HPA) and variations in activity in other areas of the brain.

Again, that first reference gives a pretty comprehensive overview of the mechanisms involved.

To answer the actual question about the fluttering feeling, as Kevin mentioned, it's hypothesised that this is caused by reduced peristalsis in the intestines as a result of sympathetic stimulation. I don't have an academic reference for this but there are plenty of non-academic sources that talk about it (a quick Google of butterflies in stomach and physiology will probably show them).

A lot of the mechanisms noted above can contribute to, sensitise for or cause sympathetic activation. For example, panic attacks and anxiety, mentioned earlier with the serotonin relationship, can cause the same feeling.

1. 
   

   Boer, et al. Love is more than just a kiss: a neurobiological perspective on love and affection. Neuroscience. 2012. 201:114-124.

   
   


2. 
   

   Marazziti, et al. Hormonal changes when falling in love. Psychoneuroendocrinology. 2004. 29(7):931-936.

   
   
   


3. 
   

   Guyton and Hall. Medical Physiology. 11th ed. Elsevier Saunders.

   
   

etiquette - What to do when you discover a mistake in the archived copy of your PhD thesis?

I've just defended my PhD in mathematics and started a postdoc. While working on an improvement of one of the results of my thesis, I realized that there are several minor mistakes and a big bug in a proof that invalids a minor result in the thesis (about 3-4 pages out of 110). Unfortunately neither I nor my advisor or referees figured it out the mistake. Though the result is minor, it is announced in the introduction and the manuscript is on-line on an ArXiv-like server, so that I could publish a new version but not cancel the one on-line.

What is the best thing to do? Upload an errata? Upload a "revised" version of the thesis? Publish a "revised version" of the thesis on my web-page?

Can this damage my future career, making me look not "reliable" as a researcher?

zoology - What is this droplet of liquid that comes out of a mosquito?

I have been looking at pictures of different species of mosquito and several times I came across pictures where the mosquito seems to be secreting some kind of fluid.

In the pictures one can clearly see that the mosquito both secretes transparent fluid and blood.

• What kind of fluid is the transparent stuff? Could it be plasma from the host's blood?



• Why does the mosquito do it?

Answer

Short answer
Excretion of blood and urine may prevent overheating by reducing body temperature through evaporative coolong (akin to perspiration). Excretion of blood and urine also concentrates the ingested blood.

Background
Female Anopheles mosquitoes seek blood for nutrients necessary to egg production. The cold-blooded insects may excrete some freshly ingested blood as a way to avoid overheating when consuming blood as warm as 104 degrees Fahrenheit (40°C). It is thought that excretion of a droplet of fluid aids in evaporative cooling, similar to perspiration in humans, to reduce the animal's temperature. The excretion of urine may serve a similar purpose, namely avoiding overheating during blood ingestion. By keeping the urine or blood droplet attached to the abdomen, excessive heat can be eliminated (Lahonde & Lazarri, 2012).

In the malaria mosquito (Anopheles stephens) the excretion of fluids has been investigated in detail. Females ingest blood meals that are equivalent to more than twice their unfed body mass. Engorged animals can fly only with great difficulty, making them more prone to predation. The blood meal serves primarily as a source of protein for egg development, but it also contains considerable amounts of unwanted salts and water that threaten haemolymph homeostasis. To counter this, a rapid natriuresis and diuresis commences even before the blood meal is completed, and ∼40% of the imbibed plasma volume and salt are voided within 1–2 h of feeding (Coast et al., 2005).

<sub>References

- Coast et al. Exp Biol (2005); 208: 3281-91
- Lahonde & Lazarri, Curr Biol (2012); 22: 40–5</sub>

<sub>Further readings
- Do mosquitoes urinate on you when they bite you?</sub>

travel - What are the benefits of getting a PhD in statistics?

I've been working as a statistician in the marketing world for two years, and I have an M.S. in applied math. I want to change industries a bit (maybe epidemiology or engineering) and I also want to live overseas (ideally, a job where I'd live in one country for a few years and then move on to another).

So, my question is: to accomplish these life goals, does it make sense to get a PhD? Or, is there some other route that would be more beneficial?

Answer

A doctoral degree is a credential signifying largely that you are capable of doing independent research at the highest possible level. It is not, in an of itself, a ticket to working in a particular industry or in a particular location any more than a bachelor's or a master's degree. In fact, PhD holders may have substantially more challenges in those aspects, because the additional qualifications make them unattractive for many positions in conventional businesses and industries. (You are unlikely to find a PhD working in a sales division of a multinational conglomerate, for instance.)

The reason to get a PhD is because you are interested in problem solving and doing original work. If this doesn't describe your motivation, I would recommend against pursuing a graduate degree, because it will be a very long few years of your life which are not guaranteed to achieve the objectives you've laid out.

code - Is it plagiarism to use an online tutorial as the basis for completing a programming assignment?

Let's suppose that you were assigned a programming project, which is considered from your teacher/professor, not easy. However, you manage to find an online tutorial, that guides you step-by-step through the process needed (so the source code you have written doesn't have much difference from the one on that tutorial).

The final solution is based on this tutorial, but you have also added your own information, corrected some minor errors, etc. I don't know if this matters, but you know exactly what every single line of your code does, you are able to explain and answer complex questions, etc.

Is that considered plagiarism, and if yes, why? If not, how can somebody support that on a teacher/professor?

Answer

Using online material to learn is not plagiarism.

This is a great way to learn (e.g, worked examples and subgoal labeling) and is a common way for instructors to try to teach something. Am I plagiarizing every time I use a common design pattern? No.

However, copying and pasting code from online is. It gets a little fuzzy when working on simple assignments that can be found easily online because it could be weakly argued that you are recalling it from memory. I would definitely not be concerned about this, especially if you think you understand the code and were not trying to cheat.

If you're genuinely concerned, you could even discuss it with your instructor and they might realize that they are not spending enough time discussing a certain process or giving you enough practice material.

EDIT: Based on your clarification in the comments, if this is something more specific/arcane and not a tutorial on something general, then just cite it. I have done this in my programming courses before. I added a comment at the top of my code linking to the material I referenced and gave a very brief description of what it is and how I used it.

microbiology - Plasmid choosing

To design a experiment in feeding of C. elegans. It has to choose a plasmid vector to insert the gene of interest that can feed to C. elegans. Many paper are using pL4440 for the feeding vector, saying it is the first used in feeding C. elegan and because of the two T7 promotor, so it easy to perform the experiment. There also paper saying T3 promotor is not fit for feeding in C. elegans. I am curious about why T3 is not fit? and because I didn't see many paper using other vector to perform the feeding experiment in C. elegan. So I wonder that is it ok if I choose a plasmid that has two T7 promotor and is used to express in worms like pLT61, will it influence the feeding or the efficiency so that people use pL4440 for feeding in C.elegan? Or is people use pL4440 vector because it is specific designed to the feeding experiment of C. elegan? Thank you!

career path - If I abandon my PhD program, will it prevent me from continuing elsewhere?

After some bad experiences in a master's program, I decided to become a PhD student in the same program. My plan was to finish a paper and leave as soon as possible, meanwhile earning the recommendations that my bad early experiences prevented. That's basically been the situation for a couple years now - longer than I ever expected. At this point, I'm finally finish my projects and I've presented at a couple conferences. I genuinely like the professor I'm working with now. However, I never intended to specialize in this research area; the idea of doing my PhD in this area is very disappointing to me. And (selfishly?), I very much want to move to a new institution.

At this point, I'm not sure what to do. My ideal situation would be to finish my current projects and move to a new institution to work in a field I was more excited about. However, I'm afraid that if I reveal my desires the professor I'm working with will try to sabotage me. I'm also concerned that leaving now will look strange on a graduate application: why admit a quitter? I'm also starting to feel a little old to be starting a new program.

I'd really like to just be done with all this, but the question I keep asking myself is, "Why get a PhD in something you're not interested in?" Maybe, though, there are good reasons.

I'd appreciate any advice you may have.

botany - How do plant galls form?

I am curious how Gall Wasps, bacteria and other organisms induce galls to form.

Specifically, what chemicals induce gall formation?

Answer

I'd like to add to Amy's excellent answer.

Generally, galls are induced by the forced accumulation of plant hormones at different levels to those naturally maintained by the plant, in a localised area. Usually the hormones targeted are auxins and cytokinins which are both involved in the regulation of normal growth patterns; disrupting these patterns leads to disorganised growth, or in some cases a differently organised growth. There are several methods that I know of:

• The gall inducer directly synthesising the hormone.


• The inducer chemically inducing the host to synthesise more hormone.


• The inducer chemically inducing the host to transport more hormone to the site.


• The inducer genetically modifying the host to cause synthesis of the hormone in the host cell.

Some examples of the different methods:

Direct production: The bacterium Pseudomonas savastanoi directly produces indole-3-acetic acid (IAA, a type of auxin). This direct accumulation has been shown to be responsible for gall formation in oleander knot disease. Some key papers: Palm et al. 1989, link 1; Glickman et al. 1998, link 2.

Chemical induction of transport: Root-knot nematode worms induce root gall formation in clover. They probably do so by producing flavonoids which up-regulate transportation of auxin into cells (see link 3).

Genetic induction: As already mentioned by Amy, Agrobacterium tumefaciens is a very well characterised example of induction by genetic modification, however, A. tumefaciens is also known to directly produce auxins in large quantities. Another interesting example of genetic modification is in viral gall-inducers. They are not so well studied as their bacterial counterparts, but in some cases (e.g. white clover mosaic potexvirus) it has been shown that virus infection initially leads to a complex change in the types of cytokinins produced by the plant (e.g. Clarke, 1999; see link 4). It has also been shown that if cytokinins are applied exogenously (i.e. injected into the plant) after viral infection, that the virus cannot replicate well. This suggests that the virus is manipulating the host's hormone production in a complex way.

There is also the interesting case of Rhodococcus fascians, which seems to produce a chemical which is not structurally similar to any known cytokinin, and yet has similar effects (Goethals et al., 2001; link 5).

You specifically asked about gall wasps, but unfortunately this mechanism is, as far as I can tell, not completely known. It is speculated (e.g. in Shorthouse & Rohrfritsch, 1992; link 6) that this involves direct injection of phytohormones. The evidence to support this is simply that other insects, particularly aphids, excrete phytohormones in their salivary sheaths when they inject them into a plant.

Finally, I'll just say that the fact that gall induction is carried out by bacteria, viruses, nematodes, fungi and wasps, and that some mechanisms are shared across all those associations, demonstrates the ability of evolution to converge on the most elegant solution to a problem. It also shows that plants are so great, everyone wants a piece (but I would say that, because I'm a plant biologist).

References:

1. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC209694/


2. http://apsjournals.apsnet.org/doi/abs/10.1094/MPMI.1998.11.2.156



3. http://www.publish.csiro.au/?paper=PP98157


4. http://www.plantphysiol.org/content/120/2/547.full


5. http://www.annualreviews.org/doi/full/10.1146/annurev.phyto.39.1.27


6. http://www.nhbs.com/biology_of_insect_induced_galls_tefno_3838.html

mathematics - In a math talk, is it better to display the number of slides left?

In a math talk (at a seminar or a conference, not teaching) that uses projected slides, is it better to display the number of slides left or not? What are the pros and cons? Some people tell me they like it, others prefer when it doesn't appear. I'd like to have some objective comments about this.

For some context, talks in math are typically one hour long, so the number of slides can be large. I like to cut talks into a few short sections. Right now I'm using the following layout, displayed at the top of every slide (from the "Frankfurt" beamer theme):

The current slide in the current section is highlighted, as well as the title of the current section.

Letter of Rec. for future University application

I'm getting my Software Engineer degree in one year here in my country, and I want to continue my studies with a Master degree in the US. Since here in my country is not a common practice to ask or write such letters, I'm not sure about some details. I have two main concerns about them:

1) How important is the written date of the letter? (It's OK to get one now, dated accordingly, if I will be submitting it in say, 2 years?)

2) Must the letter be always addressed? (It's OK to be generic, not addressed at anyone in particular? -At this moment I don't know what University I would like to apply-)

I'm asking those two questions because currently I'm developing an important software for the local Police (the 911 emergency line) and I think this could be a nice vouch for my technical skills, however since I'm changing jobs in a few weeks it's possible I won't stay in touch anymore with the Chief, or maybe this Chief won't be around in the future to ask him. This also because now I can ask for it and get it in paper, with the official letterhead and seal/stamp, so that will be a proof of authenticity.

Let's say my idea is to get this letter now and save it for later. Of course this would be a field expertise type of letter. Thanks!

administration - I left college in the last semester (did not finish), but the college "transferred military experience to credits" and gave me a diploma. Normal?

When I was in community college (2016), I wasn't on good terms with the school. I was harassed occasionally and complained about it very forcefully to representatives of the administration. I passed my classes, but didn't do homework and had an average GPA. In my last semester, I decided to stop going due to continuing issues with the faculty.

After a few months, I got a diploma in the mail. I called them and asked about it and they said it was all on the up and up, and that the VA representative had taken it upon himself to transfer some of my military experience into credits (my remaining requirements were very basic, like P.E.), which is what pushed me over the edge.

I still have a hard time believing that I could graduate without knowing it. The VA rep was new and had recently replaced the old one, and I'm stoked he took it upon himself to transfer those credits over, but I am curious if this is a normal thing? Has this ever happened to anyone else? Am I worrying too much? I don't want to look a gift horse in the mouth, but I also am afraid there could have been some mistake.

The reason I'm worried about it now is that I want to go back to school for a CS degree in the near future now that I've matured a little and have a better idea of what I enjoy learning. If there's any chance I need to be worried about my previous degree I want to know about it.

Answer

I still have a hard time believing that I could graduate without knowing it.

Me too. I would request a transcript and perhaps investigate to see whether "transferring military experience to credits" is something that routinely happens. It would be nice to document your concerns and get a written response from the college saying that everything is on the up-and-up. When documenting everything, I suggest not going into detail about your issues with the teachers; that is a separate issue.

I am curious if this is a normal thing? Am I worrying too much?

I can say that it is entirely abnormal for well-ranked, 4-year colleges in the US. However, community colleges are a different beast. While I can't say anything for sure, I can speculate:

• They may have wanted to boost their graduation rates, and looked for "almost-done" students that they could convert to "done"


• Perhaps your VA rep is just an awesome guy who helped you out.


• Maybe there were legal issues with the harassment case.


• Or, it's possible that something improper was done, and it will eventually cause problems for you.

Short answer: I suspect all is OK, but I would still try to document what happened and get the college to state in writing that your degree was not awarded in error.

Edit: I do agree with the other answers that you should proceed with your application to 4-year schools; don't let this slow you down. I just think it's worth protecting yourself...for example, the diploma-generation system could be different than the degree-verification system, and they might disagree about whether you finished...best to have the whole thing documented in case something comes up.

literature - Visualization tool for paper citations

Does anyone know if there is a tool that takes a paper (pdf) and is able to produce a directed graph of the citations, and if possible take the papers that are cited and use the citations of those papers and include it in the graph. So it is easy to see what is an important paper, and what I've missed and so on.

An example I hardcoded:

Answer

I'm also on a saga to look for this tool, hopefully the answers in this thread can end all the search. Here is what I know.

There used to be a software called RefViz that does what you exactly want. It was released by Thomson at a price of about US$295. Unfortunately, the response wasn't too good and it seems the product has been discontinued for more than five years. I used to use this software quite often to generate some themes from the literature pool. Since it was discontinued I have moved away from this type of relational analysis.

Instem has another product OmniViz, which remains in the market. OmniViz is like RefViz on steroids, and is much more capable. The price is also higher, reaching about US$1000 for an educational copy. Apart from literature relation, it can also be applied to genomics and that perhaps explains the high price. Instem has also produced a text-specific version of Omniviz [Txtviz] (http://www.txtviz.com) that is designed specifically to support people wading through large volumes of textual documents to find specific themes and areas of interest.

If you're tight on budget, try Google "citation map software" and you should be able to find other cheaper alternatives, like SciMAT, which is free.

Thomson has also hosted an online citation map, which does not hook up to your literature library, but if you click on any indexed article on Web of Science, you can get a network consisted of the cited and citing articles. If you'd like to see how much impact a certain article has, it's a good tool as well.

A more rudimentary way is to make the network yourself using mind mapping software. I have been using the brainstorming function in Qiqqa and it's not too shabby as a thought generator.

Last but not least, I'd also like to advocate for a large piece of A3 size paper, a good black or sepia felt tip pen, a box of color pencil, and some fun attitude to draw your own. I got the most out of this method, to be honest. When using the online tool or software I feel I am just producing a thing, but when I use my hands to make a network of articles that I feel important, I am also thinking. I guess person-to-person it's different.

Just remember whatever software we use, the relevance is based on algorithm. It's just like data mining, there will be false positives and negatives. Be mindful when analyzing the so-called literature gaps that the software found, sometimes it could be a gap, sometimes it could just be a void and does not deserve attention. Strong discretion along the process is necessary.

evolution - Effective population size when the population sizes varies from season to season

Let's think of a species which has four generations per year and which population size changes from season to season so that the population size is 100 in summer, 200 in spring, 50 in autumn and 20 in winter for example. In such case, the effective population size $N_e$ can be calculated by:

$$N_e = \frac{n}{\sum_{i=1}^n\frac{1}{N_i}}$$

where $n$ is the number of generation per year (4 in my example) and each $N_i$ correspond to the population size in one season.

My question

Can you please provide an explanation of why this formula (based on the harmonic mean) holds true to define the effective population size?

---

source

Answer

This is derived from studying how heterozygosity changes over time. The standard equation for change in heterozygosity ($H$) with constant population size ($N$) is:

$H_t = \left(1 - \frac{1}{2N}\right)^tH_0$

When $N$ varies between generations you use the product of this formula:

$H_t = \left(1 - \frac{1}{2N_0}\right)\left(1 - \frac{1}{2N_1}\right)...\left(1 - \frac{1}{2N_{t-1}}\right)H_0 = \prod_{i=0}^{t-1}\left(1 - \frac{1}{2N_{i}}\right)H_0$

To get the overall $N_e$ you need to find the population size that gives the corresponding decrease in heterozygocity over t generations i.e:

$\left(1 - \frac{1}{2N_{e}}\right)^t = \prod_{i=0}^{t-1}\left(1 - \frac{1}{2N_{i}}\right)$

Rearranging gives:

$N_e = \frac{1}{2\left[1-\left[\prod_{i=0}^{t-1}\left(1 -\frac{1}{2N_{i}}\right)\right]^{1/t}\right]}$

This expression can be approximated by the harmonic mean, which is easy to verify with some toy data (you get small deviations if yearly population sizes are very small). The explanation given above can also be found in Hedrick (2009, p217ff), along with some nice examples that integrates the effects on effective population size from several factors.

bioinformatics - Introductory literature for synthetic / systems biology

I am a computer engineer (MSc in Computer Engineering) who's looking to switch into the field of synthetic / systems biology. I have a comprehensive layman's understanding of evolution, genetics, transcription, etc, but my academic studies have been in the areas informatics, computer science, computer engineering and mathematics.

Does anyone have a good recommendation for standard literature in the field, to get me up to speed?

evolution - Definitions of robustness and canalization

The concepts of robustness and canalization are fashionable today in the biology literature. However, I am not sure of their definitions and I am not sure either that all authors actually use the same definition.

I am therefore asking here for a the definitions of these terms or for a short review of the common definitions of robustness and canalization. How do different authors define these words? I am particularly interested in...

• 
  

  The differences between robustness and canalization (canalization seems to apply more in developmental biology than robustness who seems to be a more general concepts)

  
  


• 
  

  At what level do these concepts apply? To populations, to genotypes, to both, ..?

  
  



• 
  

  How does the concept of adaptation link to these definitions.

  
  


• 
  

  How does the concept of plasticity fits in opposition of the concepts of robustness and canalization?

  
  

Answer

As canalization is defined in your question (also in wikipedia) it means robustness.

Semantically it is possible to differentiate the two.

Robustness of a system refers to its sensitivity to perturbations. In other words small differences in parameters would not affect the steady state of the system (parameter changes in a physically plausible range would not lead to bifurcations).

By system I mean a set of entities connected to each other in a defined fashion. For example an ecosystem in which different species are connected to each other by interactions of the food chain. At steady state a system configuration (for instance- 10 foxes, 100 rabbits, 10000 grasses, 1000 honeybees etc) remains constant over time (that, however, doesn't mean it is static). Or in case of development a system may be the body defined by a set of certain phenotypes.

Canalization/channelization refers to mechanisms that make the system follow a certain trajectory. So if you see it mathematically canalization keeps the trajectory dictated by a given set of eigenvectors. In case of development you may call mechanisms such as dosage compensation, functional compensation by isoforms, parallel metabolic flux channels etc as canalizing mechanisms.

So in contemporary usage we can call a system robust (a property of a system) whereas we should address mechanisms that help to preserve trajectories as canalizations. The final aim of canalization is to render robustness to the system but it is not the only mechanism that is responsible for robustness (for e.g. the steady state may just be independent of certain parameters).

Robustness is a property of the system and is dependent on how the different entities of the system are coupled and what their interaction parameters are (rates etc).

You should note that these are parlances that are adopted by different groups in the scientific community and may perhaps mean the same thing- this is merely my attempt to remove redundancy of terms by the means of semantics.

Now, plasticity is a different concept altogether. Plasticity is in a way opposite to robustness. This means that the qualitative nature of the system can change if certain parameters are tweaked. However, the system should still maintain its stability. In a stable system mild perturbations from steady state will result in system going back to that steady state - like a ball in a well. However, a system may inherently allow for multiple steady states (like switches), and depending on certain parameters the system can be in either of the states (but if pushed too far then the system can go to another stable steady state). This is called multistability.

NOTE: some people also use the term plastic to mean "responsive". The above definition may not be exhaustive or the most perfect.

phd - Mathematics research status in India

I am an Indian student. I am not related to any kind of mathematics research. So I do not have proper idea about it. I may join in as a PhD after a few months. I want to get a picture of the research status in India.

India has several mathematics research centres, institutions and universities. I want to know the status of mathematics research in India. How many and which of them are of international standard? What about the impact factor of their mathematics publication? What is the status of computer science, which is almost neglected by Indian Mathematicians. Is my idea true? I know that none of our institutions and universities in top 200 of the world ranking. Please give me some idea on it and sufficient resource so that I can convince myself.

Suppose I have completed a PhD in India. Will it be accepted internationally. When? Why and Why not?

Answer

You have a lot of questions all interspersed within your question block so I will try my best to answer. Here is a disclaimer:

Disclaimer: I am a past graduate student of the Indian Statistical Institute

Mathematics research, especially in theory, is pretty good in India. The top institutions (in no order of ranking) are:

1. Indian Institute of Science, Bangalore


2. Indian Statistical Institute (Kolkata, Delhi, Bangalore, Chennai)


3. Tata Institute of Fundamental Research (Mumbai, Bangalore)


4. Indian Institute of Technology (KGP, Kanpur, Delhi, Mumbai, Chennai)


5. Institute of Mathematical Sciences, Chennai


6. Chennai Mathematical Institute, Chennai

All of these are quite good internationally and attract the best Indian students. The entrance exams are quite tough and many of the BS, MS students go on to do PhDs in top world institutions. Those who stay, are also quite good and publish papers in the usual top journals. The problem is neither funding nor red tape in my opinion.

The problem is that compared to most "top" mathematics departments, these institutes are rather small (i.e. ISI Bangalore had ~only 20 full time faculty in my time and of those, 10 published regularly). You see, its only in recent years, that regular publications have become quite the norm and its usually being driven by younger faculty (usually those who have done their PhDs from US or Europe).

Please see him, him and him for reference in theory and on the applied, computing side, him [He is my MS thesis adviser] This is one small example from one school. I can assure you that the situation is similar in the other schools that I mentioned.

Most Indian PhDs go on to do postdocs internationally. Why just last year, we had a postdoc (who finished his PhD in ISI Kolkata and was joining IIT Bombay this year) in the ML lab here. He was great and very smart.

In conclusion, if you get a PhD in Mathematics in India and do good research while you are at it, I don't see why you shouldn't get international postdocs. Tenure track job positions will be restricted to the Indian subcontinent and south east Asia because USA and Europe have their own PhD glut problem. But, thats cool because most of these schools I mentioned are hiring very well. In fact, I plan to apply for several tenure track positions in CS departments in India when I graduate.

publications - Emerging science citation index (ESCI) listed vs SCI listed journals - worthyness to publish

As I know 'Emerging science citation index (ESCI) listed journals' will not receive an impact factor from 'Thompson Reuters'. Further, Science citation indexed (SCI) and Science citation index expanded (SCIE) journals receive impact factors.

Suppose I'm gonna apply for a scholarship for a PhD and that scholarship requires me to have some contribution to the world as a researcher, is there a probability that they will ever consider a research published in a 'SCI' or 'SCIE' listed journal than 'ESCI' listed journal? provided those journals are from reputed publishers.

And is it worth to publish in a 'ESCI' journal? or am I just wasting my precious paper in a non-worthy journal? any other factors to be considered when publishing papers?

P.S: Suppose, my study area as 'Construction Management and Economics'

publications - Not being a first author diminishes the contribution of co-authors?

If a group of students (say, 3 students), produces a work which has been accepted to a reputable conference. All of them contributed equally to the project,from implementation to writing and proof reading of the paper. How should one decide who should be the first author. Even if the names are listed in alphabetical order, so by not being the first author, does it affect the prospects for the other two in any means ? My field of research is computer science.

(This question has been partly inspired by the flurry of questions on ASE, regarding the importance of being the first author)

Answer

It depends on the subfield of computer science. For example, if the paper is in theoretical computer science, then author order is alphabetical, and the equal work put in by the authors is not negated by the author ordering. If in a discipline where author order is meaningful, then it's standard practice to (say) order the authors alphabetically and add a footnote saying that all authors contributed equally to the work.

vision - Seeing strange things in light

I have noticed that if you look directly at tubelight (I have only white ones in my home) and close your eyes little, you see little random shaped colourless things sometimes with slow speed and sometimes with falling down.

They are shaped like circles with something in between and in chains of random length.

My father has also seen them. So, I am sure I am not imagining things. What the hell are they?

Answer

Those are floaters. These are objects floating in the vitreous humour that fills the eyeball. They typically look like:

career path - To enroll in to a PhD Program at the age of 65

As a retired school teacher, and to become a professor at a university. Is it okay to get into a PhD program at the age of 65 and complete it to become a professor? Or is it too late and I can’t get employed at a university?

internship - Can I work as a software engineer and be a PhD student?

I'm a master student, my master's background is about IT, signal processing, and Telecommunications. It's a "research master", which means that we're trained more to do research than be an IT engineers/specialists.

I've made my choice because I want to do research, but It is also important for me to work after my masters graduation, some of my professors always say that it's very difficult, even impossible to do those two things together. So I'd like some more advice. Here are my questions:

• Is it practically possible to do research and work?



• Is it a good idea to work for a year or two after my masters, and start a PhD after that?


• What kind of internships can I do, and how long should they be, so I can apply to IT companies?

PS: I've some background ans skills in Java technologies, software design, web development, and basic knowledge in networks.

conference - What should I do if I submitted an article to a predatory journal?

Call it stupidity or bad luck but I am guilty of submitting my research article to a journal which is listed in Beall's List of Predatory Publishers.

It is my first article and I don't have much experience publishing articles. I was searching for a top impact factor journal and found this one on Google and in excitement sent my article (word and pdf files) in this journal a few days ago, only to discover later that this might be a bogus journal.

Now I am worried about that what will happen to my article. What if they plagiarize my paper, or send it to another journal not giving me credit?

My question is that what should I do now? Should I send my article to a reputable journal now? What should be the process? What if it is flagged for fraud by that journal? What are my options?

Any help would be appreciated.

Answer

If the paper has not yet been accepted for publication, you are free to withdraw the paper from consideration. Depending on the policies of the journal to which you submit the article, you may need to disclose the prior submission, and explain why you withdrew the publication from consideration.

Unfortunately, there's little you can do to stop the publishers of the first journal from doing something unsavory with your article. You will need to exercise vigilance in monitoring the work in this area to ensure that the paper isn't mishandled or worse. Be sure to maintain records of all of the correspondence you have had with the journal—and make sure of all it is documentable—phone calls won't suffice here.

However, if all the journal has is a PDF of your original article, it makes it a lot harder to do anything with it: it is tedious work to convert it into the template that most publishers use without significant effort. Thus, without the original graphics and text files, it will be difficult for them to "transmit" the paper elsewhere.

postdocs - Can I apply for a post-doc in global studies in North America?

I am doing my doctorate in global studies in Germany, and would like to apply for a post-doc position in North America, especially in Canada. The topic I work on has considerable policy relevance, and I see that some North American professors are working in those areas. I am a non-EU citizen. Is there any chance that I will be accepted?

graduate admissions - How do the completion of online courses impact a Master's application?

I see places like Coursera, Udacity and EdX offer certificates upon successful completion of course work. Also most of the people doing recorded teaching at these places are famous and well known professors.

So if someone mentions those kind of course certificates in CV or application material for grad school, does it have a significant value for the applicant?

Do you consider these kind of certificates at the same level with a grade on an academic transcript?

ethics - Is it okay to publish my personal notes from a lecture?

Would it be considered ethical to publish my own personal notes from class? In addition, is there a change when the class transitions from in session to being complete (at the end of the semester)?

For example when this may be relevant, there are courses where the Professor publishes his slides onto a class portal, but excludes certain material that is only covered in class. This is to incentivize students to show up, rather than only study from the from published slides.

research process - How can a new PhD Student objectively evaluate how well they are doing?

I'm a relatively new PhD student, and I'm faced with a new (for me) situation. Before, I always had grades and the likes to tell me how good or bad I was doing: if I was at or near the top/bottom of my class, if I passed my exams or not... were all more-or-less objective indicators to tell me how I was doing.

But now that I've started to do research, I have none of that anymore, and it's quite discouraging. It's not that I need constant validation to boost my self-esteem, but rather I'm afraid that I'm not working hard enough, not learning enough... and that it's all going to crash down on me at the end ("welp, your funding has run out and you've produced nothing good enough, no PhD for you"). I sometimes find results, but they always feel rather insignificant. And the fact that I used to be good as a student whose only job was to learn about well-established topics from good professors doesn't mean I'm good enough at research, either.

I've read several Q&A's here (How should I deal with discouragement as a graduate student?, “I've somehow convinced everyone that I'm actually good at this” - how to effectively deal with Imposter Syndrome) and they've been helpful, but simply telling myself that maybe it's just the impostor syndrome talking isn't helpful – maybe I'm really an impostor, too...

Of couse I can ask my advisor from time to time, but if I start asking every month I don't think he's going to appreciate it, and if I ask that bluntly he may not want to hurt my feelings and tell me the truth. So how do I, a PhD student, can evaluate how well I'm doing?

teaching - Drawing Lines when Giving Ideas to Undergraduate Students

I teach quite a few 'unprepared' students and I find they struggle with finding source material on which to base their reports. Basically, they need to read a lot and apply theories to different companies.

Where should I draw the line when giving them advice? I certainly do not do any searching or reading/filtering for them but if they choose a company and need to report on it, is it acceptable to give them some ideas about famous events at that company which might have happened a decade ago (or more but would still be acceptable for the purposes of the report)? Or, should I require them to do search, even for old events, and if they can't, then they can't and fail?

Answer

The purpose of teaching, which includes both your lectures, later guidance on their projects and also includes evaluation, is for them to learn new skills. So, the question you should ask yourself is: what skills do I want them to learn, and how do I achieve that best?

Typically, it seems to me that (if you have enough time for it), it is very important to teach them not only to read, filter and digest information, but also to search for it (Information Age and all). So, you might want to make “searching for relevant information” a required skill. But that doesn't mean you should help them acquire it. In fact, you probably should:

• advertise it as an important part of what they are expected to learn


• help them learn it, i.e. show them how it's done


• evaluate them based on their performance

However… even if you do all that, it still doesn't mean you can't help them if they miss something. After all, if you are teaching them how to best look for information, they might realize it's a good idea to come to the expert they know in that particular field… you, their teacher. So, maybe they will come asking

here are the relevant events I found about X in the archives… do you think I missed something?

or even:

I see a spike in the data around the fall of 1974, and I have searched but couldn't find any event possibly related to that company, do you know of anything that might explain it?

in which cases you might want to answer them, if it seems they did their due diligence.

reproduction - Does any animal species have two sexes and more genders?

Are there any animal species that have two sexes and a kind of different internal diversification in two genders or more? I don't mean something like different-task-based diversity, but something biological? For example let's imagine a species with:

• 2 sexes (male and female)


• 2 gender (A and B)

and individuals can match iff they are not only of different sex but also of different gender. So you can only have Ma-Fb, Mb-Fa.

masters - Does it make sense for the professor to write a recommendation letter that is directly readable by the student?

It seems that US universities usually provide a link to the professor of the applicant, and let him/her directly upload the recommendation letter to that link, meaning that the student would have no access to it. However, when applying to Masters programs offered by German universities, I am surprised to see that they all ask the student to upload the recommendation letter in PDF format/to a text area directly, by his/her own, which seems to make little sense to me.

I'm afraid that some professors will just outright reject writing a letter which is to be handed to and viewed by the student. Or are such worries unnecessary? Is this a cultural difference between continental European and British/American system (My current university mostly follows the British/American system)? What should I do in this case. Should I ask the professors to write and hand me recommendation letters directly, or should I try to communicate with the university and let the professors email them the letter/give me a physical letter sealed within an envelop, which I will send to the university by mail later on?

Answer

Is this a cultural difference between continental European and British/American system

I cannot surely speak for all continental Europe, not even for a small portion of it and not for all fields, but speaking with a few European colleagues of mine, it appears that the expectations that we have on recommendation letters are completely different from the typical US expectations.

In particular:

1. We mostly consider recommendation letters as a mean to discriminate between those that are not able to provide any recommendation letter and those that can provide at least a couple. That is, we expect most of the people not to be able to get one (in a distant past, I wouldn't have considered one who just attended one or two classes with me eligible for a recommendation letter).


2. We don't expect recommendation letters to be more than one page long, and half a page is ok (you just have to tell me that you had worked with this person and that they are not that bad).


3. We don't expect the recommendation letters to be sent directly from the reference to the application board.


4. We consider the writing of recommendation letters as a favour to the applicant, and not as a duty of our profession.

Actually, all the recommendation letters I wrote but one were handed directly to the student (or former student). For the exception, I've received a direct request from a university to submit the recommendation through their online system: the uploading procedure, with questions to answer too, was such a hassle that I've decided that in the future I will probably decline any request for recommendation letters to be uploaded anywhere.

To answer your main question:

Should I ask the professors to write and hand me recommendation letters directly, or should I try to communicate with the university and let the professors email them the letter/give me a physical letter sealed within an envelop, which I will send to the university by mail later on?

I understand your reasons, but I'd consider this an odd thing to do. I'd simply ask the student to provide the recommendation letters.

In case the professors were reluctant to hand the letters directly to the student, I'd write an email explaining the different traditions.

reference request - Is there evidence that suggests students should take notes?

I hear a lot about good note-taking strategies vs bad note-taking strategies, and I have seen a lot of research papers on different styles of note-taking. What I haven't seen though is any study that has asked if we should even be taking notes in the first place.

Specifically I would like to know the long-term effects of taking notes vs not taking notes. It is clear to me that if someone has taken notes their entire academic career, then immediately stops, their performance will probably plummet, but how do students who have never taken notes compare to students who have always taken notes?

I would guess certain learning styles would benefit from note-taking while other learning styles are hindered by note-taking, but I would like to see some actual data on this if anyone knows anything about it. A cursory Google search didn't return anything, so I hope there is someone on here that may be able to shed some light on this.

Edit: A lot of people have taken this question to solely be asking for research on this topic. While I would most like to see actual data, I did not intend this to solely be a literature search, and people can post their anecdotal evidence, as long as it is pointed at the long-term difference in note-taking vs not taking notes.

postdocs - What is the difference between TV-L E13 and TV-L E14 positions? Is it negotiable?

I am trying to wrap my head around the German research system since I have an offer for a position. I understand the TV-L concept, and that you can go up a step depending on your prior relevant experience.

I do not however understand what distinguishes the TV-L E13 from TV-L E14 positions for postdocs. What are the differences and is it something that you can negotiate with the institute (seeing as TV-L E14 is better paid)? Sounds like there should be a difference somehow.

In my case, I have a 4.5-year-long PhD and an additional 4 years of research experience. If my understanding of the documents is correct, I would land in Grade (Stufe) 3, is that correct? If not, could anyone elaborate on how the prior experience is calculated for this purpose?

EDIT: the follow-up is now moved to a separate question

Answer

The key difference between a TVL E13 and E14 position would be the job responsibilities and required qualifications. In an academic context, E13 positions are for researchers at graduate or post-graduate level working under supervision. E14 positions have a higher responsibility in the sense that these would typically include project leadership and / or supervision tasks. Typical academic roles that should be filled at the level of an E14 position would be group leaders, principal investigators of projects, research lab managers, or just someone supervising graduate or other post-graduate researchers. Nevertheless, someone working in these roles may still get only E13 due to budget reasons.

If the position you have an offer for includes tasks at E14 level, then it certainly is something that can be asked for. Whether or not it will be possible to make it E14 will mostly depend on how the position is being funded. It may be that this was specifically budgeted as an E13 position, and then it will be difficult to change that through negotiations from your side. If the position was announced specifically as E13 then it may be a high administrative hurdle to change that. However, if the funding is just a bunch of money without detailed budget plan, it may be easier to get it as an E14 position. Especially if it is only for few years, the total salary spent need not be much higher in E14 compared to E13 because you would likely start in a lower grade (Stufe).

Regarding the grade I think that indeed with more than 8 years of research experience you should definitely get Stufe 3 in E13. The number of years could even be enough for Stufe 4, but I've heard that new hires will usually get Stufe 3 at most. However, if you get an E14 position, then I guess that you can just get Stufe 1 or maybe 2, depending on whether you have some prior experience with the E14 type of tasks I mentioned above.

As a side note, there is also the possibility to start in E13 and then being promoted to E14 if job responsibilities are accordingly and the budget is available. In that case, one would get the lowest grade in E14 where the salary is still at least as high as in the most recent E13 grade one has achieved.

writing - Why do conferences have such short page limits?

These days, most of the conferences I attend provide their proceedings on a USB stick, or online only. Yet at the same time they have a strict page limit, which is usually set to something between 4 and 8 pages. I'm curious about the rationale for such a small limit. This is probably something that varies between fields, although I've experienced it in more than one field myself (subfields of artificial intelligence and physics). It doesn't seem particularly limited to big conferences.

I realise that super-long papers would hard on the reviewers, who have to do a lot of work for a large conference. But on the other hand, a very short paper will have to leave out a lot of background and important information, which at best will make it difficult to read, and at worst will make it impossible to judge on its merits. It's also a lot more effort to write a four-page paper than a 10-page one, unless you happen to be presenting a single experimental result using an established methodology (which is rarely if ever the case in artificial intelligence and related fields).

Looking at conference proceedings from the 1950s through to the early 1980s, it seems that proceedings papers were generally much longer. As an extreme example, I know of one that's over 100 pages (it's quite a famous paper and the length seems worth it), but up to 20 pages doesn't seem uncommon. In the '90s the standard seems to have been 10 pages, at least in subfields of computer science. Although there's obviously selection bias involved, these old papers don't seem particularly longer than they need to be, and their length allows them to make rather deeper points than could be made in a modern 4-page paper.

I'd like to know the reasoning behind short page limits at conferences. Is there a school of thought that says these extreme limits lead to better-quality papers, and/or less work for the reviewers? Or is it just a holdover from the recent past, when big conferences were expected to provide a paper proceedings to every participant, who would then have to carry the whole thing home?

How much are taxes for a postdoc in the United States?

I'm being offered a postdoc position at Penn State University.

The recent rise in salary sounds good (about 4000$/month), but I wonder taxes may be not included. Any help?

publications - How does one determine priority, prominence, and impact with regard to books, rather than articles?

My background is in physics where almost 100% of the scholarly work is reported in peer-reviewed publications. Within that framework, I understand how to determine who has priority regarding ideas, how influential a paper is, how prolific an author is, etc. at a glance by looking at publication dates, citations, impact factors, etc. Usually, the only books which are written are textbooks or those aimed at a popular audience.

My experience, though, is that not all fields are this heavily skewed toward peer-reviewed articles.

Question:

• In fields that rely significantly on scholarly books, how can someone quickly determine the impact, reliability, etc. of scholarly books and scholars whose work appears primarily in books?

phd - How can I find a second supervisor?

I'm in the second half of my Phd in a technical field in Germany. As it is common in Germany, it is not a structured PhD program but an independent PhD without any course work/mentors etc. I am not very satisfied with my supervisor because he cannot help me at all, since my topic is not his primary interest and he is very busy since he is not yet a professor. I do everything alone from choosing the specialisation of my topic to writing (my first) papers, and I got used to that. I like my topic and I get the money and besides the bad supervision, my supervisor so I decided not to change the PhD. However, I would really like to find a second supervisor who could give me advise and has a better reputation in my field.

How should I approach potential professors with my request? I would not need too much help or any money, just the name of someone who is at least a little known in this field and I would be willing to do some work for them. Is it very uncommon and unlikely to find a professor who is willing to do that?

I tried once at a summer school to ask another professor and it would have worked out but I experienced afterwards that my supervisor was not at all happy about that so I have to make sure beforehand that he agrees with my choice.

human biology - If body temperature is 37°C (98.6°F), why are most people more comfortable at around 21°C (70°F)?

It may be different for other people, but for me, anything above 32°C (90°F) is very uncomfortable, and my body is inclined to seek cooler temperatures. But I would think that at 32°C, the body would have less work to do to get itself to 37°C. So why is it not comfortable in those temperatures?

My theory is this, but I don't know if it's right:

The body's abilities for warming itself are much more sophisticated than its abilities for cooling itself (which are non-existent, possibly?). So it likes to be in an environment 20-30 degrees below optimal because it can easily handle that. But up in the 32's and we're dangerously close to going over the optimal, and the body doesn't know how to get it back down after that, so we are inclined to seek safer temperatures.

Is it something like that?

Answer

The body can never stop working. If the body stops working, you die. And while the body is working it cannot avoid generating heat. Being in an environment somewhat colder than the body makes getting rid of this excess heat easier, and is thus more comfortable.

The body's abilities for warming itself are much more sophisticated than
its abilities for cooling itself (which are non-existent, possibly?).

The body can cool itself down by sweating.

authorship - Rules for notifying co-authors about re-presenting a project at a conference

I am a PhD student in molecular biology & bioinformatics in Australia. I have previously presented one of my projects as a poster at a conference. This was sent for review to all co-authors, changes made and presented.

A couple of months down the line, I was asked to present a poster at a local conference. I re-submitted the poster abstract, which was accepted. I did this without consulting my primary supervisor as I thought any dispersal of the work would be welcome. Since then, she has started to dislike the results of that project. When the conference was around the corner, and I told her I was presenting, she accused me of bad scientific conduct for presenting something in her name. I apologized, explained why I had not consulted her and retracted the poster.

She’s not dropping the matter though and seems to be using it as a target for some larger disagreements she has with me. What are the rules for re-presenting work or posters? Are there any guidelines and how serious was this accidental transgression?

publications - Esci vs scopus ? Which one to follow

Which are considered as trustworthy good quality journals , the ones indexed in esci by web of science or are the ones indexed in scopus ? There are some journals which us indexed in esci and not in scopus and vice versa. Any lead points on this ?

Answer

Not an expert on this, but my understanding of the two are:

ESCI aka. Emerging Sources Citation Index is a "lower-ranked" index. Journals listed here are being considered for the more prestigious indices SCIE, SSCI, and AHCI (note this doesn't include SCI, which is the most prestigious index). In other words, ESCI is a "feeder" index to the SCIE/SSCI/AHCI, which in turn feed into SCI. If you search the ESCI, you'll find that the most prestigious journals such as Physical Review Letters aren't actually indexed here.

Scopus is fundamentally different and is built more on inclusiveness than quality. If you look at the inclusion criteria, Scopus mostly demands regular publication, peer review, diversity in authors & editors, and online availability. It does require that the journal's articles also be cited by other journals in Scopus, but not more than that. Scopus has many, many more journals than ESCI.

So which is good? Hard to say, and depends on what you mean by 'good'. Good journals will be in Scopus, but being in Scopus doesn't mean a journal is good. Being in ESCI is a different matter, since the really good journals won't be in it, but the really bad ones won't be in it either. It's your judgment call to make.

thesis - Can my university revoke my degree after it was granted due to (corporate) data having changed?

I did my thesis using corporate data (I used to work there, they don't give their information freely or sell it), data is from 2009 to 2018.

I collect the data, analyze it, everything normal. However, after my thesis was approved and submitted, I saw that the company has modified some of their data from 2009 to 2018, historical data from the past was changed (they have valid reasons) but I am worried that if someone tries to verify the source of my information, they will find different data and think that I commit fraud or data manipulation.

My supervisor and many people told me that nothing wrong will happen because my research was in a specified period of time when data was presented like that, they also told me that after a thesis approval, no one verifies data source. They also told me that the verification of data source is done before thesis approval.

However I am still worried, because it is not common for a company to modify data from the past.

My thesis wont be published because the used data is privated, so they are allowing me to not publish it.

Any ideas of what should I do?

thesis committee - What is the chance of making a successful appeal to dismissal decision from a PhD program after failing the qualifying exam in the 2nd attempt?

I’m about to get dismissed from a PhD program because I failed in the 2nd attempt of the qualifying exam.

Currently, I'm thinking of the option to appeal the dismissal decision due to a long history of mental health problems (anxiety & depression) and have the diagnosis of Attention Deficit Hyperactivity Disorder (ADHD) just before my 2nd attempt in the exam by 10 days as determined by the school psychological counselor & confirmed by my physician assessment. I’m not sure of this could be used as a ground for my appeal because I can present evidences for this ground and not able to use other grounds such as potential bias from my adviser as he was not willing to have communication & advisement after failing the 1st exam attempt. He actually told me “just do it and best of luck!!”.

Additionally, during the exam, there was one committee member who did not attend in person (joined us via a conference video call). I was notified several times during the exam that this professor was not able to hear me especially while presenting or answering some questions (when standing next to the projector or the white board to demonstrate some answers). The academic evaluation by this professor could be biased based on the fact that could not catch up all of my answers. However, I can not use this as a ground for my appeal because simply I do not have the evidence nor the presence of non-committee member auditing person at the exam. The director of the PhD program attended all of my previous qualifying exams (the 1st part that I passed & the 2nd part that I initially failed), but not the last attempt for the 2nd part.

I’m not making an excuse of mental health issues or ADHD diagnosis, but really made great efforts to study and prepare for this exam, and I believe that I answered most of the questions with logic and scientific rationales. I did also seek a confirmation of addressing each question asked by each committee members whether they had sufficient answers or they need more elaboration from my side.

My question is: How I can a valid arguments supported by evidences from my counselor & physician on the ground of mental health issues and ADHD? The other question: What is my chance of admission if I apply in the future for another PhD program?

Answer

I'm sorry for the tough situation you find yourself in.

First things first: no one outside your university and department can speak with any authority whatsoever as to what this particular group of faculty administrators will do. At best they can speak in general terms and give general advice. That is what I will try to do. Let me also begin by indicating my own experience: I am a mathematics professor at the University of Georgia. For the last three academic years I have been the Graduate Coordinator of the mathematics department. Thus if you were in my department you would be appealing to me (more precisely, to the committee of which I am the chair).

It seems to me that you are getting overly caught up on the legalistic aspects of your "appeal." You grasp at several things that might perhaps lead to bias on the part of committee members. But let me be honest: in the kind of academic culture of which I am familiar, this is not a very good strategy. Without evidence of clear and bias that changed the result of the exam, I think it is very unlikely that (say) the director of the PhD program will do more than inquire of the faculty members whether there were any serious problems or irregularities with your exam. When they say "No," there is not really any other group that can spring into action at this point, again unless you have something much more serious to allege and more material reasons to allege it.

Here is the reality of the situation: the committee who administers a graduate qualifying exam has extremely broad latitude in deciding whether the student passes or fails. There is probably not going to be a "rubric" that they did or did not follow or anything of the sort -- rather, they are empowered to use their best judgment. To be honest about it, a student at this stage is probably not in a good intellectual position to question their decision: you don't have the experience to know whether their standard is a good one.

Rather than thinking of the appeal as an argument that you have to win, I suggest that you appeal to the sympathies of the most sympathetic faculty member in sight. In particular, I do suggest that you mention your health issues of anxiety, depression and ADHD. As a longtime faculty member and administrator, I can tell you that (i) many students have these problems, (ii) they can become significant impediments to otherwise very strong students and (iii) these issues are (happily!) not nearly as stigmatized as they used to be, to the extent that "zero sympathy" for such a student is not such a tenable position for e.g. a public university in the United States to take. If you bring medical documentation of the problems, explain the serious steps you are taking to treat the problems and ask for another chance when your health issues are under better control, then I think you have at least a fair shot at getting another chance.

Good luck.

russia - Why do Russian and Israeli universities score low in various world rankings?

Russia and Israel have good histories of science and technology.

But, I never saw any Russian and Israeli university in the top 50 list.

Currently, the top Russian university, according to QS World Ranking is, Lomonosov Moscow State University. Its position is 114. This is far worse than China. The top Chinese university Tsinghua has a position of 47. The same problem can be seen in Israeli universities.

Why do Russian and Israeli universities score low in various world rankings?

What is the problem? And, why aren't they trying to improve the situation?

          |--------|-----------|--------------|-----------------|-----------
          |QS(2015)|Times(2015)|Shanghai(2014)|Webometrics(2014)|CWUR(2014)

----------|--------|-----------|--------------|-----------------|-----------
  Russia  |   114  |    196    |      84      |       129       |    48**
----------|--------|-----------|--------------|-----------------|-----------
  Israel  |   138  |    188    |      70      |       207       |    22**
----------|--------|-----------|--------------|-----------------|-----------   

** this ranking is an exception.

entomology - What type of insect is this?

I'm naturally thinking this is a bee, but I cannot find it anywhere in any insect identifiers. I caught this picture on top of my doorway, it's about 1 1/2 inches in length, and its torso seems to be coated in a layer of hair, and the rest of its body is narrow. The thick layer of hair may or may not be accurate, I didn't want to get too close to it, but that's how it appeared at least.

What is this?

PS - Found in Kentucky, and I'm not sure why one pic shows wings and the other one doesn't...

Answer

From the general body plan, it looks like it's probably a robber fly. Here's a page of specifically Kentucky robber flies – it's possible yours could be a Bearded Robber Fly.

authorship - Not including student who contributed very little as coauthor of paper

I am a researcher in condensed-matter physics, and I recently started a research project with another professor, for which I hired a student for a six-month undergraduate internship. The student was under my supervision. During the internship she showed good motivation, but did not make any actual contribution to the progress of the project.

Finally, she started a Ph.D. with someone else. I personally took over the project, taking care of both technical and conceptual parts, which requires a lot of time and work.

I kindly invited her multiple times to double check some of my work, but she had not done anything on the project since the end of the internship.

In the past few months she started having an attitude that I find disturbing. She replies to emails once in a while, proposing new conceptual points to explore, as if I were the student and she was the supervisor. On top of that, she ignores the invitations to double check my calculations, which would require actual work on her side.

Given that she did not make any actual contribution to the project, I am inclined to not include her as an author of any eventual publication. I think that it would be definitely fair to include her in the acknowledgments, but unfair to include her as an author.

What do you think about this? How would you inform her of this decision?

bioinformatics - Software for counting fly eggs

Is there any software that could be used to rapidly (quicker than humans) count the eggs laid by Drosophila on a substrate by placing them under a microscope with a camera attached? The eggs are laid on the surface of the food and have a fairly uniform shape - we regularly have to count the number of eggs in >200 vials, which can take a over 4-5 hours per 100 vials.

I wonder if there is some software which could be linked to a microscope with mounted camera connected to a computer, the software could then count from the live feed or a quickly taken photograph. It wouldn't have to be perfect but as long as it could be as accurate as humans (which is surprisingly low from our experience - we count up to a set amount then remove the rest, e.g. if I was aiming to leave 180 eggs I would be quite happy to get anywhere between 150-200 eggs). It would be using a stereo-microscope (aka dissection microscope) with a mounted camera.

The surface of the food with eggs looks something like this -> purely for illustration, taken with iPhone - real images on microscope would be able to get closer (food surface could fill screen) and have more uniform lighting to give better contrast (this was taken to show in a talk so I wanted pretty rather than practical). The bottom two quarters of the food in this picture would be similar to the real result, just much closer...