Sunday 31 March 2019

phd - How much do grades matter for a future academia position?


I am completing my PhD and I was wondering how much does the PhD coursework grades affect future academia applications? My undergraduate and master's was somewhat decent grade wise (3.8/4) in both. However, I had taken two mandatory courses during my PhD and I got B+ and A- in them. It was not because of the difficulty in the coursework, but I was burned out with courseworks from master's and did not put any effort. My GPA turned out to be 3.56. I did not take any other coursework as my qualifiers committee found my theoretical knowledge adequate for continuing with my PhD.


Back of my mind, I am concerned that this will affect my postdoc and subsequent professorship applications.


Is there any academic out there in same boat as me but have made it successfully in the professional world?





molecular biology - Does a man contain all the genes needed to make a woman?


This question is brought on by a Sci Fi novel I am thinking about writing. The plot device involves a colonist in charge of building a population on a new planet who loses his supply of embryos and so forth in the landing. With the artificial "wombs" intact, he populates the planet with clones of himself.


If he wanted to introduce enough variation (without making up new genes, only rearranging) in the population to allow them to be able to reproduce naturally without inbreeding problems, would he be able to? In particular, could he make a woman? Alternately, could a woman (without a Y chromosome) do the the inverse?


At the risk of introducing bias into the answers, the plot as it stands assumes he is a male and he CAN'T do any of the above and he is restricted to clones.



Answer




This answer also involves some speculations as the question is about a good theoretical framework for a science fiction.


You can find in this post about how sperm can be used to produce embryonic stem cells. It would still require an oocyte for doing that.


The question now is- Can you produce oocytes from a male?


You may fuse two X bearing haploid spermatids to form a diploid cell with XX. This cell will also have mitochondria and ribosomes — seems like a decent candidate. Gametogenesis has not been shown to happen in-vitro. Moreover a zygote will need a lot more cytoplasmic resources that you can get from a fused spermatid.


Plus there are imprinting issues as already pointed out by Chris.


Conclusion: Next to impossible


For your question "Does a man contain all the genes needed to make a women": yes he has but does not have the biological machinery to do that (exclusive of the womb).


However if you choose to send a female astronaut for this mission then there may be some hope. As Chris said, there are problems with homotypic fusions because of imprinting issues. But with a supply of ova there can be other ways:



  • Make clones using SCNT: limitation is that there would be very little variability.


  • Erase imprinting marks and fuse two oocytes: This has not been done yet but this is possible. At this moment we have technology (still incipient for therapy grade), for targeted genome editing. The basic principle involves fusing a DNA-endonuclease with a sequence specific DNA Binding Domain (DBD). Examples include Zinc Finger Nuclease, TALENs and Crispr-Cas. This study demonstrates an engineered system that can deaminate RNA in a sequence specific manner. Based on a similar principle it should be possible to link DNA-(cytosine/adenine)- methyltransferase or DNA-(cytosine/adenine)-demethylase to a sequence specific DBD 1. This system can be used for targeted epigenetic modification. This would have a little more variation than cloning because of meiotic recombination. Limitation is that there won't be any males, this would perhaps become an Amazonian Planet.


Make sure that your space-shuttle has a good biolab facility :P




1 Imprinting is generally implemented by DNA methylation which happens mostly on cytosines.


Main mechanism of the evolution of sexual dimorphism


Sexual dimorphism is very common and (normally) requires the evolution of sex-specific genetic variation/regulation so the genetic correlation between the sexes can be <1. Is there consensus as to how this type of variation predominantly spreads?


I can see it could evolve by drift and selection and I expect it is predominantly via selection (sexually antagonistic selection for different optimal genotypes)- We typically associate sex differences in traits with sex differences in selection (ecological, sexual selection...).




funding - Do universities typically cover publication fees associated with open access publications?


I am an undergraduate student in a private Indian university. Last semester I worked on a research project with another undergrad student and under the mentorship of a PhD scholar.


We have submitted a paper to an Elsevier journal which charges a mandatory open-access fee of $500 on acceptance of the paper. In such cases, does the university typically cover these costs or are they borne by the authors of the paper?


Which department of the university should I contact to ask for funding for the same?




How should I start Undergraduate Research in Mathematics?


Dear Academic SE advisers,


I am a college sophomore in US with double majors in mathematics and microbiology. My algorithmic biology research got me passionate about the number theory and analysis, and I have been pursuing a mathematics major starting on this Spring semester. I have been independently self-studying the number theory textbooks written by Niven/Zuckerman/Montgomery, Apostol, and Ireland/Rosen on this semester. As this semester progressed, I discovered that I am more interested in the pure mathematics than applied aspects (computational biology, cryptography, etc.). I want to pursue a career as analytic number theorist and prove the Collatz conjecture and Erdos-Straus conjecture.


I have been thinking about doing the number-theory research on my university (research university; huge mathematics department). I have been self-studying the NT by myself and also regularly attending the professional and graduate seminars on number theory but I did not do any pure mathematics research as an undergraduate. Should I visit NT professors in my university and ask them about if I can do undergraduate research under them? If research is not possible (perhaps due to my lacking maturity), should I request of doing independent reading under them and later proceed with the research? How should I ask them? What should I address? If even independent reading is not desirable to them, what should I ask to them or do in my own?


As for my mathematical background, I have been taking Calculus II (computational) and discrete mathematics. I will be taking calculus III (vector calc.) on Summer, followed by Analysis I, Probability, Theoretical Linear Algebra on Fall 2015. As for my self-studying on this semester, I have been studying NT textbooks (mentioned above), proof methodologies, and basic linear algebra.


Thank you very much for your time, and I look forward to your advice!


Sincerely,


PK




gene expression - Imperfect dosage compensation


Dosage compensation is used to make up for different copy numbers of the major sex chromosomes in males and females (One X or Z chromosome in one and two in the other). Two main mechanisms of dosage compensation exist, inactivation and upregulation.


But dosage compensation is not entirely perfect, the amount of gene product from an upregulated X/Z-linked genes in the heterogametic sex is not exactly that of the two in the homogametic sex.




"In Drosophila, the male-specific lethal (MSL) ribonucleoprotein complex mediates dosage compensation by upregulating transcription from the single male X chromosome approximately twofold."



On average how well is dosage compensation performed? What is the variance like:




  • within a single chromosome (between genes)?




  • within species?





  • between species?






How do people peer-review many papers?



I am an Assistant Professor of Chemistry. I try to be an active peer-reviewer but on average it takes a few hours to review a manuscript (reading, some searches in the literature, checking some relevant reference, and finally writing the report).


I review 2-3 papers per month and I need to spend some time outside my working hours. In various blogs, articles, websites like publons.com, I see it is not uncommon to review 10-20 papers per month.


Then, I came to the conclusion that I am doing something wrong. Because by my calculations, it is impossible to peer-review many papers along with various tasks of an academic.




language - Dealing with listening/talking to researchers with difficult accents


Often, when speaking English in research, you can find a great variety of (mostly, non-native) accents. Since I started moving in academic circles and a more international environment, I slowly learned to understand some of the accents much better. I can currently understand well most mild accents and some specific accents even if they are strong, but there are still both researchers with very strong accents and types of accents I have a very hard time understanding.


As networking, communicating, and generally talking to other researchers is very important, it got me wondering about what I can to to overcome this "accent barrier".


I've encountered this "accent barrier" in at least three different settings, and there's always problems arising for that:





  • speakers and presenters on conferences (or other big events)


    I usually try and decide from the slides (and what I can understand) how relevant I think the presented material is for me, and then I would read the paper later on my own.


    Still, it means that I could miss some interesting papers, miss some of the authors insight on the problem only mentioned in the presentation and loose a certain amount of time, because listening to a talk is much faster than reading (especially if one just wants to understand the basic idea).




  • poster sessions and social events on conferences / other manifestations


    This one is a bit more tricky since it's more personal interaction. I would usually try and ask the person to clarify or reformulate the question, and then if I still don't understand try talking about something related to "keywords" that I succeeded to identify. If it's a social occasion, I would try to look attentive, smile, and excuse myself the first acceptable opportunity I get.


    And again, I might be missing on some great ideas this way. Missing making some potentially useful contacts with the people from the community, and even possibly looking rude if I didn't understand something crucial.





  • interactions with people from you team/close environment.


    With this one, I'm totally at a loss. I know how much team dynamics is important. If something like that happened, I would probably try and avoid one-on-one communication with that person as much as possible. Still, it would probably make me feel constantly uncomfortable.




What are some suggestions on how to act in such situations? They generally make me feel uncomfortable, and often afraid that I'll offend somebody. Again, I do believe that a little practice and effort can go a long way to understanding different accents, especially when they are not too strong. But (and I guess this also depends on ones mother tongue) I think a lot of people have problems with (probably different) strong accents.



Answer



I'm not a native English speaker but I do understand your frustration. Here are some of my experiences:


Embrace the elephant in the room


Time to time I found people around me are too "polite" to not tell me that they don't understand what I say. I have had a course evaluation saying that "the instructor is great but time to time I had hard time understand some words he said. For example, it took me a few weeks to realize he meant 'result' when he said 'ray-sult'." I was actually amazed by how much money this student spent to be confused.



Now, at the beginning of the course, I surrender myself and introduce the elephant. "I have accent, and if any of my pronunciations is off, you're more than welcome to correct me. Your input will help me to become a better speaker." Then move on.


I think the situation is the same in the native speaker's shoes. If you have trouble understanding a colleague. Tactfully ask for a few repetitions in an informal conversation, and then confess that you sometimes may not catch the full gist of the speech, and proceed to ask for a blanket excuse in the future should you need another repetition again.


"Fully understand" is likely an illusion


Your point about missing important materials in conference is well taken. Here are two reflections I have: i) realize that even you get the whole sentence, it's still a foreign language to the speaker and there will always be some loss in translation. ii) In a conference, it's probably hard to pick up all the little bits of information. On this point, you can Zen that over like watching a firework; let that go. Or if the curiosity is killing you, approach the speaker after the talk and clarify. If the conversation goes well you can consider exchanging business cards, and ask for a copy of their presentation over the e-mail.


Hold on to an ad hoc interpreter


When I teach in foreign countries, there would be English speakers whose speeches are beyond my cognitive reach. This is how I deal with it: i) Keep smiling, and rephrase the question as best as I can, and I know I'd fail, then repeat step i) for a few more times and keep calm and smiling, ii) eventually some participants who are more proficient would volunteer to translate. If no one does, embrace the elephant in the room and say "I guess I'm a bit stuck here, would anyone tell me what I missed in the question?" iii) once the question is clarified, answer it, facing the original questioner. For myself, I prefer to slowly pace up to the board, and write down my talking points. I think this would enhance the questioner's understanding if he/she has trouble listening to my speech.


Often enough, no one would help. And the questioner may just wave his/her hand and give up. Don't be frustrated. Invite the person to stay and talk, and perhaps then you can employ things like paper and pen to better understand each other.


Use writing


When communicating with colleagues who have heavy accents, I'd also rely a bit more on writing. Using e-mails, or using a white board in a meeting may help. On that note, I also bring a stack of index cards with me to meetings and classes.


Use international "language"



Smile, drawing, ... etc. are always good substitute or supplement to verbal communication. Avoid using very specific body gestures because one friendly gesture here may deem insulting in another culture.


Learn some foreign languages


It's actually quite interesting that comparing to my colleagues who are native speakers, I actually have an easier time filtering other countries' accents. I attributed to the fact that when sitting through English classes, our teachers put extra emphasis on highlightin how our mother tongue may cause some English words to be mispronounced. Then in university I picked up a couple foreign languages, and then now I have virtually no problem listening to people from those countries speaking English.


It may actually be impractical to learn all the languages. Here are a couple tricks I have used: First, just learn their basic pronunciation system first and if you have time, figure out how to say some basic general words. In the process, evaluate how the system may work if it's used to pronounce English. For example, Japanese system does not differentiate r and l, so you may expect hearing "running" and "learning" or "lighting" and "writing" pronounced identically. Mandarin does not have the -th and Th-, so Mandarin speakers may compensate with -ve and F- (e.g. A "fief" instead of a "thief".) On the contrary, Mandarin has an elaborated series of s or s-like sounds: si, zi, and ci, with different tongue-teeth positions and amounts of air blowing through the lips. So, you may expect emphasis on some syllables that would have been only lightly pronounced if spoken by a native speaker. Italian speakers, on the other hand, tend to clearly pronounce syllable-by-syllable and attach an -e or -a after some words. Once we put the same nouns spelled in English and Italian side by side, the reason would become apparent.


Second, read some books on how to get rid of accents or how to speak in British and American accent. Most of these books would have a chapter or so dedicated to explain major mistakes made by speakers from different systems. For example, Japanese speakers may have an extra "-gu" after all words ending with -ing; Chinese speakers may not distinguish clearly between -s and -th. These tips are not for native speakers, but by learning some major traits, native speakers can quickly filter the noise and get to the content.


Make an effort


It takes time to understand accents. But as you speak to a certain foreign person more and more, you should be more at ease. This is particularly important when dealing with your colleagues. Keep talking and keep categorizing their speech traits, and you'll get better at talking to them. Most of these advices may make you feel vulnerable or even stupid, but as an ESL and also a foreign language learner, when it comes to language, I think we cannot be overly reserved.


How do I recognise a peer-reviewed journal article?


I have lots of research papers, but can I tell which of them are peer-reviewed. Also, on Google Scholar, is there any way of finding only peer-reviewed articles?




Saturday 30 March 2019

authorship - How to handle Co-author who is not listening the suggestions to improve the paper quality


Assume I am involved with a work and the lead author is writing a paper. However, after every draft version, I see that not all my comments are well addressed in the revised version. I expect that if the comments or major suggestions are not addressed, then some explanation must be given. During the previous conversation, the coauthor did not raise any doubts or concerns about my suggestions. Thus I pointed out these issues in the paper again and they again fell on deaf ears this loop continues.




  • As I already spent a huge amount of time on this paper and made a significant contribution, I don't want to withdraw my coauthorship.

  • Topic is relatively new, in addition the current version is good enough to have a decent chance of getting accepted into a medium level conference.

  • Some minor issues (may be major) are bother me. I am not sure whether I am wrong. However, there is no discussion on on my concerns even after they are explicitly highlighted.


Should I just let the paper go? or make some statement? I don't want to burn bridges with any of my coauthors.



Answer



I have had this problem on a few occasions. Usually I got ignored over suggestions on points the lead author did not want to discuss directly because (i) s(he) felt (s)he was on the right side; (ii) s(he) felt (s)he was on the wrong side but wanted to push their version nonetheless; (iii) s(he) felt I was not in a position to criticise that part.


In all cases I demanded for an explanation, and this is why I can answer your question here. So, my first suggestion is that you contact this person demanding an explanation. (Mind that most people don't do these actions -- questioning parts of manuscripts where they are co-authors, and later seek to understand why they got ignored -- and that most lead authors prefer having passive "co-authors".)


How did I react in such situations described above? I will briefly explain:



(i) I tried to make my point clearer, which subtly meant I was trying to prove the lead author wrong. The lead author always insisted on their point without seeming to listen to what I said, while emphasising on how they took my suggestions on other points. I had to let these issues go, and they got published, and as a result I do not fully agree with some of the papers I participated in.


(ii) I insisted. This will make the lead author uncomfortable, and you will have to make sure this person understands you're not cornering him/her. Typically there is a clear mismatch with data or logic that the lead author doesn't want to hear aloud. Usually I got the problem fixed, usually the lead author wasn't happy and is now unlikely to collaborate with me in the future. I think that is OK, given the circumstances. Once I had to let it go.


(iii) This is the most common situation. Typically it involves a collaborator from a different field under strong influence of their bossy PI, where you're not sure which of the two is doing the writing or even answering to your emails. They do not appreciate being questioned "on their turf". You have to consider the possibility you're wrong there. Which I think is irrelevant, because if you are wrong then there's all the more reason you deserve a clear, logical answer. In such cases I insisted, and was authoritatively told to "keep to my business". I insisted again, and got ignored, and had to let it go. Usually the lead author apparently did see my point but was told by their PI (i.e. the last author) what to do. As a result the lead authors in these cases made sure to communicate they were open to collaborate with me in the future, while their boss cut communication.


Anyway, hope that helps. In the long run you're selecting whom you can work with.


biochemistry - Role of calcium chloride during competent cell preparation


I am aware of the fact that $CaCl_2$ settles down on the cell wall making it less negative may be by forming bond with Teichoic acid. Also due to the positive charge it attracts DNA (DNA is negatively charged due to phosphate group). But is there anything else the $CaCl_2$ does? Also if its the work of $CaCl_2$ why we are adding $MgCl_2$ first in the standard protocol of the making competent cell preparation chemically?




peer review - How should I handle reviewing a paper that is very similar to something I am working on?


I was sent a paper to review recently. I decided to review the paper and saw that part of the paper is on a very similar method that I have been working on recently. Not the wording, of course, but the main ideas.


One of the problems is that they did not mention that part in the abstract, so I didn't know about it when I accepted the review. An even worse problem is that their paper is poorly written, full of wrong theorems, terminology etc. so I have no choice but to recommend rejection.


I know reviews are anonymous. But I want to avoid two things:



  • Them reporting me for a plagiarizing or stealing their idea.


  • Them thinking that I have stolen their idea, even if they do not necessarily report me.


What should I do?



Answer



I am going to answer based on an implicit assumption I feel much of your question hinges on:



One of the problems is, they did not mention that part in the abstract, therefore I have accepted.



This sounds like had you known that their work is so similar to yours, you would have rejected the review.


However, I would argue that that cannot possibly be in the interest of the review system.



Yes, you could argue for a conflict of interest, but it is the conflict of interest that exists generally, based on the simple fact that other people beside you do research in the same or similar topics as you. It is not a conflict of interest on a personal level (e.g. you being part of the team whose paper is being reviewed).


Instead, it is a conflict of interest that, in theory, should quite often exist in the review process - for reviews to be meaningful, reviewers need to be familiar with the topic to some extent, and thus, a similarity of the research topics between authors and reviewers is hardly avoidable.


I see your concerns about what the authors of the paper under review might be thinking, though you might have to brush them aside for the time being. However, what you can do is draw the benefit from being the reviewer and thus having early access to a manuscript:



  • While your method may be very similar, it is most probably not exactly the same. When describing your method, try and insert a few sentences that focus particularly on a few aspects that you do differently from them.

  • For future publications you might write on similar topics, keep in mind that there may be a similar publication by those authors around that you can cite.


This has advantages for both sides:



  • You increase the chances to include a relevant citation that you might otherwise miss (and thus the authors' chances of being cited by you are increased).


  • Even though you cannot yet cite the work of the other authors, your clear description of some different aspects serves as a way to "preemptively" establish the differences between your work and theirs.

  • If they happen to publish a revised version of their paper after your work has appeared, you have already provided them with quite a straightforward foundation for describing their differences to your work.




In the comments, the concern has been voiced that even without the assumption of plagiarism, the authors of the other paper might still feel by rejecting their work, you intentionally stalled their progress for long enough so you could publish your own very similar work first, and now it's their problem to care about the prior art.


However, there are some aspects of good scientific practice that speak against that line of reasoning:



  • You do not provide an unjustified judgement, you provide a review. If you choose to reject the paper, you have the opportunity to describe objectively and in detail why you deem the work in its current state not ready for publication.

  • The other authors have not yet published their work in a properly citeable fashion, but that still just means you have plausible deniability on your side when you are asked whether you knew about the other work. Scientific integrity still demands that you consider the existing prior work, published or not, which is exactly what you are doing by specifically describing some aspects that you do differently than the reviewed paper, as described above.



graduate school - When does a PhD end?


When does a PhD end? I know this is a very general question on this forum, but let us consider a CS-engineering group. What is the usual and primary consideration for letting the student finish officially?



Is it the number of years spent, when the professor feels nothing more useful will come out of working on the problem (or of the student!)?


Is it the logical conclusion of the problem and the thesis? A student works to complete a problem in 3 years and publishes a couple of journal papers, and finds there is no more to the problem. Will he be allowed to finish or forced to work on some tangential problem simply to prolong his PhD?



Answer



As a general rule, my PhD students need to do two things to get a PhD:




  • Publish 3-4 papers on a coherent topic, mostly in top-tier theoretical computer science conferences, including at least one paper without me as a co-author (and preferably at least one paper that was previously rejected).




  • Jump a bunch of administrative hurdles: don't screw up classes, don't screw up TAing, pass quals, gather a committee, propose a thesis, write a thesis, defend a thesis.





That's it. In my experience, most PhD students do way more than this.


A couple of comments on the original question:




  • Very few students "finish" their thesis topic. Equivalently: If a research question can be closed in just one or two papers, it's probably not a good thesis topic. Good research opens as many new problems as it solves.




  • Reaching the point where further collaboration with a student is unproductive means the student-advisor relationship has failed. Sometimes students really do exhaust their research potential, despite their advisors' efforts; in my experience, those students usually don't get PhDs. (Most successful students reach "critical mass" long before they finish.) More often, this happens because the advisor isn't giving the student enough appropriate guidance.





human biology - What effect does the Barr body have, in relation to female Turner syndrome?


Why do persons with Turner syndrome have developmental abnormalities, when normal XX-females do not, even though they only have 1 active X chromosome? From what I know, one X-chromosome is inactivated into a Barr body in normal XX-females, but these obviously don't show the symptoms of Turner syndrome. What function does the inactive chromosome have?



Answer



The reason is that X-inactivation is not complete (Carrell & Willard, 2005; Ahn & Lee, 2008), and as many as 15-25% of X-linked genes escape silencing (Carrell & Willard, 2005; Cheng et al, 2005). This means that some genes on the Barr body are expressed in XX-females, although often at lower levels compared to the active X-chromosome, and this is part of the normal gene dosage. The "purpose" of X-inactivation is usually dosage compensation, so that genes are expressed equally in males and females (and then actually upregulated in both sexes to balance autosomal genes, see e.g. Dementyeva et al, 2009). However, this is not true for all genes, and the ones that normally escape X-inactivation will be expressed in the incorrect dosage in X0 females. Some of these genes are thought to contribute to the symptoms of Turner syndrome.


It is also likely that the genes that escape silencing are involved in sex-linked traits, as stated in Carrell & Willard (2005):




Such genes are potential contributors to sexually dimorphic traits, to phenotypic variability among females heterozygous for X-linked conditions, and to clinical abnormalities in patients with abnormal X chromosomes.
... ...
However, as many of the genes that escape from inactivation do not have Y-linked homologues, strict dosage compensation may not be necessary for all genes on the chromosome. Such characteristic genomic differences should be recognized as a factor for explaining sex-specific phenotypes both in complex disease as well as in normal, sexually dimorphic traits.



Cheng et al (2005) also point out that the expression of the genes that escape silencing is tissue-dependent, which suggests that the role these genes play in the symptoms of Turner syndrome is also tissue dependent.


Friday 29 March 2019

evolution - Short-term Lamarckism in asexual single cell organisms


I was reading through the Karr et al. (2012) whole-cell computational model. One of the things they did was to induce single-gene disruptions in their model. They observed several to be fatal, but:



In some cases (Figure 6B, fifth column), the time required for the levels of specific proteins to fall to lethal levels was greater than one generation (Figures 6C and 6D).



As far as I understand this is because when a single-cell divides, daughters get not only get a copy of the mother DNA, but also have their initial levels of proteins and RNA set to those of their mother (or similar, with some statistical fluctuation).


To me this screams of Lamarkism: if an organism during its lifetime came in contact with an environment that caused a greater expression of some protein that in had at birth, its children will also have a higher initial expression of the same protein. In other words, the trait of "level of this protein" seems to be being passed down in a Lamarkian way. Is my understanding correct, or am I missing the point?


If my understanding is correct, then what are some standard methods to account for this short-term Lamarkism in mathematical models of evolution?





Notes




  • I am primarily interested in mathematical (or other formal) treatments of this. I have a background in mathematics and some work in mathematical modeling for population biology and evolutionary game theory. I have no background in biochemistry or microbiology. I would appreciate answers or references that cater to this awkward background but I am not adverse to plowing through some microbio if it is for something awesome.




  • Similar partial arguments can be made for non-single-cell and sexual organism by considering hormone expressions of the mother during pregnancy, as in this answer. I am satisfied with an explanation for asexual single-cell organisms, but bonus points if it can also say something about non-single-cell and/or sexual organisms.




  • Follow up question on modeling the mechanism behind this: Macromolecule levels in daughter cells after fission






Answer



This phenomenon is well known and can be observed in several species. In fact, if you look at the time it takes for E. coli to change its transcription program in order to react to the environment (signal->transcription->translation), you will find it can be longer than its ~20 minute doubling time. You can indeed think of it as a form of Lamarckism. However, it is part of a field that has been booming in the last ~10 years, known as epigenetics.


Epigenetics is a field of research that deals with hereditary information that is passed by non-genetic mechanisms, i.e. not in the DNA sequence. This includes several mechanisms including passing of proteins/RNA, chemical modifications of DNA (methylation) and chromatin (histone modification). It turns out that epigenetic effects can be observed in virtually all species (including human) and affected phenotypes can be significant (leading to disease, for example).


This is a very interesting field of research and is very wide, so I would recommend reading a bit. Specifically regarding protein/RNA passing, I believe this is somewhat less deeply studied, perhaps due to the fact that the effect decreases exponentially (due to dilution), can be limited by protein/RNA stability and some measurement difficulties. However, I think I recall mathematical treatment of this in Prof. Uri Alon's book. You can also catch his systems biology course online on youtube, which I think touches on some of this material.


withdraw - Withdrawing from course in a PhD Program (i.e. W on PhD Transcripts)


I'm already in a PhD program and, just one week after Add/Drop, both my teaching and research loads increased due to unforeseen circumstances. I have a course which would be helpful for my area exam, but I'm confident I can just teach myself and am considering withdrawing from it since it would be nice to have fewer deadlines looming over me. It's this weird grey area where I could probably make it through the semester, but this would basically require I get less out of my other 2 courses (which are exactly in the area I want to specialize in), not be able to teach as well, not be able to focus as much on research, and just be overall slightly more stressed.


Are there any repercussions to having a W on my transcript as a PhD student?



The only thing I can forsee is maybe external fellowship applications, but I am in my first year so I'm hoping they'd be understanding (it isn't like withdrawing makes it so that I am taking fewer classes than most grad students).


Thanks!


tl;dr: Would having a W on your PhD transcript be problematic in some way?




biochemistry - What inactivates pepsin in infants?



In infants, rennin helps in digestion of milk. Pepsin is also present in their stomach.


Why do infants need rennin for milk digestion, at the first place? Why does pepsin not act on the milk proteins in infants? Does the production quantity of rennin play a role in inhibiting the action of pepsin?



Answer



EDIT: Thanks a lot to @abukaj for pointing out the mistake in my answer (and to @paracetamol for asking such a beautiful question). I am rewriting my answer to incorporate the (hopefully) correct background knowledge this time.


NEW ANSWER: As @paracetamol and @AlanBoyd (in their answer) pointed out the lack of credible support for the claim that infants produce rennin/chymosin, the previous answer attributing the digestion of casein in infants to chymosin had to be corrected. So, lets now look at the other possible candidates for casein (or, more specifically, $\kappa$-casein) digestion in infants.


As Martin et. al. (2016) claim, milk casein has some bioactive roles, such as forming masses with calcium and phosphorus1. Also, infant milk formulas mostly have higher casein content than human breast milk, making the former harder to digest than the latter. Back to the digestion point, human breast milk is known to contain many proteases in itself, including anionic trypsin, elastase, plasmin, cathepsin and kallikrein, while prothrombin has also been identified in human colostrums2. In fact, Ferranti et. al. (2004) also identified fragments of casein created by plasmin cleavage3. However, Chatterton et. al. (2004) were able to detect $\beta$-casein after 1 hour of in vivo gastric digestion in 8 day old infants, but not in 28 day old infants, suggesting the increase of digestive capacity of the infants4. This increase can be attributed to the development of gastric acid production system in the infants. For the case of newborns, Nakai and Li-Chan (1987) suggested that Pepsin C, also called gastricsin, can hydrolyze casein at the pH range of 4-5 (the lowest pH newborns can reach)5. However, the buffering effect of human and bovine milk proteins does not allow the gastric pH to reach the optimum pH required for activity of pepsin A and pepsin C.


How, then, is casein digested by infants at all? This is summarized (to some extent) by Chatterton et. al. (2013), according to which, although gastric pH is unable to reach the optimum pH for pepsin activity, it is sufficient for minor initial digestion of human milk proteins. This causes the release of glycomacropeptide, the C-terminal portion of casein. The combination of this initial digestion and the gastric pH, close to the pI of caseins (~ pH 4.6) causes precipitation of caseins and slowing down of their digestion. The casein peptides, on the other hand, are absorbed into plasma where they show a number of biological activities, including inflammation modulation and blood pressure regulation6.


Thus, even though infants lack chymosin and a fully mature digestive system, this is compensated by a combination of proteases in breast milk and the slower digestion process until the digestive system of the infants develops completely.


Infant Digestive Systemsource


References:





  1. Martin CR, Ling PR, Blackburn GL. Review of Infant Feeding: Key Features of Breast Milk and Infant Formula. Nutrients. 2016;8(5):279. Published 2016 May 11. doi:10.3390/nu8050279




  2. Dallas DC, Underwood MA, Zivkovic AM, German JB. Digestion of Protein in Premature and Term Infants. J Nutr Disord Ther. 2012;2(3):112. doi:10.4172/2161-0509.1000112




  3. Ferranti, Pasquale & Vittoria Traisci, Maria & Picariello, Gianluca & Nasi, Antonella & Boschi, Velia & Siervo, Mario & Falconi, Claudio & Chianese, Lina & Addeo, Francesco. (2004). Casein proteolysis in human milk: Tracing the pattern of casein breakdown and the formation of potential bioactive peptides. The Journal of dairy research. 71. 74-87.





  4. Chatterton DEW, Rasmussen JT, Heegaard CW, Sørensen ES, Petersen TE. In vitro digestion of novel milk protein ingredients for use in infant formulas: research on biological functions. Trends in Food Science & Technology. 2004;15:373–383




  5. Nakai, S. and Li-Chan, E. (1987) "Effect of Clotting in Stomachs of Infants on Protein Digestibility of Milk," Food Structure: Vol. 6: No. 2, Article 8.




  6. Chatterton, D. E. W., Nguyen, D. N., Bering, S. B., & Sangild, P. T. (2013). Anti-inflammatory mechanisms of bioactive milk proteins in the intestine of newborns. The International Journal of Biochemistry & Cell Biology, 45(8), 1730–1747





ethics - Should I attend a job interview after I've already accepted another offer?


I applied for several postdoc positions recently. One made an offer which I accepted. Since then I've been invited for an interview for one of the other positions. Is there any benefit to attending? Is it an opportunity to make potentially useful contacts (in a relatively small field)? I should add that I have no experience with academic interviews (the position I secured was through contacts). Expenses will be paid.



Answer



Once you've accepted a job offer, you are supposed to inform other places that you've applied that you would like to withdraw from consideration.


If they still want to invite you over to give a talk knowing that you can not be considered for the position, go ahead. But, you must tell them.


To do otherwise would be a serious breach of ethics. You do not want to gain a reputation as someone who engages in unethical behavior (don't assume they won't find out).



job - Why would a top department hire a less experienced researcher for a tenure-track position?


Suppose that a top-N department at a big research university (for very small N) has the choice between two candidates for a tenure-track position:



  1. Candidate A: a bright young researcher just done writing her dissertation, and

  2. Candidate B: a more seasoned veteran with a several years of successful teaching, advising, and grant writing her belt (though not already tenured).


In other words, suppose Candidate B has already demonstrated that, in addition to doing great research, she can successfully navigate other important aspects of the job. Candidate A seems like a bigger gamble: perhaps she will succeed in these other roles... and perhaps not! Assume that the department in question can essentially hire whomever it wants, with very little competition from other institutions.



Question: What incentive would such a department have for hiring A instead of B?


I ask this question, of course, because I am a young candidate about to interview for a job at a top department, and I know that I am competing with more seasoned candidates. How do I make a compelling case, despite my relative lack of experience? What are some potential pitfalls to look out for during an interview? (E.g., questions that might expose my relative naiveté?!) Do top departments really hire freshly-minted PhDs for tenure-track positions? Or are they just panning for gold?


Thanks!



Answer




  • Candidate A might have a research agenda (either based on her dissertation, or on her formulated research plan) that fits better with the research agendas of other people in the hiring department, or with strategic priorities of the department or even other departments at the university.

  • Candidate A might already have collaborated with members of the hiring department, maybe in writing grant proposals.

  • Candidate A might be cheaper, in terms of salary, lab space, funding or anything else the hiring department may need to cough up.

  • The hiring department may be afraid that the "superstar" candidate B has so many more attractive offers that she would not accept an offer at this department at all, so they would rather not expend the time to go through the entire process with her.

  • Candidate A might just have better contacts, because her Ph.D. advisor is big friends with the dean of the hiring department, or (less sinister) the dean has met candidate A at a conference and been very impressed with her presentation.



My advice: do a little research on the people and the priorities at your target department, and emphasize unobtrusively in your cover letter and research plan how you could collaborate and find synergies. And tap your network. Good luck!


What's the smallest size a human eye can see?


During a biology experiment at school, where we would look at waterweeds under a microscope, my teacher said something about that it's impossible for the human eye to see the cells without a magnifying glass of some sort. So, I saw that as a challenge, and decided to check if I could see the cells. And after holding the leaves really close to my face, I was indeed able to see tiny rectangles.


Since I was curious about it now, I decided to look some more things up. First, I tried to find out the actual size of waterweed cells. Based on this 640x enlarged image, which features cells of 5mm wide and 10 - 15mm long in the picture (which corresponds with of roughly 8µm wide and 15µm long).


I left this in the back of my head for a long time then, but I just looked at my cotton sleeve, and noticed tiny fibers. Not the ones that are woven together, but ones that are standing out from it. So, after looking it up, it turns out that cotton fibers are 10 µm wide.



So, I wondered, what is the smallest size a human eye can actually see? According to a whole bunch of sources all across the internet, it's either 200-400µm, 100µm, or 58-75µm. I also hear 'the width of a human hair' very often, but those can range from 17 to 181µm.



Answer



Very nice question!


First of all, the 'smallest size' that a human eye can perceive is called visual acuity, and can be expressed in various ways. It cannot simply be expressed by means of size measures, as objects with a fixed size are perceived as smaller when viewed from a distance (perspective). A familiar example is the train track:


perspective


Hence, visual acuity has to be measured as a function of viewing distance, i.e, in degrees of visual view. Measured in degrees, the visual acuity of the average normally sighted person is 1/60 degree, or 1 minute of arc (1 MAR) (Webvision, chapter "Visual Acuity", by Kalloniatis & Luu).


Using the basic structure of the eye and some trigonometry one can deduce the smallest visible size :


basic structure of the eye


The trigonometric formula becomes: $2d \times tan(\frac{\alpha}{2})$ with d being the viewing distance and alpha ($\alpha$) the visual acuity expressed in radians ($\pi \times \frac{degrees}{180}$) (NDT resource center).


Assuming the closest distance an adult can focus (~100 mm) and an average maximal acuity of 1 MAR, the smallest visible size boils down to 29 microns.



A young child can focus at distances down to ~50 mm, and can have a visual acuity of 0.4 MAR, which yields 6 microns.


Note that 1 MAR encompasses 288 microns on the retina, and some 180 photoreceptors. The optical limitations of the eye (such as diffraction by the lens and light scatter by the neural cells in the retina) limits the resolution of the human eye below the theoretical 'pixel limit' of the eye.


So to sum up, depending on one's age, one should be able to see targets in the order of 6 - 29 microns. The lower bounds of this range are indeed in the range of the waterweed cells and cloth fibers you describe.


PS - the values described are representative under ideal conditions, i.e., under situations of abundant lighting and high contrast.


affiliation - Should we translate non-english university names?



In my country, several universities are prefixed by "Universidade Federal", which can be translated to "Federal University" (e.g., "Universidade Federal do Rio de Janeiro" to "Federal University of Rio de Janeiro"). When publishing a paper, should we translate this part of the name?


This is a obscure topic; I have some teachers that use "Federal University" and others that use "Universidade Federal". Once I heard that it is better to keep the original name of the university because it helps to keep its identity. However, even translated, it still is very easy to find. If you Google for both names, they will come up in the first positions of the ranking.


Should we translate or keep unstranslated?



Answer



The first thing to do is to check if the university has any recommendations about this. If none exist, then the second aspect is to consider if the university is well known under one or another form of the name. The purpose of providing an affiliation and proper address is for the sake of communication. Before e-mail and Internet, most correspondence went by post so a proper address was very important. Now e-mail is used, which means the affiliation is mostly to identify the author and the author's affiliation. Web sites are usually bilingual so finding the university or department is possible in both English and the native language. Most will probably use the English translation because it makes most sense if the remainder of the paper is in English. A point to make is that if one uses the native language for affiliation etc. then problems will arise for those not familiar with, for example, Cyrillic, Chinese or Japanese. So it seems the best way to communicate affiliation/address is to use English translations that are hopefully officially accepted by the university.


neuroscience - Why is there no solid evidence (histological, fMRI) that the vestibular hair cells of the inner ear contribute to 53% of the respiratory drive?


There are these papers which strongly imply that the inner ear hair cells, and not the medulla, is primarily the driving factor in the CO2 drive reflex


https://www.ncbi.nlm.nih.gov/pubmed/21130842



https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3988803/


But every fMRI study done on chemoreceptors has shown only areas of the brain and carotid bodies light up in response to CO2. I could not find any fMRI study papers showing that the inner ears light up in response to CO2 or any histological evidence that the hair cells of the inner ear are chemosensitive and play a larger role in chemosensation than the brain like these studies are trying to imply. It is said the central chemoreceptors in the brain contribute to 85% of the CO2 drive reflex and the peripheral chemoreceptors contribute 15%, which seems to leave little room for the inner ear hair cells to play such a vital and significant part.




biochemistry - Finding a template/oligo combination for my first PCR experiment


I'm an information technology engineer. I love biology so I research biological topics and have an interest in PCR. That's why I have decided to create a PCR machine.


Everything is done now and I want to do my first experiment to see if it works or not. I would be very happy if someone could give me any suggestions for testing it at home. Which oligo should I use for testing in the easiest way? I mean a template DNA for testing that is easy to find and extract.




Thursday 28 March 2019

publications - Is it ethical to submit a paper with the name of a co-author who cannot be contacted?


The paper in question is based on research my collaborator X and I did together some months ago. Our respective contributions to the research were around 2/3 for X and 1/3 for me. In terms of the actual text of the paper, X wrote about 1/3 and I wrote about 2/3.



During the writing of the actual paper, X decided to leave academia. I can no longer contact X: emails to the old address go undelivered and there is no forwarding address for physical mail. Attempts to find X through web searches and contact X through mutual acquaintances have been unsuccessful. X has thus not seen a complete draft of the paper, only the sections that were actually written by X.


In these circumstances, is it ethical for me to submit a paper with X's name on it, without a complete version having been checked by X and without X's approval?


If I do submit it, should it contain a note of the fact that X was unable to check the completed paper? I am considering the hypothetical possibility that I could have inadvertently introduced an error while writing the complete paper (and such an error might survive through peer-review and into publication); responsibility for such an error should be mine alone.


There is no possibility of separating out my contribution into a separate paper. Either the work has to be published as a whole or not at all.


I am in a field where alphabetical listing of authors is standard, so there is no question of the order of authors.




thesis - line chart or column chart



I want to show the average response time based on number of tasks on a device on a chart. So the x-axis is "number of tasks" and y-axis is "average response time".


My question is which charts I can use? a line chart or a column chart?




Wednesday 27 March 2019

evolution - Has any flying creature evolved into a sea creature?


I am talking about a creature that has evolved true flight. Has any such creature evolved into a sea creature, that permanently dwells on water (like fully aquatic fish) and doesn't come out? According to the theory of evolution, many sea creatures of the deep past evolved into land animals and some of them went a step further, evolving flight. I am talking about the reverse process, excluding semi-aquatic or semi-terrestrial animals.





publications - I'd like to use a figure from a paper; what's the best way to do this?


So, I've seen a really nice figure in a paper; what's the best way to 'get a copy'?


Will it be on the publisher's website? Do I need to draw my own version? Email the author?


And, finally, how does the answer vary for (a) those wishing to republish the figure in their own work, (b) those not wishing to publish the figure e.g. for student coursework.




Answer



Unless the paper is available under a very permissive license, such as Creative Commons Attribution, you will need to seek permission. (There may be other legal possibilities, such as fair use or fair dealing, but that's a little subtle. See this story for more information on that.)


The copyright owner is the person you need permission from. Who that is will generally be marked on the published paper (often it is the publisher, and sometimes the author). If the publisher holds the copyright, then it is still polite to ask permission from the authors as well, although this is not legally required.


Big commercial publishers will often have a department for dealing with this, typically with a name like "Permissions". If you can't find such a department, then you can try just writing to the journal in question (look at their web page to try to find e-mail addresses).


If you are lucky, they will quickly approve your use of the figure. If you are not lucky, they will ask for money.



And, finally, how does the answer vary for (a) those wishing to republish the figure in their own work,



There are definitely legal issues here.




(b) those not wishing to publish the figure e.g. for student coursework.



If you never make the work available to the public, then it is hard to imagine that the copyright owner will ever learn about it or complain (and they would look foolish if they tried to sue someone for using their figure in a homework assignment). However, you still have a moral obligation to cite the source of the figure.


My MS thesis advisor wants me to delay my graduation for one semester. What should I do?



I planned to graduate this summer, and I went through all the process of applying for graduation and my advisor signs all of these.



  • Now I have just 2 weeks to meet the deadline to officially graduate this summer. I have emailed by advisor to help me prepare my final results, proofread my thesis document. This is 2 weeks back, and I don't have any reply so far.

  • I get an email from my advisor saying that I can't delay and have to postpone my graduation next semester. "It is best for you to make an official decision to cancel your graduation, since it is getting too close to the oral defense deadline as well as reviewing thesis."


I am OK to graduate next semester, but what I can't bear to understand is the carelessness of my advisor. I have to pay again for a whole new semester because of this.


Any advice what I should be doing at this moment?



Answer



If you don't have any problems with graduating next semester then just do that. It will give you more time to refine your submissions and to prep for the defense. A little annoying, granted, but it could be a blessing in disguise too.


As for working with your adviser, what's done is done. Perhaps they were delayed in their responses but you may have to accept some of the responsibility here as well, I think. It takes some time to make all of the arrangements for finalizing graduation. It's not like undergrad where they can just look at the transcript and say "120cu, good to go". Heck, just getting a defense scheduled can be a major undertaking. Especially if you're trying to squeeze in under the wire. Stack the university processing and thesis review times on top of that and you're really cutting it close.



I can certainly understand your frustration (my M.S. was delayed by a semester due to a similarly inane set of circumstances which led to all kinds of fun) but my suggestion to you and anyone in a similar situation is to take a deep breath, relax, and use the time that you have to prep as best you can.


Aside: This type of advice question is not a very good fit to the normal SO format. I wanted to provide a response since I suspect that many people have gotten into similar situations but have fair warning that it may get flagged.


publications - Is an emphasis on "novelty" necessary in academic papers?


I often come across papers which have a 'Novel' in their titles. In the content the authors go out of their way to explain how their work is the first to the best of their knowledge to come up with the results.


Isn't novelty a necessity in research papers? Is a separate emphasis really needed? What is the best way to convey novelty without sounding extravagant?



Answer



The authors need to make it clear that the paper makes a contribution and to be explicit about what that contribution is. Otherwise the work is not original and does not deserve to be published. (This excludes survey papers and such things.)


The emphasis on novelty need not, however, be placed so explicitly in the title.


Good ways of emphasizing the novelty are



  • Include a short discussion at the end of the introduction stating explicitly what the contributions of the paper are.

  • Back this up with evidence in the body of the paper.


  • A proper comparison with related work. (As El Cid's answer states.)


Tuesday 26 March 2019

advisor - My adviser is leaving: what should I do as a third year PhD student




I am a third year PhD student at one of Universities, say school A, in the USA. I've already taken my qualifying exam and I'm planning to take my general exam next quarter. My adviser notified me yesterday that she accepted and offer from another university, say school B, and leaving my school in Sep.


She gave me two options:



  • Apply for school B. She said "Given the rules at school B, you have to start from scratch i.e., I have to take course and take qualifying exam again". In addition, I have to take GRE and TOEFL and go through the admission process. Still, there is no guarantee they will admit me.

  • Stay at my current school and she continues supervising me. However, my department at school A does not guarantee the funding (in the form of Teaching Assistant).


It is worth noting that I maintained a very good relationship with my department and my adviser and I have a good research record and TA evaluation.


In general, how do you think I need to approach this situation?


In particular,

- does that make sense that school B say I have to start from scratch even if I am a third year PhD student who passed qualifying exam from an equally reputable school?


After pondering this situation for a little bit, I came with a plan. That is,



  • I take my general exam next quarter,

  • I stay at my current school for two quarters (because I have to pass a certain dissertation credits)

  • Move to school B as a PhD visiting student for one or two semester.

  • Get my PhD from my current school


Does this plan make sense?


I would greatly appreciate if you share your thought and experience with me.




Answer



This situation is very tricky. It is not clear what is your current school level, if it is above or bellow NW (NW is a decent school, but definitely it is not say UChicago).


If you are from a bellow or comparable level school, I would say to go ahead with the transition. The tricky thing in that case would be to get admitted, but as your advisor is moving, unless it is a very steep jump in the rankings, most likely she can talk to the co-director of graduate studies and pull some strings.


Regarding the formalities you've mentioned, in my experience, there is a big difference between plain rules and practice. There is a chance that NW thinks highly about itself and formally will not recognize your credits (again, it depends where you are moving from). Nevertheless, you might get over that. Most likely your studies will be expedited, you will be able to retake generals pretty soon (if you even have to, maybe they'll just setup some committee and you just need to give a short talk to present your research, as you already do research probably), so nothing will be from scratch and your studies haven't been in vein, the nullstellensatz is the same no matter if you are in Chicago,Boston,Princeton or Palo Alto. and you will have the bonus of graduating from a better school, which is a huge aspect if you are considering academic career. GRE should be extremly easy for you by now, and if you are able to do proper TA job, you should pass Toefl as well, those should be very minor problems from your perspective (how did you got into grad school without GRE?).


If you are from a better school, this is kind of tricky, maybe there's another prof. who can step in to be co-advisor? You are only 3rd year, not 4-5th year, probably you invested less than 1.5 years in research so far. Being stuck without funding for the next 3 years (either way, NW or staying, you will probably finish up in 6 years, maybe even 7, sorry about that, not fair, but that's life, this is a major implication over your studies). I don't understand your relationship statement, you didn't know that your advisor is considering moving? The application process for academic jobs usually takes more than 6 months


All those hopes about your advisor funding in NW is wishful thinking that can have really disastrous outcomes. The startup grant most universities give to incoming profs are usually for moving, setting up office and some research visits, those are not in the level of NSF grants (or better - Simons/ERC). NW is located on Evanston - affluent suburb of Chicago, cost of living there is not zero (that's not CAL, but still not epsilon, 1 bdroom can easily go for $1800+), and considering this moving situation, are you sure she will commit so much of her own funds to bring you over? I guess support from your home institution is not a possibility as this are planning on terminating your TAship. Regarding the other funding options, some NSF stuff have strings attached (RTG, or supporting only students from their own school), it is too risky to consider this, especially as you are speaking about events which are probably 2 years into the future.


I believe that for the time being, you should continue with the application procedure to NW and if and when the admittance letter will come, set up a conference call between NW director of grad studies, your advisor and yourself and try to setup a better plan for you. If NW decide not to admit you, all those talks are hypothetical, either you will have funding for a visit or not, but you will need to stay in your own school.


publications - Citing paywalled articles accessed via illegal web sharing


There are a few sites which offer paid articles for free. It’s something unethical, especially for those who upload to that site, but for me, it’s good for expanding knowledge.


As a readers, can we cite those documents, and can the editorial board know that I’m using those articles?



Answer





  1. Nobody will know how you have gained access to the article. Feel free to cite articles found via whatever sources.




  2. It might not even be illegal to download content from the website; check your local laws and Berne convention (if your country is signed up) to be sure. In any case, this is unlikely to affect your reputation in any way.





  3. Remember to cite the source appropriately; a journal or a book, not a pirate website or any other medium. The pirate website is usually not the publisher. You do not cite the university that has bought access to research (probably funded by public sources and peer reviewed by academicians funded by public sources), or the colleguage who shows you an article, or the library that contained a copy of the article; these all have the same role as pirate website.




  4. You might not want to be vocal about using such a website. Some people still see it as ethically questionable. That said, using various pirate websites is increasingly common, and the status of many academic publishers among academians seems to have taken some hits, so many researchers will not care about how you get your articles.




  5. You also have the ethics tag on the question. The ethics of pirating digital material are a polarized subject. You might want to do your own research here, or ask a new question for what the main arguments for both sides are, if it has not been asked already. Some people say that pirating material is analogous to physical theft, while others say that intellectual monopoly laws are bad and breaking them creates more good than ill. (I happen to think the laws are far too strong and harm humanity, and should be weakened substantially or entirely removed.) I strongly suggest reading on the matter until you have found strong statements of both points of view to come to an informed decision.





cell biology - Life cycle of proteins


I try to get a picture of the life cycle of a protein (considered as a specific molecule).


This is how I can imagine it:





  1. After the cell is born a protein molecule is synthesized by gene expression for the very first time de novo. This happens at a specific point in time and in space, typically at an ribosome, which may be located anywhere inside the cell.




  2. From the location of its generation (combination or recombination, see below) the protein travels to its final destination, e.g. as an ion channel in the cell membrane. (But possibly it was already synthesized very close to its point of use.) Or it just floats around in the cytosol. (Possibly, it gathers some other biomolecules around it.)




  3. Whereever it arrives or not: the protein lives and works for some time.




  4. Eventually, it gets damaged (= looses small functional units), but gets repaired in situ. Continue with 3.





  5. Eventually, it gets marked by ubiquitin and destructed in a controlled manner. Continue with 7.




  6. Eventually, it decays spontaneously (= splits into some larger fragments).




  7. Its fragments are released (in case it was bound) and start again to float around in the cytosol.





  8. Eventually, its (or other proteins') fragments are recombined (at specific points in time and in space, possibly at "re-factories" comparable to the ribosome-"factories"). Continue with 2.




Is this rough picture of the life-cycle of a protein essentially correct?


If so: What is known about the time ranges in which these processes take place? Especially: How long is the effective life and working time of typical proteins? Are there proteins that live and work only for minutes or hours, and others that live for months or years? (Specific examples are welcome!)




teaching - Course assessment for programming courses


Next year, I will be teaching a course that has a significant programming component. While I have taught other courses before, it will be my first time teaching a programming course. Consequently, I was wondering: what is a typical design of the course assessment for a programming course, e.g., intro to Java/Python programming? In particular, how many assessment tasks are there, and how are they weighted? The assessment tasks that I have in mind would include individual assignments, group projects, and individual assessment (quizzes or a final exam). Are there other assessment tasks that are typically present in a programming course?


(I have taken a few programming courses in the past---unfortunately that was more than 10 years ago so, so my memory of my classes is quite hazy at this point.)


Response to comment: ask your colleagues who have taught similar courses



Unfortunately, my department is focused on an academic discipline where programming is not central, thus, most of the courses in my department do not involve any programming at all. Also, the course that I will be teaching is a new course that I am in the process of developing, thus I have a lot of freedom about deciding how to design the course assessment. Nevertheless, Nate Eldredge's suggestion is helpful in that I can ask the one or two colleagues in my department who are teaching programming courses (different contexts, different languages) how they assess students.




biochemistry - Why would an Eadie-Hofstee Plot be non-linear?



Besides cooperativity between multiple active sites on an enzyme, what are the other reasons for the Eadie-Hofstee plot to be non-linear?




teaching - Under what circumstances would a professor be offended at students taping or recording his or her lecture?


Are there any policies on taping or recording or even streaming a professor's lecture?


What do professors think about students who do this?


Obviously, most circumstances the professor would never find out, but there was this one instance when a professor got really angry because a student was recording him without his permission.


I don't understand why he would be offended, most likely the student is only using it for review and not commercial purposes as the nature of the class is quite obscure, could anyone shed a light?



Answer



I do not believe it had anything to do with the act of being recorded by itself. Most universities are beginning a process of recording lectures for later consumption by the students anyway.



Instead in this case it is likely because the professor was unaware they were being recorded. They may do or say something that they regret or which gets them into trouble. If however they knew beforehand that they were being recorded it would be unlikely that they would do that since they know the repercussions would be more severe. I think it was an instinctive reaction to protect themselves from others using the recording against them.


collaboration - How much of my ongoing unpublished research should I disclose to others?


As part of my PhD, I have already published a paper and am working to expand it further. Recently, a PhD student (who I didn't know) from another university contacted me regarding my paper. He showed interest in the paper and the direction that I'm working on, wanted me to explain it further and, if possible, share the framework that I developed and used for experiment so that he could use it for his own research.


Although I like to help him as it will be nice if we can come up with some collaboration, I'm afraid that it might turn into an competition instead if he decides to pursue the same direction as mine alone. Since I'm still working on it without any concrete result, it is possible for him to solve it first and publish papers. I'm not saying that he might steal my ideas/tools since he can put my name in an acknowledgement.


So, my question is to what extent I should share or disclose my current research which is in progress.



Answer



Great question! I found myself in similar situations as a student and likewise as a mentor for other students when talking with people working on similar topics.


A favourite quote of mine is from George Bernard Shaw:




“If you have an apple and I have an apple and we exchange these apples then you and I will still each have one apple. But if you have an idea and I have an idea and we exchange these ideas, then each of us will have two ideas.”



I believe this is an ideal philosophy for research in a sense that ideally, everyone should gain from the free exchange of ideas.


However, as you gain experience, you realize that it can be just an ideal.




My first experience concerning the cost of openly sharing results was when I was a PhD student. Early on, I had the basics of what seemed like an important result for the community and had some initial results. My supervisor urged me to try and publish but the paper was borderline rejected from the conference with comments like "nice idea but still too early". I thus published it as a poster in the informal proceedings. In the meanwhile, my supervisor and I had been in conversation about how to progress further, get more results and mature the work. He presented the poster, spoke with various people and told me that he had had lots of interesting conversations: lengthy conversations with two senior researchers in particular.


I continued working on the problem. My supervisor and I had some difference of opinion on the direction the work should go in (theoretical vs. applied CS basically). We got bogged down in some theoretical questions where I felt the impact could be on simplifying the problem and working on the applied side. I missed the next deadline for the conference in our area but lo and behold, two papers were published that pretty much had developed the applied side of the idea. I read the two papers and realized that both had, in parallel, at the same venue, developed the ideas I had been working on ... with one or two interesting side observations. Both works were from groups of the two senior researchers my supervisor had talked to. One cited my informal/preliminary results as an inspiration, the other didn't cite it at all.


Four years later, the first paper now has 175 citations in Google Scholar, the second paper has 100, my paper has 41. I published a later paper on the topic that's doing a little better, but for sure, the early birds had taken the worm.


In part I'm happy that the idea was developed and they did add new ideas, and I've worked on various things since, but I honestly still regret not having formally marked the idea further before my supervisor exposed it. I also regret not being more urgent in getting the full work published.





This is not to suggest that you should stay tight-lipped at conferences or turn down all collaborations, but if you're worried about someone entering into competition with you, you might want to listen to that concern. I don't think it's at all unreasonable to not share every idea you have when you attend a conference. There are plenty of anecdotes of tight-lipped researchers: for example, nobody knew what Andrew Wiles was working on for several years while he was working towards a proof of Fermat's Last Theorem.


If you think the person is someone you can trust and someone who could help in a collaboration, listen to your gut. Test the water and see how knowledgeable they are or how they could contribute. Be careful if you have co-authors, not to talk about their ideas. If you want to collaborate, perhaps publish a technical report or a pre-print to mark your ideas first.


If in doubt, you don't have to tell them about your ideas straight away. Maybe stay quiet for the conference and email them later if you think you want to work together or to tell them about your ideas.


publications - Citing (or not) a flawed or incomprehensible paper or preprint


Is there a good practice of citing (or not) a paper or preprint that you consider flawed (or at best - totally incomprehensible)?


Once I had a problem of that sort. I wrote a paper on a topic, which was not very popular. Even if I was not using other's results directly, I wanted to cite a few papers solving very similar issues.


Then I had a dilemma if to cite a preprint tackling the same problem, using methods I don't understand (with a feeling that it is incomplete, flawed or just extremely badly written).


Ii that case it is better to:



  • simply drop it,


  • cite but make it explicit that you are just mentioning it, not using their results,

  • or cite making it explicit that you have serious doubts on its content?


EDIT:


By a preprint I understand sth which is archived on arXiv or sth similar.




Monday 25 March 2019

evolution - What is meant in biology by the term "evolved"?



A student asked me this the other day and I thought that I would ask it again here. If one organism is said to be "more evolved" than another, what exactly does this mean?



Answer



"More evolved" is actually meaningless in all contexts. See terdon's answer for a good explanation.


In the strictest sense, an organism can be said to be more divergent than another when comparing both to an outgroup, such that there is an inferred most common ancestor in reference to which to make the comparison. In this case, one organism is more divergent if there are more changes to this organism than the other, relative to the reference point.


However, when speaking, many people get lazy, and use "more evolved" as shorthand, wishing it to mean something like "more divergent". Even "more divergent" is meaningless in the following contexts:



  • when there is no outgroup understood

  • when describing increasing complexity (obligate parasites have lost complexity and have had more evolutionary changes than their non-parasitic relatives)

  • when the outgroup is poorly chosen. Mammal vs reptile comparisons should not, in general, use prokaryotes as the outgroup.



Edited 2013/12/06 to reflect the precision in the answer by terdon.


publications - Is it allowed to submit accepted and published journal articles in Elsevier, to arXiv?


As arXiv allows submitting research articles which helps in increasing its visibility. I was wondering if it is alright to submit accepted and published journal articles in Elsevier (Expert Systems with Applications, International Journal of Medical Informatics) to arXiv?



Answer



You can easily find the answer following the author guidelines of Elsevier, starting from the link you provided. On https://www.elsevier.com/about/company-information/policies/sharing they explicitly state:



Authors can update their preprints on arXiv or RePEc with their accepted manuscript .




thesis - Will an off-topic Masters hurt my chances of a PhD place?


I have just completed the third year of an integrated master's degree (a three-year undergraduate degree plus an additional year of study at a master's degree level, with the final degree being an MPhys) in Astrophysics at a UK university. This summer I have to decide the topic of my final year dissertation, which counts for 50% of my final year.


I am almost certain I would like to continue in research and hence I am also starting to look for PhD places. I am very interested in cosmology, but with no idea of a specific area I want to go into and so I had thought of doing something in the field for my Master's dissertation, to get an idea of what it would be like to perform cosmology research.


However, the university I am at does not have a research group in this area and no facilities or expertise either. I have approached a potential supervisor (the lecturer who taught my one cosmology module, who is a plasma physicist), but he has told me that it is entirely up to me to decide on a topic/ question, which I am wary of doing due to my complete inexperience and lack of knowledge.


So, my question is this: if I decide to do my Master's dissertation on a different topic (eg solar physics), will I be at a disadvantage when applying for cosmology PhDs?




Answer



Don't ask us.


Contact your favourite three prospective universities for your cosmology PhD. Better still, contact your favourite three supervisors for your cosmology PhD. Ask them:




  1. What Master's dissertation topic will prepare me best for my intended cosmology studies?




  2. What Master's dissertation topic will make me most likely to be successful when applying to study a cosmology PhD?





(The first question is much more interesting than the second).


You will find enthusiasm for engaging with your question and your situation, because you are expressing specific interest in their field and because you are not asking them to decide anything about your application – since you have not applied. Quite a lot of people in senior levels in cosmology are interested in cosmology and are glad to find interest in cosmology in other people.


Sunday 24 March 2019

publications - Recommended tools for graphs and charts


I have seen a couple of images in several papers like those attached below. These images are really expressive also nice i.e. look very scientific. I have no idea how to generate such images since I have in the past used powerpoint/excel. I'd appreciate some pointers on the tools for generating such images or even better ones.


UPDATE Just to clarify about duplicated question(s), this question is quite specific to graphs like those that combine several features concisely into a line /bar graph or scatter plot e.t.c. (as provided in the attached images). Some similar questions e.g. this one is about illustrations as seen in the answers provided. I think my question is different, so are the answers provided different from those in the referenced question.



example 01


example 02



Answer



There are quite a few options here, with varying levels of user-friendliness. Some I have used are:



  • Grace: Quite simple to use, you input values through a *.dat file, and can manipulate plots through a GUI. I think it's Unix OS only (Linux, MacOS). Speculation: The figures in the question look like they were made in Grace.

  • gnuplot: Works on Windows as well as Linux and Mac. A little bit more of a step up in difficulty, as you are manipulating figures either through a script or in a terminal/command prompt.

  • Matplotlib: Also works on Windows, Linux and (probably) Mac. Requires some knowledge of Python, since it is a Python package. Also generates figures through a script or IPython console. Found this to be a bit easier than gnuplot. Very good documentation.


networking - Making time to catch up with people at a conference


I am attending a number of short (two and three day) conferences this fall. In the past I have scheduled meetings (e.g., time to chat and catch up over meals and coffee breaks) with people prior to the conference in an attempt to maximize my ability to catch up with colleagues/friends. This approach, however, doesn't work for me. To often meetings get cancelled and if I fill in my schedule too much it is hard to reschedule. Other times I have taken the play it by ear approach and catch up with who I catch up with.



Is there a good strategy for catching up with colleagues whom you already know well (I am not asking about strategies for meeting new people)?



Answer



Skip the talks


Except for meals, most of the time at a conference is taken up by scheduled talks. Don't go to them.


Ok, go to some of them. But if you want to get some work done, catch up with a colleague during a coffee break, take a look at the schedule, find a session (or two, or three) that seem extra boring, and agree to skip them. Use that time to go to a coffee shop, or sit in a quite space in the conference center.


learning - Where to continue my research-oriented studies after Bachelor's Degree in Computer Science?


I have a bachelor's degree in computer science. I am looking for an appropriate master program. I am interested in algorithms.


My question is not about where I should continue my education. My question is about how exactly should I search for the place to study for my master's degree. I simply don't know where should I start. I don't know what my first step should be. I don't have any experience living abroad.


Right now in order to choose the place I consider just few parameters.





  1. I am interested in algorithms, almost every university that offers master degree in computer science would be an appropriate choice.




  2. Fee. It's really a problem. I didn't find universities in Europe that offer master's degree study for free, few of them offer applying for scholarship. But I am not sure I have a good chance to get one, and obviously it doesn't cover all fee. I don't have citizenship in a European country so I assume it's going to be harder to apply.




What's your experience? Did you try to apply to scholarship? What's your opinion? Can I start doing research and hope for funds.


In Canada there are few places without fee, therefore it should be very competitive, but at least there is a chance. Usually they ask for GRE in mathematics and computer science; sometimes for IELTS. What's your opinion? I assume you should be really perfect in your field in order to get applied.



In China, very interesting option, without fee or with minimal fee plus one year to get a new language. It looks very attractive, especially with approach of Chinese government to education, as I know there are many programs for free. The only problem is to get the minimal communication in Chinese which may take up to a year according to experience of others.


Addendum:


According to responses I decided to update my post.


I earned my bachelor degree 3 years ago, I have a good job, and I work as a programmer. Throughout the last year I am taking courses of master degree in my domestic university. I have one day off in week for studies. Three years is a long break but I feel the power is back. In my place it's not common that employer will pay for studies, of course I have some savings but this is not going to cover fee, and all spendings for at least two years.


I would like to go to research master. Right now I am not ready to get good grade at GRE, but I am working on it. I am not fluent in English, but in my opinion more important to be good in my field of study.



Answer



The reason why you're not seeing scholarships for study at the master's level in Europe is that the master's degree is not viewed as the prerequisite for PhD study, but instead as the direct continuation of the bachelor's degree. As a result, you're expected to move on to the master's program, and usually at the same location you did your bachelor's degree. That means there really isn't a call for a lot of scholarship to fund master's study. However, it is possible to finance one's stay in a European university, as many schools offer part-time positions for master's students working in a research group for some number of hours per week.


However, in the US and several other countries, gaining admission to a PhD program is a good way to get your master's studies funded, as the funding is normally provided for the entirety of your graduate tenure, rather than just the PhD portion.


To get in to most programs in English-speaking countries, you will need to show evidence of a good scholastic record as well as good English skills, as evidenced by the IELTS or TOEFL. If those aren't in place, it's going to be very difficult for you to be competitive, and almost impossible to be competitive for a scholarship or fellowship.


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...