publications - PI published my work after I graduated without informing me (and with a different first author)

When leaving with my PhD I left a sizable amount of unpublished work, most of which was 95% or better complete. After several attempts over the past 2 years to find out his plans for publishing I all but gave up. Then tonight a google notification told me they were adding a pub on google scholar. It was my work (that I had written a manuscript in 2012) with someone else as a first author. I'm on the paper but was never informed or reviewed a manuscript. Im concerned because I still have presumably 3 more papers pending that could turn out the same way.

I would like to see 3 things happen.

• Reordering of authorship or at least an unbiased remediation/explanation of the current.


• Access to the submission process (including establishing agreed upon authorship requirements) or at least advanced notice should some other work be published in the future.


• I would love (but most likely won’t get) acknowledgment/censure by the institution, as this is not the first time the PI has acted dishonestly in this regard, and likely not the last.

I am looking for advice on who to contact, and how to approach the situation such that my claim is heard.

To clarify a few points: In my field it is customary for the author who contributed most both experimentally and conceptually to be listed first, followed by other contributing authors in roughly descending order of involvement. Lastly the PI (the Principle Investigator who oversees the work, funds the lab, the major professor involved, ect) is listed.

This order is largely taken into account when assessing a researchers body of work, as it is not common for papers in the field to have a breakdown of contributions by author in the text like in some other related fields.

Also common in the field is the ownership of the scholarship by the institution. This work was written up and published in my thesis. Additionally I prepared and formatted, and made available to the PI a manuscript for journal publication. Unfortunately, I cannot publish without the PI's approval, and I thought he was unable to publish without my approval.

job search - What to do after being denied tenure?

What do you do if after 6 years of being an assistant professor, you come up for, and are denied tenure?

How hard is it to get a job in industry, when you are middle aged and have no relevant work experience? How hard is it to get another job in academia? Who wants to hire someone who was denied tenure at their home institution?

Am I able to change my GPA once I submit a graduate school application?

I am wondering if I apply to graduate school in US in fall and lets say the due date to submit the application is December 1 and fall quarter grades are posted two weeks after that. Now I am wondering am I be able to update my GPA after positing the fall quarter grades,which is after submitting the application?

biochemistry - Why is allolactose the LacI inducer?

For what reason(s) is allolactose, instead of lactose, the "natural" inducer of lac operon repressor?

Answer

When lactose is present in a cell, some of it is enzymatically converted by $\beta$-galactosidase from the $\beta(1,4)$ linkage (typical of lactose) to the $\beta(1,6)$ glycosidic linkage (becoming allolactose). Allolactose and other analogues can then bind LacI to induce the appropriate conformational change and unbind the lac operator (one such review here).

Why does allolactose act as a signal of lactose presence instead of just lactose? From the perspective of the lac operon, there is no operational difference between lactose and allolactose -- either way one molecule binds LacI and cannot be metabolized while bound. The full paradox is explained by Edgel and summarized by well-known biochemistry textbook author and scientist, Larry Moran, on his personal blog. The short version is that neither allolactose nor lactose are the intended substrates for $\beta$-gal and instead a different sugar entirely is the "natural" inducer and substrate.

1. 
   
   

   Juers DH, Matthews BW, Huber RE. LacZ β-galactosidase: structure and function of an enzyme of historical and molecular biological importance. Protein Sci. 2012 1792-807.

   
   


2. 
   

   Egel R. The 'lac' operon: an irrelevant paradox? Trends Genet. 1988 Feb;4(2):31.

   
   

neuroscience - Is there a correlation between total neurons and intelligence?

Thanks for looking.

First off, I am not a biologist, just a curious layman, so I apologize in advance if this isn't a "good" question. Please don't downvote me into oblivion.

I read today that the human brain has about 100 billion neurons and that got me wondering: is that number pretty standard for everyone or does someone like say, Einstein, have many more neurons than this daft poster.

Is there a correlation between total neuron count and intelligence, or does intelligence depend more on the way neurons are used--or some other factor like previous experience--rather than their total count?

There are two very valid points-of-view posted as answers below, but it sounds like we simply don't have a solid answer to this question at this point in time, so I hesitate to select a "correct" answer.

publications - Is it inappropriate for an author to copy and paste from his/her original paper in an extension paper?

I am currently a referee for a paper. One of the authors of the paper had written an earlier paper, which I will refer to as the "original paper," and the paper which I am now refereeing is an extension of the original paper, which I will refer to as the "extension paper."

I have found that large portions of the extension paper are copied from his original paper. In particular, a whole section of definitions is copied from his original paper; and some paragraphs in the introduction and literature review are copied wholesale or with slight modifications from the original paper.

Is it acceptable for an academic paper to copy paragraphs and even a section from an earlier paper by the same author?

My intuition suggests that it is acceptable to copy the definition section, with an acknowledgement that it came from the original paper, since definitions are standard. But it seems strange to me for the introduction and literature review to be too similar to the original paper.

Answer

The answer depends on the relationship between the papers, and I'm not sure which applies based on the information in your question. In computer science, at least, there are two general cases:

• 
  

  The extension paper is the "extended journal version" of a previously published short-form work such as a conference paper, workshop paper, or extended abstract. In this case, the rule of thumb is typically at least 30% new material. The extended paper will often contain large chunks verbatim, as it is expected to supersede the original paper, rather than existing as a separate work.

  
  


• 
  
  

  The extension paper is a separate work: in this case, extensive reuse of material is self-plagiarism. Two exceptions: first, related work, methods, and definitional material may often be reused as long as it is appropriate to do so---the material should be appropriately customized to fit the new environment. If the author would just be paraphrasing for the sake of paraphrasing, though, it's not necessary. Second, introductory material may be partially shared, though it should be more heavily customized for the new context.

  
  

In all cases except for minor reuse of related work material, the extension paper must declare a clear and explicit relationship with the prior paper.

Note that many other fields do not have the notion of a "journal version" and thus have much stricter standards.

conference - Business cards for graduate students

It's come up in our lab that we should probably have business cards for when we attend conferences, however, we've been given very little guidance for what is appropriate for a graduate student.

Some questions that have come up:

1. Should we be trying to standardize the cards to look like the official university's cards? (e.g., with the university logo, etc)?


2. Related to the first question, should we be going for standardized or for something that will make us stand out?


3. Should we be putting our current status on the card? It seems like if we haven't hit ABD yet then it might be counterproductive because then we'd have to buy new ones each time we made progress.


4. Should we be adding our research interests directly on the card? What about advisor?



5. Any other information (other than contact/website) that we should be including or tips on this?

Answer

I would standardize them and simply put the most relevant information on them. My (dated) business card looks like this:

Now I think it has a little bit more information than needed; fax is almost certainly not needed, but there might be circumstances where it's handy to have the mailing address. But important are:

• University + department


• Academic homepage


• E-mail address



• Perhaps phone number


• The fact that you're a PhD student.

I wouldn't add too much information on them. Business cards are for core info, nothing more; they might get crowded otherwise.

My own business card is outdated: a university reform means I'm no longer at the Department of Space Science, but at the Department of Computer Science, Electrical and Space Engineering, Division of Space Technology. But I don't care, because the e-mail address is still correct, and the new department/division wouldn't even fit on a business card ;)

microbiology - How much weight/volume do microbes occupy within the human body?

Microorganisms constitute the bulk of all the biomass on Earth. I weighed myself yesterday, and wondered how much less I would weigh if I were completely free of bacteria and microbes, inside and out.

Approximately how much weight and volume do microbes occupy within the average human body? How were these values obtained?

Answer

@AlanBoyd's calculations are reasonable, I think the estimate is off though. The human microbome includes other bacteria which are not necessarily E.coli equivalent.

The human microbome projects give estimates that microbes are 1-3% total body mass. i.e. several pounds of bacteria.

The GI tract alone has most of the microbome mass - faeces is ~60% intestinal flora/fauna by dry weight, which for many adults alone must be hundreds of grams at any given moment.

independent researcher - What Affiliation to put for Amateur scientist who is an alumni out of school for 15 years?

I am an amateur scientist who wants to submit a paper to a peer reviewed journal. While I have an under grad degree... it was in business and I have been out of school for 15 years. Do I put my undergraduate university as my affiliation because I was educated there? It would be nice to put something.

job search - What is the importance of postdoctoral teaching experience for US tenure-track jobs?

I'm a math Ph.D student in the US who has just accepted a four year postdoc--NSF postdoc at a US school interrupted by a year in Europe. For better or for worse, I am only slated to teach for two semesters in those four years--likely during the second semester of my 3rd year and 1st semester of my 4th.

I am planning to apply for tenure track positions in the US afterwards and am wondering whether the relative lack of teaching as a postdoc will adversely affect my application.

Should I be looking for volunteer teaching opportunities?

If it matters as a graduate student I had fairly extensive teaching experience, serving as sole instructor for courses in various levels of calculus, multi-variable calculus, and linear algebra for four years in addition to mentoring REU students and grading/TA-ing graduate and advanced undergraduate courses.

entomology - Small mottled beetle identification

I live in Chapel Hill, North Carolina, and recently started seeing a bunch of these little guys in my house. They're about 1/8" long (estimate), with brown/black zigzag stripes; it's possible they're babies, but over the last two weeks their size has remained consistent so this seems unlikely.

publications - Order of authors in a paper

I have worked on few research labs and performed research as a master's student with PhD students and faced similar issues.

It has been papers that I have contributed most of the work for that paper, including producing results, and writing. Yet the PhD student wants to put my name second due to seniority.

When I first got involved I understood that the order of the paper authors is important in showing the amount of contribution. It feels extremely demotivating to know someone else is getting credit for the very hard work I done and makes me want to stop being involved in research.

Questions:

• What is the best practice to decide the author order for CS/AI/ML related conferences?


• When everyone has contributed equally and ordering by name, is it the first name or last name you order by?


• When the order of the authors doesn't match the level of contribution, what is a good way to bring it up and to who?

Answer

Rule #1: Always try to pin these types of things down before performing the work.

Rule #2: Understand that academia (graduate school) is run on an implicit pecking order:

Departmental pressures and requirements > Advisor > PhD Student > Master's Student

This makes complying to Rule #1 very difficult in practice. Every early career researcher runs into the issue you have described in some form. (Not that this makes such practices right). People higher than you in the pecking order will use administrative leverage to get what they want.

Advisor: "I am the first author on this paper." (And if you disagree, you'll have to find a new advisor and lose a year's worth of work).

Department: "Give Professor Smith what she wants or we will not sign off on your degree."

PhD Student: "Collect this data for me. (And then try to convince someone that you actually did the work and not me)."

The order of attribution should be based on the order of contribution in most CS-based fields. Equal contributions are noted by alphabetical order of the authors' surnames, sometimes with a footnote indicating equal contribution.

I would bring the issue up first with the PhD student directly. I would then speak with his/her advisor. The advisor is essentially the court of last resort. An advisor also will be able to help with the navigation of what actually constitutes authorship for each party. At the very least, your own advisor should (hopefully) be able to help you obtain credit for your work in the form of a chapter in your thesis or something.

Going forward, I would be firm in establishing what the authorship expectations will be on any work you do. You will at times be forced to balance fairness in authorship and expediency in obtaining your degree.

I will note that I take the pecking order things into account when I interview applicants for a job. I care much less about author order and much more about what the person actually did for the paper. Thus, if the OP applied to a job with me, I would likely give his research the same weight whether he was first or second author. I fully understand that superiors sometimes take advantage of their underlings.

Where to find journals or other publications for my work?

I have written papers on the topic of network security. Now I am trying to find a place to publish one of them. Is there a list of publications by topic, somewhere? If I come across such a list, how can I determine the reputation of the various publications?

Answer

Try Google Scholar Metrics. I guess the topic you are looking for would fall under Computer Security & Cryptography.

phd - Should you cite somebody's Transfer Report? (Confirmation Report)

Context: At UK universities at least, before progressing from the first year of your PhD (or transferring from an MPhil to a PhD), it is required to write a fairly substantial report detailing the research done so far and the outline the research direction over the remainder of the PhD. It's usually known as the Transfer/Confirmation/Upgrade Report.

Is it appropriate to reference these kinds of reports when writing: a) Your own Transfer Report, and b) Published research articles? I have never come across one referenced in a paper before, whereas I have seen references to PhD theses, Masters, and undergraduate dissertations.

Answer

If it is published somewhere, then you should feel free to cite it. However, if it's not, then you have a challenge. You might cite it as, more or less, "Author. Title. Transfer Report, University, Year. (unpublished personal communication)" Which indicates that you friend or colleague gave you a copy in which you first found the information you are referencing.

I think such an approach gives your colleague credit and gives readers at least some hope of being able to track down a copy if they want to verify your claims about what it says.

graduate admissions - Deadline For PhD offer while waiting for other results

I have been offered a PhD position with full funding from my backup university, however they gave me a deadline of April 5th to either accept or decline their offer. I am still waiting for replies from other more prestigious universities. What should I do?

Answer

There are generally two things you can do - and you can and should do both at once.

1) Try to extend the deadline. Contact the people who've offered you the position and ask for extra time. They aren't going to give you an infinite amount of time, but ask for ideally how long you'd like - say, an extra two weeks? - with the expectation that they might be willing to give you less time than that. They might say, "Sorry, we can't extend the deadline" or "we can only extend the deadline X days" - but hey, that little bit of extra time could be very important! If you are polite it can't really endanger your offer at any place you'd want to dare attend, and they could always say yes. Just be 'reasonable' in your request - asking for an extension until days before the academic year starts won't be granted and might encourage them to give you no extension at all.

2) Contact the programs you haven't heard from and let them know you've received other offers, and that you'd really like to still consider their program - but you are on a deadline. Inquire if you'll be able to get an answer from them before your deadline. Everyone in the process understand that candidates who get in anywhere often get multiple offers, and deadlines don't always sync up. If you've had contact with a prospective adviser at the institution, consider CC'ing them as well (on the chance that they have already made a decision but the institution is being slow).

There's not really anything to lose if you act professionally, and potentially a great deal to gain. You could get an extension, you could get an early response from other programs, you could find out responses were sent but did not reach you - or worst case scenario you end up in exactly the same position as you are in right now.

citations - What are the downsides of using DOIs in reference sections of publications?

Few papers use DOIs in the reference section (example below). What are the downsides of using DOIs when listing references?

---

A typical example from one of the main conferences in the natural language processing field showing no DOI:

gender - Should I write that a student is a feminist in my recommendation letter?

I'm in the process of writing a recommendation letter for a female student to be admitted to some honors program within the university.

She is fantastic and I assume that she will get admitted with or without my help, so my question isn't necessarily specific to this particular letter, but I do remember feeling curious about this, so now's a good time to ask, I guess!

It's this one line in my letter that made me scratch my head a little bit. The line in question would like to say something like, "she is very interested in advancing women and other minorities in the STEM field," which is a quality that I approve of heartily.

The problem is, I am not sure if everyone in academia feels the same way about this as I do. Perhaps there is that one grumpy old professor from the Old Boys' Club who absolutely hates "feminists" and maybe I am inadvertently hurting her chances.

Sure, I could word it carefully so that it doesn't set off the feminist trigger in most people, but I still have that nagging feeling of "what if" in my head.

Just to make sure that I am not misunderstood, I also support gender equality, and I do not want to discourage anyone from saying so, but recommendation letters are a delicate thing that need to appeal to everyone, and I do not want to hurt anyone's chances, most of all not of these fantastic women that I want to brag about to everyone.

Answer

First of all, your title doesn't quite match the rest of your question. In your suggested quote you write "she is very interested in advancing women and other minorities in the STEM field," whereas according to the title you are asking whether you should write "She is a feminist." Sadly, these things will not evoke equivalent responses in all parties -- the word "feminist" has unpleasant connotations in certain circles nowadays, more so than a generation ago. (By the way, I am a feminist, and it makes me sick that the word is now taken in this way. But it is by many, and so I think it is too loaded a word to use about someone else in such a context.)

The purpose of a recommendation letter is to successfully convey your impression of the recommended party. In particular, if you feel strongly that the recommended party should get the position being applied for, then you want to write the letter that maximizes the chance of that happening (while staying appropriate, professional and truthful, of course). With that in mind: how relevant "she is very interested in advancing women and other minorities in the STEM field" to the honors program the student is applying to? Is this advancement one of the activities that students in the program will be participating in? Or, beyond interest, does the candidate have a record of activities and/or accomplishments in advancing women and other minorities in the STEM field? If the answer to either question is yes, I would suggest that you fill in further details accordingly: this is part of your argument that she is great fit for the program. If not, then: are students selected for the honors program because of their progressive views -- or, much more cynically put, because of the alignment of their political and social views with those of the administrators of the program? Probably not, right? In particular, because "She is fantastic and I assume that she will get admitted," then I don't think you need to help her out in this particular way. There is some risk that even a feminist could read "she is very interested in advancing women and other minorities in the STEM field" as a bit of a consolation prize. Again, write the strongest letter you can.

advisor - Is it appropriate for assistant professors to supervise PhD students?

As pointed out in another question, the general tendency today as compared from classical times is to make junior professors (at assistant level) more and more independent. However, I wonder that assistant professors (common in the US university) supervise PhD students.

The philosophy of academic ranking is to prepare academics for academic/scientific tasks.

Although, academics normally have postdoc experience before their appointment as assistant professors, it is not mandatory. Moreover, postdoc experience is not experience conducive for the supervising of students.

In relation to the above is it wrong that an inexperienced assistant professor (who is not far from his PhD studentship days) can take control of one or several PhD students?

Does it reduce the quality of the education/research?

Answer

Isn't it wrong that an inexperienced assistant professor (who is not far from his PhD studentship days) can take control of one or several PhD students? Don't it reduce the education/research quality?

For certain institutes I've been in, I would find myself asking the opposite question: isn't it wrong for senior professors to supervise students when they have little time for them?

Of course it is not always the case that full professors have no time for their students, but I have seen it happen many times: I've seen cases where students were meeting their official full professor supervisors once a month (or less frequently) and putting names of supervisors on papers that the supervisors had never read. This seems to me to be prevalent in research institutes where the hierarchy tree has a high branching factor to get value out of available funds (few Full Professors, lots of PostDocs / Assistant Professors, even more PhD students and Research Assistants, etc.); in such cases, the priority for senior professors is getting funding for and managing projects. In my case, when I was a PostDoc in such an institute, I was doing the day-to-day supervision of a number of students whose supervisor(s) had no time for them.

Of course it varies from place to place. But my hypothesis is that by the time you reach the Assistant Professor level, either you will have the necessary skills and personality to be a good supervisor, or you will probably never have those skills.

In summary: I don't believe that seniority amongst professors is a good predictor for quality of supervision.

How to search for upcoming conferences that will be held in a specific subject

What is the best way to search for conferences all over world? I need to participate in one in the near future.

graduate admissions - Unhappy with my PhD program in my home country, thinking about applying to another university in UK

My problem is a bit unusual and I would love to get some advice…

I'm a first year PhD student in social-sciences and I already got my proposal approved. I moved back to my home country (where I am currently doing a PhD) after completing an undergraduate and an MSc. I am very unhappy here.

I would like to have a future as an academic. The only reason I decided to a PhD in my home country and not abroad was because I was determined to try, stay, and make it work here, but recently I been thinking it was a mistake. I am thinking more and more about discontinuing my program here and applying for doctoral studies in the UK, as a new student (after a bit of online research I found that they rarely accept a transfer and it is best to start as a new student).

I would love to get your thoughts regarding my situation,

1. 
   

   I am considering sending an email to a potential supervisor but I am not sure how to explain why I want to drop-out of my current PhD program without talking my university down? How do you suggest I do that?

   
   


2. 
   

   Did anyone had a similar experience or have some advice?

   
   

publications - Strategy for submission of articles to highly ranked journals

I am working on a research project that all total will probably end up lasting about two years. As the research progresses, I am writing articles about each new discovery/study, with each article becoming more relevant to current interesting trends (for lack of a better description).

What I mean by this is that in the plan for publications my group has, the first article discusses just the structure, dynamics, etc. of some new interesting carbon/silicon/etc. system. The second article will elaborate on this for an even more novel, more developed structure than the first. Then the last article will (hopefully) provide a deep new insight into how this structure can be used for energy storage/transport/etc.

As I'm sure you can tell, each article gets more interesting, and thus I think each article has a better chance than the previous one of making it into a more highly ranked journal. Our current strategy is to submit the article to a succession of less prestigious journals (each getting rejected) until it eventually gets into one. This way, it ends up getting into the journal it probably deserves to be in, and not something lower, and there's always the chance it is accepted into a highly ranked journal as well.

However, I am curious if this is a bad idea in the long run. Will editors remember "Oh, they already submitted articles to us twice and got rejected; what are they doing it for again?" Will they be quicker to dismiss the next article they receive even though it is higher-quality/deeper research than the previous one?

Or do the editors give each new submission a fair chance for acceptance, with no memory of previous submissions?

I know some of you all are journal editors, so any insight you can reveal to me about your thought process would be quite appreciated.

When does a paid research assistant become a co-author?

What amount of work should a well compensated research assistant put into a paper before they're included as a co-author? Is there any norm? Suppose this is a field where 1 to 3 authors on any given journal paper is the standard amount (e.g., economics/finance/econometrics).

What if they do 30% of the paper? What if the paper requires (model building, programming, writing), and each component is about 33% of the paper, and the RA does all of one of these and helps a bit with another one of these?

I would think the answer is never, unless it was an unusually large contribution or the professor was feeling nice. I think this because otherwise they would've just gotten an experienced co-author who could bring much more to the table who they also don't have to compensate with any $$.

Answer

The decision of whether someone should be a coauthor is completely independent of monetary compensation: authorship depends on what sort of intellectual contribution each person has made, and it would be unethical to treat them differently based on their job (paid assistant, student, colleague, amateur, etc.).

People in different roles may be treated differently based on their contributions. For example, an assistant who does no creative or insightful work, but instead just carries out explicit instructions in a straightforward way, should generally not be a coauthor. (Still, the assistant should be thanked by name in the acknowledgments.) When the assistant's work starts to involve exercising nontrivial skill and judgment, coauthorship may be appropriate. If the assistant is doing a serious part of the creative intellectual work, then coauthorship is mandatory, even if the supervisor's role is deeper.

citations - On citing "common knowledge" statements

I am an undergraduate student with no experience at all.

If you are writing a research paper, that you are planning to submit for publication, how do you state that a particular statement/fact is commonly known to all and it's dicoverer/inventor is not known, and that there exists no research paper that introduced the concept but there do exist various books/websites that discuss the very concepts and a few derivatives of the concept?

I am not able to cite a particular statement/bunch of statements as I am not able to find any research paper related to that at all.

The particular thing in question is: https://math.stackexchange.com/questions/161661/source-of-probably-the-most-simplest-math-trick

What should I do?

Answer

You don't need to cite common knowledge. If you think it is common knowledge, wait for the reviewer to ask for a reference, before going to all the trouble of sorting out the history. Often if a reviewer doesn't think the statement is common knowledge he/she will suggest a reference or provide a conflicting reference.

ethology - Why social animals attack odd members of their own group?

Some social animals are known for attacking odd members of their own group, for example, chicken:

If you have a large group of one type of chicken, they will usually gang up on the one or two others that do not look like they do. They recognize color differences the most and will beat up on the odd chickens in a group.

Of course the same behavior is most commonly observed in humans, where any difference can be a reason for aggressiveness.

Why this behavior developed and still exists and how it is called?

cell biology - Why is saltatory conduction in myelinated axons faster than continuous conduction in unmyelinated axons?

How does spacing apart sodium and potassium channels allow the action potential to travel faster down the axon? This is the reason always cited for saltatory conduction and myelination, but my mental model of conduction tells me that the density of ion gates along the axon should not affect the speed of the AP.

To illustrate, consider a myelinated axon. A wave of Na$^+$ from action potential site 1, a node of Ranvier, rushes into and quickly diffuses down the axon. (It travels in both directions, but backwards is still in the refractory period.) It diffuses through the myelinated region, its concentration always diminishing. Before it attenuates too much, however, it happens upon node of Ranvier 2, where it triggers another action potential. A new wave of Na$^+$ rushes in and the cycle repeats. This should be plain so far.

Now imagine that there is actually a node of Ranvier halfway between node 1 and 2, called node 1.5. The wave of Na$^+$, on its way to node 2, happens to trigger an action potential at node 1.5, from which a wave of Na$^+$ pours in and either boosts the original wave or replaces it by taking its momentum. Now the reinforced wave proceeds to node 2 and triggers it just as soon as, perhaps even sooner than, if node 1.5 had not existed. Repeatedly insert nodes at higher densities until the situation is simply lack of myelination, and we conclude that unmyelinated axons can transmit an action-potential-triggering wave of Na+ as fast as or faster than a myelinated one.

In short, my point of confusion is this: I cannot see how a higher density of gated channels can possibly slow down the wavefront of Na+ that triggers action potentials. If anything, the additional influxes of Na+ should speed up the all-important wavefront, assuming that new waves really "either boost the original wave or replace it by taking its momentum", and also assuming that the wavefront of Na$^+$ is really all-important for signal transmission, and also assuming that the mere presence of (voltage?) gated ion channels in the membrane does not significantly retard the wavefront.

But the usual explanation for why saltatory conduction is faster than continuous conduction (a fact I hope is empirically and unambiguously established) relies on the putative slowing effect of ion channels on the signal fore. Please explain this effect in more detail, if it is not a misconception.

Answer

Myelination acts as an electrical insulator and allows saltatory propagation.

• By reducing membrane capacitance and increasing membrane resistance, myelination increases the velocity of signal (i.e., Action Potential) propagation.

If you want to see a really wonderfully simplified explanation, see this Quora post by Edward Claro Mader. Four great figures that Edward created show this phenomenon simply:

Decreased Membrane Capacitance:

---

Increased Membrane Resistance:

---

So you're right: myelination speeds up electrical conduction. Unmyelinated axon conduction velocities range from about 0.5 - 10 m/s, while myelinated axons can conduct at velocities up to 150 m/s -- that's 10-30x faster!!

But why? ...

Let's Look at Action Potentials & Signal Propagation:

You can get a background of this process in numerous places (e.g., here), so I will just mention this briefly:

• 
  

  When the neuron is at rest, ions are distributed so that the inside of the neuron cell is more negatively charged than the outside. This creates an electrical potential, called the resting membrane potential, across the cell membrane.

  
  


• 
  

  Sodium and potassium channels in the cell membrane control the flow of positively charged sodium (NA$^+$) and potassium (K$^+$) ions in/out of the cell to maintain this negative charge.

  
  


• 
  

  During depolarization, the cell membrane essentially becomes more permeable allowing NA$^+$ to enter the cell. This causes that section of axon to have a positive charge relative to the outside.

  
  
  


• 
  

  When this positive voltage is great enough (i.e., when an action potential is created), the influx triggers the same behavior in the neighboring section of the axon. Gradually, this positive charge on the inside of the cell moves down the length of the axon to the axon terminals.

  
  

The Main Takeaway:

In this process, action potential generation occurs repeatedly along the length of the axon.

It's important to note two things about action potential propagation:

1. Each action potential takes time to occur.


2. The charge (i.e., voltage) that is created dissipates with $ \uparrow $ distance.

Time for some Math & Physics:

In fact, we have equations to calculate both the time a voltage change takes to occur and how current flow decreases with distance.

• You can read more about the mathematics behind this and passive membrane properties in general here and here.

Importantly, these equations rely on two constants: length and time.

The time constant, $\tau$, characterizes how rapidly current flow changes the membrane potential. $\tau$ is calculated as:

$$\tau = r_mc_m$$

where r$_m$ and c$_m$ are the resistance and capacitance, respectively, of the plasma membrane.

• 
  

  Resistance? Capacitance? Huh?...

  
  
  
  
  • 
    

    Resistance = the measure of the difficulty to pass an electric current through a conductor.

    
    
  
  
  • 
    
    

    Capacitance = the ability of a structure to store electrical charge.

    
    
    
    
    • A capacitor consists of two conducting regions separated by an insulator. A capacitor works by accumulating a charge on one of the conducting surfaces, which ultimately results in an accumulation of oppositely charged ions on the other side of the surface. In a cellular sense, increased capacitance requires a greater ion concentration difference across the membrane.
    
    
    
    
  
  
  
  


• 
  

  The values of r$_m$ and c$_m$ depend, in part, on the size of the neuron:

  
  
  
  
  
  • Larger cells have lower resistances and larger capacitances.
  
  
  
  

Importantly, however, is that these variables also rely on membrane structure.

• 
  

  c$_m$ (the capacitance of the membrane) decreases as you separate the positive and negative charges. This could be the result of additional cellular structures (e.g., sheaths of fat) separating intracellular and extracellular charges.

  
  


• 
  
  

  r$_m$ (the resistance of the membrane potential) is the inverse of the permeability of the membrane.

  
  
  
  
  • 
    

    The higher the permeability, the lower the resistance.

    
    
  
  
  • 
    

    Lower membrane resistance means you lose ions quicker and therefore signals travel less far

    
    
  
  
  
  

But why? This is where that length constant becomes important. The length constant, $\lambda$, can be simplified to:

$$ \lambda = \sqrt {\frac {r_m}{r_e + r_i} } $$

where, again r$_m$ represents the resistance of the membrane and r$_e$ and r$_i$ are the extracellular and intracellular resistances, respectively. (Note: r$_e$ and r$_i$ are typically very small).

Basically, if the membrane resistance r$_m$ is increased (perhaps due to lower average "leakage" of current across the membrane) $\lambda$ becomes larger (i.e., the distance ions travel before "leaking" out of the cell increases), and the distance a voltage travels gets longer.

Why am I telling you all of this??

How are the time constant and the space constant related to propagation velocity of action potentials?

The propagation velocity is directly proportional to the space constant and inversely proportional to the time constant. In summary:

• 
  
  

  The smaller the time constant, the more rapidly a depolarization will affect the adjacent region. If a depolarization more rapidly affects an adjacent region, it will bring the adjacent region to threshold sooner.

  
  
  
  
  • Therefore, the smaller the time constant, the more rapid will be the propagation velocity.
  
  
  
  


• 
  

  If the space constant is large, a potential change at one point would spread a greater distance along the axon and bring distance regions to threshold sooner.

  
  
  
  
  • Therefore, the greater the space constant, the more rapidly distant regions will be brought to threshold and the more rapid will be the propagation velocity.
  
  
  
  
  

Sooo....

1. 
   

   If you increase the layer of cells around the membrane, you decrease the electric field imparted by extracellular ions, which allows intracellular ions to move more freely in the axon. In other words, you decrease the capacitance.

   
   
   
   
   • As a result, you have more cations available to depolarize other parts of the membrane.
   
   
   
   



2. 
   

   If you decrease the permeability of the membrane (i.e., if you prevent ion pumps from moving ions in/out of the axon), you increase the resistance of the axon membrane, which allows for the voltage created in the action potential to travel farther before dissipating.

   
   
   
   
   • By allowing the voltage to spread farther before necessitating the generation of another action potential, you reduce the time it takes for signal propagation.
   
   
   
   

In other words, if you "block" ion pumps and decrease the concentration of anions near the axon membrane, you increase membrane resistance (r$_m$) and decrease membrane capacitance (c$_m$), respectively. Together, this decreases the time of electronic conductance through the axon (and thus increase conduction velocity).

Finally, to Myelin!

Myelin greatly speeds up action potential conduction because of exactly that reason: myelin acts as an electrical insulator!

• 
  

  Myelin sheath reduces membrane capacitance and increases membrane resistance in the inter-node intervals, thus allowing a fast, saltatory movement of action potentials from node to node.

  
  


• 
  

  Essentially, myelination of axons reduces the ability for electrical current to leak out of the axon. More specifically, myelin prevents ions from entering or leaving the axon along myelinated segments. As a result, a local current can flow passively along a greater distance of axon.

  
  

So instead of having to contantly generate new action potentials along each segment of the axon, the ionic current from an action potential at one node of Ranvier provokes another action potential at the next node. This apparent "hopping" of the action potential from node to node is known as saltatory conduction.

So Why not Just Myelinate the Entire Axon??

The length of axons' myelinated segments is important to the success of saltatory conduction. They should be as long as possible to maximize the speed of conduction, but not so long that the arriving signal is too weak to provoke an action potential at the next node of Ranvier. The nodes also can't be too frequent because, although adding a new node to the axon would increase its ability to generate sodium current, it would also increase the capacitance and thus diminish the effectiveness of other nearby nodes.

---

Sources:

1. 
   

   Purves D, Augustine GJ, Fitzpatrick D, et al., eds. (2001). Neuroscience. 2nd edition. Sinauer Associates, Sunderland, MA.

   
   


2. 
   
   

   The Brain: Understanding Neurobiology

   
   


3. 
   

   Byrne, J.H. Chapter 3: Propagation of the Action Potential. Neuroscience Online. Univ. Texas.

   
   


4. 
   

   Understanding the Passive Properties of a Simple Neuron

   
   


5. 
   

   Quora

   
   
   


6. 
   

   Wikipedia

   
   

publications - At what stage of research career one can write a 'review article'?

At what stage of research career one can write a 'review article'?

Obviously a graduate student in the beginning stages cannot/may not write one. But how experienced does one need to be before attempting to write reviews? Does authoring a number of papers in the relevant field equips one for that?

Can a graduate student publish a review article? Do acceptance of review article (for publication) depends on the reputation of the author or co-authors?

EDIT: As @JeffE has pointed out anyone can write a review article; the question is about getting this write-up published.

Answer

First, I'll remark that (at least in fields close to me: physics and chemistry), the process for submitting review articles is typically handled in a different way than other articles (which I'll call “research articles”). Review articles take a lot of effort to write, and that their publication may depend not only on intrinsic quality and scientific criteria, but also on editorial policy: if the journal has already hosted a review on a given topic, it is unlikely to publish another soon afterwards. So, the common practice is to come to an agreement with the editor before writing the full article. Either the editor contacts a scientist to offer him to write a review on a given topic, either an author sends an abstract to the editor asking if the journal would welcome such a review (with no guarantee as to the results of the peer-review process, of course).

This has an important consequence for your question: you can actually ask the editor of the journal of your dreams if a review by you and your co-authors would be welcome. Practices may differ between fields, journals and editors, but asking exactly the person who is going to make the decision is the right course.

Then, we come to what I would call the “customs”. It is indeed typical to gain some authority in your field before writing review articles. This usually means working for a few years in a given field, publishing some articles of your own, in short: getting noticed by your community. As such, it is not a typical thing to do for a graduate student. Maybe at the end of your PhD, jointly with your adviser. Most probably, later in your career: either as an experienced post-doc, or after having gained a faculty position.

With more than a few years of experience, my personal experience is that you perfectly write reviews (and the editors will accept if the work is good). However, it gets easier with seniority, as you will (i) more easily have your work accepted in more prestigious journals, and especially (ii) more easily get invitations to write reviews.

errors erratum - I made a huge technical mistake in an arXiv paper... How bad is it?

I made a huge technical mistake in a paper I published on arXiv... How bad is it in academia?

graduate admissions - Statement of purpose: how important is correctness of grammar and punctuation?

English is not my first language, and I am concerned that my statement of purpose might contain some grammatical and punctuation mistakes that neither Microsoft word nor I can see. What is the best way to overcome this problem, and to what degree does this affect the admissions committee decision putting into consideration that English isn't my first language?

P.S. I don't have any native English-speaking friends and I don't trust companies or online sites to see my statement of purpose to check its correctness.

Answer

If the written question above is a genuine reflection of your English spelling and grammar abilities, then I strongly suggest you seek professional services to assist if you are in any way concerned about your abilities having an adverse impact on your application.

This application is clearly a very important step in determining your future, and if it is so important and you have concerns, it is not worth leaving it to chance. If you have no suitable friends, use a professional service. Plenty of other native-English speaking applicants who are competing for spaces with you will have done so.

I can't say for certain how a selection committee will factor your English as a second language. It is likely to depend on the institution and the course you are applying for.

publications - Why do tenured professors still publish in pay-walled venues?

I wonder why tenured professors still publish in pay-walled venues. I can understand that non-tenured professors are publication pressured, but once one gets tenured, why should one still place knowledge behind walls?

proteins - What type of mutation causes Progeria?

I'm doing my High School biology final on Progeria, and am wondering what type of mutation causes this disease.

I know that the LMNA gene codes for the "prelamin A" protein, and that protein contains a farnesyl group that is then not able to be removed (in the case of Progeria). The abnormal form (with the farnesyl still attached) of prelamin A is then called progerin, and attaches to the nuclear rim resulting in an abnormally formed cell nucleus, making mitosis impossible.

Is this a structural mutation? What sort of mutation is this?

Thanks in advance.

Answer

Hutchinson–Gilford progeria syndrome is almost always due to to a de novo mutation (i.e. not an inherited mutation) in the lamin A gene (LMNA). The mutation responsible is a C-to-T substitution at position 1824. Remarkably this doesn't change the encoded amino acid but rather creates a new splice donor site in the RNA transcript. When this splice site is used it results in the deletion of information corresponding to about 50 amino acids internal to the protein and near to the C terminus.

During biogenesis of normal lamin A a C-terminal -CAAX motif is recognised as a signal for isoprenylation, in this case farnesylation. The added lipid group acts as a C-terminal membrane anchor. However this anchor is subsequently removed when the protein is proteolytically cleaved near the C-terminus, removing 15 amino acids including the C-terminal cysteine (by this point the three C-terminal residues have been trimmed away). The cleavage site for this final modification is missing in HGPS lamin A so the farnesyl group cannot be removed. The accumulation of unprocessed lamin A causes the observed defects in the nuclear membrane.

Eriksson et al. (2003) Recurrent de novo point mutations in lamin A cause Hutchinson-Gilford progeria syndrome. Nature 423: 293-298

Capell et al. (2005) Inhibiting farnesylation of progerin prevents the characteristic nuclear blebbing of Hutchinson-Gilford progeria syndrome. Proc. Natl. Acad. Sci. USA 102: 12879-12884

marine biology - What are the buoyancy control mechanisms of Chambered nautilus?

I'm currently working on an underwater robot and was hoping to use the principle used by the nautilus for buoyancy control. So how do the Chambered nautilus control its buoyancy?

graduate admissions - Advice - MS in mathematics to increase competitiveness for PhD programs?

I am a senior maths major (computer science minor) who is pretty worried about the next step in my academic career. First, let me state that I'm about as sure as I can be that I want to get a PhD in mathematics. Unfortunately, I didn't realize what the field entailed, or my passion for it, until I had made many really poor decisions - mostly in the form of bad attendance. For example, I basically just showed up for tests in calc 2, 3, linear algebra, and differential equations, and consequently, my field of potential letters of recommendation is quite small. To make things worse, I come from a party school - I need letters!

I've had one professor (abstract algebra) offer to write me a letter, and I've taken my advanced calc sequence under a professor who I think could write me a good recommendation (adv calc 2 was a graduate course; had [i think] the highest grade out of about 15 students). I'm also taking topology (graduate level) this semester, and am hoping to impress my way to a third letter.

My GPA is okay - cumulative about 3.61; math is all A's and one C in linear algebra. I've also been working through a few books (Spivak's "Calculus" and "Calculus on Manifolds," and am about to start Birkhoff and Maclane's "Survey of Modern Algebra." Although I love the material, and enjoy learning it, the independent studying probably stems from some feeling of inadequacy due to my past immaturity.

I got a 169/170 Q, 165/170 V on the general GRE. Also, I think I can crack 80% on the subject test, but am not overly confident about this. One glaring hole is that I have done zero research, and have done nothing extracurricular - I literally have nothing "extra" going for me.

My concern is that I've seen the resumes of many people accepted to top universities (PhD track), and I just don't stack up. But if my goal is to become a professor one day, it seems that where I go to school is extremely important. So should I just hope that I can get accepted into a top 30-50 school, or would it be beneficial to consider improving my resume in a solid Masters program so that better schools become available?

And if a masters is a viable option, what caliber of school would I need to excel at in order to be a competitive applicant for a top 10 PhD program?

graduate admissions - Are student records accessible by university officials?

Application forms for graduate school usually contain some vague statements regarding the extents of usage of one's social security number. Some people believe that educational records at other institutes are private information and the universities should have access to the educational records that the applicant would disclose to them ONLY. (Regardless of potential consequences and/or ethical justification for actions of either party.)

My question is, having the applicant's social security number, can schools see which schools/programs the applicant has attended, for how long, and the courses that were taken in the past? If so, is this a common practice? That is, do graduate offices commonly check with social security information to make sure that the records from each previously attended institute is included in the application?

Answer

I believe your question is really about the existence of some sort of central database where all student records can be searched, if one has a key like a Social Security Number (SSN).

I do not believe any such system exists as I have never heard of it and if it did exist, it would likely run afoul of FERPA mentioned in the comments.

Basically, the only way one school would know you were at another school is if you (or someone else) tells them. Having your SSN does allow people to find out information from you but that is mostly from credit reporting agencies. If you borrow money from the school and they report it to the agencies, someone might be able to find out some information that way, but I can't imagine they would find out the program you were in.

human biology - Can one die from pain?

Is it possible that a human or any other creature can die from pain?

I googled and found different answers. Some articles say Yes while others say No.

Answer

I very much doubt it. You may however die from whatever's causing the pain. The reason you feel pain is so you stop doing whatever is causing the pain. Hence someone knows not to touch a hot fire because it is painful. But the pain itself is not actually the danger - it's the fire burning away skin. So pain is actually a good thing, a survival mechanism. So for something that is meant to prevent death it's hard to imagine it doing the opposite.

Perhaps if you were in SO much pain you may be unable to breath and paralysed - but even then I still think you'd go unconscious before that would happen, and you'd start breathing again, etc.

The only other thing I can imagine is having a cardiac event, and the heart stopping. Again, this would be because of stress. Other than that - you may commit suicide on account of insufferable pain, however it's a different situation.

However pain never comes on its own for no reason, just like smoke needs a fire. In this case it's the fire - not the smoke, that will kill you!

People who've ever been in a desperate or life threatening situation like a car accident, have often walked on a broken leg for example - feeling no pain. In this case the body was giving them a chance to escape what might have been a lion, etc.

In short, no - I don't think you can. However I cannot give a 100% correct answer. It would take just one example to prove that however!

evolution - Why do parasites sometimes kill their hosts?

It's bothered me for a while now. I understand why a parasitoid would do this, as it only temporarily requires the host, and that not all parasites kill their hosts.

There seems to be no evolutionary advantage in killing a host, because the parasite relies on the host for resources. Yet some organisms, usually microscopic pathogens, seem to fatally damage the host with no immediate benefit to themselves. Why is this?

I know this is asking for a broad soft answer, but I don't want the question to get bogged down by a specific species, although bonus points for using examples.

Answer

I can think of several (non-exclusive and probably non-exhaustive) hypotheses:

1. 
   

   Maladaptive. It is maladaptive. Maybe because it is a virus coming from another species (e.g. SIV and HIV) or because it is not adapted to our modern lifespan.

   
   


2. 
   

   Benefit of the host immune system to the parasite. Some parasites might benefit from host immune defence (e.g. sneezing helps bacteria to spread) and death is a consequence of the selection for increasing disease symptoms to the host.

   
   


3. 
   
   

   Pathogen's and host's fate. The pathogen's fate is not linked to the host's fate. This is especially true if the pathogens spread well (easily jump from one host to another) I guess or for parasitoïd because the pathogen leaves its parasitic life after the death of its single host.

   
   


4. 
   

   intra- and inter-host selection. Among hosts, there might have a selection for reducing resource consumptions and therefore for decreasing the probability for the host to die. But within a host (among individuals of a parasite population or even among parasite species), it is a prisoner's dilemma (tragedy of the commons). The more you invest in foraging, the more competitive you are. This might not be adaptative at the population level but it is at the individual level. We might think of this prisoner's dilemma happening among individuals of a single parasite species or among several parasite species. You may want to have a look at the work of Martin Nowak on the subject incl. Consider for example his book; Evolutionary Dynamics.

   
   


5. 
   

   Consequence of harming on trade-offs. Harming an individual will cause him not to spend energy into reproduction in order that more energy is available for the pathogen use. Moreover, by causing symptoms, the infected individual will be sexually less attractive and will again have less opportunity to spend energy into reproduction.

   
   


6. 
   

   The pathogen does not mean much harm. When fighting pathogens, many of the symptoms we experience (such as fever typically) are actually caused by the immune system and not the pathogen itself. A maladaptive overreaction of the immune system can cause our death.

   
   
   

The book Why we get sick by Randolph Nesse and George Williams, will probably interest you.

united kingdom - When referring to study at Oxford why is the word "read" used?

When reading about people who have studied at Oxford the word "read" is used instead of study. Example:

"He read Philosophy, Politics and Economics at Oxford"

Why when discussing study at Oxford (and maybe other universities) is the word "read" used?

Answer

This is just a peculiarity of British English that read can have this particular meaning. The New Oxford American Dictionary says:

read
3. chiefly Brit. study (an academic subject) at a university: I'm reading English at Cambridge
[ no obj. ]: he went to Manchester to read for a BA in Economics.

So, it's more about language itself than the official title of the diploma or an academic custom.

---

— Hey, wait, but where does this idea come up to associate “read” with “learn, understand”? Surely there is a reason? And why is it English only?

Well, as it turns out, the meaning of “learn, understand, think, explain” is actually the original meaning of the Old English word from which we inherited read! The Old English word is rædan (“explain”, amongst its meanings), from Proto-Germanic raedanan, from Proto-Indo-European root re(i)- (“to reason, count”).

Now, in many languages, the words derived from this root kept their original meaning. In German, raten means “to advise, counsel”; in Icelandic, ráða means “advise, decide, solve”.

Now, at some point something in Old English went sideways. Wiktionary states very clearly:

The development from “advise, interpret” to “interpret letters, read” is unique to English

Etymonline is more specific:

Transference to “understand the meaning of written symbols” is unique to Old English and (perhaps under English influence) Old Norse raða. Most languages use a word rooted in the idea of "gather up" as their word for "read" (cf. French lire, from Latin legere).

Now, the original meaning of the word read is retained in some contexts in British English, but was lost in other forms of the English language, such as American English.

---

As a summary, the hard question is not really “why can read mean study”, but instead: why did read come to mean “read”?

^{(source for the above: my memory, which is backed by the most excellent Etymonline)}

publications - Why publish a research paper when a blog post or a lecture slide can have more citation count than a journal paper?

I am quite surprised to find that a lecture slide for a course has 133 citations from highly reputable researchers across the world. The main contribution of the lecture slides (which seems to be the reason for the citations) appears in 1 line on 1 page of the slide out of 30 slides. (Citation count according to Google Scholar)

What is the point of even publishing a paper and going through the painstaking process of peer review and editing if you can just write some blog post or a lecture slide on some hot topic and accumulate citation counts (which is crucial for securing funding, etc.)?

chromosome - What are the total number of alleles for a single trait?

Humans receive a copy of gene from both parents and each gene has an alternative form called allele. Does every person possess two genes and four alleles for a single trait?

ethics - Is it ethical to cherry-pick reviewers based on their previous reviews of your manuscript?

The academic review process is usually supposed to be blind, in that authors are not told the identity of the reviewers. But frequently it is possible to guess who has reviewed your work, or the reviewers themselves may let you know informally.

Say my manuscript is rejected from journal A after one very positive and one more critical review, and I think I know who the reviewers were. After some revisions I submit to journal B, who ask me for a suggested list of reviewers. Is it ethical to list the reviewer whom I suspect gave the positive review the first time, but replace the one I suspect has a negative opinion of my work with another reviewer? What if the positive reviewer is someone whom I did not originally suggest to journal A - is it ethical to suggest him/her to journal B in the light of their previous review?

Answer

There are ZERO ethics involved. First, you suspect, but do not know, who the original reviewers were. You may be right, you may be wrong.

Next, suggestions for potential reviewers are just that -- suggestions. It is the responsibility of the editor to pick appropriate reviewers, and your suggestions are just one potential source of information in the process of doing so.

I'd say even if you recommend people who you respect to referee your papers, they'll surprise you regularly with critical reviews (if they're doing their job).

The biggest ethical quandry you can get into in the process of recommending referees is probably some sort of pre-arrangement with those you suggest. This is to be avoided as less than stellar behavior.

writing style - Can cited works hold grammatical positions in sentences?

Though I read this style quite often, I was recently told unambiguously by a reviewer that I was NOT supposed to use citations "as if they are objects in a sentence." The following sentence is an example of what the reviewer considered unacceptable:

We analyzed the data using the Wilmerding method, guided by [12].

The references section might include the following:

[12] Smith, D., Marshawn, J., & Devenshaw, A. 2011. Techniques and Procedures for Applying the Wilmerding Method. Prince Publications, Inc, New York, NY.

The Wilmerding method¹ is not a step-by-step algorithm that can be precisely followed as if by a machine, and thus [12] does not provide a step-by-step algorithmic description but rather guidance for using the method. [12] is a relatively slim but authoritative textbook about how to use the Wilmerding method.

Within this question, for the purpose of discussion, I have intentionally put [12] in grammatical positions where it's an important element of the sentence and the sentence would make less sense without the reference. Sometimes that seems to be the most efficient way to communicate the intended message. Is using a reference as a grammatical sentence element like this OK? Why might this not be considered acceptable? Should I be rewording those sentences? Is it enough of a violation to be worth passing the note on to authors of papers I review?

I considered posting this on EL&U but it seems more specific to academia than general English usage, and the comment came from a content reviewer rather than a copy editor. This question is related but it seems to be more about when to put authors names' in vs. outside of the parentheses in an APA-like style.

The numbered citation style (as opposed to following APA, for example) is required by the venue.

_{1: Fictionalized for the purpose of this discussion}

publications - How are journals evaluated?

How are journals evaluated?

A researcher is evaluated on the basis of his/her publications. If a researcher has good publications in his/her PhD he/she is offered a Post-Doc position and eventually a faculty position.

My question is:

How is a journal judged?How does a faculty search committee evaluate a person's publications based on the journals where one has published?Is it done on the basis of impact factors of journals?

Answer

I feel it may differ from country to country, or even from institution to institution. It may also differ across disciplines. Where I am working, there is what is called journal reputability assessment guideline, which outlines several criteria in assessing journals in which a faculty has published articles. These include the following.

1. Journal impact factor (JIF) - journals with higher JIF are given higher weights.


2. The current volume of the journal - as in JIF, journals with higher volumes currently are assigned higher weights.


3. Indexing - journals indexed in known indexing services are considered more trustworthy and hence are given more weight than journals not indexed in known indexing services.


4. Publisher - though assessment of this criterion is more subjective, journals considered as being published by popular publishers get more weight while those considered as being published by less known publishers are given lesser weights.


5. DOI number - journals assigning digital object identifier (DOI) to their articles are given more weights.


6. ISSN number - if the journal has an ISSN number (though it is less likely that a journal will not have one), it is rated more positively (i.e., it gets higher weight).


7. The composition of the editorial team and editorial policy - this is also subjective; journals considered to have a high profile editorial team/board and standard editorial policy are assigned higher weights than those otherwise.


8. Regularity and continuity of publications - Journals that publish regularly and without interruption between volumes or issues are assessed more positively (i.e., get higher weights) than those with irregularity and discontinuity in publishing.

So, the bottom line is, the criteria may differ and the way the evaluation is accomplished could also be different, but universities have such set of criteria for assessing journals.

Double PhD: is it really worth it?

Is it possible to have a double PhD even if the university you are originally applying for doesn't focus on this category? A double PhD is not the same thing as two PhDs. For example, the medical school at the University of Groningen describes its double PhD program as follows:

A Double Degree (DD) PhD means that you will obtain your PhD degree from two different institutions, i.e. a double diploma, sometimes also referred to as a "dual award". A double degree (two diplomas, each of which issued by a single university) should not be confused with a "joint degree" (one diploma issued by multiple institutions).

I'm applying for a PhD position on a university and it does not have a explicit double PhD program (although I know there are some people on another field that held a double PhD from this same university). However, this double PhD degree would be very helpful to me considering my future plans.

From this, I was wondering: could I receive a double PhD if I find a second advisor from another university? Or the universities need to be associated upfront? In this case, if the university I'm apply on does not have an explicit double PhD program, it is possible (for legal issues of diploma printing) to just associate with another university?

My second question is: for an advisor, what is the advantages of having a part-time student? For last, the thesis needs to be approved for both universities... how this happens? I would have to present for both?

Answer

First, a note for those who are not familiar with the terms. In general, double degree or joint degree are degrees awarded by two different universities within a student mobility agreement. They do not refer to the pursue of two independent degrees, as described in this question.

At the Master's level the tradition of double degrees is well established within the EU, and has been going on for more than twenty years, probably 30, since the establishment of the Erasmus programme. Currently, the major EU programme supporting joint degrees is the Erasmus Mundus. The Erasmus+ guide, p. 109, describes the framework of the Erasmus Mundus Joint Master degree. Of course, individual universities can set up joint degrees outside of this programme, especially when one of the partner universities is outside the EU.

At the PhD level things are much less established. As far as I know, the idea of a double PhD degree has emerged only in the last 3-4 years. Before, it was totally unheard of, at least in my country (Italy). Though students are usually encouraged -- and funded -- to spend a period abroad (typically from 6 months to 1 year), this is done within an agreement between two research groups, and not at the university level (though it should be approved by the PhD programme committee).

Usually, to obtain a double PhD degree a student should follow a shared path between two partnering universities. For instance, the two universities might agree that the student shall spend two consecutive years in one university under the supervision of X, and two other consecutive years in the second university under the supervision of Y; that the coursework should be divided equally between the two universities; that the student should defend their thesis in front of a joint committee (or in front of two committees separately); etc.

Since at the PhD level things are much less established with respect to the Master's, I will answer on the basis of my experience: I have a student who is pursuing a double PhD degree; one who initially asked me to do that; and I know a couple of other students from other advisors who are pursuing it.

None of the universities I know of have an explicit double-degree programme for PhDs. In fact, the double degree is usually proposed by a student who thinks, in this way, to strengthen their PhD or to facilitate the immigration in another country. This means that the double degree should be set up on a case-by-case basis, which usually brings about a bureaucratic nightmare, especially for the PhD schools and the advisors. This nightmare comes from the fact that different countries, even within the same region (e.g., EU), have different requirements for what concerns programme duration, funding, coursework, publications and assessment, and finding an agreement is quite complicated.

For instance, if the PhD in one country has a duration of 3 years, and it is funded for that period, who is going to pay for an additional year in a country where the "standard" PhD duration is of 4 years? If there is an ongoing collaboration between two groups it might not be that difficult to find the money, but it could be almost impossible to set up such an agreement out of the box.

As I said, in my experience, the double degree is usually proposed by a student who thinks to strengthen their PhD. I strongly disagree with this premise, and I usually discourage my students from such an idea. A double degree is not stronger than a single one done working hard and with a good publication record. Then, whether it can facilitate or not immigration to another country is questionable: I don't think that, to date, there is sufficient statistics to know this.

As for your last questions:

for an advisor, what is the advantages of having a part-time student?

There is an advantage if there is a collaboration between two groups, otherwise there is really no advantage.

For last, the thesis needs to be approved for both universities... how this happens? I would have to present for both?

These details are really decided on a case-by-case basis, and sometimes the outcome depends on whether one university wants to appear stronger than the other and impose its criteria.

graduate school - Problems in coping with my PhD Supervisors

I'm a PhD student at a reputable institute in my country. I joined the group of a supervisor who is good at experimental and not so good in analytical front. I also have a co-supervisor who's good at analytics and numerical stuff. Neither know my research problem well.

Initially I had lot of difficulties in understanding the problem. I was a little slow in understanding the analytics. They told me to do lots of stuff here and there. All of them failed. Now I'm in my third year, supervisors are asking me "Are you really interested in your problem, or do you want to leave the course?".

Leaving course mid-way does not make sense for me. But without getting much help from supervisors and working on my own is manageable. Sometimes I get mentally disturbed by their attitude. How do I cope with these supervisors who talk so crazily and seriously at this point of time?

Answer

It would be interesting to know what is the subject or area of your research project. After 3 years, there has had to have been a passion to carry out the goals. Follow your dreams. You could be on to something that will help humankind so really take a bit of a breather and handle any doubts of your own. Visualize the future for a moment by seeing a DONE goal that you would enjoy with the same passion moving forward and having a team with you to help out. Sometimes debugging a project can be like watching grass grow. Find things similar to your dream and make a list of successful actions and put those back in and knock off trying to cope. A new strategy and approach to the supervisors will help rekindle their enthusiasm for you as it was in the beginning. Take the project back to where you were doing well. What happened just after... that is all that needs an adjustment.

evolution - Do the claims in this paper have any degree of validity?

The paper The waiting time problem in a model hominin population talks about a problem of waiting time, etc. Is the methodology of this numerical simulation, and the conclusion right or is it wrong?

(A quick search reveals that the first author is an intelligent design advocate and apparently believes or believed that the earth is less than 10,000 years old)

species identification - What is this insect from Brasil?

SE Brazil Atlantic rainforest Oct 2017. I'm assuming this is an early stage of an insect. It was crawling around a tree in the moss and was about 6-7mm.

Answer

This is, indeed, a nymph (what you called a young stage), but not from a cicada as you suspected: it's a nymph from a leafhopper, which are hemipterans from the Family Cicadellidae (cicadas are also hemipterans, but they belong to the Family Cicadidae). More specifically, this seems to be a sharpshooter, which are leafhoppers from the Tribe Proconiini.

Narrowing down to the Genus is more complicated, but I'd guess it is Oncometopia. Here is an image of Oncometopia orbona for comparison:

This other image (also Oncometopia orbona) is even more similar to yours:

interview - Is it fine to ask who are the search committee?

I saw that some friends know who are the search committee members before their interviews. So would it be fine to ask the department who are they? And if it was fine, why the department didn't mention their names since the beginning? Could asking about their names be taken as negative thing?! A strong applicant could say that she doesn't care who are finalizing the list or interviewing her.

Answer

In general, I would recommend against asking who the search committee is. It might give the impression that you are trying to "game the system" rather than simply put your best foot forward for everyone. That said, I don't think this is a serious faux pas.

Some departments, including my own, post a list of committee assignments on their department homepages -- mostly out of convenience for their own faculty. So you might be able to answer your question without asking.

Should I write IEEE membership in my CV?

Does it worth to add IEEE membership to my CV? It seems every body can pay a fee and become an IEEE member.

publications - How to deal with low quality software project that needs to be evaluated

I have evaluated a software project which has been created by a consortium of top scientists in the field. However, the project itself it doesn't really work, and has only been developed as a proof-of-concept rather than an end product (i.e., it works only with 2-3 scenarios).

This software application should perform 4 steps in order to successfully execute. Each step takes an input file, and produces an output file. The output file from the previous step is used as input in the current step. Initially, you start with 1 file. This file is used as input for step 1. After step 1, another file is produced. Let’s call the input file general_input_file, and the output file general_output_file. When general_input_file is loaded into the application, general_output_file should be produced. Now, I have an input file which I will call my_input_file. I expect the application to produce my_output_file. However, the application only accepts specific_input_file and will produce a specific_output_file. This means that it only works with 2 files which has been previously generated. Both files exist in the project. When I look at the part of the project which should process the general_input_file, there is a statement which looks like this: if the name of the given input file equals specific_input_file, then return specific_output_file. This is a file inside the project. Otherwise, try to process the generate_input_file and generate general_output_file. At this point the software breaks. A number of exceptions are thrown, and debugging and fixing this is beyond of the work that I’m doing.

The question is: in the paper, how do you approach this issue? And how do you argue, in the paper, that the reason you're unable to evaluate the software in a different scenario is due to the limitations of the software? What is the best wording to be used, without being offensive to the authors?

teaching - Dangers of allowing students to resubmit assignments

There are two closely related questions here:

1. 
   

   If a student submits their assignment and is unhappy with their mark, are there any dangers (which I might not be seeing) in allowing the students to do so? If I would offer for one, I would offer for all, but should I be offering it in the first place?

   
   


2. 
   
   

   If resubmits are unavailable, some students ask me to 'pre-read' or 'pre-mark' their assignment. The end result is that when they submit officially, that may actually be the second submission. Clearly doing any 'pre-marking' or the like takes time and energy and, so far, very few students have taken advantage of this until right before the submission deadline (at which point I stop because I don't have THAT much time to offer them). Are there dangers in 'pre-marking' assignments?

   
   

Note: These assignments constitute either 50% or 100% of their total mark.

One of my concerns is that the student would have lower motivation to maximize the quality of their original work and just correct what was marked as a problem area - like a production worker depending on a Quality Control Inspector and not paying as much attention to the quality of their work the first time around. Are there other issues as well?

EDIT: I should add that these are business management subjects so student answers are not easily right or wrong but more about how they justify their analysis. Therefore, there is not an issue of "giving the right answer."

Answer

Should I be offering it in the first place?

Dangers:

1. You spend even more time on assignments, limiting your time for other endeavors.


2. Students might get into a "grade grubbing" mode where they simply re-submit marginally better answers in order to improve their grade.


3. Students do a poor job initially because they know they will have a chance to re-submit, and they might as well take their chances that you'll give them decent marks for inferior work.

Benefits:

1. Overall, students spend more time on the assignments, leading to better knowledge and ability to do the work.


2. You can provide helpful information to guide them to better answers (because you're seeing first-attempts). This level of grading also takes more time.



3. Students are happier because the stress of a hard deadline isn't so bad.

I think the benefits outweigh the dangers if you're willing to put in the extra time to re-grade. As I've said in other threads, I've used auto-grading homework for a some classes (probably not relevant in your case), but I've used the strategy that I'd have deadlines for all the assignments but that the week before the final I'd re-open all the assignments and tell the students they can re-do any questions they missed. I don't tell them I'm going to do this until I do it, in order to keep students from simply waiting until the end to do all the assignments.

Are there dangers in 'pre-marking' assignments

I think it's great that you're being creative with the assignments (e.g., pre-marking, resubmittals, etc.). Again, it comes down to your time -- if you have motivated students who want pre-marking and you have the time, I can't see a problem with it. It wouldn't surprise me if the best students are the ones who want pre-marked work, but then again I've had some less-capable students jump at chances like that to do better.