Tuesday, 31 October 2017

microbiology - How many eukaryotes are there on Earth?


I have been reading:



William B. Whitman, David C. Coleman, and William J. Wiebe, "Prokaryotes: The unseen majority", Proc. Natl. Acad. Sci. USA 95, pp. 6578–6583, June 1998. [Full Text] [PDF]



wherein they estimate the number of prokaryote cells on Earth to be of the order of $10^{31}$.


I can't seem to find any equivalent data for eukaryote one-celled life. Are there any estimates for the number of one-celled eukaryotic living things on Earth? Do any other estimates confirm or tell against the reference I have cited above?



Answer



Could not fit in a comment....


To make sure we all understand your question...



Is your question how many (eukaryote) species are currently living? or How many (eukaryote) cells are currently living??


Just a hint to answer the question


Micheal Lynch, in his book (On the Origin of Genome Architecture) at page 3, Box 1.1 tries to answer the question How much DNA is there on earth?. He ends up with an estimation of a total length of DNA on earth of $10^{24}$ km for procaryotes, $10^{25}$ km for eukaryote (of which $\frac{1}{1000}$% is accounted to humans). This sums up to a total DNA length of $10^{12}$ light-years, or 10 times the diameter of the known universe!


In his calculations, he estimates that the total number of procaryote cells at $10^{30}$ (citing Whitman et al. 1998 as you did). He estimates the total number of eukaryote species to $10^7$, i.e. 6 times the number of known eukaryote species. However, he doesn't directly give any reference for this estimate but he refers to different chapters in the book that contain lots of references.


...I hope that helps...


epidemiology - How is it possible to even hope for an ebola epidemic of this current size to remain contained to a relatively small part of Africa?


As of 2014-09-14 at least 5347 cases of ebola have been identitied. Some estimates are much higher. While experts are sounding the alarm to try to get sufficient resources to contain the outbreak, some people are also speaking very hopefully about containment to roughly the current affected area. This article puts the risk of the outbreak reaching the United States as low as 3%. I'm not an expert in the field, but it seems like there are almost countless ways in which an increased number of cases increases the risk of further exponential growth. It's encouraging to hear that in countries with better healthcare, death rates would likely be much lower, but at this point, isn't it inevitable that the outbreak will run its course as a global pandemic?



For example, which of these possibilities is just my imagination, or likely so improbable that we don't need to worry about it?




  1. Scared carriers not yet showing symptoms sneak or force their way across boarders to unaffected regions.




  2. Objects, food, or water touched by the infected go unnoticed until they end up leaving the containment zone.




  3. If it can jump from bats or monkeys, thousands of infected humans increase points of contact to create vectors into other species, perhaps one that will travel unnoticed far beyond the containment zone.





  4. After months of the same security precautions day in and day out, airport checkpoints, and other points of entry become lazy, and let infected through.




With numbers as high as they are, and possibly higher than we even know, is this really containable at all?



Answer



This is too long for a comment, so my thoughts about this here. The CDC Director said a few days ago after a visit in Africa "The window of opportunity is closing".





  1. This can happen. However, you are not getting contagious unless you show symptoms. This is different in other diseases like chicken pox or measles where you spread the virus before showing symptoms. So there has to be a lot of awareness. Also doctors need to be very careful with patients showing these symptoms. This is most likely one of the main reasons for the wide spreading of the disease.




  2. Same problem as in 1. Theoretically this is easy to prevent, but in a situation of chaos this can cause problems. But since infected people which show symptoms will not handle large amounts of food, this is most likely less of a problem.




  3. Every crossing of a species-barrier is a rare event. Double-crossings are even less likely. So I don't think this is a problem. Besides this, we already have to independent Ebola outbreaks which has never happened before. One is the one in West-Africa, the other one is happening in the Democratic Republic of Congo. Both are independent cross-overs.




  4. This can cause problems. The advantage of the first world is that we have functional health care systems. They allow better care for the persons and also better isolation of contact persons. I think it is unlikely that it would spread widely. The perspective will be different, if the virus makes the jump into the densely populated regions in South-East Asia. There a lot of people live closely together, this can cause real problems. Fortunately for us the virus is not highly contagious. To infect yourself you need unprotected contact to the body fluids (blood, stool, feces, sweat etc.) of infected persons.





publications - Is it acceptable to extend results from an arXiv paper that has not appeared in a journal?


In general, building on unpublished work of another author, which he may have told you in confidence, or you may encountered as a reviewer or by word of mouth or other informal means, is not an acceptable practice. Does the same apply if the author has uploaded his work on arXiv?


Here's a specific scenario: Suppose I submit a paper for review to a journal. The paper has results that could possibly be extended, however, the idea for extension is either not obvious or is not compatible with the theme of the paper, so I may plan to keep it for a later paper. If I put the paper on arXiv would it be considered ok if someone else extends my results? This would ruin the theme of the other paper I wanted to write with the extension.


If this happened to me it would make me uncomfortable, as if my confidence has been breached. I don't know if this feeling is justified. This feeling stems from my view of arXiv. My personal theory is that arXiv is an informal medium, unlike journals and conferences, and in that sense it is no different from other channels of informal communication. It allows for structured and faster dissemination of work (thus inform the ongoing work of others), in addition to establishing priority of results, but that does not grant it a formal status. I think an author should exercise restraint in extending results from arXiv, and apply the same standards that he would if he were to encounter the work through classical informal channels.


Of course, this is just my theory. I would like to hear what others have to say about this issue.





cheating - What is the rationale behind requiring a meeting before filing academic misconduct charges?


Some universities have a rule that, for example, "if it appears that a student in your class may be guilty of academic misconduct, you must promptly ask the student to meet with you informally to discuss your concerns." The quote is taken from one such university, the University of Wisconsin. UW's Academic Misconduct Guide for Instructors goes on to say: "You can discuss the matter with the student in person, by telephone, or online. During this meeting, you should explain why you believe the student may have committed academic misconduct and give the student an opportunity to respond. It is not necessary to inform the student in writing before this meeting."


What is the rationale behind this type of requirement?


Bonus: How common is this? When did universities in the US start instituting this type of requirement?




publications - What to do if my paper is incorrectly cited in a journal?


Recently I got a cite in a research paper where the author cited my work as [first name] et al, where it should have been [last name] et al. Is there any problem for indexing purpose? should I contact the journal editor about this incident and ask for correction?



Answer



Yes, that's a problem, and you will absolutely want to fix it. The problem is that it's actually a two-stage problem to correct:



  • First, you will need to contact the journal to fix the citation.

  • Then, after the citation has been corrected in the article, you'll need to submit a correction request to the various citation trackers (such as ISI and Scopus). They will need to fix your citation in their database, if the article has already been entered.


Note: It may or may not be possible to correct the journal—the editors may or may not be willing to issue a correction to fix a reference. However, it may be possible to correct the reference with the citation indices, even if it's not correct in the journal. However, the road will be tougher; you'll need to show that the paper that should be cited is indisputably yours.


Monday, 30 October 2017

graduate admissions - Can I be admitted to a master's in the USA after a 3-year European bachelor's program?


I am an Indian citizen and I'm planning to go for my bachelors to Germany. Since schooling in Germany is 13 years in length, I'll study 1 year in India before going there. I wanted to ask that after completing my Bachelor's in Germany, will I be eligible to apply for Masters in USA straightaway right after my BS (I plan to pursue a BS in Computer Science). I had this doubt in my mind as BS in Germany would be 3 years compared to that in USA which is 4 years.




Sunday, 29 October 2017

Should I omit some of my qualifications in my application materials to "surprise" with during an interview?


I am applying for a fellowship so that I can pursue a PhD in the US. The selection process includes an interview for shortlisted candidates.


I like to save the best for the last in order to surprise the audience. I think surprise, wherever it is used, has a good effect. I have a poster based on my undergraduate dissertation, which is said to be very attractive. It is inspired by the poster of Michael Barton, which is introduced by the Better Poster blog. I think I can use it to surprise the fellowship selection committee.


Now, should I apply this strategy to the interviewers? That means I will keep the information of what I've done in the SOP as minimal as possible, just enough to pass the first selection round to get to the face-to-face round. At this round, I will show them my poster and hope they will be favorably impressed.


Should I use this strategy?




I think I should quote my comment on Hans Adler's answer here:



I just take my A0 size poster in to the interview room. During the interview, professors will test my knowledge, ask me what I've done and judge that if I'm adequate to the fellowship. In the room it will have a white board for you to outline what I've done, and this is what is poster born for. Instead of drawing figure or chart by myself, I just need to open the poster and show what's what.





Answer



Absolutely not.


Even if you turned out to be a good candidate, I would reject your application on this basis alone. You're completely wasting my time by failing to be up-front about your qualifications when you know that I have a lot of work to do in prioritising applications and arranging interviews accordingly.


If I find out, after doing all of that work, that by hiring you I will be hiring someone who routinely withholds relevant information because he wants to "surprise" me, then I know I am only hurting myself in the long run. I would instead pick an individual who is capable of being up-front and honest — someone with whom I can work without constantly wondering what he's not yet bothered to tell me.


graduate admissions - What is common in most PhD application procedures in the UK?


I am almost done with my master's degree in mathematical finance. I'm done with thesis and have one course left to take. I am taking it in a 3rd world country and am interested in applying for a PhD in stochastic analysis in the UK.


I am told that, in general, the application process for PhDs, unlike applications for masters or bachelors, involves first speaking to faculty and then to the school. Is that right? That is, when I apply I should already have a professor in the university willing to be my doctoral advisor?


The exact procedure I heard is something like:



  1. Read up various literature on your desired dissertation topic which should include several textbooks and even more for recently published articles. (If necessary, study for IELTS, GRE, etc.)

  2. Come up with a PhD proposal.


  3. Contact relevant faculty of the universities to which you intend to apply.

  4. Discuss your proposal with them if they're up to it.

  5. One of the following: Revise proposal if needed, completely change proposal or get referred to different faculty member.

  6. Actually apply to the university.


So, is that how it actually is?



Answer



Unfortunately the system in the UK is not uniform. You will really have to read each individual department's web site to know how to apply. There are, for example, Centres for Doctoral Training http://www.epsrc.ac.uk/skills/students/centres/ which you apply to like a US graduate program. I don't know if there is a good one that covers stochastic analysis but it seems likely.


It sounds like the list you give is for people who want to apply for a specific supervisor. For this route, your main issue will be funding as there is very little funding for non-UK students these days. This will also vary wildly between different universities. There may be deadlines which you have missed already if you want to start in 2015. However, simply for being accepted by a supervisor without funding the list you gave is fine.


Overall, read each department's web site on their PhD programmes, don't forget to look for any relevant Centres for Doctoral Training and good luck.



productivity - What are some good project-management tools for academics?


My advisers are starting to use Basecamp for my project, and I like most of it so far. I am wondering, though, about the arguments for and against Basecamp.




ethics - Are reviewers allowed to discuss their review with each other?


Suppose you find out that someone you know well or work with is reviewing the same journal paper you are reviewing (i.e., finding out this information on your own, and not via the journal or editor, assuming a blind process).


Can you discuss the paper? Can you discuss your reviews?



Answer



If it's a blind process, you're not meant to find out. As various people have pointed out in the comments already, discussing your review with them is therefore a big no.



One of the main principles of reviewing by several people is that you get independent opinions, so that if a particular (maybe well-known and well-respected) person doesn't like the research, they can't just make it disappear by convincing everybody else that it's bad.


For some conferences (and maybe journals?), you are able to discuss your review with the other reviewers after the initial submission. But in this case the facilities for doing this are provided by the submission system. There are two important differences to the situtation you've described though. First, your initial review will not be influenced by the discussion and second, there is a record of the conversations and changes made.


Saturday, 28 October 2017

How does hemoglobin-free blood transport oxygen?


Snails... We have some kind of huge garden snails appearing lately (read since the last 10 years or so). Try as one might, it's impossible to avoid them when driving. These snails do not appear to have red blood - I doubt they have blood at all. Wikipedia tells me blood's red colour is due to haemoglobin - which serves to transport oxygen.


How do snails (and any other animals that do not have red coloured blood) get oxygen? Or, do such animals need no oxygen at all?




Answer



Snails, like most molluscs, have a protein called hemocyanin dissolved directly in the hemolymph ("blood"). Hemocyanins are copper-containing metalloproteins: the binding site for a single O2 molecule contains two copper atoms. Unlike hemoglobin, where reversible oxygen binding is accomplished without a change in the oxidation state of the Fe(II) atoms in the heme prosthetic groups, in hemocyanin the copper undergoes a transition from colourless Cu(I) in the deoxygenated state to blue Cu(II) when oxygenated.


Incidentally, there are certain species of fish that manage with little or no hemoglobin - icefish.


publications - What can cause the date of submission status to change without a change of status "under review" for Elsevier editorial systems?


I have a paper submitted to a journal of Elsevier.


From "Manuscript Submitted" to "with editor" took one day; then it was "with editor" for five days, and then "under review". One and a half months later, the status of the paper was still "under review", but the date of status has changed.


What can cause the date in the submission system to change in the absence of a change in status?




Answer



When a paper is assigned to a reviewer, the reviewer may decline or fail to review the paper. In this case the editor will assign the paper to a new reviewer. The status date will change at the day the new review was assigned, but the status will remain the same.


job - When should you move on from a postdoc position?


Suppose that in your sub-field there are half a dozen research groups on your continent that are acknowledged to be "world class". You have had the good fortune to do your MSc research in one, and your PhD in another. You are now a postdoc in a third. Your current group is large and well-funded, and your position there is secure for the foreseeable future. You realistically hope to get a faculty position in a good research university within the next 3-5 years.


One day, you are offered a postdoc position in a second-tier research group. Should you consider taking it, in order to broaden your academic horizons? Does the answer change depending on how long you've spent in your current postdoc? Are there other relevant considerations? Assume that you cannot expect to get a better offer within the next year.


Bonus discussion points: What if you're instead offered




  • a faculty position at the second-tier institution?





  • a postdoc position at one of the first-tier institutions you've already had an association with?




  • a postdoc position at a first-tier institution that you haven't already had an association with?




I have some views on these questions that I'm happy to share, but I'd like to see what other people think first.



Answer




"Discussion" isn't really how SE is supposed to work. However, I think the answer to your questions are relatively clear-cut (at least to me):



you are offered a postdoc position in a second-tier research group. Should you consider taking it, in order to broaden your academic horizons?



Why? You have a broad horizon, you have seen three top institutions before even becoming a faculty member. Go if the new position offers you something you are currently missing (such as a nicer place to live), but I would certainly not move just for the sake of it.



[you are offered a ] a faculty position at the second-tier institution?



If I like the place, I'll take this offer without a second thought. Expecting to become faculty directly at one of the five top institutions seems too much to ask for.




a postdoc position at one of the first-tier institutions you've already had an association with?



Did you like it there better than in your current job? If yes, take the offer. If no, stay.



a postdoc position at a first-tier institution that you haven't already had an association with?



More or less same answer as for the first bullet. You have seen a lot of places already, you do not need to change jobs just for the sake of it. If there is something you think the new institution will do better, then go for it. If not, stay. There is no life achievement for visiting each top institution in your field.


virology - Does 2019-nCov really has 4 HIV insertions?


https://news.ycombinator.com/item?id=22204866


https://www.biorxiv.org/content/10.1101/2020.01.30.927871v1.full.pdf


Indian scientists have just found HIV virus-like insertions in the 2019-nCov [pdf] (biorxiv.org)


https://www.virustotal.com/gui/file/44be7e51e386396fba6dba07a2fa5dcb21d6c41a76bd6b791128a0bea07a6043/detection



The article claims that the new coronavirus is an "hybrid" of an usual coronavirus with some parts of HIV. If you mix both virus in a bottle of water, you don't get the hybrid. If both virus infect a cell simultaneously, there is a small possibility that something like this happens. I think it's so small that is not possible to do it in a laboratory even on purpose, and definitively not by accident but IANAB.


It is easier with other virus. For example mixing variants of flu, because they have (IIRC) 8 strands of DNA. There are avian, swine, human, others flu, and each of them has many subvariants. If some animal get infected with two variants at the same time, a cell may have a double infection and the viral offspring may have a mix.



But the mix is a mix of the strands of DNA, like 3 swine flu + 5 human flu. This is usual, but you must consider that there are millions and millions of animals in the wild and farms. It's more difficult to do it in a small lab, but IANAB.


The main difference is that the article claim that the usual coronavirus and the HIV parts are in a single strain, not a bunch of strains packed together.



Q: can someone peer-review this and confirm that it is wrong?




publications - Is it better to submit a paper to a journal "normal" issue, or wait 4 months and send it to a more focused "special section" of the same journal?


I am a recently PhD graduate student in computer science.


In the last months, I wrote a paper about an aspect of my thesis, with the collaboration of my former supervisor. We found a call for papers for a "special section" of an important journal, that is a section focused on the data set we are exploiting. The submission deadline was set to the end of November 2014, but surprisingly we just discovered that it has been post-poned to the end of March 2015. So a 4 months delay.


Our paper is ready and I don't know what to do with the submission.


I would prefer to submit it now to the "normal" track of the journal, to move on to new projects and close this. But my former supervisor thinks that it's better to wait and submit it to the March 2015 "special section", because he says we will have more likelihood to get it accepted, even if this will make our paper more outdated.


What should I do?



Submit it to the "normal" track now with less chances to get it published, or wait 4 months and submit it (more outdated) to the easier "special section"?



Answer



There's another alternative. You can submit to the special issue early.


Usually journals don't have "easier" submission to a special issue or section. Most journals try to have the same review and editing criteria for such contributions as they do for other articles. (Consider that having different criteria makes it harder for them to process and track such articles.) I can attest - I had a manuscript that was asked for significant revision and it didn't make the "special issue" by the time we'd revised it.


But you can submit the article and ask for inclusion in the special issue and explain that you have the manuscript done now. They will probably send it for review, etc. but it won't be published until the remainder of the special section is finished as well.


I've done this. It gets the paper off your desk and lets you move on to other things.


What are the pros and cons?:




  • Pro: Usually a special section or special issue gets added attention and publicity. I haven't seen analysis, but one would hope that articles in this section or issue would have more readers and potentially more citations than in a normal issue.





  • Con: You will have to wait for the special issue to finalize, while if you submit to the "regular" journal, publication will probably happen sooner. On the other hand, if the journal publishes accepted articles before publication, or you can put the manuscript on a pre-print server, there's little downside.




Personally, I'd submit early, indicate in the submission letter (and online forms) that the article is for the special section and be done with it.


teaching - Knowing that most students submit assignments right around the deadline, is it advisable not to set deadline that is very late at night?


Like many on this site, I use a Moodle-type online Content Management System to give assignments to my students, and receive the finished work for grading. This is in a traditional context where the students are physically present in the classroom, and the online part is seen as a simple tool to be used in addition to the classic paper-based route. Students' first class for the day usually begins at 8 a.m.


For the last few years, I put the deadline for assignment acceptance at midnight, with plenty of time (2-3 weeks) to do the work, so each student can handle his/her workload as they wish. These are young adults aged 18-25, and are in theory very much responsible for their acts. Observation gives us actual hand-in times with approximately the following distribution:



  • 1-2 days before deadline: 5%

  • 3-24 hours before: 10%

  • 1-2 hours: 10%

  • less than 1 hour: 65%

  • emails in distress after the deadline has expired saying they have encountered a computer glitch or some other excuse: 10%



Which I guess is about par for the course. :-(


So it is clear that while in theory these students are responsible young adults, in practice they tend to plan ahead in a less than stellar way. The impression that is perceived is that the online nature of the submission system makes students take slightly more liberties with deadlines than when assignments had to be handed in, in a face-to-face situation - although it is clear that even then there will always be a certain percentage of people with difficulties respecting deadlines.


OK, here is the question: without getting into considerations on whether students should plan better (and possible ways in which I and other teachers could help them do so), would changing deadline times from midnight to, for example, 10 p.m. be a good move from the standpoint of their getting enough sleep (moral considerations welcome) and actually attending class at the beginning of the next day? Do I get to patent this Great Idea?


No, that last bit was a joke. ;-)


Reactions from people who are not actually teachers, but have experienced this context as a student are also welcome.


Update


I have ended up accepting the answer by Superbest below, basically because I liked his discussion of alternative possibilities. This is a bit subjective, since many other answers are also of very high quality IMHO - and I would certainly encourage the reader to peruse all the answers given here, and the varying points of view expressed (also in comments). Much appreciated.



Answer



While I admire your concern for the students, I feel that ultimately your endeavor is quixotic.


To be sure, I see nothing wrong with making your deadline be at 10 pm. It won't change anything, so you might as well. But I wouldn't expect it to have any notable effect, and I would be wary of the slippery slope that leads to you blaming yourself for the students' errors.



The reason I am so pessimistic is that I don't think procrastination and irregular sleep are caused by deadline timing (unless the work demanded is truly overwhelming, but in college it never is). They are caused by poor personal discipline and bad habits acquired over many years leading up to the present. Regardless of what you do, the procrastinators will still invent ways to procrastinate, because the problem is rooted in their own behavior, not yours. You therefore cannot solve the problem by changing your behavior.


For instance, if you have the deadline at 10 pm, the procrastinator will drop everything that evening to work on your assignment and submit it around 10. Then he will still stay up doing the things he just postponed for the sake of your assignment. Because, recall, this person is not selectively procrastinating on your course only - they have also other courses that have deadlines. Even if all courses had the same early deadline policy, the students would still have their own errands with self-imposed deadlines at later times that they stay up for.


By the same logic that makes you consider 10 pm, we can explore other alternatives:



  • 5 pm is a fair time, since it would presumably encourage students to concentrate their last ditch effort in the typical working day. However, there will also be students who have classes right up to the deadline that day, and if they procrastinate (as some certainly shall) they will now skip class to do the assignment, which is arguably worse than staying up!

  • Noon is another time that sounds like a good idea. Being too early, you might expect that it will make students feel they have no choice but to start working on it early since the morning isn't nearly enough time, and if they can't finish it the night before they can safely go to bed, get some sleep, and finish in the morning. But realistically, the procrastinators who stay up late and hand it in at midnight now will just start working at 1 am and stay up all night to finish it.

  • 9 am can be argued for as a realistic time - it's not like you will start grading at midnight, so there isn't really a point in requiring the assignment by midnight - instead of having the students rush their submission to a deadline just so it could sit in your mailbox for several hours, you could tell them to that you will start grading at 9 am and they should have it done by then. This makes the deadline less arbitrary, since there is now a clear logic to being required to meet it (ie. you will be delayed if they don't do their part). But of course you will again have the same problem of students staying up all night because they procrastinated.


For what it's worth, I think the midnight deadline came about as codification of an unspoken tradition. Often deadlines are given as days, without time - with this, there is always much controversy about what exactly counts as meeting an August 6 deadline: Does it have to be done at the beginning of Aug 6? Does it have to be before the instructor leaves the office? Does it have to be before the end of the day, ie. before you go to sleep? Well, what if you never go to sleep, can you squeeze out a few more hours and still "meet your Aug 6 deadline" by submitting at 3:14 am on [technically] Aug 7?


Even though informally "today" means "until I go to sleep", the convention is that the date changes at midnight, which is also reinforced by how computer clocks show the date. Hence, I think the midnight deadline came about as an extension of this - it's just a date delimiter.



As for the students, since you are concerned about how late they go to sleep, surely you will agree that planning ahead and not leaving everything to the last minute is an important skill to be learned as part of tertiary education. This, then, the students must learn on their own, you cannot help them by tinkering with deadlines, since indeed the deadline is not what is preventing their learning. In fact, one could argue that you should maximize the negative reinforcement, and set the deadline at the worst possible time - say 6 am: The more misery you inflict on the procrastinators, the better they will appreciate how important it is to learn discipline, and the sooner they will take steps to unlearn their bad habits.


Granted, I'm not seriously suggesting you do the above, since it seems like it could go horribly wrong. Realistically, I could instead suggest the following:



  • Set your deadline at some reasonable, early time such as noon.

  • Secretly (ie. do not tell this part to the students) have the "real deadline" (for instance, the one you lose points for missing) be quite a bit later, say 5 pm.

  • In class, say that it is very important they not miss the deadline even by a minute (don't say why), and they should come talk to you if they feel they won't make it.

  • When they inevitably come asking for more time, be liberal with the extensions, but not before making them explain why they were late and lecturing them on the importance of planning ahead. When giving the extension, explain that they absolutely cannot miss the extended deadline, because then you would not be able to meet your own deadline for grading (whether true or not).

  • If anyone misses the noon deadline (but not the 5 pm deadline), confront them about it to discourage submitting late without asking for an extension (which allows bypassing the social discomfort of asking for more time).


With this, you might create something like a low stakes environment (you don't lose massive points just for being a few minutes late) while still creating a fair amount of social pressure to increase the likelihood of a lightbulb appearing and the student thinking, "Hey, Dr. Ward is very nice and reasonable about deadlines and everything, but maybe it's worth for me to try to stop leaving everything to the last minute?". Furthermore, if you force them into an explicit discussion about their procrastination, they have an opportunity to ask you for advice on how to plan their work.



But all of this requires quite a bit of effort from you (much more than just replacing "midnight" with "10 pm" on your syllabus). So if you are not willing to commit the energy, there isn't really much that can be achieved with quick fixes.


Is there an "Adam and Eve" for each new trait during (not just human) evolution?




Do new beneficial mutation evolve simultaneously and independently with several individuals of the same specie or only with one specimen who then transfers it to all of the specie?


In other words, when we talks about common ancestor we usually mean a specie, so for example, all earth dwelling reptiles, birds and mammals are the descendants of Tiktaalik (to the best of my knowledge), and we know that Tiktaalik was the first (or one of the first) species to come to land, but was there a first individual Tiktaalik who went to the land, like Tim Minchin's Tony the fish.



Imagine being the first dude ever to have feet...


Imagine you're a fish, and you are swimming in the ocean ... and suddenly out of nowhere Tony just goes "I'm getting out, I'm freezing, I'm just gonna pop out for a bit, maybe lie on my towel, I'll bring you an ice cream"


-"Don't bother ,Tony, you are a freak! Tony is a freak, let's go, let's ostracize him for being different"



It seems to me that from the same species of ancestors there are several descending distinct species, so it seems to me that that that there was a species of reptiles that at some point some individual of that group developed Dinosaur features and traits and whose descendants became Dinosaurs and then Birds, and another individual of that specie or a descending specie (not necessarily at the same time) developed mammary glands whose descendants became mammals, and other individuals who didn't mate with those two whose descendants remained reptiles.


Was there ever a first dinosaur with feathers who is the father or mother of all birds, or the first fish with lungs, the first monkey with opposable thumbs from whom all apes descend, or the first mammal that decided to go for a swim and all dolphins, whale and seals are his direct descendant of that first swimming mammal?


And also for traits that don't lead to speciation, was there a first human who was lactose tolerant, and all the lactose tolerant people on the world are his/her descendants, or the first person with no wisdom teeth, the first person with slanted eyes, and the first person with red/blond hair?



*- If there are gross inaccuracies and/or over-simplification in my understanding of the evolutionary process, this is because I'm not a biologist, and I would accept happily any correction.




publications - Special (non-english) character in name. What to do as author? Internationalize or not?


In German, as well as in other languages, people have Non-English characters in their names. e.g. ß, the umlauts etc..


I frequently face problems when flying, opening bank accounts, etc., particularly abroad, since replacing the ß with ss changes more more than 25% of my family name as compared to how it's written in my passport.


Obviously it is desirable to write one's name for submissions, the way one's name is written correctly. Can one expect to run into problems, and will sooner or later end up with different publications being published under different spellings of the name, or is it safe to go for the correct spelling?



Answer



First of all, always be consistent. Whatever you decide, that is what you will always have to use.



Considering the first point, might be better to strive and use your real name as it is with the non-english characters. You will have less problems in the future to prove your authorship in case questions rise. Complain to systems who do not accept your non-english characters...


Friday, 27 October 2017

career path - Why are some PhD holders unable to become professors?


Why do some people get STEM PhDs, want a professorship, and end up not getting it?


Is it only about opportunity and competition, or are there PhD candidates that are just not qualified to be professors (why?)?




Value of mathematical models in biology



Sorry if this is too much of a soft question or if it is too broad for this site.


As a person who has much more experience with math than biology, I've always been really interested in the mathematical side of biology. As I study math in biology, however, I am left with the question of "how is this actually useful?"


What kind of unique insight can mathematical models give us about biological systems that we couldn't just find experimentally?



Answer



This question is broad.


There are plenty of uses of mathematical modelling in biology.



Wikipedia


You may want to read the wikipedia article: Mathematical and Theoretical Biology.


Books


There are tons of books on theoretical biology. I am personally working in the field of population genetics, a field where much of the theory has been expressed mathematically. Here are book recommendations for this particular field.


On Biology.SE


We have a tag for mathematical-models (you used it in your post). You may want to see what kind of posts are tagged for mathematical-models.


To repeat @fileunderwater's comment, What physics knowledge can be applied to biology of organisms and ecosystems and When are population dynamics models useful? are examples of posts you may want to read.


What prevents predator overpopulation? will give you an example of an easy and classical mathematical model to describe population dynamics of predators and preys.




Personal historical/philosophical note: At some point physicists have started to describe the laws of nature with mathematical expressions and at that time many physicists didn't quite like the idea that physics could be described by math. Biology has gone through the same phase but much later. Early mathematical biologists developed the modern science of statistics (Francis Galton, Karl Pearson, Ronald Fisher). Biologists used existing mathematical tools such as diffusion processes (Kimura). Note that part of the work in the field of diffusion equations have been done by physicist (Einstein solved the 2D equations for diffusion processes). Note also that the dynamic of diffusion processes called brownian motion have been named after a biologist. Today, biology produces massive amount of data that require good computational skills to treat. The time when biologists had only to know how to recognize species is over, now there are few biologists left that aren't able to code in at least one programming language.



Thursday, 26 October 2017

biochemistry - Is there a difference between "Alpha Helix" and "Alpha subunit"?


In my biochemistry textbook the terms alpha helix and alpha subunit are both used. Are these two terms synonymous? For instance, hemoglobin has an alpha and beta subunit, are these the same thing as alpha helix and beta pleated sheet?




postdocs - Post Doc application form in France asks for very personal details, is it normal?


I'm trying to get an engineering post doc which I will conduct at a company's R&D labs, however I need to jump through all of the sponsoring university's hoops. I just received their application form and some of the questions are very personal. I thought such questions would be illegal in any European country. Are questions like your marital status, number and name of your children, date, place of birth...normal? The number of ways a candidate maybe discriminated against based on their responses would be exponential.




research process - Familiarizing oneself with state-of-the-art at the beginning of a PhD


From my research internship experiences (my previous University didn't really focus on research much) and what my current advisers told me, a general flow of a PhD is like any other long(er)-time project:



  • familiarize oneself with state-of-the-art on the subject


  • generate your own ideas (by trial-and-error) and integrate with current approaches


    (with this phase becoming a lot fuzzier the more advanced your "project" is)



  • write it up for the world to know.



As a fresh PhD student, I'm currently in the middle of familiarizing myself with the state of the art, following the advice of many older students ("be a brave soldier in the beginning and do and read everything your advisers throw/send/e-mail your way"). And I do understand the importance of it (in fact, more often than not, I love it). But, it does give one an impression of self-uselessness sometimes (I have a talk with myself every few weeks or so to remind myself of my motivation and resolve the "uselessness" issue).


So, my question is: Typically, how much time would a fresh PhD student spend on going through state-of-the-art at the beginning of his/her PhD?


And some sub-questions:



  • is it expected/typical to produce some kind of output (articles?) during this period?

  • what kind of output is expected at the end of this period?

  • what would be some indicators that this period is ending which a student himself can notice





In the end, just to provide some context: I'm doing a PhD in Europe, and we have a limit of 3 years for a PhD (sometimes extended for up to 6 months) and I'm studying Computer Science.



Answer



Your question likely indicates that you need to work on your communication with your advisor. Hasn't he told you what is expect and how you are progressing?


I will try and keep this answer focused on the question, but I apologize if it strays.


Some indicators that your are becoming familiar with the field:



  • When you talk to your supervisor you are familiar with some of the references mention and names start to mean something to you. Better familiarity is when this holds when you talk to colleagues and go to talks and seminars

  • When you have read/glanced at most of the references in articles that you read. Better is when the most exciting thing about reading new literature is finding a reference to something you didn't know about


As far as output, ideally during the course of your dissertation you should become familiar enough with the relevant literature to write a literature review article. You should feel like you could write a review at the end of the familiarization stage. Actually writing a full review is probably a bit premature, since you want the review to tie in with your eventual dissertation. I would suggest that a useful output is a dissertation proposal with a strong literature review based motivation. This is not a publishable output, but it is tangible.



human biology - What is the name of the category of viruses that affect only one side of the body?


The Varicella zoster virus causes chickenpox in children and shingles in adults.


When the virus attacks as shingles, one of its distinguishing characteristics is that it only affects one side of the body. (As shown in the link and verbally identified by a doctor I spoke to). This happens because the nerve cells themselves are infected - and are partitioned on different sides of the body.




At first the rash appears similar to the first appearance of hives; however, unlike hives, shingles causes skin changes limited to a dermatome, normally resulting in a stripe or belt-like pattern that is limited to one side of the body and does not cross the midline.[13] Zoster sine herpete ("zoster without herpes") describes a person who has all of the symptoms of shingles except this characteristic rash.[16]


From Wikipedia



My question is: What is the name of the category of viruses that affect only one side of the body?



Answer



Short answer: Viruses that affect only one side of the body are not categorized by this information.


Long Answer: For people who likes details


Several types of virus classification exists:



  • Baltimore: Classified by the type of DNA or RNA that is carried by the virus


  • Holmes: Classified by the target organisms of the viruses (plants, bacteria, animals)

  • LHT: Classified using several physical differences (More specific and complex)


For example, Shingles would be classified as:


Baltimore: Group I (double DNA stranded viruses)


Holmes: Group III Zoophaginae (animals)


LHT:




  • Order: Herpesvirales





  • Family: Herpesviridae




  • Subfamily: Alphaherpesvirinae




  • Genus: Varicellovirus





  • Specie: Human herpesvirus 3 (HHV-3)




graduate admissions - Recommendation letter from advisor with different research interest


While I was an undergrad, I wrote a paper on topic A with my advisor. Currently, I'm working in a research institution with an Economist whose work mainly lies on topic B. However, I've come to understand that I do not like A or B, but I'm more interested in topic C, and I've done some independent study on topic C. I'm thinking of asking my undergrad advisor and my current Economist for recommendation letter to apply for PhD in topic C.


How will admission committee for PhD view such recommendation letters from academics whose work is not on my current interest? That is, will it have any negative influence in my application, if I seemed to change my interest often?


To be specific, all topic A, B and C is under the field of Economics, but are vastly different from one another (especially the switch from A to B; it was like learning completely new subject). Knowledge gained from A and B can only be partially transferred to C.


Related, but does not quite answer the question that I have: Value of recommendation letters from professors in a different field. My question is more focused on the fact that two recommendation letters will show my interest in certain research topics were very short-lived.



Answer



I think it depends on exactly how long you worked with these two individuals and what you accomplished. You want strong letters, so if you worked with both of them long enough for them to assess your basic research abilities and potential to develop into an independent researcher, I think the fact that they don't work in your exact desired field won't matter much. The fact that all three topics fall under the same Economics umbrella probably makes it even less of an issue.


It is true that sustained interest in a field/topic is usually a positive. However, I think you and your recommendation letters can spin even short-lived interests into a positive thing if you demonstrate that your prior experiences in A and B were valuable from a research skills development standpoint, while also helping you narrow your research interests down to topic C. Switching topics after you start a PhD can become difficult (especially the longer you wait), so admissions committees may look favorably on any prior work that helps you discover your research passion.



Wednesday, 25 October 2017

entomology - What insect is this? (Black body two orange lines in its back and six legs)


I found this today in the library while studying. I am very curious to know whether this particular insect has a name that I can look up and find more information about:


enter image description here


Full length is almost one centimeter. It doesn't bite or anything. It has lots of small hairs in its back (similar to cockroaches and ants) and has a tail that a white sticky substance comes out from.




human biology - Why does the ring finger not move independently?


Why is it that we need to move little finger in order to move ring finger with it? For example, put your palm on a table and fold your middle finger inside. You won't be able to move your ring finger unless you move your little finger along with it. Why? Paul Gilbert and Buckethead and various other guitarists are the only people that I'm aware of that use the ring finger and looks independent. Is it possible to have surgery to make the fingers independent or is it not functional to do that?



Answer



The reason for this phenomenon is in both the muscular structure and neural connections of the little and the ring finger. Lets start with the following diagram:



hand muscles


As you see (click on the image to see full version), the fingers contain extensor muscles for movement. However, the index finger and the little finger have separate extensors, because of which they can move more independently as compared to the middle finger and ring finger, which contain a common extensor muscle called extensor digitorum. Some people lack the interconnections between these extensors, and can thus move their ring finger quite easily. One can also achieve this through practice.


Now, as to why the ring finger moves easily when moved along with another finger, have a look at another image:


finger nerves


The fingers are connected to brain via two nerves:




  • radial nerve, which connects with thumb, index finger and one side of middle finger





  • ulnar nerve, which connects with little, ring and the other side of middle finger




As you see, the branching between these nerves is what causes dependence of the fingers on each other for movement. Since the nerves for ring finger and little finger are intertwined, it becomes difficult to move each of these fingers separately. Similarly, you may find it easier to move your ring finger along with your middle finger. But you can easily move your middle finger independently because it gets signals from radial as well as ulnar nerves.


Thus, it is the combined effect of muscular and neural anatomy of ring finger which causes this effect.


PS: Since the effect is due to the neural and muscular anatomy of the ring finger, I don't think surgery would help in this case.


References:



molecular biology - basic programming and bioinformatics



As a molecular biology graduate student I have decided to learn some basic programming and bioinformatics since everybody says that it is crucial. For example, what would you learn if you need to work with RNA-Seq data, compare and interpret them?


Thanks!



Answer



Indeed the question is broad and quite hard to answer I think. I'll give a try. I very welcome editing to improve this answer.


The field of bioinformatics is a big field. Bioinformaticians need basic knowledge in



  • biology


  • molecular genetics

  • Population genetics

  • programming

  • statistics


You may find courses on statistics applied to bioinformatics here (R-language) and here (I haven't watched these sources).


How to start programming? - Python


You seem to be mostly interested in is programming. I think that Python is a very good start to get in touch with programming. Programming might look a bit scary when you don't really know what it is about but you can easily, in a few days, acquire basic knowledge in this field and already solve some pretty neat problems. Many people actually have lots of fun learning how to program. And you'll probably be amazed by all the power this tool will offer to you. I personally really enjoyed learning to programming in Python. I did it (I was mostly interested in object-oriented programming, you'll learn what it means) in a day or two with a very good source but unfortunately, this source is not available in English. But there are tons of introductory documents, you'll have no difficulty to find a good one. I'd counsel you to directly download Python and to look at online courses on khan academy or EdX (I haven't watched them).


Data analysis - R


While Python is very popular, I think that, as a biologist, it is very important that you know about R. R is a programming language which is slow (compare to Python, C, Java, …) but it is very useful for statistical analysis and visual display of data. Also, many people use R in bioinformatics (for phylogenetic analysis typically). I think that acquiring basic knowledge in R takes more time than in Python because we tend to use R because of its huge amount of already existing functions and therefore, we have to learn many of these functions before understanding that R can indeed be much more useful than Python for some tasks.



Command line - Shell script


Shell script (BASH for example) is a very specific and very important language too. Very useful for manipulating, transferring files, managing processes or pretty much anything that is happening on your computer.


Other


C and C++ are very fast and very much used as well. Perl is commonly used for genomic sequence analysis (although Perl is slowly losing users to the advantage of Python).


Usefulness of programming


You also ask about the usefulness of programming. Well, it is used in pretty much all areas of biology. It is used for analyzing empirical data, computer simulations in population genetics, graph theory, annotating DNA sequences, … I guess that 98% of biologists have at least some basic knowledge in programming. The main point about programming is that it performs calculation much faster than anything you could ever realize with your calculator. Typically, in bioinformatics, analysis of DNA sequences often asks for very intense calculation and asks for big computation power. Processes such as constructing phylogenetic trees, determining a goodness of fit of evolutionary models, annotating DNA, aligning DNA sequences, analyzing microarray and many other things are all sorts of tasks that require programming.


phd - Is a research thesis (report) with zero contribution to human knowledge acceptable?


An alternate title could be "Do we award a PhD for what the student became or for what he produced?". More precisely, if a research thesis report does not advance human knowledge, yet still shows that the student acquired the right skills of investigation, should the title of Philosophy Doctor be awarded?





  • I kind of always assumed that a thesis (PhD thesis in particular) should have some positive results (where positive means "advancing the state of human knowledge"), and that part of the art of finding a good topic of research was the art of asking the right kind of question, which would yield some positive result independently of the answer. Similar views are expressed in this other stackexchange question and the corresponding answers:



    It is an expectation that the PhD would make an original contribution and/or advance knowledge in a given field. I understand this is a universal assumption for this level of study across all universities. (...) usually a PhD is measured on its contribution to expand knowledge.





  • Nevertheless, Justin Zobel defends convincingly the opposite view in "Writing for Computer Science", p.154 of the Second Edition:



    even if good results are not achieved, the thesis should pass if you have shown the ability to undertake high-quality research. (...) A thesis with negative results can, if appropriately written, demonstrate the ability of the candidate just as well a a thesis with positive results. (...) it is you, not the research, that is the primary object of scrutiny






Is there an agreement across disciplines about this question?


I am not directly concerned (I reported positive results in my PhD thesis long ago, have many positive results to report in my "Habilitation" thesis, and I certainly aim for my students to report positive results in theirs), but I am curious about the real objective of the thesis: - as an advisor, I could suggest a more risky topic if it had the potential to teach more to the student without risking the whole graduating thing; and - as a referee or member of an evaluation committee, I have to judge students and/or their thesis...




Extreme Fictional Example


A student and advisor do the entire research work following the most rigorous scientific process for several years, only to find their efforts ruined near the end of the process either by a budget cut, the disappearance of the species they were studying, or the discovery that the problem is the consequence of an obscure results from year ago in another research community.


The student has followed and learned the scientific process, but did not contribute to human knowledge (apart from maybe improving the index of its bibliography). If the student has showed the qualities required from a good researcher, should(n't) he/she be awarded the title of "Doctor in Philosophy", independently of the contribution made to human knowledge?


This is truly a rhetorical question, and I doubt this kind of situation happens often. Yet the idea is new to me and I kind of like it, albeit I doubt the whole community would agree...





Opposite Extreme Example


Imagine that a student, stroke by luck, makes an amazing scientific discovery which deeply impact human knowledge, and can be understood by all even though the student poorly redacts it. It seems clear to me that the society would not benefit from awarding a PhD to such a student, who has not learned how to do research even though contributing to human knowledge.


On the other hand, setting two conditions for the awarding of a PhD, having learned how to do proper research AND having advanced human knowledge by using it, introduces trade-offs and compromises (which again do not serve society).



Answer



The question as currently asked is: Is a research thesis (report) with zero contribution to human knowledge acceptable?


And the answer to that question is no.


A thesis or portfolio submitted for a PhD or higher doctorate must make a novel contribution to human knowledge. It must also demonstrate that the applicant has acquired the appropriate level of research skills.


Some negative results do advance human knowledge. So a thesis with negative results and no positive results may make a novel contribution to human knowledge. e.g. demonstration of absence of an effect is a negative result, but can be a distinct and significant contribution to new knowledge (particularly if the effect was previously believed to exist).


However, just spending the time, putting in the effort, and churning out the right quantity of work, is not in and of itself sufficient.


Basis for this



This is based on a combination of my employer's guidelines, my experiences as a PhD supervisor, and advice from my colleagues. I hear that there are other (less well-respected) institutions that award doctorates just for putting in the effort and churning out the right quantity of work, regardless of novelty of contribution, or of demonstration of research skill


A quote from some official guidelines.


Here's a quote from the relevant part of the academic regulations for PhD examinations from UCL, University College London (pdf):



A thesis for the awards of EngD or PhD degree shall be examined in accordance with the criteria prescribed by UCL and the thesis shall demonstrate that it: ...


shows a student's capacity to pursue original research in the field of study based on a good understanding of the research techniques and concepts appropriate to the discipline; ...


represents a distinct and significant contribution to the subject, whether through the discovery of new knowledge, the connection of previously unrelated facts, the development of new theory, or the revision of older views;



graduate school - How does one keep herself updated with new research without forgetting older results?



The title is fairly generic in nature, so I'm trying to elaborate in the body. I'm interested in answers pertaining to Theoretical Computer Science (TCS), but I'm certain the question would be equally relevant in fields which have been around for more than a couple of decades, and hence I hope to get responses from researchers in other disciplines as well!


What I'm trying to understand is how researchers (who have been working for quite sometime) in any specialized field (like TCS) keep track of results that have already been published - not just seminal results, but also results which have a lesser (but not insignificant) impact on the field but were published years or decades before. At the same time, one has to keep track of results being published in (at least) the notable conferences in the current year as well, in order to absorb the new ideas presented there and incorporate/extend them in one's own work.


I find it kind of incredible to believe that all of the above is possible without any kind of disciplined approach to reading and subsequent assimilation of the ideas on a regular basis - which is why I'm asking members of academia about their experiences/practices on this. In particular:



  1. How frequently (if at all) do you revisit "classic" results?

  2. Do you keep written/electronic notes on a regular basis to keep track of continuing progress in a field (say, for instance, inapproximability results for geometric problems) - or do you prefer to keep it all in your mind?

  3. To keep track of current state of art, do you only attend/read Tier-I conferences, or do you get useful ideas from results published in Tier-II/III conferences as well?

  4. What kind of time/resources would you typically set aside for reading, as opposed to working on a problem?


In short, I'm trying to find what kind of things would you expect a top researcher to "know" off the top of his head, and at what level of depth - and how would you go trying to maintain that level of perception over the years?



(I understand that the question IS subjective, but I'm hoping that it satisfies the guidelines for a "good subjective" question!)



Answer



Here are a few additions to Suresh's list (converted from a comment at TCSgrad's suggestion):




  • Don't even try to remember details. Just remember that somebody published something related, and use Google (or Mendeley or Papers) to find the paper again when you need it.




  • Chase references. Interesting papers tend to cite other interesting papers. When you read any paper, also look at the papers in its bibliography.





  • Chase citations. Interesting papers tend to be cited by other interesting papers. When you read the paper, find other papers that cite it (via Google Scholar, for example) and look at them, too.




  • Follow whims. If you see a paper with an interesting word in the title, or an interesting figure on the first page, at least read the abstract.




  • Don't try to read everything. That's impossible. Just try to read a little more.





  • Stop reading. Eventually you have to do your own research. Don't worry about reinventing the wheel; sometimes the best (and even fastest) way to understand what someone else did is to ignore them, figure it out yourself, and then read their paper.




Tuesday, 24 October 2017

gel electrophoresis - How to do western analysis to lung tissue?


I am working with lungs from mice, and I want to do a western blot analysis to my samples. I am having trouble with this because my images turn out very "messy", with a high background. Perhaps I should filter my samples following their homogenization? Has anyone had this problem and knows how to avoid it? What is the best method to homogenize the samples?




ethics - First-year PhD giving a talk among well-established researchers in the field


I am currently a first-year Ph.D. student, before that (as I have posted about before) I was forced to leave my Ph.D. program after one year because of a bullying supervisor. Previously, I made a good relationship with other researchers in my field and other scientific volunteering activities.


Now, there is a workshop at a highly ranked conference, and I asked about the possibility of sending a paper for the workshop. They don't solicit papers, however, I have a good relationship with the professor who is the main organizer of the workshop, and they voluntarily asked me to be a speaker in the workshop for 30 minutes.


The other speakers are the most well-established researchers in my field, I felt excited but afraid in the same time. I don't have yet any publications concerning the current research. I don't know if I should apologize, maybe the professor does not know that I have been kicked out from the earlier program. I don't know what I should do, all the speakers are the elite and I think I am not deserving to be among them as I don't have the same experience.


Should I try or would this be counterproductive to my future career?


EDIT 1


Thanks for answers encouraging me to try, while there are pragmatic answers that I don't have to waste the audience time, honestly, I have self low esteem since all peers have papers published in top journals and conferences, I don't know why the organizers listed me as a speaker, I am not doing great as other students or there is no indication in the right moment that I am doing fantastic research.



Answer



Let's flip this question around and imagine that you, as a first year anthropology PhD student, are now visiting your high school. One of the students asked your former teachers if you would be interested in a local, anthropology-related research project they were doing (e.g., they could be investigating the attitudes of people towards those who are HIV positive, and contrasting how that varies between countries). The teacher promptly arranged for them to give a talk on their results while you were there.


The student feels excited but afraid at having to give this talk. She knows she doesn't have the pedigree you have, she doesn't know if she should apologize, maybe you don't know she flunked her latest exam, and she thinks she is not deserving to be giving the talk because she doesn't have as much experience as you. Should she go ahead and give the talk or would it be counterproductive to her future career?



I'm pretty confident you will say she should go ahead, and the same applies to you. These well-established researchers probably know (or can tell) you're a PhD student, and will not demand that you have done groundbreaking work on par with theirs. Instead of focusing on all the things that could go wrong, think of all the things that could go right: you get to present your work to a well-established audience. They're the people you most want to know your results. You get to network with them. You get to practice skills that you'll undoubtedly need later in your career. What's the worst that can happen anyway? Even if you give a truly atrocious talk they'll probably all have forgotten about it by next year.


tl; dr: stop worrying and do it.


What are the benefits/detriments to graduate students joining unions?


The graduate students at my university (a relatively large state school in the US) are considering joining a union. To help decide whether to sign a union card in support of joining the union, I'm interested in more information about how unions have helped graduate students at other universities. What are some improvements to graduate life gained by graduate students at other universities upon joining a union?


I'm also interested in information about how unions have hurt graduate students at other universities. What are some detriments to graduate life caused by graduate students joining a union?


I'm primarily interested in student-body-wide benefits/detriments, instead of student-specific or faculty/administrator-specific claims (e.g. "my advisor treated me better with the union behind me" or "my students have stopped working since they joined a union" is not what I'm looking for).



Answer



I went to graduate school in mathematics at a university with a TA union. I think the main effect was to level off graduate student compensation across disciplines -- so, the union was apparently a great boon to those in the humanities, but I heard that compensation for math TA's would likely be higher if not for the union.


Another benefit to the union was that it instilled (for many) a sense of camaraderie and common cause. Union events were fun, and they served beer. It was a good way to get to know your fellow graduate students.


The main disadvantage was that dues had to be paid, around $200 a year (most of which went straight to the AFT). This is not a lot, but on our salary it did mean something. Dues were mandatory, even if you opted out of the union -- although state politicians have since seen to it that this is no longer true.


Another potential disadvantage is that union dues went (in part) to political contributions to union-friendly politicians. I didn't mind, but this tended to alienate graduate students who were more politically conservative than me.


There was occasional heated rhetoric when I was there, and even more after I left, but overall the union didn't seem to do much good or harm. Mostly, I remember the beer.



publications - Advisor publishing students' work as sole author - ethics and motivation


This is a question about my advisor (supervisor, professor) in a lab, where I am a graduate research assistant, and had done research together with a PhD student, as a part of his dissertation. The student happened to be one of my close friends. The professor wanted to write a journal paper based on the results of his dissertation with that candidate. This was kind of near the end of his PhD program (three weeks before final defense). At that time he said that he was already stressed out about defense and will write the paper after the event as it won't take him more than a week.


After he graduated, he had asked the professor about the journal paper but the professor kind of brushed it under the carpet saying he is looking for CFPs (call for papers) where they can write and never got back to him, despite his constant inquiries.


For his research on human-computer interaction, I had developed applications which formed the core of his project. So my advisor asked me if I was interested in writing the paper and she convinced me that since I developed the applications (that formed basis of the research) it was fair enough that I write it. But after a week, she ignored me and wrote the paper herself and submitted it to the journal.



I came to know last week that my advisor wrote the paper herself and got it published. This professor is an assistant professor trying to get tenure. I am trying to understand the motivation behind this behavior.


My questions:



  1. The journal paper was published by my professor as sole author. Won't the paper count towards her tenure if she wrote it with a graduate student or will it count towards higher credit if she is the sole author?

  2. Is it ethical to publish the paper based on my friend's dissertation? (I mean it is legal, because she will be referencing his PhD dissertation, but is it ethical or common in academia to sidestep the original author?)

  3. Should I be listed as co-author for all papers coming out of this research because I developed the applications that formed basis for this research? I mean the concept for them was not mine, but I did program them.



Answer



Before anything else: Don't walk. Run.


There are almost certainly details of this story that you have omitted, or that you have unintentionally embellished, or that you are unaware of, and clarifying those details here would be inappropriate. What is clear is that your relationship with your advisor is completely broken. Get help, and get out.




Q1) Wont the paper count towards her tenure if she wrote it with a graduated student or will it count towards higher credit if she is the sole author?



All publications count toward tenure, whether solo, with colleagues, with current students, with former students, or with strangers from Zanzibar.



Q2) Is it ethical to publish the paper based on my friend's dissertation? (i mean it is legal, because she will be referencing his phd dissertation but is it ethical to sideshaft the original author)



There are a few different possibilities here:





  1. Your advisor's submission does not report your friend's thesis work as her own, but rather builds on your friend's work in a novel direction. In this case, your advisor's submission is ethical, but perhaps a bit unfriendly. After all, the success of her students is a significant component of her upcoming tenure case.




  2. The results in your friend's dissertation are the main topic of your advisor's submission, but your friend did not make a significant and novel contribution, and therefore does not deserve coauthorship. But in this case, your friend also does not deserve a PhD, and your advisor's signing his thesis was unethical. This possibility seems highly unlikely; passing a thesis defense generally requires the unanimous approval of the entire thesis committee.




  3. Your friend made a significant and novel contribution, which is the main topic of your advisor's paper. In this case, your advisor is being grossly unethical. Fortunately, since your friend's dissertation is easily accessible online (Isn't it?), any competent referee or editor should quickly spot the intellectual theft. That would just be stupid.






I came to know last week that my advisor wrote the paper herself and got it published.



If you believe that your advisor has stolen credit for another person's work—your friend, her former student, or a stranger from Zanzibar—it would be appropriate for you (or better yet, your friend) to speak discreetly to your department head or another trusted senior faculty member, with both the original dissertation and your advisor's publication in hand, asking them to clarify the ethical boundaries. Do not accuse; such accusations are very serious, and your advisor's colleagues may react defensively on her behalf. Instead, explain the delicacy of the situation and ask for guidance. And then listen.


They may react badly anyway, but then you have your answer.


If they agree that your advisor has acted unethically, get out of the way. This is not your fight.



Is it common in academia to do this?



No. I won't claim they never happen, obviously, but serious breaches of ethical behavior, at the level you are accusing, are extremely rare.




Q3 One more question i have is should i be listed as co-author for all papers coming out of this research because i developed the apps that formed basis for this research. I mean the concept for them was not mine but i did program them.



That is a more subtle question. As a general rule, I would say no. Of course you deserve credit for your contributions, but only once for each contribution. If your contribution is a key piece of software, then the first paper that uses that software should describe that software in detail and include you as a coauthor. If you walk away after that first paper, later work that relies on your software—by your advisor or anyone else—need not list you as a coauthor; you already got credit. With good reason, Stephen Wolfram is not a coauthor on every paper that uses Mathematica. You should of course be cited in any paper that uses, builds on, or improves your work, but that's a separate issue from coauthorship.


But reality is rarely so cut and dried. Is moving the software to a new platform a sufficient contribution? Optimizing the underlying algorithms? Adding a new, easy-to-implement feature suggested by your advisor? Adding a new, hard-to-implement feature suggested by your advisor? Adding support for a new input device? I have no idea. You and your advisor should have agreed in advance on the contribution required for you to be a coauthor.


Normally, if you had not had this conversation already, I would recommend having it now, but it sounds like it may be too late for that. You may be better off simply walking away and finding a new advisor that you can trust.


Monday, 23 October 2017

database - The best free and most up to date phylogenetic tree on the internet?


I found phylogenetic tree in wikipedia is lacks of accuracy. It actually confusing with versions. Some terms was not scientifically accurate with dna analysis anymore


So are there anyone know where is the most updated datasource on the internet?



Answer



Available ressources


I would recommend oneZoom.org is probably the best ressource. oneZoom.org is based on openTreeOfLife.org (for phylogenetic relationships) and eol.org (Encyclopedia Of Life) (mainly for the pictures I think). If you do not fancy to much the display and links of oneZoom/org, then I would just recommend openTreeOfLife.org.


There is also tolweb.org but it is not as nicely updated as openTreeOfLife.org (and therefore openTreeOfLife.org) and the dates are harder to find.


Particularities of oneZoom.org



I particularly like that for each node oneZoom.org offers links to



  • wikipedia

  • encyclopedia of life

  • the red list

  • NCBI


, which makes it a very appreciable tool. oneZoom.org has the advantage of a nice display (although a bit slow to load IMO) and is easy to navigate and get time to the Most Recent Common Ancestor of a lineage.


I also like that you can just add the species name after "#" in the URL and it will jump to its node. Here is the Kagu for example.


Potential issues in oneZoom.org



Of course, oneZoom.org contain a few mistakes! Some of them are unintentional (wrong picture, misrepresentation of what is known from the literature, fail to update information), some of them are caused by lack of knowledge of true phylogenetic relationships. oneZoom.org does not say how certain we are that a given speciation event is correct or correctly dated, it just display the best estimates we have. If a specific node is of interest to you, you will need to go to the scientific literature which will give you much more information about what we know and what we roughly guess.


grades - Should a marker TA handle students' marking issues by email?


I am a university marker TA. The instructor requires TAs to meet students if they have marking issues. But I found most students just come to meet me for better grades, not to ask questions, and some are tough to handle; they just insist they should get better grades.


I feel that is annoying. Is it a better idea to handle the cases by email, and let them talk to the instructor if they have further questions?




graduate admissions - Is it unwise to contact the professor directly before getting admitted to a program in US?


In his answer of Details an applicant should include/exclude in an introductory letter to a prospective grad school adviser?, aeismail says



If the program in question is in the US, for instance, you should probably never contact the professor directly until after you've been admitted into the program in question. Since admissions decisions are handled centrally, it's just a waste of time.



Now I'm surprised with this, and I think I'm not the only one. For many times, not only in this site, but also in real-life examples in my university, I have seen that my friends get accepted through contacting professors beforehand, and those professors are helpful and willing to get you through the adcom. Recall it back, they don't go to US, but I don't think US should be an exception.


Why is it an exception? Why do the "admissions decisions are handled centrally", unlike other universities in the world, where the weight of the professors is heavier? Isn't that sorting the applications by score not good as checking their ability directly through interview? And who is the most suitable interviewer, if not the one who will advise you in the future?



Answer



Let me answer this question from the perspective of our school. If a school does things differently the answer you're quoting might be very appropriate, but not in our case.



Our admission decisions are made by our department, and essentially everyone is on the admissions committee - we share the load of evaluating applications. So, there could be great benefit of talking to a professor ahead of time. If one faculty member strongly desires a particular candidate, that student will generally get admitted, assuming they meet our qualifications. (Note that, as a small school, we have enough capacity to take more students than we do because we don't get tons of qualified applications. Also, we almost always have TA funding available for qualified students. But this really varies from one university to another.)


So, this establishes that, at some schools, talking to potential advisors ahead of time can be very valuable. The interest of working with a particular advisor can also (and should) go into the personal statement. I read so many personal statements that you can tell are completely generic, with different school names copy and pasted in. So, when someone says something specific about my research area, I take notice, and I think other faculty do too.


The real issue is that I get so many requests from random students to look at their CV. Many of them have very little connection to my work and are probably mass-emailing professors. This should be avoided.


@Anonymous' answer has the right idea here. A few months ago a student contacted me with a list of publications and a precise statement of interest about my work. We exchanged a few e-mails and I looked at his work. Another student tracked me down after a talk at a conference and talked to me in more detail about the work. These were both appropriate ways to contact me that may benefit the students in the future.


publications - ESCI Journals vs SCI & SCIE Journals


Three years ago I published 2 papers in the open access journals with APC that are indexed in Emerging Sources Citations Index (ESCI), Directory of Open Access Journals (DOAJ) and Scopus. This was according to the university directions to publish fully open access. I have to admit that, three years ago, I was new to the research career and I blindly went by the general guidelines the university has towards publishing. Now, when I am trying for other academic positions, they are increasingly looking for publications in Science Citation Index (SCI) or Science Citation Index Expanded (SCIE) category of journals. In this category, I have only one publication. Moreover, I see that the papers published in ESCI journals, in general, haven't received much attention compared to the ones published in SCI or SCIE. So my question is,




  1. Is it possible to reuse some of the results that I published in ESCI journals and add additional case studies and try to publish in SCI or SCIE journals (with proper acknowledgment to the old paper)? Will this be a good strategy or it is considered as a duplicate publication?





  2. This is more of a general question. If all science has to be published in SCI/SCIE indexed journals, then why do some top reputable publishers promote the ESCI journal category? With the move to fully open access, SCI / SCIE index journals open access fee are very high compared to the open access journals in ESCI category. This is an important factor for some people to choose the ESCI journals. How do the other academicians see this?




Note: The journals that I published are within manufacturing category.




etiquette - In what situations would it be appropriate to include one's photograph in a CV?


I think I have only seen one CV where a photograph of the CV owner was included. I personally wouldn't want to put my photograph in my CV, but I was wondering, in what situations would including a photo if oneself within the CV be appropriate?



Answer



In the United States, you should never include a photo in an academic CV. It comes across as somewhat inappropriate, like you are deliberately drawing attention to your appearance and hoping it will influence the decision. (I know that's not actually the intent, but many people's gut reaction upon seeing the photo will be "Why is the applicant showing me this? Do they think I should know what they look like before making a decision? How is that supposed to be relevant?") If you are from a country in which photos are often included, then that will be understood as a reasonable explanation, but it will stand out as foreign. If you aren't from such a country, then it will look bad.


graduate admissions - Does high school success in Math have a correlation with Undergrad success in Mathematics?


I will start in freshman in a fairly good undergrad institution in August 2018. I am planning to major in Mathematics. However this school attracts the most brilliant high schoolers in Math. This includes IMO gold and silver medalists. Participation in IMO guarantees admission to this school. I have already planned to go to graduate school. However seeing the enormous competition I am pretty skeptical of my chances. Usually the best student of our school in a given year has a fair shot at Princeton. Looking at my result I might have barely crept in their freshman batch. I do have 1 month left, shall I start on standard Math textbooks like Rudin, Munkres, Dummit and Foote or are the IMO medalists way ahead of me?




Sunday, 22 October 2017

Can vitamin B17 cure cancer?


I have heard that a 'vitamin B17' can cure cancer, but that the medical industry never talks about it, since making it legal would cause them loss of billions. But I have never found a reliable report on whether B17 really works or not. There is a question on 'vitamin B17' deficiency as a cause of cancer (see this post), however, not on 'vitamin B17' as a possible medication for cancer. What are the proposed mechanisms? And is there evidence that 'vitamin B17' really works in curing cancer?



Answer



Laetrile/Amygdalin has been claimed to be a suitable treatment for 'cancer' (which is a summary term for an extremely heterogeneous class of diseases). Even though laetrile/amygdalin in these claims is often called a vitamin, it in fact is not a vitamin as the molecule is not essential for the metabolism (Greenberg (1980)).


The claimed effects of laetrile/amygdalin are not only based on supplementing the molecule to balance a putative deficiency (with the false assumption that it is in fact necessary), though. Both other putative mechanisms are based on reactions that form HCN/cyanide: the enzyme $\beta$-Glucosidase breaks down laetrile/amygdalin and this reaction releases HCN. The argument now is that tumour cells have higher levels of $\beta$-Glucosidase which leads to accumulation of cyanide in tumour cells - with the effect of killing the tumour cells selectively. This would be great... if healthy and tumour cells actually had different levels of the enzyme. Unfortunately, they seem to have similarly low levels of $\beta$-Glucosidase (Greenberg (1980)). Even more problematic, Greenberg (1980) also reports elevated levels of $\beta$-Glucosidase in the liver and small intestine ... and you would not really want to release cyanide there.


There is a second mechanism, though: The enzyme $\beta$-Glucuronidase is claimed to be at higher levels in cancer tissue than in healthy tissues (leading to the same desirable effect described above). But again, there does not seem to be a difference in enzyme levels between healthy and cancer tissues (Dorr and Paxinos (1977)), and even more: $\beta$-Glucuronidase does not even break down the molecule as laetrile/amygdalin has a glucoside bond - so there is not even any cyanide release in that case (Holzbecher et al. (1984)).


Additionally, there is no clinical evidence that laetrile/amygdalin is an appropriate treatment for any form of cancer. This topic has been reviewed substantially (see Milazzo et al. (2006) for a review and this fairly recent Cochrane review by Milazzo and Horneber (2015)) and none of the studies included and analysed indicate any positive effect of laetrile/amygdalin. On the contrary, the in vivo cyanide formation after laetrile/amygdalin uptake makes the treatment very dangerous as it can lead to cyanide poisoning (and death, eventually) - especially after oral uptake due to higher $\beta$-Glucosidase concentrations in the digestive system. The authors of the Cochrane review therefore conclude that



The claims that laetrile or amygdalin have beneficial effects for cancer patients are not currently supported by sound clinical data. There is a considerable risk of serious adverse effects from cyanide poisoning after laetrile or amygdalin, especially after oral ingestion. The risk–benefit balance of laetrile or amygdalin as a treatment for cancer is therefore unambiguously negative.




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...