Thursday, 28 February 2019

peer review - Can reviewing papers help increase your credibility as a researcher?


I was wondering if reviewing papers for established journals was a way to increase ones credibility as a researcher?


My question is related to the fact that the journal editors, that are (frequently) known scientists in your domain, will read the review you made.


I was wondering if we can therefore assume that they will, to some degree, evaluate your reviewing work, and therefore yourself as a scientist, based on your review? Lets imagine I know the editor, and I might want to have a position in his/her lab, then my reviewing work might weight in my evaluation?



Answer



Just to add to the other answers with some other points to think about in terms of profile:





  • Reviewers for conferences are often made explicit as Programme Committee members. People who do good work in the PC eventually become Senior Programme Committee members, then Track Chairs, then Programme Chairs, then General Chairs, etc. Even PC membership for good conferences helps your academic profile, where higher-up positions help even more.




  • Journals work a little differently since reviews are solicited directly and are typically not noted anywhere public (with the exception of some journals employing a transparent peer-review model). But in my case, I was invited to the Editorial Board of a new journal in my area on the basis of my reviewing work for them. If you do good reviews, editors will notice. (Of course, this might not always result in an EB membership, but ...)




  • Conferences and journals (at least in CS) sometimes award "Best Reviewer" awards. I've picked up a couple of these and they look good in CVs.





Of course, reviewing in a community is an excellent way of keeping your finger on the pulse of not only what are the hot topics, but how papers in the area are evaluated (this is esp. true for serving in committees of conferences where seeing how the sausages are made is an enlightening experience).


(And on a more philosophical note: I always saw reviewing a bit like seeding in Bittorrent. Submitting lots of papers for review but never doing reviews is plain greedy. Complaining about the quality of the reviews you get and then doing crappy reviews is hypocritical. ... not so related to the question, but it's good to vent now and again.)


undergraduate - Which is preferable, to go to graduate school at same school as undergrad or to go to a lower-ranked school?


I've heard from people that generally, it's a bad idea to go to the same school as your undergrad to get your graduate education.


However, in the situation that you get into only your undergrad school and a few much-lower ranked grad schools, what would be the better school to pursue?



Answer




I've heard from people that generally, it's a bad idea to go to the same school as your undergrad to get your graduate education.




The word "generally" is commonly used in two rather different senses. The first sense is "typically", "most often". The second sense -- perhaps more common in mathematical and scientific writing -- is "always", or "in the largest possible scope which might be applied". The quoted advice is valid if "generally" is construed in the former sense, not the latter. To briefly explain: on the one hand, there are advantages to acquiring a diversity of experience. "Great University X" will do its business in a way which is slightly different from "Great University Y". Experiencing this is very valuable, because if you stay in academia you will probably be affiliated with several more universities, different from each of these. If all of your student experience is at a single place, you will have subconsciously internalized the universality of your experience, and you'll be in for a rude awakening when you learn that what is obviously best to you is not the practice in your new environment. Then too, by going to different great universities, you meet different great people (many of whom will know each other and will be in transit to/from other great universities), both students and faculty. This is also very valuable.


On the other hand, there are situations where it is most advantageous to stay where you are. For instance there are sometimes personal, family or financial considerations. Even neglecting these, there are times that the university you attended as an undergraduate is truly the uniquely best option for you to continue your studies, or the best option among those available to you. If you are an undergraduate at UCLA, if you want to study analysis, and if you did not get admitted to Berkeley, MIT, Chicago, Princeton or Stanford, then staying where you are sounds like an excellent (perhaps optimal) choice academically. If you've already done successful research with a top faculty member at your current program and you truly want to continue that research most of all: yes, think seriously about staying right where you are.


The other answer says that graduate school rankings is "a little ridiculous". While I don't really disagree, let me try to put a finer point on that: grad school rankings are ridiculous if you take them too seriously, and especially if you regard them as a strict linear ranking. It does not matter that US News and World Report currently thinks that MIT is the best mathematics department in the US whereas in past years it used to think it was some combination of Harvard / Princeton / Berkeley. It would be more honest and more helpful if they simply recorded that these departments and several others (Chicago, Stanford,...) are in the uppermost echelon of graduate programs in mathematics. Asking whether Harvard is better than Stanford is ridiculous: it depends upon what you're studying. (If you want to study analysis, don't go to Harvard unless you know you want to work with the one faculty member there who does that.)


Students should be thinking of departments in terms of echelons. Within a given echelon, ranking is not helpful. However, barring some truly exceptional circumstances you want to go to a program in the top echelon that accepts you. As a corollary to this: if your undergraduate institution is in the top 10, and every other program you've gotten into isn't in the top 30, then yes, I think you should stay where you are, unless you have a very good reason to go to a lower-ranked department (best reason: there is a superstar there that has agreed to work with you).


Finally though I have to say that I find it slightly odd that the OP has apparently gone to a top department, been admitted as a student to that top department, but not at any other department of comparable quality. That suggests to me that her application is not as strong as it could be, as those who know her in real life apparently value her more highly.


how to evaluate the quality of scientific journal?




Hope that the question is not a duplicate, I could not find anything similar.


I am doing a PhD in mathematical economics but I usually look at math journals and I am trying to adapt some technical methods from there to economics when it is necessary.


What I am always curious about, as I am not familiar at all with mathematics journals, I don't know which journal is a good quality journal in mathematics (as there exists a huge bunch of journal in mathematics, if I am not wrong) I don't know if the paper published in the journal is a really credible reference.


Besides Google Scholar citations, what are the best ways to understand if a journal (in the field of mathematics or other) is a well ranked journal ?



Answer



There is no straight answer, since as Tom commented, "good quality" can have several meanings. Further, a journal can be considered good for a specific domain and not for another.


What I usually do:



  • Check the impact factor (and compare it with "known good" journals),


  • see some of the published works (Usually to discard automatically accepted stuff that has horrible english and worse results...)

  • Talk to other people with more experience. In your case, what do you advisor thinks? Or any other professors that usually publish in that area?


Another interesting concept is if the journal is correct for your work.


Nature is an awesome journal, but I caters to specific domains and requires a very high quality article. Sometimes it makes more sense to send the work to a "less good" journal that is specific to your domain and which "matches" the level of your work. As long as there is a proper review involved, it works.


(For instance, sometimes you don't have time to further develop something, or there is not much more to be done/improved, etc... instead of "losing" the work, you publish it in a "reputable", "less good" venue)


The ability to match work <-> journal is important and comes from experience. If you don't have it yet, ask for the help of someone who does. That's why advisors are there! :)


salary - How are instructors compensated for teaching a Massive Open Online Course (MOOC)?


This question prompted me to wonder what compensation comes with teaching a MOOC. Most of these seem to be sponsored by universities, but my university doesn't offer them and neither did my PhD institution so I have no first-hand experience on the instructor-side.


Obviously, most participants do not pay for them (some do, I guess, but I have no idea how many and they're obviously paying much less than university tuition). So, it seems unlikely that teaching such courses pays for the instructors time.



Thus, I ask: does teaching these come with compensation of any kind? Salary/bonus? Teaching load reduction? Release from service? Teaching assistants for the courses? I'm interested in compensation either from one's university or from the MOOC provider (Coursera, Udacity, edX, etc.).




physiology - How does extracellular potassium ion concentration and calcium ion concentration affect the excitability of a cell?



When extracellular $K^+$ concentration increase by a certain amount, excitability of cells is higher because the resting potential shifts toward a higher equilibrium potential of $K^+$, therefore causing depolarization. However, when there concentration of extracellular $Ca^{2+}$ increases, excitability of cells decreases. If $Ca^{2+}$ and $K^+$ are both positively charged ions, what is the cause behind their opposite physiological effects?


I'm not a biology student, so detailed answers would be kindly appreciated. Thank you!




Wednesday, 27 February 2019

writing - How to reduce a paper's size for a page limited conference?


This is a usual problem of mine, I have a page limited conference (usually 8) and my paper is 15 pages long, or in a less dramatic case 10.




  1. How do you go about taking stuff off the paper. Do you have any rule of thumb?




  2. How do you know what is "irrelevant" enough for you to take it out of the paper?






Answer



Before you go about the longer process of deciding "what to delete," have you first tried to remove the "dead weight?" Academic writing is often quite leaden in style, and can be trimmed quite substantially. Following Strunk's commandment to "omit needless words" can often cut down a page or two out of your manuscript without sacrificing "actual" content.


If, having pruned your text, you find you still need to reduce things, ask yourself the following question:



What information do I want my readers to retain?



Then ask yourself:



What sections of the paper do not provide information necessary for the reader?




Those should be a fairly good guide about what to delete.


international - Feasibility of moving from US to France for a postdoc opportunity


Recently I ran across an international postdoctoral opportunity, which seems quite interesting to me. While I would prefer to stay in academia in United States, there are various factors that enable me to consider that opportunity, including potential for work on an interesting and important topic as well as an opportunity to immerse myself in somewhat different cultural, language and, perhaps, academic environment (thanks to my relative freedom from family obligations at the present time).


The problem is that the opportunity is at one of the universities in France, which creates several issues (beyond the obvious one of being accepted). The issues (and corresponding questions) are somewhat specific to my situation, but, at the same time, likely rather common to many people, who are originally from non-Francophone countries. Specifically, I'm concerned about the following.





  • How feasible is to consider such an opportunity from the foreign language perspective? I am talking about the fact that I practically do not speak French (discounting a very limited number of popular words and phrases)? While English language is considered a de facto universal language of science, I expect this aspect of academic environment to vary significantly from country to country (probably much less from university to university, even in major cities).




  • Combining that assumption with my, perhaps, incorrect knowledge that English is not as popular second language in France as in some other European countries, such as Sweden, this aspect brings an additional potential challenge of everyday living in a foreign language environment. I am aware of the fascinating approach of learning languages by immersing yourself in different cultural/language environment, but I'm not sure that it is such a good idea under the circumstances, considering that a postdoc position is demanding enough already. Thus, I am curious about the following question: is that a real challenge and to what extent?




  • How feasible is to consider such opportunity from the perspective of me being a US citizen without French work visa or similar documents in hand. I realize that, typically, AFAIK, selected international candidates' visa documents are processed by hosting universities. However, the question is this: how significantly the potential burden [financially and time-wise] of visa processing and, perhaps, relocation negatively impact hiring committees' decisions and, thus, reduce international postdoctoral candidates' chances to be offered a position of interest? I am interested in answers to this question from both general and local (France) perspective.







arthropod - Identification of an insect found near Shirdi, Maharashtra


Insect found inhouse near Shirdi


I found the insect nside house near Shirdi, Maharashtra. I have captured the image




cv - What to write in an impressive about me section


Can you give me some suggestion on how to write an impressive about me section in my cv?


I know I'm supposed to give relevant information (I'm a scientist, by the way) which is not directly covered by my academic background and career, but basically I don't have a clue about what to include (for example, should I add the description of some traits of my personality?).


I'm particularly thinking about some sections of the second page of this one www.teemeurope.eu/documents/europeanCVformat.doc namely PERSONAL SKILLS AND COMPETENCES and OTHER SKILLS AND COMPETENCES and the linkedin profile



Answer




It looks like what you are being asked for here is sort of a hybrid between an academic and conventional CV. I dislike this sort of form filling CV but if its what you've got to do...


Personal skills and similar sections generally are looking for your soft/transferable skills. Good communications, team-working etc. Try and not just state these but add some qualification e.g I'm good team working which I have developed/demonstrated during whatever project or competition or something. It's very easy to say you have some skill but far more convincing if you can demonstrate it. Similarly be prepared to defend anything you say in an interview.


For an academic CV you should focus more on your publications and academic work etc. and keep your personal skills section fairly short. When given silly form type CVs to complete don't feel obliged to complete all the sections. I would definitely just remove the Artistic skills section if I was doing this (I have none!).


Here is a similar template which also has some basic instructions and an example (admittedly non-scientific) http://europass.cedefop.europa.eu/en/documents/curriculum-vitae/templates-instructions


For advice on writing actual academic CVs see http://www.careers.ox.ac.uk/wp-content/uploads/2012/10/Academic-CV-2012.pdf


phd - Supervisor not approving submission because of coauthor he didn't approve of


Okay I'm pretty desperate here.


I'm a PhD student. I had a cosupervisor (Prof Y) that my supervisor (and head of center, Prof X) removed (without consulting me) from my project and assigned (again without consulting me) another cosupervisor (Prof Z). The assigning of cosupervisors to a PhD project at my university happens with a form that both the new cosupervisor and the student need to sign, which I did not, and thus my supervisor (Prof X) thinks he's (Prof Z) my cosupervisor, but formally he isn't.



I have a publication ready that he (Prof X) needs to approve before I submit. His major issue with the paper is the fact that as a coauthor I have added my ex-cosupervisor (Prof Y), who indeed has scientific contribution. I received an email telling me that he has not been informed that I was working with my ex-cosupervisor (Prof Y), that this is not normal practice and that he (Prof X) won't approve the submission because of this.


Does he have the right to do this? Where is the academic freedom in policing who I collaborate with to such an extreme extent?


Please let me know your thoughts. I feel like I'm losing it.


UPDATE: I've contacted the vice-dean. He's going to look into the situation as I forwarded everything to him and tell me his opinions. He was shocked that my supervisor/HoC needs to also approve submissions.


UPDATE 2: Vice-dean has encouraged change of supervisors. He will support me throughout the process and will handle all economic issues himself. I'm arming myself with all the legal matters now. I'm making a meeting with prof X to politely explain that this is happening.


UPDATE 3: I changed supervisors. I lived. I'm so much happier. Thanks for the encouragement.




Tuesday, 26 February 2019

graduate admissions - The GRE: Why does this still exist?


I did my undergraduate degree in the US and am heading to graduate school here in less than a month, so I myself have taken the Graduate Record Examinations (the general as well as two subjects tests) and I guess it always just seemed as a sort of un-avoidable formality that nothing could be done about, and so I just took it and got it over with.


In the intervening year between undergrad and the start of my Ph.D. work, however, I traveled overseas to Cambridge where I found that I was quite mistaken: the GRE is very, very avoidable. The solution is simple: don't apply to universities in the US.


By the time I had arrived there, I had already gotten it over with myself, but for most of my peers there, this was not the case, and quite a few of them had simply decided to not even bother applying to the US because of the inconvenience that comes along with that in the form of the GRE.


This made me wonder: are admissions committees at US universities aware of the number of highly qualified candidates they miss out on because of the GRE?


I could understand being willing to miss out on the potential recruitment of these students if the GRE were a significant part of one's application, but I have yet to find any US professor tell me that the GRE scores are weighted highly when it comes to making admissions decisions (perhaps I just haven't asked around enough?). In fact, I've often been told it's the least important factor when deciding whether someone should be admitted. (Indeed, my impression is that the general GRE is more or less a joke and only serves as a convenient way of tossing out applicants who would have been found un-qualified for other reasons.)


Putting aside for a moment the issue of those who decide not to apply to US universities, let's consider the inconvenience faced by those who do. Once again, if you're from the US, I can imagine simply not being aware of this (I know I wasn't), but I now know of several people who have had to fly (sometimes the flights have even been inter-continental!) in order to sit to take a GRE test. And even for those who don't (like probably most of us in the US), there is the ridiculous price: almost $200 for the general and an extra $150 per subject test. I was under the impression that admissions committees encourage people from all backgrounds to apply, rich or poor, but how can they honestly expect this to happen if even those who don't have to fly have to shell out anywhere from $300-$500 in addition to the application fee? (I personally find it a bit nuts that these tests cost several times more than the application itself.)


So, could somebody please explain to me why we still require students to take these things? Do they really add information about the applicant and their abilities that could not be found out any other way?




career path - Will taking a post-doc position harm my future chances in industry?


I am 29 years old and am about to finish my PhD thesis in the field of remote sensing (i.e. somewhere between computer sciences and geosciences in a broad sense or applied signal and image processing in a more narrow sense) at a university in central Europe.


Due to the fact that there are only few tenure positions available in science and I would rather stay in my (economically strong) home region, I want to find a position in industry in the long term. However, I have received an interesting offer for a post-doc / scientist position in a new-to-be-founded research group with great funding and cutting edge research in the applied signal processing field.


My question now is: Will some additional years in academia harm my chances concerning a job in industry?


Some additional points to consider:





  • in the post-doc position, I would be the deputy of the group leader (who is soon to receive a full professor/tenure position)




  • I'd be responsible for staff management and some budget issues (about 20% of time)




  • I'd have the chance to travel to international conferences





  • the application the signal processing research is carried out for is not directly industry-relevant




  • I have received an invitation to an interview for an R&D job at an automotive company, but it is scheduled only in 3 weeks, while I have to decide for the post-doc offer sooner rather than later






Monday, 25 February 2019

publications - How do Academic Journals protect against empirical results given by bugs?


As the title says.


My background is in Economics/Finance(mostly), many topics in those fields (and I am sure other fields) require fairly complicated programming, enough to where one can easily screw something up. How do Academic journals defend against results that are generated by bugs?


As far as I understand nobody ever sees my code, it could be hundreds or even thousands lines of garbage code without a single function in it (not to mention no unit tests) laced with bugs, and I kept "fixing" things until my results "made sense", and then happily reported them. How could a journal tell that my results are trash?



Answer




Journals never make any guarantees regarding the validity of the content published in them, though this may seem to be implied. Ideally, errors are caught during the review process. Note that this problem is not specific to programming bugs, subtle errors can occur in all kinds of settings including physical experiments. It is important to always be critical about any results in any article, even highly cited articles in top journals (though these are less likely to be wrong, they still might be).


Letters to the editor are not uncommon in my domain when questionable results are published. In a worst case scenario, published papers can get retracted after the validity of their results has been formally rejected. Retractions for this reason seem to be fairly rare, though.


This is one of the reasons why reproducible results are so important. If several independent researchers seem to reach similar conclusions, they are likely correct.


copyright - Do publishers simply waive their exclusive rights without any resistance?


Assumption based upon my experience from CS: Typically, the business model of academic publishers is to archive and disseminate papers whose authors have transferred exclusive publication rights to the publisher. Sometimes, there are limited provisions such as authors being allowed to host a copy on their personal website. In general, though, the revenue of publishers is based upon providing paid access to the papers.


This is reflected by the choice authors often face upon publication:



  • Transfer exclusive publication rights of the paper, pay nothing.


  • Retain publication rights so as to provide open access to the paper, pay a (usually substantial) fee1.


Now, the fee in the latter case is obviously the way publishers make up for their loss in revenue by not being able to restrict access to the paper to paying subscribers. This is discussed e.g. here and here.


Point of this question: Recently, the University of California has announced a "Presidential Open Access Policy" (other announcement, other article). In short, it sounds like all university employees are asked to transfer rights to their papers to the university prior to transferring rights to any commercial publisher. Furthermore, the announcements make it sound as if the consequence were that publishers simply do not receive exclusive publication rights and the university provides open access to the papers in addition to the publishers, all else apparently equal.


Now, to me, this raises a huge question mark and some speculation. In one question, I am asking here: How does this actually work? But to make things clearer and more explicit, I'm going to list the various facets of this big question one by one:



  • To my knowledge, universities weren't the obstacle so far when it came to publishing as open access. Publishers were, because they wanted exclusive rights or a substantial fee, as described above. How is it that a university policy can change this?

  • Do publishers readily provide a modified license transfer agreement because of such a policy? One that does not insist on exclusive rights? Otherwise, granting rights to the university first, and then signing an exclusive copyright transfer agreement sounds like the author is on their way to committing copyright infringement (or at least a breach of contract) themselves, rather than a witty way around the publishers' restrictions.

  • Is this actually a legal loophole that allows authors to circumvent the publishers' wishes? If so, it would seem quite an obvious loophole ("Don't want to transfer exclusive rights? Easy. Just grant someone else rights before."); why isn't everyone doing it? Is the University of California administration just the first to have the idea for some reason?

  • Do publishers just comply with this because the University of California is a comparably "big player" (as the press release states, "the UC system is responsible for over 2% of the world’s total research publications")? Even if so, what do publishers gain from complying? One might say they're not getting less, they're getting absolutely nothing.


    • And even if so, how would UC threaten them? Would they threaten to use only their in-house publisher, which offers free open access hosting in accordance with the policy?

      • Does the in-house publisher actually offer free open access hosting? It seems like UC Press relies on its sales just like commercial publishers.



    • If so, would the in-house publisher offer that hosting also to non-UC employees? Otherwise, it would seem unlikely that any journal or conference would switch to that in-house publisher, hence such a boycot would amount to banning oneself from participating in research for at least some months (if not years), until the boycot has an effect.



  • Is the University of California simply testing its limits here, as a part of an ongoing legal battle of varying degrees of copyright enforcement by publishers and varying degrees of copyright infringement by authors and their institutions?


  • Does the policy actually mean that all university departments are obliged to pay the open access publication fee to the publishers (i.e. requests by employees to get reimbursed for such a fee cannot be dismissed)? I was told (and hence cannot provide an accessible reference) for wealthy universities like the University of California, the open access publication fees in the lower thousands of dollars per paper might be negligible (?)

    • The latter speculation might not apply completely. Other wealthy universities are having issues to pay for subscriptions, and in numbers, these issues seem to be well in a range where one might get by paying all those open access fees, as well. But ... is this maybe a bureaucracy thing? Library subscriptions have to be paid from some (relatively limited) permanent account, whereas open access fees would apply upon publication and can thus be paid from (possibly much more generous) research grants?



  • Or of course: Am I missing anything crucial about the announcement?


1: For instance, ACM charges (for non-members) USD 900 per conference paper and USD 1,700 per journal paper.




publications - Thanking a "shepherd" in acknowledgments


I often find in many conference papers submitted by US research groups that paper writers would thank their "shepherd" in the acknowledgment section. What is the exact contribution of a "shepherd" to a paper submission?


I'm speaking about my domain which is computer science and I'm not sure about the situation in other domains.



Answer



CS conferences often ask a member of the Program Committee who reviewed a paper which is accepted but has some problems to help the authors fix it up for publication. This person is usually called a "shepherd" for the paper with the overt connotation to people who mind sheep in a field. The problems with such a paper can include English language problems, other kinds of bad formatting, the need for a few additional results or cases, or the elaboration of some component of the work that was insufficiently described. This is all done in order to increase the quality of the presentation of otherwise excellent work.


APA Citation of Website With No Author Mentioned


I get conflicting information about APA website citations from different sources. What is the best way to cite website documentation in APA style? For example, if I want to cite an announcement website about Apache Struts project releases (with no author given), do I cite it as: Apache Struts Team. (2018). Announcements 2018. Retrieved from https://struts.apache.org/announce-2018.html


And in-text citation would be given like this? Struts 2.3.36 was released as a "General Availability" release on October 15, 2018 (Apache Struts Team, 2018).





Masters Thesis: Self-containment



So I am currently writing my thesis in nanophysics (in particular, applications of nanomagnetism). My adviser and I had a few discussions about the inclusiveness (i.e., self-containment) of the material, quality of figures, etc. He does not seem to care about neither of these points, and just wants the thesis to be done so that 'I carry on with my research'...


I am now wondering:



  • Is it typical (or preferred) for the masters thesis to be rigor/self-contained, in terms of literature review? (I said masters only, because I assume it should typically be the case for a PhD dissertation - no?)



Answer



The best advice I heard about this is: Write the thesis in the way you would like to have had it at hand when you started your thesis. Imagine yourself in a situation that you are a master's student and want to learn about the very topic of your actual thesis. What detail do you need? What background should you give? What literature should you refer to?


I often hear students say that their advisors do not really care about these issues, and indeed it's somehow true. As an advisor, you care much more about the content. This does not mean that the presentation does not matter, but it is not that much about what background you give, but how. Do you treat simple things at length but brush over more difficult things without proper reference? Do you provide proofs for standard facts but use advanced concepts without any argument?


Sunday, 24 February 2019

publications - How to make sense of a 2019 paper published in 2016 journal issue?


I submitted a paper to a social sciences journal and it has been accepted. However, the publisher tells me it is going to be printed in the next weeks in the 2016 issue. How to make sense of this? Apparently the issue has been delayed a few years. However it will not mention the year 2019 and it is officially a 2016 paper issue. No digital copy since the journal doesn't have a webpage. Can I still put 2019 in my CV? and if I want to present it in an upcoming conference?


It is an old journal in French that might had issues with their timeframe, collecting papers, printing, and moreover getting the editing work done on ambitious projects. Is it really an issue when the work was done? If this is part of PhD research, want difference does it make if it is possible to indicate in bibliography that the work was submitted and printed in 2019?




Saturday, 23 February 2019

entomology - What small insect is this?


Lately, lots of these little bugs have been lurking in my house in Italy. Should I worry? I'm curious to know what they are. For reference, the 2 cent Euro is 18.75 mm in diameter.



Answer



It looks like a carpet beetle larvae(Anthrenus verbasci) to me. This seems to fit considering you found it in your house, which is one place they are fairly common. I would not be able to tell you if you should be worried, I am not a biologist.


reproduction - Could a sperm be altered to contain a female's genetics?


While discussing with a friend a while back on the likelihood a futanari (a woman with both fully developed and functioning sets of genitalia) existing in real life, we got into a discussion of whether a child could carry the genetics over from 2 months.


Currently (to my knowledge), for a female same-sex couple to conceive a child and for both women to be involved, one would donate an egg, the other actually gives birth, and the sperm is donated by a third party. However, this means that the child will carry over the genetics of one women in the couple and the unknown male.


I am wondering if there is a way for sperm to contain the genetic information so that way both women in a same-sex relationship could be genetically related to the child.




publications - Does Impact Factor reflect the quality of a journal?


Is the impact factor really useful for judging the quality of a journal article?



Answer




No.




To answer Paul's comment:


The title of the post asks about journals. For a well-worn list of criticisms of Impact Factor as an indicator of journal quality, see the Wikipedia article and the sources it cites. In many disciplines, important papers receive most of their citations well outside the IF's two-year window. Raw citation data can be manipulated by editorial policies, some more nefarious than others, or even by individual papers. Thomson-Reuters' calculations of Impact Factor are not reproducible, even using their own citation data. Et cetera ad nauseam. But most importantly: Having lots of citations is not the same thing as quality.


The body of the post asks about journal articles. Impact Factor is (roughly) the average number of citations to all papers published by a journal in a given time window. Even if it were a reliable measure of average quality (which it isn't), it would say nothing at all about the quality of any individual paper.


Friday, 22 February 2019

evolution - Why do adult insects have 6 legs?


Apparently, there is an advantage to having 6 legs in the insect world. What is that advantage, if anything? Why would such an advantage exist for insects, but not for other, larger land animals?


What do those middle legs do that the front and hind legs cannot, if anything? Are they really essential, or do they just generate more muscle power?





Thursday, 21 February 2019

graduate admissions - How to make a complaint about grades?



My professor announced the grades. He told us in each part what grades we had. My oral presentation for the project was way better than other students. But he just gave me 89 for oral and gave others 88. I think it is not fair at all, because most of the students were not clear or the did not consider timing. He also told me that "your presentation was very good". Also, I performed very well on the final exam but he also did not give me the 100. I think it is not fair.


How can I make a complaint? What should I write?




Wednesday, 20 February 2019

metabolism - Why our body does not produce polyunsaturated fatty acids?


Our body does not produce two polyunsaturated fatty acids (PUFA): linoleic acid and alfa-linolenic acid.


I am thinking reasons for it.


Saturated fatty acids have more energy than unsaturated. Saturated fatty acids do not need NADPH and some many other enzymes as unsaturated in beta oxidation. This means that less storage places in the body needed to have energy in the form of saturated fatty acids such as for muscles and heart.


There are four main reasons why our body does not use PUFAs as the primary source of the energy but saturated:



  • PUFAs lower metabolism and interfere with thyroid function

  • PUFAs spontaneously oxidize, speed up the process of glycation, since too much glucose

  • PUFAs decrease mitochondrial respiration - more oxygen and CO2, less lactate



where one reason is missing.


One complication of PUFA is



  • PUFAs promote diabetes, cancer, inflammation and biological stress


which cannot be thought as a reason why our body does not use PUFAs as the primary source of the energy.


There are positive sides of the PUFAs when they are used in other way. - PUFAs replace trans fats and saturated fats in certain types of foods. - PUFAs can help your body to eliminate high cholesterol levels - PUFAs decrease the risk of heart disease


There are also some types of essential fats that your body cannot produce on its own - omega-6 and omega-3 fatty acids. PUFAs are used to create these. You can get PUFAs from vegetable oil, fish and nuts for instance. Balanced diet is essential.


Normal lipid metabolism depends directly on food lipids. Both the essential fatty acids and right amounts of PUFAs can be obtained from food. Body converts the essential fatty acids to long PUFAs, which serve as the precursors of prostaglandins and leucotrienes for instance.


There are so many reasons why our body does not produce polyunsaturated fatty acids.



Why our body does not produce polyunsaturated fatty acids?




masters - Writing a letter of recommendation as a graduate student


I am a MA student who frequently works with undergraduates on projects. One student has asked me if I can write her a letter of recommendation for graduate school. Are there any risks to me submitting a letter, as opposed to her finding a faculty member (who likely would not be in the same field as her interests)? For graduate school applications how much does the position of the person writing a recommendation letter matter, as opposed to his/her academic familiarity with the student? I have already advised her to check with the programs she is applying to in case they have requirements.


Edit: I realize I left this unclear before-- she has two tenured professors willing to write letters. If I agreed to, I would be the third letter. The department is small, so there might not be too many options for an additional letter.



Answer





[H]ow much does the position of the person writing a recommendation letter matter, as opposed to his/her academic familiarity with the student?



It matters very highly. For most graduate programs it would be better to have a letter from a very eminent and trusted person which simply says "Student X's performance in my class convinces me that she will be successful in a top master's/PhD program. I highly recommend that you admit her." than a more personally insightful letter from a less well known faculty member, let alone someone who has not even completed the degree that the student is applying for. If you have not yourself completed a master's degree, how can you certify that the student will be able to do so successfully? (Well, of course it may well be that you probably can, but what degree of trust can the reader put into your letter? Not very much.)


In general, I would recommend that even postdocs and temporary faculty should defer to more senior faculty, if possible, when writing letters, and in any case the student should make sure to get at least one letter from a senior person. If someone who has a PhD (let's say) but is otherwise very junior can say something about the student that other faculty cannot, it could be a good idea to send along a letter, but it would be better to have that be an additional letter beyond the number required. However, for someone like you who has not even completed the degree the student is applying for, I would simply say that you should not write a letter for the student. If you want to help, I would recommend that you find a faculty member who is senior enough but doesn't know the student very well and give them the information that you wanted to convey in your own letter. (Don't write the letter for them! Just give them the information.) It helps of course to find a faculty member that you are comfortable with.


By the way, if you are in the habit of mentoring grad-school bound undergraduates, you would be doing them a favor if you let them know as early as possible that it is in their best interest to make significant contacts with senior faculty as well as with you.


evolution - How are new chromosomes replicated into the next generation via sexual reproduction?


If an individual has a new chromosome, which is very unlikely to happen, he will not have any luck in finding a sexual partner with this same trait. How will the offspring inherit this trait. And given that extra/fewer chromosomes are often undesirable traits (e.g. Turner Syndrome) how can it propagate?



I assume that humans and rats have different number of chromosomes, so a common ancestor must give a lineage where some individuals had a different number of chromosomes than their parents.



Answer



You are right that a person with an abnormal number of chromosomes will be unlikely to find an "equal" partner to mate with. This does not prevent a chromosome aberration from spreading though, and it is not necessary that the mutation is initially beneficial for it to spread. While it is true that many chromosomal aberrations may be detrimental and cause various syndromes, a chromosome split or multiplication may also be netural except for the matter of reproduction. A change in chromsome number will not be inherited deterministically, but can give rise to various new permutations in the offspring due to the mechanics of chromosome segregation during meiosis.


You can find a good explanation at Scienceblogs.com: http://scienceblogs.com/pharyngula/2008/04/21/basics-how-can-chromosome-numb/ :



The net result [of a chromosome split] is that although this individual is fine and healthy, a significant number of his or her gametes may carry serious chromosomal errors, which means they may have reduced fertility. They aren’t sterile, though; some of their gametes will have the full complement of genes, and can similarly produce new healthy individuals who will probably have fertility problems. (...) So our two chromosome individual will have a reduced fertility as long as he or she is breeding with the normal one chromosome organisms, but those split chromosomes can continue to spread through the population. They are not certain to spread — they’re more likely to eventually go extinct — but by chance alone there can be continued propagation of the two chromosome variant. Which leads to another misconception in the question: something doesn’t have to provide a benefit to spread through a population! Chance alone can do it. We don’t have to argue for a benefit of chromosome fission at all in order for it to happen.



science - Subtle (and not-so-subtle) humor in scientific literature



Tonight I was scrolling through my RSS aggregator (which includes subscriptions for several journals I follow) and this abstract caught my attention. The article's title, as well as the name of the software it describes, includes a subtle reference to this popular internet meme. This gave me a good laugh, and an excuse to watch that ridiculously silly video again.


But on a more serious note, this is not the first time I have seen the use of subtle (or not-so-subtle) humor in the title of a scientific journal article, conference abstract, or poster presentation. Sometimes the humor is even injected into the body of the publication itself. But in general, we as scientists are expected to write in such a way that our findings are easily communicated and easily reproducible. The focus is on clarity, objectivity, and reproducibility.


There are of course no formal rules about the use of humor in scientific literature, but are there any de facto rules? Do these de facto rules depend on the field (computer science vs genetics) or the publisher (Oxford Univ. Press vs BioMed Central) or the journal's impact factor (Nature vs Frontiers in Genetics)? Does humor even have a place in scientific literature, or would we be better off without it?



Answer



I see humorous titles in scientific articles now and again, like the "Wizard of Odds" joke in a recent commentary in Epidemiology. One should however be somewhat cautious. The general use of "marketing gimmicks" like questions in the title have been suggested to increase downloads but not actual citations - which flawed or not flawed form the basis for how both the paper and you as the author are evaluated.


Consider this finding:



The results of the current study indicate that in two prestigious scientific journals in psychology the use of exceptionally amusing titles (2 standard deviations above the average rated amusement) was associated with a substantiate ‘penalty’ of around 33% of the total number of citations. The present results were found in both of the examined journals and cannot be attributed to potential moderating effects of the title length and pleasantness, the number of authors, the year of publica- tion, and the article type (regular article vs comment).



While that might not be perfectly generalizable, I think it's pretty easy to say that being overly clever is hazardous.



Tuesday, 19 February 2019

Should I report an accepted PhD thesis in which the literature review is copied verbatim from sources?


While writing the literature review for my doctoral dissertation, I picked up a few recent dissertations on similar topics from the library to get some pointers on references and style. As I was reading some of the articles cited in one of these theses, I discovered that this person had lifted large blocks of text from the cited works verbatim. Although the original works were cited, the borrowed text was not presented as a quote, but used directly in the thesis.


I checked a few more, just out of curiosity, and realized that basically the whole literature review by this author (who graduated with a PhD two years ago) was cut-and-paste verbatim quotes strung together (and who knows how much more of the thesis is plagiarized - I only checked this one chapter).


This really ticks me off, as I (and many students like me) spend a great deal of time reworking cited information into proper coherent explanations for our projects. I happen to know the offending author's advisor pretty well, as we currently work together outside of my graduate program.


Should I say something or should I just let this person get away with plagiarizing large parts of their dissertation?




Edit:


I still don't know what I will do about this -- no-one wants to be a tattle-tale, and it really isn't any of my business how other people go about getting their doctorates. However, as I am currently writing my dissertation, it really irks me when I see someone else getting away with this, as I know from experience how much hard work goes into writing a PhD thesis.


I just have one more comment -- I ran the chapter in question through the TurnItIn software, which I have access to as an instructor at my institution. The thesis came back as 52% unoriginal. Turnitin only counts exact matches, so the 52% figure doesn't even include some of the paragraphs that I caught, where the author has changed one or two words but kept the sentence structure.



I doubt that there would be any legal consequences, even if I report the thesis for plagiarism -- it is more a question of academic dishonesty and what steps the institution that awarded the degree would take. I will show it to my advisor and see what he says before I do anything.



Answer



This is of course a sensitive issue. However, the ethically correct behavior is to notify someone responsible about the problem. Etiquette says to go to the advisor first, as the advisor is the person who, after the author who committed the plagiarism, stands to lose the most from the accusation.


However, if you feel squeamish about doing it by yourself, you can talk to your advisor about the best way to proceed.


The main issue on your part is if you will need to rely on the plagiarizer's advisor for recommendation letters. Then you should definitely proceed with caution, and with the support of your advisor, department administrators, or both.


Of course, make sure that you've done your due diligence before going public with your charges, and to have the evidence with you when you meet with anyone about this matter.


human biology - How is temperature sensed?



Can anyone summarize the mechanism by which when an object of a given temperature is placed in contact with, say, the skin on a human fingertip, the average speed of the particles of the object is converted into nerve signals to the brain?


If you can answer that, how about the format of how the temperature is encoded in the nerve signals?



Answer



In the periphery (e.g. on our fingertips), our body senses external temperature through nerve terminals, expressing certain TRP channels. These are ion channels that are sensitive to temperature (note that TRP channels can be sensitive to several things, such as pH, light, and stretch) and allow entrance of cations in the cell when the temperature is higher or lower than a certain threshold.


Six TRP channels have been described as been involved in sensing different temperature ranges1,2:



  • TRPV1 is activated at >43 °C

  • TRPV2 at >52 °C

  • TRPV3 at ~> 34-38 °C

  • TRPV4 at ~> 27-35 °C


  • TRPM8 at ~< 25-28 °C

  • TRPA1 at ~< 17 °C


Not surprisingly, TRPV1 and TRPV2 are also involved in nociception (=pain perception).


The exact molecular mechanisms by which different temperatures open different TRP channels are unclear, although some biophysical models have been proposed.3


I am not sure of the exact "format" in which sensory fibers encode different temperature, but I would assume that the neuron would fire faster the more the temperature is distant from the specific threshold (hot or cold).




1 Thermosensation and pain. - J Neurobiol. 2004 Oct;61(1):3-12.
2 Sensing hot and cold with TRP channels. - Int J Hyperthermia. 2011;27(4):388-98.
3 - Thermal gating of TRP ion channels: food for thought? - Sci STKE. 2006 Mar 14;2006(326):pe12.



graduate admissions - Selecting references for PhD applications: are industry references OK?



My background:



  • Final year computer science undergraduate in the UK.

  • Spent one year working in a scientific facility developing software for scientists. My colleagues had previous academic experience (PhDs in math or physics).

  • Researched for 3 months under professor N within my university.

  • My dissertation begins in February, so cannot use my supervisor from that.


I want to pursue a PhD, and am at the stage of applying for programmes. However, each programme requires "two academic references", and am unable to come up with a second one (professor N being the first) that would provide the best application.


Giving many of you read references, and recruit PhD students, which of the following references would you prefer receiving:




  1. A senior software developer where I previously worked (he has a PhD in physics), but I feel this is not "academic".

  2. My personal tutor (a professor who helps with any personal or professional problems), whom I have not seen in a few months, but have used for references before (to get the aforementioned job).

  3. Professor B who has taught me over the past three months, but whom I am not close with (on a personal or professional level).


I know my question is a bit specific, so perhaps to generalise:


Q. Is it acceptable to have industrial references when applying for PhD positions, or should I instead use university professors as reference? Even if they may result in a generic reference letter.


Q. How can I speak with professor B to avoid him writing a generic reference letter about me?




Monday, 18 February 2019

industry - Balancing an internet startup and a tenure track professorship


What should do or consider to simultaneously succeed at my new professorship and my internet startup?


I am starting a tenure track professorship in the fall. I am also on the team of an internet startup which has received an initial round of funding. I have expressly limited my availability to the startup to the amount my university allows faculty to consult. That said, this is not consulting, and no explicit rules regarding my situation are on the books beyond broad conflict of interest rules.



I am not alone in this decision to pursue academic and startup success together, and as I talk to others starting this path I see common questions as to what challenges we will face.


What factors should a dual academic/startup founder consider, especially pre-tenure? I'm especially interested in advice from professors with a startup.



Answer



I have done both, and let me tell you it boils down to how hard you want to fall into entrepreneurship.


I did research for my own sake and did teaching, to see students smile when their code compiled; but let me warn you with peace and love that both startups and doing research/teaching are both very stressful. So:


If you want to be serious about startup, you will eventually be very busy with it and not so much time doing research. However, if you want to use "I'm part of a startup" just to open a presentation or conversation then you can do both.


It might sound harsh, but you have no idea how hard a startup will be, both in terms of operations and people management.


What is 'Impact' anyway? Lets consider the word "impact" that you mentioned. What is it? Well:


Researcher: if you are a researcher it is very simple: the rank of the journal you are publishing shows the impact of your work. There is a difference if I publish my work as a poster in a conference, or publish it in a journal in THE Nature.


Startup: What is the impact here? Well, do you remember the "Green energy" back in 2005-2006; "social network" in 2007, "the cloud" in 2010, or "Big Data" in 2012; or "Crypto" in 2017? What all these things have in common? The fact that someone decided that they are the "next big thing" and the rest are following. Why the are following? Well they can get funded easier if they are "crypto-based" startup back in summer of 2017. The game is to get funding by promising an impact. Who and how they can deliver this, is totally different thing and in most cases, they are BS.



Philosophical: Lets think about this philosophically. You could create the better toilet paper, and have an impact everywhere, is this something you are looking for? You could write a research paper that most people or no one in your field cares. At the same time, you could get funded and create a successful or unsuccessful startup. What I'm trying to say here is that: you could succeed or fail at anything, at least choose something that you look forward to; so you don't switch as soon as you fail.


molecular biology - How long can I store extracted RNA?


If I extract RNA from a (leaf tissue) sample using a one-step phenol:chloroform extraction, how long can those samples be stored at -80°C? And how many times can I defrost and refreeze them before they will become degraded?



Answer



I've found that extracted RNA using commercial kits has stayed stable for many years at -80 C. I would certainly aliquot it before freezing however as RNA is particularly sensitive to freeze-thaw cleavage.


publications - How can I timestamp my paper without violating double-blind review?


I submitted a paper to a top tier conference and it did not get accepted. The paper contains an original idea, and I am afraid that the paper could get plagiarized between the time I send it to another conference after incorporating reviewer's suggestions and making some modifications. Such things have happened in the past to a few students in my department.


I had considered posting the paper on arxiv as a means of timestamping before sending it to the aforementioned conference, but didn't, as this would have violated the double-blind review requirements of the conference. (The conference chair replied to my query as follows:)



The submission of a paper in the arxhiv.org system is not strictly speaking a double-submission, but rather a violation of a double-blind submission required in this conference, as the reviewers will be able to find your name (and those of the coauthors) if they do a simple search in Google. Thus, I am quite certain it will be rejected, and I do not consider it an acceptable practice in this conference's submission to be fair with all the submissions in order to handle them equally during the review process by the reviewers.



Hence I had not posted it on arxiv. Now this paper has been rejected and I would like to timestamp this paper now, while still being able to send a modified version to some conferences in the future (including those that follow a double-blind review).


Is there a mechanism by which I can timestamp my paper that does not violate the blind review requirements?


Edit: The paper was in computer science, if that matters. A related question "How can I time-stamp my data without publishing it?" asks about ways to timestamp while keeping the information in the paper private or hidden to avoid plagiarism. However my question is about ways to timestamp such that it is still possible to publish the information while not violating blind review.




Answer



The most typical way to time-stamp a piece of work is to place it in a public repository: arXiv is a good example when it applies; many institutions also have a technical memo or technical report system in place. Although this may technically violate certain interpretations of double-blind submissions, as noted in the comments blinding of authorship is pretty iffy in many cases. Moreover, in practice this will only be violated if the reviewers actively go looking, particularly if you put it in an institutional repository rather than a global one like arXiv. I would thus advise that if you are worried about date-stamping, just do it and let the double-blind nitpickers complain if they even notice.


One other consideration: certain publications (particularly certain journals) do have a policy against accepting material that is already available online. While this is in my view an insane policy, if you find yourself dealing with such, one way to handle with it is to put up a shortened version of the work, i.e., extended abstract, as the date-stamped pre-print.


evolution - The evolutionary process in bird wings, especially with regard to winglets


In this answer on aviation.SE a comparison is made between the shapes of airplanes wings and the shapes of birds wings. It concludes with the following remark:



After all, no bird has winglets. Not a single one.



In addition to be a disputable assertion (the wing tips such as the eagle's could be considered akin to a "winglet" of the fanned type) this has stricken me as based on a quite wrong assumption of how evolution works.


I tried to make my point in the comments only to reach this point:




So you consider evolved wings as not mature. The winglet modification is just waiting to happen? Nature never tried it, in >100 million years of biological flight? Could be, yes. But is extremely unlikely. That settles it for me.



Am I correct in identifying this in a wrong interpretation of the evolutionary process?


As I understand the evolutionary process, the current bird wings are not necessarily perfect, are simply the version that so far has given the best advantage. The lack of "winglets" in birds cannot then be explained simply by assuming that they do not improve the wing, but it could also be that there has never been an evolutionary pressure to evolve them or that since birds flap their wings they would be detrimental instead of beneficial or whatever other reason.


Is my understanding of the evolutionary process correct? if not, where am I at fault?




As a small addendum, another user cited the "Spandrels" in comparison to the above debate, could someone explain what could have been the meaning of the comparison?



Answer



I looked up winglets so I had context for this answer. I'm interpreting winglets as the vertical tips at the end of airplane wings. If so, then you are correct. The spread primary feathers of soaring birds like eagles function as winglets (Tucker 1993). Airbus has a biomimicry web page devoted to some of the biological designs, including winglets, they incorporated into their airplane designs. Some studies suggest airplant winglets do increase efficiency (e.g., Hossain et al. 2011), but there is still some debate.



From the aviation.se answer:



Look at birds: They use two different wingtip designs. I guess we will both agree that those designs are mature after millions of years of evolution. And still there are two distinct wing tip shapes: One is the "fingered" wingtip with large, spread-out feathers, and one is the pointed tip you find from seagulls to albatrosses. Why is there not one, mature design?


This has to do with the environment they are used in. Seabirds fly in an unobstructed environment with steady winds and need to stay aloft for longer duration. All other birds have to cope with trees obstructing a straight flight path and gusts from hills, or those trees. They need to maneuver quickly and cope with gusty winds. This is helped by a reduced span and the possibility to fold the outer wing in or fan it out in an instance. Hence the fingered wingtip.



Although bird wings do tend to match his descriptions, he is not correct that these correspond entirely to ocean-going birds vs all other birds. Many inland birds have pointed wings, including swallows, nightjars, swifts, and falcons. Some seagoing birds have winglets, such as pelicans and cormorants. While wing type is shaped by natural selection in a given environment, it also reflects the evolutionary history of the birds.


There is not "one, mature design" because wings many different shapes and sizeshave evolved under varying selective pressures. For example, the long pointed wings of ocean-going albatrosses are excellent for gliding with little energy expenditure but they are lousy for taking flight or for landing. Other wings are shorter and broader, providing greater maneuverability in the woods. In this sense, there is no perfect wing. Each has evolved for different evolutionary reasons.


The main question


From the aviation.SE thread:




the fact that no random mutation has produced a winglet* in birds is in no way a demonstration that airplanes do not benefit from them, there is no logical relationship. [*even though the "fanned" design you refer, such as the eagle's, can be considered a form of optimum winglet] – Federico



followed by this response:



So you consider evolved wings as not mature. The winglet modification is just waiting to happen? Nature never tried it, in >100 million years of biological flight? Could be, yes. But is extremely unlikely. That settles it for me...



Federico is correct. The basic wing type was set long ago as birds evolved from non-avian dinosaurs. Comparisons of modern bird wings with fossils suggest that the basic structure of bird wings has not changed very much since then. The current structure may be the best that has evolved by natural selection so far but that does not mean the wing cannot be improved further. As you noted, mutations could occur in existing genes that lead to further improvements of the structure and function of the wings. If those mutations never occur, then the improvements won't occur. This is one constraint of the evolutionary process (Hoffman 2014). Natural selection can only work with existing traits, using existing genes and genetic variation.


Another consideration is that wings for powered flight have evolved independently at least four times (birds, bats, insects, pterosaurs). Each time, a different type of wing evolved. Is one better than another? Bat wings have aerodynamic properties very different from birds but function very well for bats (Hedenstrom et al. 2009). Along the lines of your argument above, each wing type perhaps is (or was for pterosaurs) optimum given the environmental circumstances and evolutionary constraints. That doesn't mean they could not be improved. If a wing evolves again in some organismal group in the distant evolutionary future, odds are very good that the structure will be different from those that have evolved so far. Perhaps that wing will be even more efficient than current wings.


Spandrels




Another user cited the "Spandrels" in comparison to the above debate, could someone explain what could have been the meaning of the comparison?



The use of "spandrels" in evolutionary biology stems back to a well-known paper by Stephen Jay Gould and Richard C. Lewontin called "The spandrels of San Marco and the Panglossian paradigm: a critique of the adaptionist programme", published in 1979 (Gould and Lewontin 1979). A spandrel is the space that forms between two adjacent arches or between an arch and a rectangular shape. The spandrel emerges as a result of putting two arches next to each other and filling the space. It results from the joining of two arches. It was not specifically designed as part of the arch. Gould and Lewontin claim that evolutionary biologists are too quick to assign adaptive value to every trait on an organism, and argue that not every trait results directly from adaptation. Instead, they say, the trait may be a "spandrel" that emerged as a by-product of other traits. The "spandrel trait" has no adaptive value in and of itself.


The use of spandrels in the comments of the aviation discussion is not clear to me. Clearly, the person intended the evolutionary meaning, mentioning the paper by name. But I cannot tell at all the person's intent.


Edits: Incorporated comments by @Federico and @Andrew - thanks. I corrected horrendous typos and attempted to add clarity.


Citations


Hedenstrom, A. et al. 2009. Bird or bat: comparing airframe design and flight performance. Bioinspiration & Biomimetics 4 015001. doi:10.1088/1748-3182/4/1/015001


Hoffmann, A.A. 2014. Evolutionary limits and constraints. Pp. 247-252. In: The Princeton Guide to Evolution, Princeton University Press, USA.


Hossain et al. 2011. Drag analysis of an aircraft wing model with and without bird feather like winglet. International Journal of Mechanical, Aerospace, Industrial and Mechatronics Engineering 5: 30-35.


Tucker, V.A. 1993. Gliding birds: Reducion of induced drag by wing tip slots between the primary feathers. Journal of Experimental Biology 180: 285-310.



human biology - How did the cardiovascular system evolve?


How has evolution created our blood, lungs and the heart?


We can't exist without blood, which transports the oxygen to all areas of our body. However, the blood needs a lung, which gives it the oxygen to transport. The blood also needs something which lets it flow through the whole body, which are our veins. And in order to allow the blood to flow through our veins, an organ is needed to pump the blood, which is our heart. We also need a brain which controls all that, and the brain in turn needs the blood in order to function right.


Evolution makes very slow steps....."it just doesn't jump". So, How did evolution manage to create all that?




Answer



While others have addressed the big picture aspects of your question, I think it would be useful to look at the specifics.


Have a look at the heart (or more accurately, the hearts) of the earthworm: enter image description here


They're nothing more than veins with some pumping muscles wrapped around them. It seems almost a stretch to call them hearts, they are shaped so different from what we think of as a heart proper.


Also, note the earthworm's lungs, or rather, lack of them. It doesn't have any! Why not? It doesn't need them. It gets enough oxygen through its skin via osmosis. It's only larger organisms that need dedicated systems to concentrate oxygen from the surrounding environment.


So, the worm has a simpler system (no chambered heart, no lungs) that works.


All vertebrates descended from a common ancestor that was very similar to this earthworm. It had simple hearts, and no lungs. You can follow the evolution of the human heart through fish heart: enter image description here


which is a more sophisticated pumping vessel with two chambers.


Amphibians evolved from fish, reptiles from amphibians, and mammals from reptiles. In this diagram, you will find that the heart becomes more sophisticated and efficient in each: enter image description here


So, this should give you a good idea of the evolution of the human heart from simpler, working system. I won't take the time to draw out the evolution of blood vessels or lungs; maybe someone else will, or you can google them yourself, the information is readily out there. But they all follow the same pattern: gradual, incremental improvements on working, simpler systems.



Sunday, 17 February 2019

How to cite a technical report for a double blind review process?


Some conferences follow the double-blind review process. As such, you cannot reveal your identity to the reviewers. Further, these conferences restrict the number of pages, say to at most 8 pages.


I am facing the following problem: I would like to submit a paper to some of these conferences but I have a paper that is 10-pages long; containing 2 pages of appendices (proofs). I am thinking to write a technical report and put these appendices in it. So now I have the paper to submit (8 pages) which of course cites the technical report (10 pages). How can I cite the technical report to not violate the double-blind review process?



Answer




I hate to suggest it here, but in some ways your best option is to work to rewrite the paper within the page limits. It can be a difficult task to use fewer words without losing meaning, but it is part of the history of good writing to work at that. George Bernard Shaw famously said "I'm sorry this letter is so long, I didn't have time to make it shorter."


Mathematical proofs, if that is what it is, can often be shortened, especially if the techniques are standard and the audience is sophisticated.


But the prose in the other ten pages may be more amenable to reworking.


If you can do it the reviewers will be happier as will the rest of your audience.


Saturday, 16 February 2019

peer review - Under what circumstances is there a conflict of interest for a researcher to be a reviewer of a submitted academic paper?


If I were asked to review a paper, under what circumstances would I be expected to decline out of a conflict of interest? Could I review a paper for someone...




  • I have collaborated with N years ago?

  • Who I am currently collaborating with, but we have not yet published a paper together?

  • Who is currently or was once in the same institution as I?



Answer



The answer to your question depends on context. I find three key elements to the decision of whether or not to declare conflict of interest:



  1. Formal rules: some venues have an explicit conflict of interest policy; if so, abide by it.

  2. Size of reviewer pool: sometimes, you have an extremely specialized subject, in which the number of people qualified to review a paper at all are quite small. In such a case, one should generally be more permissive.

  3. Formality of venue: conflict of interest for a journal or top conference is generally more strict than for less formal venues like workshops, especially for ones intended to discuss early-stage work where all you're really looking for is a sanity check.



Now, to address some specifics:



  • I generally hold that it's a bad idea to review one's current or recent collaborators except in the most informal of venues.

  • Co-authors is often the same as one's collaborators, but not always --- one might be collaborating but not yet be published together, or might be a very distant co-author (for example, I'm not going to worry about conflict of interest with most of the co-authors on my 600+ author paper).

  • I also don't generally count co-organization as collaboration, since that's often a fairly narrow relationship.

  • Being at the same institution (currently or in the recent past) may or may not be a conflict depending on how close the organization is: in some places different departments might as well be different institutions; in others, it's one tight family.

  • Being funded by an organization is almost certainly a conflict of interest.


publications - Using home address when submitting an article with no affiliation?


If you're submitting information for an article, and you have no institution affiliation, what should you use? I was asked for an address and all I have is an home address. That seems a bit weird to use, however.



Answer



I did a quick search to see what other independent researchers do for Nature journals, which include an author address.Specifically, I searched Google for



site:nature.com "author details" "independent researcher"




I found that authors who are independent researchers sometimes list just their city for their address, or



Independent researcher, City, Country



See for example here and here. Some do appear to give their home address, e.g. here and here.


Can both a grad. student & faculty member cosign a recommendation letter?


Can two people, a professor and a graduate student, sign a recommendation letter? The concern here is that the professor knows little about the student and the graduate student knows all about the student.



My concern here is that if the professor is contacted, he will not be able to provide further information, where as if I was listed as the primary contact: I could.



Answer



Like Noah, I had a situation where two advisors co-signed a letter of recommendation. I should mention that the people reviewing the letter found this an unusual situation—and had claimed that they had not seen that in twenty years of reading recommendation letters. So this is definitely not standard practice. I suspect it would be memorable, but I am not sure it would be actually useful.


However, the difference was that my two co-signers were equal in rank. Your situation has a professor with a graduate student providing most of the insights. I suspect you will need to have the professor adapt the graduate student's comments, and then sign the letter. In the case where feedback is needed, the professor would then need to get the relevant details from the graduate student.


Friday, 15 February 2019

grades - What can a professor do about an exam that was too long for the allotted time, after the students have completed it?


I just finished a midterm exam. It was very easy but I was only able to finish about 3/4 of it. And I rushed through some parts in the final moments.


Talking with other students, there's a consensus that there wasn't enough time. Some of us mentioned this to the professor as we were leaving, and he acknowledged it.


What can the professor do to remedy this situation?



Answer



I found myself in a position similar to your instructor's. I considered and rejected several possibilities:




  • Adjusting the curve or grading scale to compensate can be unfair to students who cannot read and understand English quickly, especially if the exam is text-heavy or the students are not native English speakers. The result of this approach is that the exam grade reflects speed of English reading comprehension more than mastery of the course material.

  • Dropping the lowest exam grade, or allowing a grade on another assessment to compensate for the midterm exam grade, only works if there are other assessments that cover the material that was on the midterm exam. Otherwise, a student could get an A in the course without having mastered some of the learning objectives.

  • Adding another assessment that wasn't on the syllabus, or adjusting other assessments to cover the material that was on the midterm (in violation of the syllabus), isn't fair either, especially to students who have other commitments and need to make plans in advance and schedule their time very carefully.


Ultimately, I decided that the fairest approach is to give students another opportunity (but not in the form of a required assessment) to demonstrate mastery of the course material. Depending on the course format, the size of the class, etc., several possibilities are:



  • Allow students to submit a correction to their exam, and earn partial credit for answers that they didn't complete correctly on the exam but did successfully in the correction. There is a possibility that students will receive unauthorized assistance on this correction, though.

  • Same as previous suggestion, but have the students explain their corrections in an oral exam. This reduces their ability to benefit from unauthorized assistance, since by questioning the students it is easier to see who really understands what they are saying. However, it is unfair to students who get nervous or have trouble expressing themselves in an oral exam.

  • Grade the original exam on a curve, but allow students to take a makeup exam covering the same material, if they feel like their "curved" grade doesn't reflect their knowledge of the material. For students who take the makeup exam, the makeup exam grade replaces the curved exam grade. This may be unfair to students who have limited time to review for and take another exam, possibly because of outside commitments, and have to manage their school and other commitments very carefully.



As you can see, none of these are perfectly fair, either. Depending on the particular circumstances (and possibly with input from the class), an instructor may decide which is the least unfair.


journals - What does "Awaiting Reviewer Scores" mean within the context of a ScholarOne submission system?


I submitted a paper to a Taylor and Francis journal that uses the ScholarOne submission system. The manuscript status has changed from "Under Review" to "Awaiting Reviewer Scores".


What does this change mean? What is the flow chart of the different statuses for a manuscript?




Fear of someone having the same idea and doing the research before you do


I am a young researcher, and recently, I find that the drive to publish and advance my career has created an unhealthy mindset. In particular, I find that when I have a good idea, I am worried that someone will have the same idea, carry out the analysis, and publish before I do. While this worry has greatly speeded up my research, sometimes I feel it is unhealthy, in that my work becomes more sloppy, my analysis is less careful, I check for errors less, and as a result I'm more prone to making mistakes. I think this is an undesirable outcome, because it can potentially reduce the quality of my research results.


However, the tradeoff is real - the more time one spends vetting one's results for accuracy and making improvements large or small, the later one publishes, and the risk of getting preempted is higher. Even if one is still able to publish, not being the first will reduce the impact of your publication.


I am interested in hearing what others think about this, and approaches to dealing with and think about this issue, to have a healthy mindset and research environment.



Answer



I worked on a project during the summer and fall of 2014 that I never published. Someone else beat me to it, publishing a very good and very thorough paper that did everything I had thought to do and more.


Do I regret that time I spent on that project? Not at all. I learned some useful new methods that I have since been able to apply to other ideas. I have a much deeper understanding of this problem than I would have just from reading my competitor's paper, and I'm sure that will come in handy someday. I've taken my version of the idea in a totally different direction, and it's stronger for it.



I suggest you consider the potential consequences of being "scooped":




  • Maybe you'll read their work and discover that although it seems very similar, the details are fundamentally different. Great! You'll cite the work in your own paper. The fact that other people are paying attention to this area shows that it's relevant and helps motivate your paper. Also see: Scoopage




  • Maybe you'll read their work and discover that it actually does accomplish everything you set out to do. Now you get to be flexible and take your project in a different direction. After you've done some preliminary work in this new direction, get in touch with them and propose a collaboration, which is likely to make your own work even stronger.




Know that being scooped doesn't necessarily mean everything you have done is wasted. (This article has some more advice on moving on from being scooped.)



Also, there are steps you can take to help avoid being scooped (although you can't guarantee anything, of course):




  • Know your strengths. If you're working in a crowded area, what can you contribute that you already have some expertise in? If you can apply what you already have to something new and interesting, you're ahead of those people who don't already have that expertise.




  • Read a lot. Identify the people in your field who are doing similar work, talk to them at conferences, generally keep track of what they are working on, so that you're less likely to be caught off guard.




  • Be open about what you are working on: give talks, poster presentations, chat with people at conferences, etc. about your ongoing work. If everybody in your field knows "LCW is working on X," then people interested in X may come to you for collaboration instead of working independently. When you do publish (a careful, accurate, not-sloppy paper), everyone working in the area will know about it and will probably cite it in their own work.





These are measures that can help alleviate your anxiety and improve the quality of your research.


Thursday, 14 February 2019

publications - Is it appropriate to add a co-author at the stage revise & resubmit?


Context


I've submitted a paper - it was sort of a side-product of my main project - to a high ranked journal from an adjacent field. Recently I got a revise & resubmit that was close to a reject, but the editor sounded really interested in the paper being multidisciplinary. I'm suggested to contextualize my research stronger within the journal's field. I feel like getting one of my experienced in that particular field colleagues involved in the revision in order to get the paper accepted.




The question


If a person helps you a lot during the revision, are you allowed to include him as co-author?



Answer



Absolutely you can add a coauthor in revision, if there is good reason for doing so: in fact, I have recently done so myself on a paper where revision involved some new experiments with the aid of a colleague not previously involved.



Most journals that I know consider authorship changes routine and even explicitly support such changes by asking you to review and, if necessary, modify author lists as part of submitting a revision through their system.


Wednesday, 13 February 2019

biochemistry - How does botulinum toxin enter the blood stream from the digestive tract?


To my understanding, large polypeptides such as botulinum toxin cannot pass the intestinal lining intact. How, then, can it enter the bloodstream and cause botulism poisoning?



Answer



Transcytosis is a process by which large macromolecules are transported across a cell, such as those in the intestinal epithelium. It is used by many toxins and even whole organisms to enter the body. Botulinum toxin also apparently uses this mechanism. I'm not sure how detailed of an answer you want, but the linked to-review is pretty in-depth.


publications - What do you do when you find yourselves with an unreadable/inaccessible paper?


Since I started my life in Academia, I sometimes found that there are some seminal papers to which I cannot get any access.


Either they are very old, and the journal that published them charges for it, or they are simply not to be found anywhere in the internet. I have to admit I never went to look for the physical copy in the library, but I'm not sure they would have it either.


When I asked a labmate about a reference he had in his paper and I could not find, and that seemed to be ubiquitous in any other paper in the area, he mentioned me he had never read it, but that reviewers usually demand that you should put that seminal reference.


How do you try and solve this problem?



Answer





  • Search the web for it: open archives, search engine, authors webpages, whatever (you've probably done that already…)

  • Ask the contact author for a copy, which she'll usually be very happy to provide. I regularly get such requests from other researchers in my field, and it feels very good to know that people are actually interested in your work.

  • If the contact author doesn't respond, try the senior author, then other authors.

  • Try your local library. Look into their database, and also ask the librarian there if the document might be available through loan from other libraries. I've never had much success doing that, but you never know…

  • Ask a few colleagues at different institutions if they can get it for free (see this question). If you have friends at large/famous/well-funded US universities (Princeton, Harvard, …), they probably have a more comprehensive access than you.

  • If it's a really important paper, pay for it!


Whatever happens, make sure you make a copy for others in your lab/group, and archive it. When I started my PhD, there was a folder (the heavy paper type, not the computer type) labeled “important but hard to find papers” that the group had accumulated along the years. It was the most treasured object in the whole lab.


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...