Tuesday 28 February 2017

advisor - Supervisor delays publication over style questions for years – can I remove him from the authors list?


I did my PhD four years back. I was funded from my home country and I have done all the work. I started writing papers before submitting my thesis.


I am sending my supervisor drafts every year until now. Altogether I have now done 32 drafts. Since last year alone, I have rewritten my paper 12 times but he still is not happy to submit it and not willing to make any changes by himself. He is even not letting me to show it to the reviewers.


My supervisor is a lecturer and I was his first PhD student. I acquired the opinion of two professors (one of them is my 2nd supervisor and is a co-author) recently about the quaility of paper and they recommended to send it to a good journal (impact factor of 10 and above). After many years of struggle my supervisor wished to publish it in a journal with an impact factor less than 1. Above all he is not willing to pay publication costs and he is not allowing me to try for good journal. I am the one who did all the work, who paid for work, who wrote paper and who is paying for publication costs and i am not allowed to try any good journal.


One thing about his recomened changes: He did not ask repeating any experiments, redoing any analysis or revisiting any conclusions. It’s only text style that is being changed over last four years. I contacted the university services and they told me that I don’t qualify for university help as they only cover two years post PhD duration.



What can I do now? Can I publish my work without him as co author. Can I just acknowlege him for hosting me and remove his name from the author list?




computer science - Are open-book exams generally a superior way to test understanding on practical courses?


I understand why it would be a bad idea to allow math students access to paper materials as it is necessary for students to know the basic math formulas by heart.


But what about advanced practical courses where it is important to "understand" rather than "know"? For example, knowing statistical formulas won't help if you haven't understood how to apply them. Knowing STL commands by heart is also useless for programming, unless you're actually good at programming. Intel's x86 developer manual won't help a complete newbie in Assembly programming.


Therefore the question is whether it is reasonable to believe that good courses should be focused on "understanding" the subject rather than "memorizing" it, meaning that the instructor should have no problems with his students using paper materials on the exam?



Answer



You might find this article on a computer science class valuable (1). The tl;dr is that sections allowed student-prep notes showed no overall improvement, but mostly because many students didn't bother to create good student-prep notes. Good notes = good grades.


A quick browse of a review/ meta-analysis article on the topic (2), indicates that open-note exams can decrease student anxiety, and that student-prepared notes tend to produce larger improvements than open-book exams.


As an instructor, I've found students often spend energy only where they feel it is needed. I would recommend providing sample exam questions (as a group activity in class?) that gives students a good idea of what will be required and what sorts of notes would be helpful. This will help them expend the energy in preparation instead of frantic in-exam page-flipping.


Thanks for wanting to trigger deep learning in students!




  1. Duncan, D.G. (2007). Student performance shows slight improvement when open notes are used during information system exams. Journal of Information Technology Education, 6, 361–370.

  2. Larwin, Karen H., Jennifer Gorman, and David A. Larwin. "Assessing the Impact of Testing Aids on Post-Secondary Student Performance: A Meta-Analytic Investigation." Educational Psychology Review 25.3 (2013): 429-443.


Adding a citation after paper is accepted


I am a junior researcher in mathematics. I worked simultaneously on proving Theorem A and Theorem B. They both generalize Theorem X in two different directions. Theorem X was proved several years ago (not by me). The proofs of Theorem A and Theorem B use very different techniques, and so I decided ahead of time to write one paper for each.


I finished proving Theorem A before I finished proving Theorem B. Then, I submitted Paper A to a journal (and the arXiv) proving Theorem A. Paper A includes a survey of related problems in the introduction. After a short while, I managed to prove Theorem B, and two months after the submission of Paper A, I submitted Paper B (to a different journal, and also to the arXiv). Now, six months after the submission of Paper A, it is accepted with requests for minor corrections. There is no response yet regarding Paper B.



In this situation, is it a reasonable/common to add one/two sentences to the survey in introduction of Paper A, explaining and citing the arXiv prepreint of Paper B, in addition to the minor corrections the referees asked for? (and letting the editor and referees know that I did that in my answer to their reports which comes along with the corrected manuscript).




Note that I am not asking if it is ok to cite a preprint. This is something I do, and so do other people, at least in math. My question is about making a change, after acceptance, which was not asked by the referees and the editor.



Answer



Of course it's ok. Even if the paper is accepted, but some minor corrections are required (I guess the reviewer noted that after these corrections the paper can be accepted without sending the revised manuscript to them again), your work on it has not not yet finished, and you are free to make modifications that you consider appropriate - not only those that the referee asked for. So if you found something that the reviewers didn't ask for, but adding it to the text improves the quality/completeness/etc. of the paper, you definitely should do it.


Talking in general: in the meanwhile you could obtain some new data, could perform the experiments on different equipment, apply another method to confirm/strenghten the results, or some of your colleagues pointed out you have some minor error or that some part is unclear, or you found some other relevant works that you want to compare your results to - all of this can be done even in such an almost-accepted stage.


Finally, it could also happen that you'd need to add some extra sentence to keep your overall style consistent after the requested corrections, or to make a more natural transition between two parts of the text; this would also be perfectly fine, even if - strictly speaking - that's not precisely what the referee asked for.


Overall - aim at the highest quality of the article that you can achieve at the moment.


Monday 27 February 2017

publications - In text listing style - how to use? Any downsides?


I'm currently considering to use a in line (in text) listing style, such as:


'Some things are quite good. (i) Thing A can do this and that, which is awesome because of this and that. (ii) Thing B can do, ... . (iv) Some people also say that this and that, therefore thing Z is great.'


I've got more important points already highlighted through bullets, therefore I don't want to use bullets again for this minor information, plus I want to logically link the single points through sentences, but still provide an easy way to pick out the key words quickly.


First question: I've seen this style in quite a few papers. Is it considered to be a "good" style, or are there any downsides to this approach? Should I not use this style? Does the reader get confused by this?


Second question: Shall the brackets and latin number be bold, only the number, or nothing?


Third question: Should I place the enumeration element right infront of the keyword, or at the beginning of the sentence containing the keyword?



Answer





  • If the numbers are never used, or if the technique is overused, then this can be considered bad style. I would not use it in the example above, for instance.

  • You can use whatever style you want. There is no reason that they are bold. Sometimes the leading parenthesis is dropped, sometimes both. It's best to consult the style guidelines for the relevant publishers.

  • Put the enumeration element in front of the sentence or phrase under consideration. Try it out, if you put it near the keyword, then you'll have spurious sentence elements in illogical positions.


publications - Should I withdraw my paper because the editor is delaying the report?



I am clearly disheartened by the editor's behaviour:


I sent a manuscript for peer review nearly three months back to an Elsevier journal with impact factor 0.625 in mathematics.


I inquired about the status of my manuscript after 1.5 months since it was still showing "With Editor " status.


The editor said review process is on and a decision can be obtained after 1 month.


After 1 month I again inquired about its status, to which the editor said that the report can be obtained in a few days.


But, since then, nearly 3 weeks have passed, but I did not get the report. I have mailed the editor 2 times and the associate editor 1 time but no one replied.


The status is still showing With Editor.


Why is the editor behaving this way with me? I am waiting anxiously for my report as it matters a lot to me.


Are they avoiding my mails intentionally by not replying?


What is their aim? Do they want me to withdraw my paper? Should I withdraw my paper because the editor is behaving so badly with me?



NOTE: Also, if the editor is busy, why is the associate editor not replying?


My question is not a duplicate of submission review is taking too long because I never asked why my review process is taking long.


My question was



If the Editor said that I will get a report in a few days , why did he not keep his/her word and now when I am sending him mails, why is he/she not responding?



The two questions are clearly different as far as my knowledge goes.



Answer



The situation is sub-optimal, but not as bad as you seem to think. Remember that being an editor to a scientific journal, even one published by Elsevier, is often a volunteer job. Moreover, the editors have no control over how long the reviewers take to review your article. (which reminds me...) So what they gave you was only a guess. If the guess was wrong, then that happens. What seems to worry you the most was the status of your paper. I would not worry about that. Sometimes editors use these function to track submission and sometimes they don't. If they do, then the status is probably fairly accurate, if they don't then it means nothing.


My suggestion is to think about publishing your article until you submit the article. After that you just forget about it (don't look at the journal website, don't think about it), because there is nothing you can do. Instead, focus on writing the next article. Only when you get your rejection letter, you start thinking about it again, and improve the paper and submit it to the next journal.



graduate admissions - Should I take a "positive, but not enthusiastically strong" letter of recommendation?


I'm currently applying for a Masters degree in a competitive program, and most things on my application are going well.


The problem I'm having is with securing a letter of recommendation - I have already secured two strong letters, one from a workplace manager in the field that I am applying for and another from a professor in an unrelated field. Regarding the third letter, a professor that I spoke to said that he could write a "positive, but not enthusiastically strong" recommendation.


From reading up on answers here and on other sites, it seems that in most cases I should look elsewhere for a letter. However, in my case I do not yet have a letter from a professor in the field that I am applying for. There are a few other professors in the field that I will reach out to, but assuming that they reject my request, should I take this letter?


Another option that I have is to secure a strong third letter from another manager at my workplace. Would taking a third letter from a work manager be better? I am leaning towards this being the case, but I also do not want to jeopardize my application by not having a letter from a professor directly in the field I am applying to.




graduate admissions - If I cannot get sufficient recommendation letters, what can I do?


I know you should build a good network with your professors as early as possible, not only it will help your study, but also you can get great recommendation letter from them.


But not all students aim at graduate school when they start their undergraduate, for example, I only became interest in research and decide on going to graduate school after my third year of undergraduate. At that time, I have done a research project with a professor and certainly I can ask him for one. However, most schools require 2-3 recommendation letters.



I know a good recommendation letter should speak about the candidate research potential instead of 'did well in my class', but in my case, only my undergraduate adviser can speak about that. What should I do besides asking recommendation letter from professors I get A grade in their classes?



Answer



Of course, the best solution to this problem is not to have it in the first place. Being proactive and thinking about the future is sometimes a rare talent, especially in 18 year olds fresh out of high school, but then again grad school is supposed to select the exceptional individuals.


There is a world of difference between a recommendation from someone you worked with, and from a mere acquaintance. The latter kind rarely benefits your application in a meaningful way, and can sometimes even hurt it. No matter how enthusiastic your instructor is, unless the course is at least a project-centric course (eg. grade is based entirely on your individual term project), they will not be able to make a good, in depth argument for your abilities, and the recommendation will therefore be weak.


The point of the recommendation is that the admissions committee will read it, and decide whether you have potential to be a good researcher. How can they, if the recommendation does not talk about your research at all? And how much better if instead of hinting at your potential indirectly by citing course performance, the recommender can just say "this person has potential to be a great researcher because I have personally seen that they are good at research"?


This is why there is a qualitative difference. This can be a big problem when applying to a very selective program. What if you apply to a program where the committee has a philosophy that "an application is only as strong as its weakest link"? Even if you are quite exceptional otherwise, you can get eliminated early on because there are many other applicants who are also exceptional, but don't have a recommendation problem.


Also, similar to how a lukewarm recommendation can mean "I think this person is a bad candidate, but I am not being negative out of politeness", a recommendation from someone who only taught a course can mean "this person is a slacker who never bothered to do real work, so they can't find any supervisors to recommend them".


The best way to remedy is really to obtain more "good" recommenders. Because you want people who supervised you, the solution is obvious: You haven't been supervised by enough people who will vouch for you; you must undertake more projects and be supervised by other people whose recommendation will carry weight.


If still in school, look for faculty whose lab you can work in. If that is difficult, try approaching a former (or current) instructor with an idea for a theoretical or computational project (this requires less commitment from them, so they may be easier to convince). It doesn't necessarily have to be original research, so long as you can come up with a relatively long term (at least half a year) project where you are the primary contributor. It could also be (more) valuable to spend a summer working in a lab at a different university.


If out of school, delay your application by 1-3 years, and look for work as a lab tech at a university, institute or private company. Make sure not to displease your boss.



A related problem is working for a long time with the same person, for instance an undergrad who spends 3 years in the same lab. This is actually better, because you can accomplish much more in 3 years, and you can have a very impressive project to sell yourself with. The issue is that you will have only one supervisor - but hopefully after 3 years, you will have networked with collaborators and other scientists and will not have a problem there.


graduate school - What are the advantages and disadvantages of having multiple advisers?


Could multiple advisers mean that it might be easier for you to get funding? (since you're not just limited to one person?) Could it also mean that you get more overall input in your project (the input of 3 different people), and that maybe your project will be geared in a way that it's "interesting" to more people, and consequently might also get more citations that way?


They might pull your project in different directions, but how much is this really a concern?


And what about the special case where they explicitly expressed the desire to interact with each other more through the student? (this was actually the case in my situation).



Answer



The answer (as in case of most answers in academia.SE) is it depends, often widely from case-to-case. Unless presented with an exceptional example, I would generally view having more than two advisers as a major hindrance - the perceived benefit of having another source of ideas is negated heavily by the communications overhead between them, and the scope for misunderstandings about their role, which might cause the student to be either overloaded in multiple (possibly conflicting) areas, or languishing without any significant guidance. The rest of my answer is based on the assumption that the number of advisers is 2.





  1. What is the defined role of the said advisers - are they equally responsible for guiding the student towards completion of their graduate studies (as I've been told is the case in some European schools/research schools), or is one of them the principal guide and the other a co-guide? The amount of time/effort invested by each would depend on their perception of how much they are actually responsible for the student's growth as a researcher.




  2. As with most social interactions, it would help greatly if there is a good (or at least professional) working relationship between the 2 guides, as well as a healthy overlap of research areas - a new student might not be able to handle multiple research problems in completely different areas at the same time (without affecting the time to graduate, or the quality of results).




  3. Assuming the student publishes with both of them independently, it would look good on her CV that she can produce publishable research with multiple established researchers. This could also have the side-effect of enhancing the student's research network - as a lot of papers (in CS at least) have more than 2 authors, and often collaborating on an paper could lead to more papers/research done with the same set of persons in future.





graduate admissions - Should I mention a professor's name in my SOP for MSc if the professor is only taking PhDs?


Some facts:





  • I am applying for a Master's program in Computer Science at a university in US.




  • My research interests exactly match with the professor's.



  • I am applying to the university because of the professor.

  • The professor is only taking PhD/PostDoc students in his group.


  • He has just joined after completing his PostDoc and there is no information on the website if he will take any courses.





  • Chances of directly doing a PhD with him are very less based on my profile.




The problem:


I understand that whether or not I should write his name or mention some of his work depends on if he will be able to advise me during the program which is exactly what I do not know.




  • Can having discussions with him during his office hours be a good enough primary reason to study there?





  • What could be the possible reasons that a professor is not taking any Master's student? Is there a good chance that if I get an admit, my regular interaction with him, interest, and work will make him take me in his group with PhDs?






Sunday 26 February 2017

botany - What is the largest perennial herbaceous plant?


What is the largest perennial herbaceous plant? My guess would be some kind of banana or bamboo.




Answer



The tallest banana species is Musa Ingens (15m) which grows in the forest of Papua New Guinea and Indonesia. It also claimed as the the world's largest herbaceous plant. http://www.thestatworld.com/2015/12/musa-ingens-the-tallest-banana-plant-in-world.html


publications - How/when to become independent in research as a graduate student?


I am in the last months of my MSc and I have done my thesis. I have published some conference papers but most of them were literature reviews. My MSc thesis is about solving wave equations by means of method of potentials and boundary elements. I am interested in pursuing research in another field (differential equations) but I have no idea how to start any topic that may lead to a journal publication.


By asking this question, I want to understand how a research student, whether a recently graduated MSc student or a PhD student, can start searching for a new research topic and develop some researches based on his own interests. Specially, I would like to know:




  • To what extent should a graduate student be dependent on faculty members? How can he be more independent and start his own research activities?

  • Is it a good idea that the graduate work on another topic with the faculty member or work independently on a more recent research topic?

  • If the person is in a research group or at the university, is it a good idea or is it ethical that he develop his own research interests, besides to the topics which are being developed in that institute?

  • How should a graduate student manage this and make some progress in the research fields of his own interest? (In particular, sometimes the faculty members are not interested in the topics you are interested in and the person has to start his own research activity.)


And also, if this research is part of his independent research, at the time of publishing what affiliation should be used in the publications. Should it be "Independent Scholar" as mentioned in this link or something else? This is important in academic publications, because sometimes, the person is in a research group, but he is publishing a paper as part of his own researches not the things he is doing in that institute; in this case, has he mention that institute's affiliation or use his own one? So please make it clear that how the affiliation would be when the person does research independently in the cases like when he is not working in a research group or he is working with a professor or research group but his publication is output of his own research activities? It is a little unclear.



Answer



Context: I'm an older PhD student (mid-50s) and had a couple of publications before entering the PhD program. I'm in an interdisciplinary field where there are few well-established research programs. It's very common for PhD students to embark on their own research interests that are different from their advisers. Myself, I started submitting papers after my first semester based on class projects and side projects. I even developed a paper that started as my answer to a question on our Candidacy Exam. I was a research assistant for three years with sole responsibility for a very complex Agent-based Modeling simulation.



To what extent should a graduate student be dependent on faculty members? How can he be more independent and start his own research activities?




Start as soon as possible to develop your own intellectual curiosity. This involves thinking hard about the research in your field relative to the fundamental questions in the field. This is more than "picking sides" in intellectual debates. It involves developing mental models of your field, the various research methods, research questions, and research results. What's important? What is not?


You might start with a single important paper. Look at the section of the paper where they describe opportunities for further research, or maybe limitations. Read other papers that critique this important paper. All the time, you should be asking yourself: "What do I think should be done to improve/extend/solidify this research?"


You could also start with a survey paper, which often include extensive discussions of future research directions.


As soon as possible, you should put your intellectual curiosity into action. I'm fond of class projects and papers for that but not all disciplines have courses that support project work. Either way, "directed reading" courses are ideal settings to write conference or journal papers of your choice under the supervision of a professor (not necessarily your adviser).



Is it a good idea [to do] the graduate work on another topic with the faculty member or work independently on a more recent research topic?



If your intellectual curiosity leads you to research questions/methods that can be successfully done in collaboration with a faculty member, then approach them and suggest a collaboration. If, like me, your interests and ideas lead elsewhere, then do your research independently.




If the person is in a research group or at the university, is it a good idea or is it ethical that he develop his own research interests, besides to the topics which are being developed in that institute?



It's a good idea to develop and invest in your own research interests if they diverge from your research group. There is no problem with ethics if you are open and forthcoming about what you are doing and why. This might go against the cultural norms of the university or research group, but you should make decisions you feel good about in terms of your ethics and values. If other people aren't happy with them or push back, then my view is that is their problem. If they have power, you may suffer negative consequences. So be it. Don't bow before people in power just because they are in power.



How should a graduate student manage this and make some progress in the research fields of his own interest? (In particular, sometimes the faculty members are not interested in the topics you are interested in and the person has to start his own research activity.)



Make a work plan. What is your output (results, papers, articles)? Where will you submit it? In what sequence? How much time will it take -- daily, weekly, monthly? If you can't make a plan that answers these questions, recruit a mentor. It could be anyone who you respect and who knows your field, maybe faculty at your university or maybe someone far distant.


In general, the more you can weave your independent research into your other activities and projects, the better off you will be. That's why I like class projects. But same goes for research assistant work, industry work, or other work. Look for as much synergy between all these activities as you can.



[...] if this research is part of his independent research, [...] what affiliation should be used in the publications? Should it be "Independent Scholar" as mentioned in this link or something else?




No, you shouldn't use "Independent Scholar" as affiliation as long as you have an official affiliation as a graduate student, post-doc, or other. You should always use your primary affiliation, even if it is Physics and your paper is in Art History. The exception is if you have multiple official affiliations (e.g. Visiting Researcher) and your research was done at or was supported by these other affiliated institutions.


publications - Why do we not reinvent the journal system?



I am very surprised that I could not find any similar question here.


It seems to me that researchers from all universities are willing to write papers about their research for free and hand them into a journal to gain reputation. On the other hand, some other researcher do voluntary check the paper in order to examine if the paper is acceptable for the journal. Therefore, the main work is done by researches.


The remaining work for the journal is to offer a platform where researchers can communicate and making sure that the reviewer is selected anonymous and to bundle many articles to a journal.


Now everyone has to pay a huge amounts for the papers, they are not accessible for free to the general public, even though that most researchers are financed by taxes and only the journal is making profit.


Now I wonder, should it not be possible to create a network page for researchers which contains methods to imitate the review process of a paper? So that all papers can be downloaded at the website for free. I guess most researchers would be very happy if everyone could read their work. Also the money that is spend on journals by universities could be spend to this huge network page instead in order to keep it running.



Answer



Please meet the Open Access movement. In the last twenty years, many scholars and librarians did try to address the problem you pose. It is, in fact, a huge issue, and things like this don't change overnight.


The OA movement focused on two main strategies:





  • Publishing in peer reviewed open journals (gold open access): the idea is to create a brand new journal (or to change the model of an old one) which will provide articles free for the readers, without the current subscription model in which libraries (meaning, taxpayers) pay. The crucial factor of Gold OA is the presence of peer review: organize real journals costs a lot of money, and at the moment the major business model is APG (author processing charges), meaning that the author (often, the faculty behind it) pays for being published and cover the journal costs. We're still in transition, and there are a lot of drawbacks: there are predatory publishers who try to scam authors, and big publishers offer the "open access option" charging huge fees (this is also called double dipping, because a hybrid (both Open and Closed) journal will receive the money from subscriptions and the money from the authors. It is important to remark, also, that big publishers make a lot of money with subscriptions and they are actively challenging the open access model. PLoS, for example, is one of the new Gold OA publishers.




  • Self-archiving in repositories (green open access): it is the model of arXiv, Repec, and thousands of other repositories. They can be "institutional" or "disciplinary", and they accept mostly pre-prints, but also post-print articles.




Of course, there are some experiments in the field:




References



Full disclosure: I've worked as a digital librarian in managing OA journals from University of Bologna. I'm biased towards OA and open knowledge in general. Please keep it mind that my answers reflect these bias.


Saturday 25 February 2017

endocrinology - Euthyrodism and goitre


I read in Tortora and Derrickson that goitre is associated with euthyrodism.


How is that possible?



Answer



In this context, euthyroidism refers to the amount of hormone present.


What is a goiter:




The term “goiter” simply refers to the abnormal enlargement of the thyroid gland. It is important to know that the presence of a goiter does not necessarily mean that the thyroid gland is malfunctioning. A goiter can occur in a gland that is producing too much hormone (hyperthyroidism), too little hormone (hypothyroidism), or the correct amount of hormone (euthyroidism). A goiter indicates there is a condition present which is causing the thyroid to grow abnormally.



See also here and here for more of the same info.


ETA: According to this:



Chronic lymphocytic thyroiditis (CLT), also known as Hashimoto thyroiditis, is an autoimmune, inflammatory process that causes up to 55% to 65% of all euthyroid goitres...



Although, as the link I already gave above state, regular ol' iodine deficiency can still cause euthyroid goiter.


human biology - How does the brain know where a signal came from? What is the addressing system


I am an electronic engineer so I am thinking about this from an electronics outlook.


How does the addressing system work, As I see it, the nervous system is small parallel branches attached to larger "serial" lines (spinal cord).


The serial line is then attached to the brain, but how does it then figure out where the message came from and then get the message back to the place it came from.


If I were to build a robot I would have an addressing system with each message and maybe some kind of error checking to make sure the messages don't become corrupted, but as it's not an electronic system I don't see how the brain could possibly do this. unless it is a fully parallel system and there is a single wire going from every sensor back to the CPU..




Answer



The brain knows where a sensory signal came from by what neuron is doing the signalling. The incoming neuron is dedicated to signals from one source and, since it is not shared by other sources, does not need to have an encoding as to what the source was. When your toe touches something, the sensation causes a pulse which, amazingly, travels along a single nerve cell (neuron) up to the brain stem. That neuron has its nucleus at a dorsal root ganglion located by the spinal cord, and has a fiber (axon) that extends to the source (toe) and another extending up to the brain stem. This pathway is called the PCML pathway and the Wikipedia article has some readable details. This page has a schematic and tabular summary, while this site has a good descriptive overview.


If a robot were built along the same sort of design, to determine what was happening at 1000 places in its body, it would have 1000 wires running to its central computer. You probably wouldn't choose to use such a design, but then you probably wouldn't be designing a robot that has to build itself from raw materials.


biochemistry - How do ants follow each other?


I was observing ants in my house.They all were going in a straight line and also some of the ants were coming back through the the same line.



I took some water and rubbed the line with my finger, then the ants were not able to follow each other. Looks like they were confused.


My assumption is that they may had secreted some chemical .


Am I right ? If yes, then which chemical is that and how it is secreted?



Answer



The chemical we are talking about here is called pheromone, trail pheromone to be specific.



A pheromone is a secreted or excreted chemical factor that triggers a social response in members of the same species. Pheromones are chemicals capable of acting outside the body of the secreting individual to impact the behavior of the receiving individuals.1



Pheromones are of mainly 9 types (13 exactly, but 4 not so common) which are:




  • Aggregation pheromones

  • Alarm pheromones

  • Epideictic pheromones

  • Releaser pheromones

  • Signal pheromones

  • Primer pheromones

  • Territorial pheromones

  • Trail pheromones

  • Sex pheromones

  • Nasonov pheromones


  • Royal pheromones

  • Calming pheromones

  • Necromones2


Ants, and many other animals, use trail pheromones to mark their trail as a guide for others in their gang. Other ants, catching the signal of trail pheromone, follow the way it goes and reach their gang leader. Trail pheromones are volatile compounds, so it is not very likely that you would see ants following the exactly same path tomorrow or a week later. All ants release trail pheromones, so as long as ants are going through that path, the trail signal will keep getting stronger and will also tell lost ants "Hey, bro! We are going this way. Don't you want to join us?" See, for example, here3:


trail pheromone working


In the beginning, different ants follow different paths, but as soon as an ant finds the shortest path, all ants join it on that path, due to which pheromones on other paths evaporates and finally, they all walk in straight line.


Of course, trail pheromones are very useful for organisms who have lost their way home, but you know, other organisms, like their predators, are not just sitting and watching them. Some predators can also catch pheromones and find out where the whole team is going, to attack them all at once. Such chemicals are known as kairomones. See this4:



A kairomone is a semiochemical, emitted by an organism, which mediates interspecific interactions in a way that benefits an individual of another species which receives it, and harms the emitter.




Semiochemical is just a type of pheromone which a species X releases, but a species Y can also respond to its presence. Its just like when you walk on road and say "Whoa! Seems like a pizza delivery van just passed by" (obviously, smell of pizza is not by a pheromone ;)


The trail pheromones released by army ants can also be detected by a blind snake or a forest beetle, leading it right inside their nest. Obviously, all semiochemicals are not bad. Chemicals like synomones (helping both species) and allomones (just the opposite of kairomones) are also present5, but they are beyond this question's scope.


References:



  1. Medical Definition of Pheromone

  2. Types of Pheromones - Wikipedia

  3. Life in Wireframe - Ant Algoithms

  4. Kairomones - Wikipedia

  5. These Pheromones Get The Animals That Secrete Them Killed



What is the easiest way to check for plagiarism in student essay papers?


I've had to grade quite a few essay papers in the classes I've taught, and I've suspected some may have plagiarized but I never really pursued check on them because it would be too time consuming to check their sources and pursue any/all possible sources where they may have copied from.


What's the easiest way to check for plagiarism? Is there a search engine tool that one could use to upload a paper and check for it? I doubt it, but other than that, I don't know of any other way to check for it than to put in more effort than I have time for.




citations - how reference a translation of an already translated text?


Somebody wrote a text in Latin, let’s call her Alice and let’s call the text De Nihilo. This text was then translated into German by Bob. In my work, I translate Bob’s translation into English.


In the author–date system of the CMoS style, I have adopted this solution for referencing a translation of an already translated text:



My own translation of the following translation from Bob. (Bob 1987; translation in German of De Nihilo by Bob).¹





¹ “[Latin Text]” (Alice 47BC).



Is my solution the correct one?




evolution - How did butterflies evolve to have eyes on their wings?


Some butterflies, such as the UK native Peacock butterfly (Google Image Search) have markings on their wings that look just like eyes, complete with a white fleck to imitate a convex, transparency effect, as though the "eye" is reflecting sunlight.


Presumably, this pattern is designed to deter prospective predators, because the predator will see a creature with massive eyes looking at them and think twice before attacking.


But how did the pattern evolve? Was the first one a fluke / a genetic mutation that happened to work, or is there another explanation?


For possible bonus points, is there any way of telling when this occurred, and therefore making a guess as to which creature's eye is being imitated?




Answer



There has been quite a bit of study on the development of eyespots. How did they evolve is still unclear, but several experiments have elucidated the molecular mechanisms underlying their formation.


The Wikipedia page about eyespots gives a good basic introduction and some interesting references.


So, first of all, how does an eyespot form?


During the development of wings, eyespots arise at specific locations called foci (singular focus).


If you take cells from a focus in a developing wing, and transplant them into another region of the wing, an eyespot will develop at the transplanted site.


Transplanted focus Adapted from: Pattern Formation on Lepidopteran Wings: Determination of an Eyespot - Nijhout, Dev. Biol, 1980


The photo on the left is a normal wing from an adult Buckeye butterfly, Precis coenia. In the middle and right photos, some cells of the big eyespots have been transplanted in a new position during development. As you can see, a third eyespot develops. Note that the middle photo is from an autograph, that is, the cells were transplanted on the same wing. This results in a shrinkage of the normal eyespot. In the right picture, instead, cells were transplanted in another individual, and this does not result in shrinkage of the eyespot.


The authors conclude that:




It is evident from these experiments that the development of the large eyespot on the forewing of Precis coenia depends on the presence of a small group of cells that lie at or near its center. This group of cells corresponds to a "focus": a small region, occurring in each wing cell, that is postulated to be responsible for the induction of most color pattern elements in butterflies and moths (Nijhout, 1978). Cautery experiments establish an upper limit for the size of this focus in the neighborhood of 300 epidermal cells, though it is probable that the actual size of the focus is much smaller.



They further speculate that a specific morphogen may be involved:



The response of the eyespot pattern to cautery or transplantation of the focus is most readily interpreted if we assume that the focus is the source of a morphogen that is somehow able to induce synthesis of specific pigments.



The idea that a morphogen was involved has been confirmed in later years.


From: Development, plasticity and evolution of butterfly eyespot patterns - Brakefield et al., Nature, 1996



The focus is proposed to be a signalling source for a morphogen, the levels of which determine the pigmentation of surrounding cells. Recent investigations have indicated that regulatory genes, such as the Distalless homeobox gene, are specifically espressed in the eyespot focus.




Wing development


During the development of the wing the expression of the Distalless (Dll) protein (shown in green in the picture) corresponds to the location of the future eyespots.


Several mutations exist that will provoke changes in the eyespots patterns. Some of this with the evoking names of Cyclops, Spotty and Bigeye were analysed in the paper.


Now, without going much into insects genetics (which is far from being my domain of interest), you can clearly see that, although the number, position and size of the foci are affected by the mutations, their position always correspond with an increased expression of Dll during development.


wing pattern mutants
Left column: ventral hindwing patterns of a wild type (top), Cyclops (middle) and Bigeye mutants. Right column: forewing pattern in a wild type (top) and Cyclops mutant (bottom).


From the conclusion of the paper (bold mine):



The selection experiments on B. anynana rapidly produced dramatic differences in eyespot size which were due to genes of small phenotypic effect. The mutants described here show that genes also exist with large phenotypic effect on eyespot development (including size) that have no perceptible effect on other wing or body patterns. It is likely that the evolution of eyespot patterns in nature involves both genes with large and small effects on eyespots development. [...]

These observations suggest that the regulation of the eyespot developmental pathway is such that eyespot patterns can evolve rapidly and independently of other wing-pattern elements and body structures.



Finally, another interesting read is:


Wings, Horns, and Butterfly Eyespots: How Do Complex Traits Evolve? - Monteiro and Podlaha - PLoS Biol., 2009


where the authors propose that:



Complex traits require co-ordinated expression of many transcription factors and signaling pathways to guide their development. Creating a developmental program de novo would involve linking many genes one-by-one, requiring each mutation to drift into fixation, or to confer some selective advantage at every intermediate step in order to spread in the population. While this lengthy process is not completely unlikely, it could be circumvented with fewer steps by recruiting a top regulator of an already existing gene network, i.e., by means of gene network co-option. Subsequent modifications of the co-opted network could further optimize its role in the new developmental context.



Friday 24 February 2017

publications - Selecting Journals or Conferences to publish research work



I am working on a multidisciplinary subject which involves mechanical engineering, chemical engineering and chemistry. I have a decent amount of research completed and now I need to select a journal to publish my work. How do I select a good journal to publish my papers? Also for the same topic I need to select conference to present. How do I select that too?



Answer



In general if you are looking for a journal where to publish a specific type of manuscript do a survey of the material you have referenced. Where are those articles published? You should pay special attention to articles that are multidisciplinary such as yours. The next step if you are uncertain about the appropriateness is to e-mail the journal editors of journals and ask if they consider multidisciplinary articles. I do not think you should send the manuscript to them because they usually do not have time to read anything substantial just to answer a question but do paste in your title, author list and abstract.


As of conferences, I cannot see a patented answer. If a conference is a recurring event you can always go back to collections of abstracts to see if other multidisciplinary papers have been presented. Another option is to see if you cannot organize your own session at a larger conference that permits sessions.


Why do open access consortia affiliate themselves with questionable publishers


The open access publishing world has a number of predatory publishers. Many know about Beall's list which identifies publishers and journals that engage in questionable practices. The existence of these questionable publishers and journals makes choosing a quality open access journal difficult. Consortia like the Open Access Scholarly Publishers Association and the Directory of Open Access Journals seem to promise a level of scrutiny. For example, members of OASPA include the Royal Society and PLoS and while I cannot find a link confirming it, it seems like the AIP is also a member. To me these are above the board legitimate and well respected publishers. There are also members, like Frontiers, that I am not sure how I feel about. I like that Frontiers is trying to push an innovative model of publishing, but I am not sure that I want them to have a large say in defining "good" open access publishing practices. Finally, there are members like MDPI which Beall classifies as predatory and Hindawi which while it never made Beall's list, did make his "watch list".


I think I have two questions. First, why do these consortia affiliate themselves with questionable publishers? Second, how can the academic community pressure open access consortia to consider their members carefully?




Answer




Why do these consortia affiliate themselves with questionable publishers?



Hindawi is a founding member of the OASPA and MDPI, whichever opinion we might have about the quality of its journals, is a major player in the OA business. The OASPA apparently conducted an internal investigation about MDPI and seem to be happy about the results. The question might be more: is the OASPA questionable?



how can the academic community pressure open access consortia to consider their members carefully?



I would recommend not to consider open access consortia as relevant. Then, not submitting papers, not serving on the editorial board, and refusing reviewing tasks for sketchy journals.


On a more general level, one thing we could do is reduce the demand for low-quality, pay-for-publish 'OA' journals by challenging the hiring policies based on publication volume in our local institutions.



protocol - circularizing DNA molecules?


I have been reading about next-generation sequencing technologies that can sequence long reads. Even though the origin of my question is sequencing technologies, the question I am asking is about the basics of DNA biochemistry.


One of the issues in manipulating DNA samples seems to be the ability to circularize long linear DNA molecules into circular DNA molecules. What are the technical challenges of circularising DNA molecules longer than 50Kbp?



Answer



For ligation of a linear molecule to occur, the two ends must come together at the active site of the DNA ligase. In a simple molecular cloning experiment the aim is usually to avoid recircularisation of a cut plasmid vector, and instead to get a new fragment of DNA inserted into the vector. However because the ends of the linearised circular plasmid are tethered together (by being ends of the same molecule) they are more likely to encounter each other than they are to encounter the end of an incoming fragment. This is usually overcome, in part, by increasing the relative concentration of the target fragment.


If you are aiming to recircularise a long fragment then the opposite effect will come into play: the ends of individual long molecules will be much more independent and so the end of another molecule will be likely to compete successfully for ligation. In theory this effect could be overcome by reducing the DNA concentration, but I assume that this is impractical for other reasons.



Thursday 23 February 2017

graduate admissions - How to ask for a recommendation letter?


The recommendation letters seem to be one of the most important aspects of the application.



  1. First of, how will I manage to ask a professor to write a recommendation letter for 5 colleges I am intending to apply to?



  2. Does it make a difference for the professor what school I am applying to (ivy league or not)?




  3. What criteria should I use when picking the professors that will write a good recommendation?




  4. I live in a different country at the moment. Should I go and meet them in person to ask for this?




  5. I burned a few bridges, but how can I influence their opinion at this point and show them how much I have grown after college and how much better I have become and it is partially thanks to them?





I am really scared of asking them. Any tips or advice is greatly appreciated it.



Answer




I have not been a very good student while attending college. Whenever attendance was not mandatory I would probably miss class. My grades were a lot better than people attending every day but it has been cases I attended only few times a class over the entire semester. But my GPA has been 3.8 and did a double major (Both were science majors, 20 credits a semester, in a reputable school).



It sounds like you were a very good student in some ways: first, a 3.8 GPA is excellent. Second, to get those kinds of grades while rarely attending class except when it is required demonstrates a talent in learning and understanding independently: this is very beneficial for graduate school. On the other hand, if you are rarely showing up for class, you are missing most of the benefit of being enrolled in a university. Moreover, a class that you can mostly ace without showing up for might be the right class for a student who is trying to get a degree with minimal effort; it is exactly the wrong class for a student who wants to pursue a professional academic career. The vast majority of students who are going to the very top programs have all of your talent and are using their time as undergraduates to dramatically increase their knowledge and skills.



But I am sure that all of them don't think high of me, in terms of achieving a master's degree.... I went to office hours and was respectful of them. The problem is that I did not act in a very professional manner towards them. I had many personal issues and was still discovering myself at the time, but this is all excuses nobody will understand.




I'm not sure that your old professors do not think highly of you, professionally speaking, and you haven't said enough to explain why you think that. I would describe a large percentage of the undergraduate students I've interacted at with as "respectful but not very professional". Most faculty figure out pretty quickly that they can't expect 18-22 years young adults to behave according to the professional standards of academia (or other adult, professional life). Someone who is 20 years old, intelligent and successful in their coursework but somewhat unprofessional has a good chance to become a 25 year old graduate student who is intelligent, successful in their research and more professional. When it comes to evaluating undergraduates, when tend to look for unprofessionalism and immaturity that impedes their studies and acquisition of the material.


I agree with Brian Tompsett that a large range of suboptimal student behaviors will not factor into recommendation letters (though some will). I think the real problem is not that you necessarily have "burned bridges" with your instructors (although I don't know exactly what you did...) but rather that you failed to cultivate positive relationships with them outside of the classroom. As far as I can see, you have a good shot at getting routinely-good letters from your professors: the kind of letter that says that the student did well in the courses they took, as evidenced by their very high grades....and doesn't say much else. These kind of letters, written by faculty at a reputable institution, ought to get you into a graduate program somewhere, but in my experience will leave you far short of the top places (the Ivy League and others of the same caliber).


Here are (necessarily brief) answers to your questions:



First of[f], how will I manage to ask a professor to write a recommendation letter for 5 colleges I am intending to apply to?



You should begin by composing an email briefly explaining that you are applying to graduate programs and X and would like a recommendation letter. Let the email sit for a day or two and then reread it to make sure that it doesn't sound weird. Then send it. Don't overthink this.



Does it make a difference for the professor what school I am applying to (ivy league or not)?




In my field (mathematics), faculty usually write just one letter and send it to everyone. If they have a substantial professional relationship with faculty at one or more of the institutions being applied to, they might separately contact their, um, contacts at these places, or they may in turn be contacted by them. That's about it. The job of the "one letter" is to calibrate rather precisely the student's potential. For instance, I recently wrote a letter for a student in which I meant to indicate (without saying it in so many words) that they should be a strong candidate for admission at a top 20 program but less so for a top 10 one.



What criteria should I use when picking the professors that will write a good recommendation?



There are whole questions on this site about this, but: you want to strike a good balance between someone who (i) knows you well, (ii) has good things to say about you and (iii) has a status in the academic community that lends weight to what they say. In practice, students who have not been very mindful about cultivating strong relationships with their instructors end up in a situation in which the number of faculty members who could possibly write such a letter is not much larger than the number of letters needed, so it's not such a difficult task.



I live in a different country at the moment. Should I go and meet them in person to ask for this?



It's really up to you, but to my mind this is not worth a serious or long trip. If your email communications are not resulting in faculty agreeing to write letters, maybe reevaluate.




I burned a few bridges, but how can I influence their opinion at this point and show them how much I have grown after college and how much better I have become and it is partially thanks to them?



To be honest, I don't think there's that much spin you can put on the situation at this point. The faculty are writing based on their past interactions with you as an undergraduate, not based on the person you are now or who you aspire to be (there are already parts of the application for you to address that). If you have subsequent academic work or accomplishments, you should certainly convey that to them, but if you're asking how to talk them into writing you a stronger letter...Sorry, I don't think you can.


Good luck.


ethics - Publishing previous results from a previous lab


I just looked over this article from Retraction Watch.


To make a long story short, a student used previous data from their former lab and then published it without the PI's permission or knowledge.


While the above is a rather extreme example of poor ethics, I'm curious where the line gets drawn regarding the ownership of research. I can understand if the data was produced in one environment and then get published in another. What about reagents (clones come to mind) that were produced in a previous lab and then were transported to a new lab? What about ideas that were developed in one lab and then taken to another?



Answer



I think that so long as the principal investigator is actively involved in the planning, performance, or analysis of the research being funded, it is the duty of any researcher working in that group to determine the PI's status as a co-author. However, only if there is no active intellectual activity taking place—in other words, it's an entirely self-driven initiative, then it might be possible to say that the PI doesn't merit co-author status. (Even then, though, the provision of financial support should be clearly recognized.)


Wednesday 22 February 2017

graduate school - Does your Alma Mater and U.S. News Rankings Really Affect Future Job Opportunities?


I'm in the process of trying to decide on which graduate program to attend. I am pursuing a Master's level degree in Computer Science in hopes of furthering my web development career. I would love to be able to teach web development/programming at a community college someday after getting a few more years of industry experience (teaching requires at least a Master's degree). Previously I taught secondary science before transitioning into web development.


I've been accepted to the following programs:


Boston University - Master's in Computer Information Systems / Web Application Development (U.S. News ranked #51 nationally)


Brandeis University - Master's of Software Engineering (U.S. News ranked #31 nationally)


University of Bridgeport - Master's of Computer Science (not ranked nationally)


I keep going back and forth in regards to which program I should choose. University of Bridgeport seems to have a good curriculum and it looks like it will be cheaper (I may get a scholarship), but I'm concerned that it's not viewed as a "top" school. I would be happy to pay for a more expensive school if it helped provide greater opportunities in the future.


Do you find that going to a "better" school has affected your resume to the point that you may have more teaching opportunities after school? I realize that a certain school won't earn me the actual position, but having a highly regarded school on my resume MAY lead me to getting more interviews. Any insights are greatly appreciated.


Thanks and have a good day.





ethics - Is it normal/ethical for student grades to be assigned according to quotas?


In my undergraduate Physics courses, I have heard from my Professor last semester that he got in trouble from the physics department for passing too many students.


This semester, the TA in the lab portion of my class (who grades our lab reports) came flapping around a memo he got, also from the Physics department, stating that the average grade needed to be 75% and he will now be grading accordingly, after a few weeks of normal grading.


I typically spend up to 4-5 hours on these reports, typing up formulas and doing analysis, calculations, etc. I have gotten a 100 on every lab report in my first semester and up to that point in the second. Now, after the ultimatum, I'm losing points for things I didn't before, and being asked for additional analysis that has never been required. I already spend as much time as I can, and this harsh grading feels out of nowhere and undeserved.


Questions:




  1. Is this normal that teachers have quotas?





  2. Should it affect students who actually put in the work?




  3. Does this seem like an ethical issue of arbitrary grading that I should bring up to the department or my professor?





Answer



Yes, this is (unfortunately) fairly normal in the sense that it is done at a number of locations.



The places I've heard it done, the main concern is at a department level, with courses of many sections, in which instructor difficulty has high variability; some instructors are "hard" and others "easy". Admittedly, this causes some initial level of unfairness in the luck of the draw as regards who each student gets for an instructor. The fixed-statistic doctrine forces the harsh instructors to scale up grades to look more like other sections, and so forth (this reduces student complaints to the dean/department). The resulting counter-unfairness is that if lots of legitimately strong students all get in the same section at once, they will be effectively penalized... however this becomes somewhat masked because the grade-data is now mangled, and all you have left are subjective student complaints that are likely ignored. I know that I've had multiple sections of the same course in a semester, taught identically, with wildly varying outcomes (40% passing in one section and 80% in the other).


I think the gold-standard way of handling this would be to have joint tests that are team-graded (i.e., same one or two professors grading each problem and verifying each others' judgement). However, that is logistically expensive and rarely done by tenured academics, I think.


My father had a similar down-grading in a college class, for similar reasons, circa 1966 and he hasn't stopped complaining about it yet.


research process - White Paper & MS in Mechanical Engineering?


I am a Mechanical Engineering student & want to pursue Master of Science with specialization in Design/CAD. Recently I have come across white papers on website of some companies about their products. My friend told me that publishing a white paper would be beneficial for my MS applications. So I wanted to know: 1. What exactly is the scope of a white paper? 2. What sort of topic/information must one put in the paper? 3. How to publish a white paper (I mean is there a Journal for white papers or any other standard)? 4. How much effect does it have in showing my research aptitude compared to a scientific publication/ research paper?




thesis - When to use inline versus displayed equations in a publication?



On a publication (thesis, paper, other), when should I write an equation inline and when should it be separated and numbered from the text?


I've seen publications containing both styles, but I don't know if there is a rule to choose among them. My field is applied computer science.



Answer



A numbered equation always takes a separate line, so there is no question here — if you need to refer to some equation later in the text, it deserves a separate line and it needs a number.


If your equation is as long as a line, or even longer, then again — it should always be placed out-of-text.


To answer the rest of your question, we should think a little how we (e.g. your readers) read inline equations, and how we read equations on separate lines. First of all, inline equations merge into the text, and provide some smoothness (it is just like you speak and draw on a whiteboard at the same time). In contrast, equations of a separate line break the text (just like you write a long equation on a whiteboard and take a big pause to let your audience reflect on it).


If there are no pauses in the text, it is hard to comprehend. Too many pauses raise similar problems, because it becomes difficult to focus on the most important pieces then. My advice is to think about the role of each equation and put only the most important equations in a spotlight of a separate line.


faculty application - What is the appropriate length and specificity for a teaching statement?


A colleague and friend has been approached by another institution (a state university in the U.S.) seeking to fill a position. My friend, who is putting a package together, has asked me to review his teaching statement. Evidently, this was a good idea.


I read the statement, and, quite frankly, I wasn't too impressed. He and I are quite candid with each other, so I'm not too worried about what might otherwise be a delicate issue: me telling him how much it needs to be polished.


That said, I'll admit: I have very little experience with teaching statements (either writing them, or reading them). I'm not usually on faculty hiring committees; I don't want to give him bad advice out of ignorance.


My questions are:


1) What is an ideal length? (So far, I've narrowed it down to half a page is too little, and three pages is too much.) Would a single page be considered too thin?



2) How detailed should it be? My friend talked about different courses he has taught, even mentioning one course by its catalog number. I initially thought that generalities would be better. In other words, instead of saying something along the lines of:



Teaching styles should be adaptable, based on the student demographics in the class. For example, in my Intro to Programming course at Urbandale College, I taught had mostly freshman, but the Programming Languages course I taught at Westerville University, CSCI 352, was a more advanced course with juniors and seniors...



my gut instinct tells me it would be better to say something more general, such as:



Teaching styles should be adaptable, based on the student demographics in the class. For example, I've taught some courses with mostly freshman, and other more advanced courses with juniors and seniors...



but perhaps I'd be dishing out out some bad advice if I recommended a more general wording; maybe applicants are expected to weave such details into their teaching statements.



Answer




My answer comes from Mathematics, but probably it's quite similar.


1) 1-2 pages is pretty typical.


2) My general advice is to include details and concrete examples where possible (though course numbers are not necessary). One problem with just being general is such statements feel very generic, and lack any real content in the sense that they don't distinguish you, in the same way many political speeches turn out.


funding - Donating money to scientific research after my death


I'm lucky - I probably won't have to provide for any loved ones after I die (they can take care of themselves). That means I can use my assets on whatever I want, and most likely, that will be science. The exact amount I can spare depends on how much longer I have to live, but an order of magnitude estimate is $10 million.


I understand that most funding requires proposals from the scientists, which are then peer reviewed. I'm not particularly interested in that. Instead I'm thinking of finding people working on what I'm most interested in (cosmology) and funding them to do whatever they want, trusting in their integrity to use the funds appropriately.


Questions:



  1. Is it better to use the funds as a one-shot lump sum, or make it sustainable (that is, keep the principal, and use only the interest on that for funding)?

  2. What is a good amount to provide a single professor? Is it better to provide one researcher with the $10 million, or ten different researchers with $1 million, or some other number?

  3. How do I go about this? Can I just ask for the professors' bank account numbers, and write in my will to transfer $X into that account?

  4. I'd like to talk to the professors, preferably face-to-face, to assess their character. Are the professors likely to be willing to talk?



EDIT: Thanks for answers. I'll need to think about it. I'm not keen on funding PhD students since there're already too many graduates and too few permanent positions. I'm also not keen on funding a fellowship because when I wrote my own applications there were so very many fellowships, many of which required their own separate application. I'm hoping to make things easy.


I also want to free some scientists from spending so much of their time writing funding proposals. Endowing a chair is a possibility but that ties the money to a single university, which is again something I need to think about. Hopefully there'll be many more years before I die to sort all these out, and thanks again for answers.



Answer



Funding people instead of projects is in fact a good idea if you are interested in a supporting fundamental research problems to be addressed. There are multiple ways to go about this, and it's a reasonably well established principle, so you might want to search around a bit how other funding organizations and (non-profit) foundations approach this.



  1. Lump sum vs. funding from interest is really a choice between aiming at one or two breakthroughs within a period of 5 to 10 years vs. continuously supporting research in a specific field, on a smaller scale, over 50 to 100 years. This relates to the answer of the next questions...

  2. Amount to give to a single professor: A strategy for short term funding (using up the capital) would be to fund the establishment of a new research group, i.e., pay the salary of someone early in their career (assistant or associate professor level) plus some funds for research staff (PhD students and post-docs). I would recommend a funding level of $2M (that is what the Consolidator Grant of the European Research Council provides for a period of 5 years) to $5M per professor, depending on how much expensive equipment and materials are needed to do this research. That means you could fund 2 to 5 such groups. After the period of funding at that level, these persons should have achieved sufficient research results to be self-sustainable, though you cannot be sure that they will continue working on the kind of questions you aimed to fund. For long term funding, I would recommend donating the whole sum as a Financial endowment (see Endowed professorships) to one university. If you assume an interest rate of 1 %, it will pay $100k per year, which might be just enough to pay a professor's salary, or, if the university agrees to pay the professor, could be used to fund 1 - 2 PhD students or post-docs working with the professor.

  3. How to spend the money: Don't transfer that money to a professor's private account. Professors get research budgets from their universities, and if the funder wants to, the spending restrictions can be extremely flexible while still making sure that the money is only used on research related costs. So you either need to make an agreement with a university for them to administer the money according to the stipulations you agree on, or set up a foundation that administers the money and pays it to universities, who then put it in the research budget of the professors that it's meant to support. For the first option, you may want to contact a university's alumni or financial office, or maybe the dean of a department in the area you'd like to support.

  4. Don't plan to select the persons you're funding yourself. First, it's better to fund young researchers, and if you talk to potential candidates while you still can do it, I'd hope that these will be old, or at least senior researchers, by the time the money becomes available. Instead, choose the persons that will do the selection. In the endowment case, that would be the university department that gets the endowment. Make sure that the general research direction and overall functioning of the department fits to your aims, and only select them if you're reasonably confident that they will use the money according to your aims. In the non-profit foundation case, I'd suggest setting up an advisory board with reputable scientists in the field you'd like to fund, and let them run the selection. Keep in mind that the composition of this group (institutions they come from, character, etc.) will be an important factor in who they select for funding. If this is going to operate over a longer time, make sure that there are regulations in place how new persons can enter the advisory board when you won't be there anymore.



Tuesday 21 February 2017

An alternate cure for AIDS?


Is is possible to cure AIDS patients by using white blood cells of blood cancer, by fooling HIV to attack a false target?


Is it possible to wrap HIV in a physical boundary, such that it has no interaction out side the wrapper, so the functionality of the cell will not be affected by HIV?. Since all cells in out body are replaced within three years, after 3 years, the HIV affected victim will have fresh HIV free cells.



Answer



What would you choose when your treating physician gives you the option: leukemia or antiviral treatment? HIV is not lethal anymore these days, at the least life expectancy can be substantially prolonged. Admittedly, treatment is life long and not a cure, but you'll live.


Leukemia on the other hand, is life threatening and needs immediate treatment. Treatments for leukemia are primarily chemotherapy, and perhaps radiation therapy, biological therapy, targeted therapy, and stem cell transplant, all of which are by no means guaranteed to be curative.


But interestingly: a Berlin leukemia patient with HIV was actually cured after receiving chemotherapy and having received HIV-resistant stem cells to repopulate his white blood cells (Source: Medicine Net). The donor carried the relatively rare mutation called CCR5delta32. People with this mutation lack functional CCR5, the protein that HIV most often uses to enter cells.



Why is this not a standard treatment? The Berlin patient serves as a good example, because the patient suffered intestinal and neurological symptoms due to the chemotherapy. And besides being dangerous in itself, chemo is truly a grueling experience to go through. And in fact, this patient was the only instance in which this approach was followed (Source: Medicine Net).


citation style - How to cite indirect sources in CSE/CBE (name–year) system?


I’m writing my first review paper and I don’t know much about the CSE system. I couldn’t find the indirect citation rule for CSE (but for others). So how do I cite indirectly in this style?




Is there any appropriate way to offer cash to a lecturer or TA for private tutoring?


Due to financial issues, I've had to work in order to support myself alongside my degree, and unfortunately due to work obligations I've had to miss some lectures and classes. Due to not spending much time at the university, I also don't have many friends who would be willing to help me catch up.


Would it be appropriate in any way to ask the lecturer or the class TA to help me on a 1-on-1 basis? I think I've managed to fall behind sufficiently far that I would need several hours of help to catch up -- could I possibly suggest to the professor that I can offer you £50/hour for your time? I don't want it to be construed as bribery or anything inappropriate -- I just want to pay the person fairly for his/her time.


Is there an appropriate way to do this? I know that in my high school some students paid teachers for 1-on-1 tutoring, but I'm not sure how it works in university?


For context, I'm in the United Kingdom, I'm doing a master's degree, and the end-of-term examinations are administered anonymously (i.e. the person grading does not know whose paper he/she is grading).




Monday 20 February 2017

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


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


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


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



Answer



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


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




It's supposedly some unknown research center somewhere in Europe



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


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


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



Online material on the cnrs isn't helpful at all



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



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


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


phd - What are the main goals of administering preliminary / qualifying exams to graduate students?


If I were a Spanish Major as an undergraduate and decide to pursue a PhD in a completely unrelated field (like Theoretical Physics), it makes sense to give a qualifying exam to check that I had the necessary skills to begin the program. But if I'm coming from a B.S in math to a PhD program also in math, it doesn't seem to make sense to give a qualifying exam, as if the knowledge I gained in my undergraduate was insufficient. I presume that one is accepted into a PhD program because he/she has already demonstrated the "qualifying" skills. Thus, I'm baffled by the notion of the qualifying / prelim exam. I'm curious about the ultimate goals of these exams, and how they relate to the professional development of a graduate student.



Answer




This answer serves mainly to corroborate @Anonymous Mathematician's answer.


As she says, the most important thing to realize is that there are two different kinds of exams that go under the name "prelims / quals". The first of these generally:


(i) tests undergraduate material
(ii) is administered soon after arrival in the graduate program
(iii) used to be used for preliminary weed-out purposes but is now -- at least, in most programs I know about -- used almost entirely for diagnostic purposes.


Probably (iii) is most important: once upon a time, many graduate programs -- even excellent ones, like Berkeley (in fact, especially Berkeley) -- admitted lots of students, as in up to 50% more than were expected to finish. The idea was to give a large group of people, including those with less than sterling (or ivy) pedigrees, a fair shot. Then after a small amount of time in the program -- maybe a year or less -- they would take a "prelim" exam, and a significant portion would fail and leave.


This is no longer the way graduate programs work (at least not in North America, which is what I am primarily familiar with, but to the best of my meager knowledge they don't work that way in other parts of the world either). We pay much closer attention to each student we admit now than in the scenario above, and further our program is judged on retention and completion rates. A graduate program in 2012 who dismissed a third or more of its incoming class every year would look disastrously bad by these sorts of metrics. So this "weedout prelim" is, as far as I know, a thing of the past.


In the graduate program at UGA we still give a "prelim exam" to all entering graduate students, but as I said above we use it almost entirely for diagnostic purposes. In fact we have a certain graduate course designed entirely for students who didn't do well on the prelim, whose purpose is to shore up their undergraduate knowledge ASAP. Other than being encouraged to take this course, there are no direct consequences of failing the prelim (in fact, I'm not sure that one "passes" or "fails" the prelim in any technical sense).


In contrast, most of the "qualifying exams" that you hear graduate students talking about are something entirely different. They:


(i) test graduate level material; in particular, most students do not enter equipped with the knowledge to pass most qualifying exams.

(ii) occupy students' attention for a while: in our program, students have up to three years to pass their qualifying exams.
(iii) really must be passed in order for students to advance in the program, in most cases.


I hope this answers your question. Let me say though that the scores on the "prelim" exam -- i.e., the undergraduate level exam that I mentioned first -- are often all over the place. All of our entering students have at least an undergraduate degree in mathematics. So, unfortunately, no, an undergraduate degree in mathematics is not a guarantee of ability to do undergraduate level mathematics...at least not to the satisfaction of a decent mathematics graduate program. (And a student who does poorly on this entering prelim may yet succeed in doing PhD level mathematics a little later on: that is, the fault often seems to lie with the undergraduate program more than the student.)


evolution - Are there any multicellular forms of life which exist without consuming other forms of life in some manner?

The title is the question. If additional specificity is needed I will add clarification here. Are there any multicellular forms of life whic...