publications - Can I publish a review article if I only have a Master degree?

I read many articles about specific area and I feel like I can write a review article. So, is that ok if I only have a Master degree? can some journals accept that? (I will be the sole author)

europe - European style PhD in the US

1. 
   

   I'm wondering are there any PhD programs (specifically in machine learning) in the US that are structured more like the European ones, i.e. where you immediately start doing research and don't spend your first two years or so on something very similar to Masters' program (lots of coursework, less research). I have already a Master's degree and research experience and would like to start working on my thesis from the start.

   
   



2. 
   

   Also I'm wondering are there any non-university research institutions in the US that grant PhDs? (For example, something like German Max Planck research institutes)

   
   

Thank you!

Answer

Many graduate programs in the US allow you to either waive coursework by claiming prior credits, or waive coursework by taking a series of examinations. If that's a primary concern, you should look into programs that offer such a format for what's usually called the "breadth" or "comprehensive" requirement.

In answer to your second question, the Toyota Technical Institute in Chicago is a non-university research institute that offers a Ph.D program in Machine Learning.

publications - What to do when principal investigator publishes your work without putting you down as a coauthor?

Say I am post-doc in the USA, and my PI (principal investigator) just published a review I wrote, with pictures I took of my experiments without putting my name as the author. What tools do I have at my disposal to get what is rightfully mine?

human biology - Why is the opposite of plantar flexion called "dorsiflexion"?

Why is the action of flexing the foot so that the toes move anteriorly/superiorly (i.e. in the direction opposite that which they move during plantar flexion) described as "dorsiflexion?" In the same vein, why is the top surface of the foot called the "dorsal surface?"

If anything, the action opposite to plantar flexion moves the foot in the ventral direction, doesn't it? And surely if you've ever seen a human in the anatomical position, you can see that there's nothing dorsal about the top surface of the foot - it's superior, perhaps, but by no means dorsal.

Answer

Anatomical terms must be able to fit a wide variety of organisms, from insects to fish, dogs, horses, chimpanzees to humans. That's why the terms are sometimes confusing to people who are thinking only of bipedal humans.

In anatomy, the dorsum is the upper side of animals that typically run fly, swim or crawl in a horizontal position. In vertebrates the dorsum contains the backbone. In such an animal the "ground side" is the ventrum.

Due to varied orientation on quadrupedal mammals (where the term is more appropriately used) the "back"-side of the hand, the "top"-side of the foot and the upper surface of the tongue are referred to by the term dorsum.

Does this picture help? Note the dorsal surfaces of the body, muzzle, feet.

In anatomy, the sole of the foot is called the plantar surface. The top of the foot is called the dorsum of the foot. (Imagine us walking on all fours like apes.) Therefore when you extend your foot, it's called plantar flexion; when you flex your foot upwards towards your head, it's called dorsiflexion.

Similarly, the arteries feeding the bottom of your foot form the plantar arch. Those feeding the top are the dorsal artery (or the dorsalis pedis).

Because anatomy must describe other animals than ourselves with other orientations, it must be consistent. In a quadruped, the dorsum of the tongue and the feet do actually point to it's "back" surface. See the picture below:

Lynxes have big paws, so it's more obvious that the surface facing the backbone is appropriately called the dorsum of the paw/foot. This picture is particularly interesting because it shows three degrees of dorsiflexion and one paw in full plantar flexion.

In humans, the "back" is actually the posterior surface, because we are not primarily in a horizontal orientation. The ventral surface is called "anterior". Thus we speak of the anterior chest wall and the posterior chest wall, not the dorsal and ventral surfaces, although those designations would still be entirely correct.

How does rate of evolution/innovation scale with population size?

I understand that there will be many other factors that affect rate of evolution/innovation. However, other things being equal, how will the rate of evolution vary between two populations of different sizes? Does doubling the population size double the rate of introduction of new traits?

Is this answerable for evolving life in general, or do different forms of life have different scaling laws? For example, is it different for sexual and asexual life?

cell biology - Was the mitochondrion or chloroplast first?

I still don't know if the mitochondrion or chloroplast was first? I've looked for it on the internet and in various books but haven't found anything. Does anyone have the answer and a theory which backs up this answer?

Answer

Mitochondria evolved before chloroplasts.

We know this because Mitochondria form a monophyletic group: e.g. all life with mitochondria traces back to a single common ancestor (source). Since the group with chloroplasts groups within this clade, it must be the case that either (a) chloroplasts were obtained by an organism that already had mitochondria or (b) chloroplasts were independently lost by multiple lineages within the Eukaryotic clade and then many of these lineages re-acquired chloroplasts by secondary endosymbiosis. Since (a) is a (much) more parsimonious explanation it is the one it makes sense to accept.

phd - Can a supervisor extend the paper and change the order of authors?

Background: In my area, people extend their conference paper to a journal version by adding only 30% contribution. This means that you get a second paper, with the same content (introduction, related works, motivation, etc). Secondly, the order of authors matter in my area.

Story: I published a conference paper, which is one of major contributions to my PhD, and I planned to prepare an extension of that paper to be submitted to a journal. However, I postpone the extension, as I was busy with my other projects (also related to my PhD). Recently, my supervisor has secretly given the (almost) extended paper to another person to do the extension and has submitted it with a different order of names.

My supervisor and the person who extended the paper did not tell me anything about it and kept everything secret, until the last minute of submission. Although my supervisor knew that I had planned to do the extension, he ignored all my previous efforts. He even sent my already extended version to this person. However, I should acknowledge that both of them had minor contributions to the initial paper, but I am not sure if that gives them the right to extend it.

The question is whether my supervisor had the right to do so? He knew that I have planned to do the extension (as I had already extended some parts of it --I added 4-5 pages of a proof of a theorem and extended experiments).

Answer

If the paper was submitted without your knowledge and agreement, this is a serious problem. All co-authors are supposed to know about and approve a paper that they are listed on before it is submitted. This would be an ethical breach by your supervisor. I would at least raise it as a concern with them. This is something that you could potentially raise with others, as well, such as someone else at your instutation, or even the journal. Consider the consequences before you do anything, though: it's likely to have a major impact on your relationship with your supervisor, and therefore your PhD studies.

Beyond that, the situation is much more of a gray area. Clearly the way things were handled, particularly the lack of communication with you, was not optimal. But it's not so clear that it was "wrong" beyond that.

• The PI directs the research of the group and has the authority to decide that someone else will now take the lead on a collaborative project.


• It is a judgment call who should be first author. If the other researcher made a significant contribution and put together the draft of this paper, they may have a legitimate case to be first author. At least, it may be ambiguous enough that it would be hard to challenge. Also, someone might feel that the first author on this paper should be the one who did the most on the revision/extension rather than the one who did the most overall. After all, you already got first author recognition for the primary piece of work on the conference paper. In a series of related papers that build on each other, who did the most recent work may be considered most relevant to authorship position.

Don't be too quick to assume intent. Your talk of the supervisor keeping things "secret" implies intent to sneakily do this behind your back. I wouldn't necessarily assume that.

Perhaps your advisor is just poor at communication/management, and this was an oversight. This is quite common; many professors are not good at managing a group of people. Even submitting the paper without your knowledge may be an oversight (it shouldn't happen, but it does happen).

The advisor might even think they are doing you a favor by taking some work off your shoulders and getting something done that has been delayed.

Talk to them and make them aware of your concerns and see if you can arrive at a constructive solution. It may be too late to undo what is happening here, but hopefully you can agree on a better way of working in the future.

If, after attempting to discuss this, you feel that your supervisor is acting in bad faith, you may want to escalate the situation. But only do this as a last resort.

genetics - How much of my ancestry will match with my brother?

Recently, my brother (full sibling) got his ancestry checked from MyHeritageDNA. They have a similar service like 23 and me and I've found out that both companies are offering the basic service almost the same, with some add-ons which are different.

My question is that if I (I'm a male) send my DNA sample to either organization, how different should I expect the results to be?

human biology - What causes the development of antibiotic-resistant strains of bacteria?

I understand bacteria have become resistant to antibiotics due to selection pressures, but how do resistant bacteria process antibiotics when exposed to it, compared to non-resistant bacteria. Also, what research is being conducted to combat bacteria resistant to antibiotics?

Answer

Bacteria usually gain resistance mechanisms through horizontal gene transfer (such as conjugation and phage infection). The four main mechanisms in which bacteria elude antibiotics are:

1. Drug Inactivation: For example, E. coli can produce beta-lactamase that inactivate many lactam based antibiotics such as penicillin.


2. Alteration of Target Site: Mutations in genes encoding for target sites can reduce drug binding affinity. Example: Random mutations in DNA gyrase and topoisomerase IV reduces binding affinity to fluoroquinolone.


3. Alteration of Metabolic Pathways: Many drugs target certain parts of metabolic pathways by inactivating enzymes or sequestering substrates. Bacteria can use alternative metabolic pathways or find ways to uptake the necessary nutrients from the environment.


4. Reduced drug accumulation: Caused by reduced drug permeability or the ability of the bacteria to transport drugs out of the cell (for example, tetA encodes for a tetracycline efflux transporter). They can gain these abilities through conjugation, phage infection (transduction), or uptake of environmental DNA (transformation).

Wikipedia has a pretty extensive and comprehensive article on antibiotic resistance. There's also a good list of references. http://en.wikipedia.org/wiki/Antibiotic_resistance

Why does arxiv.org not assign DOIs?

I know that arXiv have their own identifier system, but considering how widely adopted DOI is, why do they not use DOI perhaps as a supplement to their own identifier?

job search - How to make leaving a PhD program seem like a positive thing on a resume

I have a feeling this question has been posted before, but I wanted to ask as my situation is slightly different. I've recently decided to leave my PhD program in the social sciences in order to look for work. I've basically come to the conclusion after completing 3 full years, courses, and fieldwork that I don't want to be an academic but would rather put my skills to use with NGOs, non-profits, or the public sector. In many ways, the last hurdle of the PhD (i.e. writing the dissertation) seemed more like a barrier to what I wanted to do, rather than something that would bring me closer to it. I left because I wanted to go in a new direction, not because I wasn't sure that I was capable of finishing.

Anyways, my main concern right now is how to present this discrepancy on my resume. As I've been a TA and doing research projects since getting my MA, I've decided to list my years as a TA, and the rest under the position of "Researcher." I figure that the situation is a little too complex to really explain in a resume or cover letter, and that most employers will be able to read between the lines that I was probably in a PhD program. I've basically been marketing myself on my resumes/cover letters as a "researcher" with lots of research projects under my belt, without specifically stating under the "education" section that I have a partially finished PhD. My motivation behind the "researcher" title is that during my graduate studies I designed, proposed and carried out individual research on a number of projects.

I guess I should qualify this by mentioning that my PhD studies were in the social sciences, and there seems to be a bit more leeway in terms of describing what we do. All of my dissertation research was funded by a fellowship, and all of my various other research projects (where I wasn't principal investigator) were the result of competitions funded by grants. I have always designed my own research projects, which is why I didn't think it was a bad idea to go with "researcher", and my references could verify that.

It looks like this title would be a little confusing given the circumstances, so I think I'm going to use "Graduate Student Researcher", "PhD Researcher" or something similar in the future. I guess this seems like it gives a more accurate representation of what kinds of things I was doing. I figure that the 4 years of MA/PhD work on research projects gives me (and any other former graduate student) skills that are valid to most employers. I just want to be able to address this discrepancy honestly and enthusiastically in an interview, rather than clumsily addressing it in a cover letter/resume. What do you guys think? Is this the right strategy to take?

digestive system - What is an simple way to burn glucose for visible effect?

I want to make a partially working model of the digestive system that could digest complex carbohydrates. My ultimate goal is to be able to cut up some bread, put it into the model, operate it, and eventually see some effect equivelent to glucose being used in a muscle. I obviously have a very limited buget. How could I simulate glucose being burned in some way that has a visible effect?

Edit: I'm specifically looking for some way glucose can be used to achieve some visible effect that makes sense as a metaphor for combustion, without dangerous/expensive chemicals.

phd - From whom do I get references when my original advisor leaves academia?

This is similar to a previously asked question, but deals specifically with addressing the problem on the CV. My adviser had a bit of a personal meltdown and left the department while I was finishing analysis of field data/writing up. His students were assigned the following year to a non-tenured professor. This new professor was of little help to me my last year of writing up, sat on my dissertation with no comments for over 6 months and only produced comments after I went to the departmental chair. He did not think much of the type work I was doing and went so far as to say so during my defense. I will add here that I have a number of publications (>5) including single authored ones-which for my field is significant- as well as an excellent track record of funding and in presenting my research. I have a strong CV but have had no success thus far in securing a job. I once saw one of the letters he had written for me (it needed to be included in a single PDF so he had to send it to me) and it was terrible. It talked mostly about him and how he really did not know me well and with a few generic sounding "he will no doubt exceed" sentences that just sounded fake. Months later a colleague suggested that I find a different reference than my adviser (but was not clear as to why).

So, my question is this: since committees will no doubt look at my list of referees and wonder at my lack of an adviser-I have taken to including a short "note" in the "reference contact information" section explaining that 1) my original adviser left academia at the end of my time as a student and 2) that my new adviser was up for tenure the year I defended and very busy and was in a different field than mine, so instead "below are three people who are in a better position to judge me on my research, teaching, writing skills".

Is this providing too much information or is this instead ensuring that rather than questioning and then rejecting my application the committees will stop and think "oh okay, I can see why the applicant did not include their adviser"?

citations - Should one cite during university exams?

As the title suggests, it's not a usual practice but should one do it? All I know that one can study for an exam and simply write the answers needed in order to succeed, no one tells us to include the names of authors of the ideas we memorized to write (except rarely).

graduate admissions - Ways to spend gap year/semester before applying to mathematics PhD

I was just reading in the answers to some other questions (here and here) that it's not necessarily disadvantageous (and it may even be advantageous) to take a year or semester off after finishing my bachelor's degree before applying to math PhD programs, but I'm not really sure what to do during that year. If the below section is too long, the TL;DR version is: What are my options?

I honestly hadn't looked into any other options since I was planning on going straight to math PhD programs after I earn my Bachelor's degree in May of 2016, but this fall while I was dealing with some personal issues I ended up dropping one of the two graduate math classes I was enrolled in and I missed the September GRE math subject test (as well as the deadline for the October subject test).

While I'm planning this spring to take the GRE math subject test (for real this time) and enroll in another one or two graduate math classes, it's looking like I might have a better chance at PhD program admissions if I wait to apply for admission in the Spring or Fall of 2017, rather than the Fall of 2016. I might apply to a couple of PhD programs for Fall 2016 admission, but I don't want to spend a lot of money on application fees when my application isn't as strong as it could be.

If I do end up taking a semester or a full year off, I want to figure out something productive to do so that the time won't be wasted. I came up with a few options: applying to PhD programs abroad that don't require the GRE (I speak English and Russian, so Canada, England, and Russia), applying to less competitive US PhD programs, or working a full- or part-time job (teaching? computer science?) and using that money to pay for simultaneously taking one or two graduate math classes.

However, I'm not sure if it's kosher to apply for a PhD program if I only plan on staying for a semester or a year. On the other hand, I don't know how feasible it is to both work and take graduate math classes, so I'm pretty uncertain about what to do. Does anyone have advice about the options I have?

Answer

Options I can think of (I bet there are even more than these):

• 
  

  Take some upper level undergrad, or first-year grad, math classes as an unmatriculated student

  
  


• 
  
  

  Audit some classes (this saves you some money -- you don't get credit, but you learn the material)

  
  


• 
  

  Apply for a master's, in a program that doesn't require a math GRE (for example, with some quick googling, I found a good program in statistics that doesn't require the math GRE)

  
  


• 
  

  Take or audit some non-math classes that you find interesting

  
  


• 
  

  Become a K-12 substitute teacher (this only requires a Bachelor's degree)

  
  
  


• 
  

  Be a Vista volunteer

  
  


• 
  

  Get a job and build up a bit of savings, to make it easier to get through grad school on a TA stipend

  
  


• 
  

  Study abroad for a year but not as part of a PhD program for the reasons you mentioned

  
  

Note, if you are working full time, I find that one challenging class at a time is enough. If you are working 20 hours a week, depending on the type of job, maybe two challenging classes would work comfortably. I remember taking data structures and linear algebra at the same time while I was working a 40-hour week, and I went a little nuts. In retrospect, it would have been better to negotiate a reduced number of hours at work.

databases - Do all versions of an arXiv paper appear in Google Scholar?

I know that new arXiv papers usually appear in Google Scholar within a few days or weeks. My question is: if someone submits a replacement of his/her arXiv paper, does the new version of the paper also appear in Google Scholar?

Answer

Remember that the way the arxiv works, the default paper identifier goes to the most recent version that's been uploaded. So even if Google Scholar caches an older version, it's using the same URL. Now if you make changes like changing the title and/or material parts of the abstract, then it might take a while for the new title to percolate through the search indices.

publications - What should I do if I found a citation error in a published paper?

I've found a mistake in a published paper, and am unsure what to do now.

I was looking at all cited articles from a paper over 10 years old, and found one that is citing the paper in error.

A variant of a certain protein and a fusion protein made of 2 proteins have been confused, that is the citation points to a paper on a protein which shares an abbreviation but is entirely different - this is a pretty big mistake and suggests they haven't actually read the paper they referenced!

The Elsevier journal published this in 2013 and I don't know how to report it, or what the etiquette is here. I can't see contacting the authors to be of much use as it is already printed, and they could very easily delete my email and forget about the error, whereas an editor or some such person would surely be able to take reasonable steps to address it.

For the record I'm an undergrad and have no professional link/competition/other conflict of interest with this researcher or department!

Answer

Small errors that do not affect the results or conclusions of the paper are normally handled through publication of a correction (or erratum). This is handled by the journal editor, who will be in contact with the authors for confirmation that they agree as to it being an error, and provide for the exact correction to be published.

The journal that published paper should have a policy on corrections, check it out! Physical Review Letters’s editorial policies and practices state, for example:

Errata.— The Errata section contains notices regarding errors or omissions in papers previously published. Besides the standard Erratum, several special categories of documents may appear in this section. In the online journal, each of these documents involve bidirectional links between the original article and the document in the Errata section. The category of the corrective document is indicated in its title and in the link from the original article.

The standard Erratum is a statement by the authors of the original paper that briefly describes the correction(s) and, where appropriate, any effects on the conclusions of the paper.

Thus, what you should do is:

1. Make double sure it is actually an error.


2. Then ask someone else to double check it again. Preferably someone more senior, i.e. with some experience of academic publication.


3. 
   

   Write to the corresponding author, pointing out the error. Be nice, and make real sure not to assume to worst.

   
   

   You say “this is a pretty big mistake and suggests they haven't actually read the paper they referenced”: depending on context, it could actually be something minor like a copy-paste mistake (pasting the wrong reference, when they meant another paper)

   
   
   


4. 
   

   If you do not obtain a response, or they respond but don't intend to correct the error, then consider contacting the editor.

   
   

I can understand why, as an undergrad, you would consider contacting the editor directly without writing to the authors first. However, as long as you remain professional in your correspondence with them, I think it's best to contact the authors first. It's more polite, and they may actually be able to provide you with some explanation you haven't thought of. Contacting the editor before the authors is somewhat overdoing it…

Are there people who have done so much work before PhD that they get a PhD automatically?

This question addresses why it's a bad idea to try to do a lot of independent work before PhD in the hope of finishing PhD quickly.

Nevertheless, are there famous examples of people who have done so much work before PhD that they get a PhD pretty much automatically (say, 1-2 years or less)?

Answer

The closest example I can think of is Mihai Pătraşcu. After publishing several extremely strong results as an undergraduate, Mihai earned an MS in one year and then a PhD in one year, all in computer science at MIT.

Accessing a "forgotten" Google scholar account

I have a Google scholar account A which is linked to my Google account and it all works well. But there is also another copy of me, a Google scholar account B, which says that it has a "verified email" (which is my university email). Apparently, I must have confirmed it some time in the past.

How do I access account B? I cannot access it through my Google account, which just takes me to account A. Is there some way to make it send an email to my university address that will let me access it?

Answer

I have found an answer: think hard about whether there are other Google accounts that I might have and through which I could have authorized the Scholar account.

In my case, there is a long forgotten "temporary" Google account which was created for me by Goolge during that period when they decided to merge all of its services under the Goolge+ umbrella.

graduate admissions - My advisor refuses to write me a recommendation for my PhD application unless I apply to his lab

I got my master’s degree in China and had worked for two years as a visiting student in the US. Although my master thesis’s supervisor promised to write me a recommendation letter, my visiting student advisor refused. He is the corresponding author of all my publications. What's more, research experience in his lab was included in my personal statement. He said he would offer me a recommendation letter only if I apply for his lab. When I asked whether he could recommend me for other universities, he did not reply to my email. Is there any possibility that I get an offer without his reference letter? How should I explain this to an admission committee?

graduate admissions - Discussing diversity and underrepresented groups in personal history statement for PhD application

I am applying for a PhD program in US. The university has asked to address the following in personal history statement:

How your perspectives or activities contribute to social or cultural diversity and/or make you sensitive to the experiences of underrepresented groups

Honestly, the statement does not make sense. What is social or cultural diversity? Why it is important? Who are exactly underrepresented groups? What is experiences of underrepresented groups? I would be grateful if someone help me to understand this statement and give some examples about it. Many thanks.

conference - Submitting Workshop Proposal by A first Year PhD student

I am interested in submitting a workshop proposal for a top-tier conference related to my topic. I don't know whether this could be a good idea but this year I co-organized a workshop in a top-tier conference. I handled the speaker, funding and I really enjoyed although it was for women who made a contribution in the field .

I had quite good relations with some professors. However, I don't know whether asking them that I want to submit a workshop proposal is an acceptable idea. Of course, I am doing my research and trying to come up with a paper, but I want to lead a workshop in the field since it still emerging.

Another problem, my ex-supervisor who is bully still got recognition. I found that he is going to be a chair at the conference for a specific category and cannot hide anymore and have to face him anyway.

The question is: Is it a good idea to submit a workshop proposal by a first-year Ph.D. student?

P.S.I had two years of experience in this emerging field and I have been invited for a talk the last month and feedback was positive by professor attended the workshop.

zoology - Insect identification - Is this a bedbug?

This bug was found on a couch in Cape Girardeau, Missouri. The couch, and the two beds in the room show no signs of other bugs. Is this a bed bug that I should worry about or something harmless? It was slightly larger than a common tick.

Answer

Unfortunately, you're the first I've seen on here actually to have a bed bug.

See this picture from University of Kentucky for comparison:

Here is one moving (more footage & info here):

Below is a picture from Bed-Bugs-Handbook.com demonstrating the relative size and appearance of 6 different life (molt) stages:

• From Left to Right: Nymphs to adults both before (top row) and after (bottom row) feeding and becoming engorged with blood.

General Info:

Bed bugs are parasitic insects of the cimicid family that feed exclusively on blood. Cimex lectularius (or the common bed bug) is the most well known species as it is the one that feeds primarilly on human hosts and infests human dwellings. These insects often dwell in beds, couches or other upholstered furniture, and they are also known to live in cracks and crevices in walls, behind wallpaper and wood paneling, or under carpeting (Krueger 2000).

They usually feed nocturnally, and in the absence of allergic rashes from their bites, their presence can go unnoticed. The first signs of a bed bug infestation are often the bed bugs themselves or small dark stains bed bugs can leave behind.

• See this EPA page for more information about locating bed bugs in a potential infestation.

Description

From University of Florida:

The adult bed bug is a broadly flattened, ovoid insect with greatly reduced wings (Schuh and Slater 1995). The leathery, reduced fore wings (hemelytra) are broader than they are long, with a somewhat rectangular appearance. The sides of the pronotum are covered with short, stiff hairs (Furman and Catts 1970). Before feeding, bed bugs are usually brown in color and range from 6 to 9.5 mm in length. After feeding, the body is swollen and red in color (USDA 1976).

Do you have a problem?

From Wikipedia:

Certain signs and symptoms suggest the presence of bed bugs; finding the adult insects confirms the diagnosis.

However, other than being a nuisance (e.g., having a "gross" factor + some skin conditions such as rashes), bed bugs have not been known to transmit dangerous human diseases (e.g., see Dolling 1991 and Kolb et al. 2009)

What to do:

Below, are a number of reputable and useful resources for handling and ridding yourself of bed bug infestations:

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Finally, a quick search for "bed bug" on this site as well as visiting this reddit page can provide info for a myriad of species that are often mistaken to be bed bugs (e.g., carpet beetle larvae, psocids, ticks, etc.). Again, unfortunately, you're the (un)lucky winner and do in fact have a definitive specimen.

---

Citations:

• 
  

  Dolling W.R. 1991. The Hemiptera. Oxford University Press, New York, New York.

  
  


• 
  

  Kolb, Adam, Glen R. Needham, Kimberly M. Neyman, & Whitney A. High. (2009). "Bedbugs". Dermatologic Therapy. 22 (4): 347–52. doi:10.1111/j.1529-8019.2009.01246.x. PMID 19580578.

  
  


• 
  

  Krueger L. 2000. Don't get bitten by the resurgence of bed bugs. Pest Control 68: 58-64.

  
  

graduate admissions - What is the difference between the promoter and the advisor?

I am applying for a Ph.D. position at Netherlands and I see that there will be a promoter and an advisor. I have never seen such a title as "promoter". What is the difference between the two titles?

Answer

As far as I understand, in the Netherlands, only full professors may be appointed "promoter", i.e. the official advisor, the super-boss if you will. Other faculty members must apparently get authorization from the university (see comment).

So if you are going to be supervised by someone who is not full professor (e.g. associate/assistant professor), that person will be appointed as "(co)advisor", while a full professor will be acting as an official advisor/promoter and will chair the doctoral examination committee.

evolution - What is the advantage of the inverted image on the retina?

Recently, I learned that the image of the world which we see actually reaches the retina inverted. This is due to the fact that the retina lies behind the focus of our eyes.

I have two questions:

1. 
   

   When the retina lies behind the focus and the lens in our eyes has a spherical shape, shouldn't left and right also be interchanged?

   
   


2. 
   

   What is the advantage of this? Why does the retina lie behind the focus and not in front of it? Or doesn’t it matter since our brain is not a real screen and it’s only a question of the correct interpretation of the electic signals?

   
   

citations - Is it appropriate to cite a paper in a language I don't understand?

Some months back I got into a situation where a paper with information that I considered important to prove a point was in a language I cannot understand. Since it was important but not crucial, I ended up not using the paper. Except for its abstract, which was in English, the entire paper was in this other language. It had graphs and images that I could understand without knowing the language.

At the time, I was tempted to use Google Translate in order to get the general idea of the paper (in more detail than what is given in the abstract), while not necessarily trusting on the specific information that the translation gave me (it can give faulty results at times). Since this would still leave me with some measure of uncertainty — there was no way for me to be sure exactly what it was saying — I thought it better to just let the paper go.

But say that in a future situation I find a crucial paper in a language I don't understand: if I use Google Translate, using the paper in a situation that does not require specific information but only it's general gist, would citing it be ethically acceptable?

(It's almost the same situation as this question, but I'm not concerned with translating the entire paper, for this would take time/resources that I simply don't have access to.)

Answer

I think the fact that the paper is in a language you don't understand is somewhat of a red herring. Sure, it will affect the specific steps you'd take to try to understand the paper, but the ethics of "to cite, or not to cite" it is no different from a paper you don't understand written in a language you speak. You're generally supposed to provide a good-faith overview of the literature, with citations as appropriate. The fact that one paper is significantly harder to understand doesn't really change that.

My view is that it behooves you to, as far as possible*, and regardless of language, at least understand at a high level what the full papers you cite contain, and the parts of papers you use on a detailed level. Google Translate will be good enough in some cases, but for other cases it's better used as a starting point. If you find yourself doubting the machine translation it's certainly best to use it as a starting point. You might want to try to clarify uncertain points with the authors, ask a colleague (who might speak the language) for help, get a professional translation of parts of the paper, or use a secondary citation.

*In some fields they even study ancient languages to understand original texts. That might be overkill...

publications - Paper rejected. Should I appeal against biased reviews?

I received a rejection letter from a relatively high-impact journal based on the feedback from three reviewers. After I reviewed their comments, I feared that their comments were biased and am not sure if I should appeal. The comments from all three reviewers are all negative, but one is more bias than the other.

The first reviewer say that I need to carry out a lot more experiments that will involve a lot of cost, which is not practical. However, in the comment, s/he only suggests one additional experiment that need to be done. The second reviewer complains about the quality of the figures, but I think they are fixable. The third reviewer complains about the novelty of the paper but I think s/he did not carefully read and understand the paper.

Is it still possible to write an appeal if all three reviewers were negative about the paper since their reason to support rejection wasn't strong?

pharmacology - Why does Penicillin only affect bacterial cell walls

I was quite fascinated by the feature Should Science Pull the Trigger on Antiviral Drugs—That Can Blast the Common Cold? in this month's Wired magazine.

They explain that Penicillin is effective at killing bacteria because it interferes with the growth of bacterial cell walls.

How does Penicillin do that exactly? And why does it not dissolve human cells as well?

Answer

Bacteria have a mesh-like structure surrounding their plasma membrane called a cell wall. The cell wall is made up of peptidoglycan polymers that form a rigid crystalline structure that helps protect the osmotic pressure of the bacterial cytoplasm.

Penicillin and other β-lactams work by inhibiting the final step of peptidoglycan synthesis, which prevents transpeptidation (crosslinking) of the peptidoglycan molecules. This leads to the death of the bacterium by osmotic pressure due to the loss of the cell wall.

This drug doesn't affect human cells because they lack a cell wall surrounding their plasma membrane.

publications - Is it unprofessional for a journal editor to be anonymous?

An editor of a journal asked me to review a paper but did not provide his/her name or institution, signing the e-mail as, essentially, "Editor of ...". The e-mail seems to be based upon a template. The sender's e-mail address is of the form AbbreviatedJournalName@PublisherName.com

The journal is reputable but not a top one. I cannot determine the editor's name from public online sources or private contacts. My best guess is that the name of the author of the e-mail is very likely to belong to the list of the editors advertised on the web page of the journal. I know nobody from this list personally through I've read and cited some of their papers.

1. 
   

   How should the editor's decision to stay anonymous be qualified? For example, was it

   
   
   
   
   • (un)ethical,
   
   
   
   • (un)professional,
   
   
   • (contrary to the) commonly accepted practice?
   
   
   
   


2. 
   

   What does this tell us about the editor or the journal?

   
   


3. 
   

   I would like to know whom I am speaking to before taking any decision. What would be the most appropriate reaction from my side, if any?

   
   

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In another circumstance, the editor of a different, top-notch journal to which I submitted is unknown to me. I corresponded only with the chief editor, and I know that the manuscript is under review, but that's it.

4. 
   

   Is it

   
   
   
   
   • (un)profesional
   
   
   • (contrary to the) commonly accepted practice
   
   
   
   
   

   for the chief editor not to reveal to an author which editor was assigned to the author's submission?

   
   


5. 
   

   I would be happy to know who is the actual editor of my submission. Is it possible (and how) to ask for that such that the question is likely to be answered?

   
   

Answer

(Due to some rearrangement of comments, etc., I'm rewriting a comment as an answer... :)

First, yes, as noted by others, on many occasions such emails are software-generated... stimulated by an on-line submission, without other human intervention. So it's not that anyone is trying to avoid revealing their identity.

At the same time, nevertheless, I myself do not find machine-generated "invitations" adequately motivating in most circumstances to get me to do volunteer work. My viewpoint is that if no human being is willing to take the trouble to invest at least their identity and a few moments for a small email, then I needn't feel an obligation to invest my (identity, even as "anonymous" reviewer, and) time.

A feature that helped me move down this path was crappy automated interfaces... (won't name names)... which tried to coerce my referee reports into a format that misrepresented my comments... and on other occasions didn't like the browser I use, etc. In particular, when dealing with the interface was a lot more trouble than carefully reading the paper? And there was no one to email about it?

But this did start me thinking about the whole arrangement. Docile free refereeing for for-profit large corporate entities upon the command of software is not the way I want to go.

publications - Assume an undergrad has something worth publishing: how might (s)he get it published?

I study undergraduate philosophy.

I wrote a paper (beyond the coursework) that presents a solution to one of the unsolved problems facing our conceptions of personal identity. I regard it as worth publishing, but I get that, as an undergrad, I may not have much of a sense of what qualifies a paper as "worth publishing." So I took a few precautions:

1. 
   

   I read the recently published arguments, and the arguments that preceded them.

   
   


2. 
   

   I critically thought about whether the argument could contribute to the field

   
   


3. 
   

   I presented the argument to some people accomplished in fields that depend on logical thinking {a physicist, a lawyer,a mathematician}. The mathematician told me of a few useful concepts in math that I should incorporate into the argument, I studied them, incorporated them, and re-presented the paper to him, and he felt it was clear and logically sound.

   
   



4. 
   

   I asked some academically successful people {two medical doctors and a Harvard mathematics graduate} for their opinion on it. They agreed with me; however, none of them had much experience publishing research.

   
   


5. I presented it to the prof.

The prof's responses seemed defensive. However, I get that I may have had a defensive bent that disposed me to regarding her criticism as her 'just responding defensively'. So I recalled the conversation to people who I believed would tell me that I had mischaracterized her responses, if they suspected that I had done so - and none of them did.

I also get that,

1. most professors -like anyone- want to make the most of their time, and that


2. most people usually see what they expect to see, and that



3. most professors probably would not expect an undergraduate paper to contain much worthwhile.

So, I suspect that most wouldn't want to read it, and that if a prof agreed to read it, an extra measure of prejudice would affect her assessment of it.

I say all of that to say that I have reason to believe I should try and publish the paper, but I didn't succeed when I tried the most obvious path to doing so (presenting it to the prof), and I don't suspect that I'd have much success asking other profs to read it.

So, how might I get a journal or a professor to give the paper a fair shake?

Answer

Here's what you should do:

1. Find an appropriate journal with a double blind review process.


2. Submit your paper.



3. See what happens.

Double blind means that you do not know the identity of the reviewers, and they do not know your identity. The ostensible purpose of this setup is to encourage reviewers to evaluate the paper based on its academic merit, rather than the pedigree of the author(s).

In reality, of course, there will always be politics in reviews, and many reviewers will nonetheless formulate theories about who you are and where you're from. Moreover, things like hot trends in the field can influence judgement—which is why it's important to identify a journal compatible in spirit with your chosen topic.

You will also be judged on the style of your writing, and the visual style of your submission. Reviewers will be much more comfortable accepting a submission that looks like a published article than one with strange typography, layout, etc. E.g., don't submit a paper written in MS Word when everybody else in your field uses LaTeX. Strange as it may seem, you will look like a nut job! Even different linguistic tone and structure can make your reviewers think you are a quack, even if your idea is legitimately awesome. In short: be a conformist when it comes to your first few submissions. Once you understand how the game is played, you can start to break the mold (hopefully for the better!).

Even accounting for everything above, there is an extremely good chance your submission will get rejected. Coming up with genuinely good ideas is hard; developing political/cultural/intellectual savvy in academia takes time and experience—especially as a lone undergrad. And rejection will sting! But the submission process will be a valuable experience nonetheless. After a few days, go back and read your reviews calmly, and think carefully about why the reviewers wrote what they did. Was the typography too bizarre? Are they protecting their political interests? Or is your idea simply not as good as you thought it was? The more papers you submit, the better you will get at answering these questions objectively and honestly. Eventually, you will master the game and can just focus on the work. I hope.

Good luck!

teaching - Is it professional for a professor to ask "surprise" questions on a test?

To clarify, I am asking if it's professional to ask questions that while relevant to the subject/course, and are related to the topic, but have not been discussed in class, assigned as homework, reading, etc. and are also not related to any prerequisite class that the students should already know. I am also not asking about "gotcha" questions where it's a quick "know it or not" fact, but rather an entire procedure, proof, or concept of some sort.

For example in class, using a formula from the textbook to solve problems, but on the exam asking for a proof of the formula that has been used.

Another example - in a foreign language class, asking about a never-before-seen word that may be related to some other, studied words or that has a similar sound/meaning in the native language.

Do such questions "make students think out of the box", or are they more likely to discourage students when they struggle with them? While in the real world there may be many problems similar to this where the problem is completely new, is this something that should be taught in an unrelated class?

Does it matter if the test in question will be graded on a curve where even if a student doesn't answer the question correctly at all, they could still get a good grade?

P.S. - this question was prompted by the comments in this answer

Answer

Among the answers given thus far, the one which is closest to my thinking is that of xLeitix, and the side note about the context applies too.

Now,

Is it professional for a professor to ask “surprise” questions on a test?

It can be professional. As I said in a comment, it's unprofessional to ask such questions with the only purpose of failing as many students as possible.

Moreover, I don't like very much the adjective surprise in the title: a surprise is something unexpected, but if a professor clearly warns the students that at the exam they will find problems which have not been solved during the course, there is no surprise. So, in the following, I will talk about "new" problems.

Exams and tests have, as their main goal, that of assessing how well students master/understand a (small portion of a) certain subject. As others have well explained, new questions or problems can give a hint on how deep this understanding is.

But apart from the above stated main goal, exams and tests might also have secondary goals:

• An exam can be an occasion for learning new stuff. The well defined separation between learning and verification, which typically happens in a course, is something that drastically comes to an end when one starts working, even in academia. Learning and verification in everyday life are really interleaved, and many times learning has to be done along a stressful verification. So, a new problem during an exam can be an occasion to continue learning in a more "unprotected" way.


• An exam can be a hint, one of the many, that what has been taught during the lessons is not the whole story, and that beyond the lessons there is much more: new problems surely deliver this message.


• For a professor, an exam is an occasion to fish for good students to whom propose a thesis. Giving new problems can be a way to find students who are capable of independent thinking.

So, I tend to give new problems at the exams keeping in mind the above points.

To avoid being too general, let's make an example related to my experience. A few years ago I taught a course about sensors, transducers and signal conditioning circuits for graduate electronic engineers. The written part of the exam consisted in one problems about designing or analyzing a signal conditioning circuit or about evaluating the measurement uncertainty of certain transducer. Due to the vastness of the topic, the course could neither describe all kind of sensors and transducers, nor all possible signal conditioning circuits. So, I decided that every exam would have been made of a new problem, where "new" meant:

• A problem about a transducer not described in the course. Indeed the exam text contained a short description of this kind of transducer.


• A problem about the analysis and/or design of signal conditioning circuit not described in the course. The students, being electronic engineers, were expected to know how to analyze electronic circuits, even of moderate complexity. In more difficult cases, hints were provided.


• A problem about a known transducer applied in an unknown way.

Exams were open books and students could bring the solutions of all previous exams and all the class notes. After the written part, if successful, there was an oral examination which was more about class material.

What was the outcome of this kind of exam? The course was in general very well received by the students, even if the exam was considered hard: the percentage of success was around 30% (the pass grade is 60%). The major complaint was about the number of exercises solved during the classes, but this happens in all kind of courses. My answer to this complaint was that there were, indeed, time constraints that prevented us to solve more problems but, anyway, whatever the number of problems solved during the course, at the exam they would have found a new one (sometimes students ask for more solved problems in the hope that these will exhaust all possible cases).

From this and other experiences along 15 years, I think that students can withstand new problems at the exams as long as the motivations are well explained and, especially, as long as the course is worth of it.

graduate admissions - Will ISIS attacks hurt my PhD application as a Muslim?

I'm a dedicated person, very passionate about physics and pursuing my PhD at a good school is crucial to my life. I've been preparing my application documents for a while now. GPA is almost 4 and Physics GRE is 980. My general GRE is at the 97 percentile. Good recommendation letters. I have other few decent ranks since high school as well. HOWEVER, I'm from the Middle East, and yes, my name is Mohammed. I can feel how the world is infuriated about the Islamic community in general, though the vast majority of Muslims are vulnerable to (and on daily basis thousands are already subjected to) similar attacks from ISIS. The majority of us, including myself, are terrified by ISIS, sorry for and mortified by these attacks by ISIS.

My question: Will these events perhaps hurt my application? If you were to decide on my application on the admission committee, how would my citizenship, religion and name affect your decision?

So grateful for any attempt to help. In fact, I'm sort of developing anxiety due to this issue.

---

EDIT: For those wondering, I'm applying only for universities in the USA.

cell biology - What is itching?

What exactly at the molecular level is itching? What physiological function does itching serve, if any? I cant remember the reference but a PLCb3 null mice lost the itch phenotype, so presumably it is mediated by the Gq-PLCbeta pathway through a cell surface GPCR. Since a physical action of scratching relieves it, could it be a case of a mechanosensitive channel at work?

masters - Creating a schematic figure based on an existing one

In the context material chapter of my masters dissertation, between other things, I must write about the state of the art on the thematic presented. There are some very expressive and simple schemes in other authors works that I would like to use. I was wondering: is it legitimate if I create schemes by myself that convey the same structure and information and reference the sources in the following manner: "Image based on [Reference]" ?. The result would be different looking (colors, shapes, and several other visual elements) schemes that would express the same content.

I've looked at How much do figures need to differ to avoid copyright claims? but I wasn't sure if the context of that question is enough for the answers to apply for me.

Thanks.

job - Principal Research Scientist vs. Senior Research Scientist?

I notice that some schools, e.g., MIT EECS, has these two non-faculty appointments, Principal Research Scientist and Senior Research Scientist.

At least true for MIT EECS:

Both of them, just as Faculty members, are PI's and can run their own research groups. One difference I know is that Principal Research Scientist's appointment is reviewed every 4 years, whereas Senior Research Scientist's is evaluated every 5 years (as per MIT's website). Yet, this doesn't tell much.

In addition, Principal Research Scientist falls under "Sponsored Research Staff Appointments" category, whereas Senior Research Scientist falls under "Academic Research Staff Appointments". Does this tell something?

What is the exact difference between them and the Faculty members (i.e., professors)?

Why aren't they just called professors?

What are the differences between these two?

Answer

According to the MIT EECS pages, there are two tracks:

• Academic Research Staff. These are mostly shorter term (such as a Postdoctoral Fellow), and are funded externally (by grants and similar).


• Sponsored Research Staff. These are longer term appointments which are funded by the department.

Senior Research Scientist is an Academic Research Staff position, because while it is long-term, it is also a position for which the researcher is expected to procure their own funding.

From 5.3, the SRS's funding:

Appointees to this rank generally are expected to raise funds to conduct research and cover their own salaries.

Principal Research Scientist is a Sponsored Research Staff position, and is funded by the department (though I'm sure they can get their own funding also, their salary is paid by the department).

From 5.2, the PRS's funding:

Funding responsibility resides with the department, laboratory, or center that is the locus of the appointment.

From 5.1 on the difference:

Two types of research appointments are described in the following sections: long-term appointments, which are classified as sponsored research staff appointments, with the exception of the Senior Research Scientist/Associate/ Engineer position; and short-term appointments, which are, in general, classified as academic research appointments.

The purpose of the campus research appointment structure is to create professional sponsored research staff categories with employee benefits and privileges in order to encourage long-term research careers at MIT. The concept of long-term professional careers, independent of classroom teaching and supported entirely from research grants, is not a new one for the American research university. This mode of research, with professionals working in departments, laboratories, and centers, is an important mechanism for universities to maintain research viability, enter new fields, and bring researchers to the campus.

It seems evident that Senior RS is basically the same position as PRS, but not funded by the department. In some cases, the PRS could earn more, because (for example) a NIH-funded SRS would be limited by NIH regulations, while a PRS who is funded by the department is only limited by whatever MIT chooses to pay them.

ecology - When are population dynamics models useful?

When are population dynamics models useful? There seems to have been a lot of research about it, but how does it help? If I need data about how a population will evolve under what conditions, I need it because I need data for a decision (such as "can we kill 50% of population X without doing too much damage?"), right? But for that, the model needs to be aware of what causes what. And for that, I have to do experiments, right? Like "let's kill a significant amount of population X and see what happens in the next ten years". I really don't get it.

Answer

Population dynamics occupies a whole subset of mathematical biology. Perhaps the most pragmatic uses for modelling population dynamics come from the fields of epidemiology for modelling disease infection and transmission through a population (one such article), or ecology modelling things like forestation, fishing dynamics, predator-prey relationships (an example). Then there are more abstract uses, when you cannot measure a population to test a hypothesis because the labour is too intensive, or it's too costly, or no such surveillance mechanism exists. Theoretical models of population dynamics are built to gain an understanding of what the system as a whole may do under certain conditions. In this sense, population models are more of a theoretical exercise or a thought experiment.

research process - What are acceptable criteria to select publications for a (systematic) review?

I'm in the very beginning of my scientific career, so I don't yet know the standards for (systematic) reviews very well. I feel I don't have so much experience that I could publish my own research in good journals (I have now just two conference papers), so I'm considering to pay close attention for 6-12 months in other peoples' works.

I have a clear research question, but given the massive amount of related papers it's difficult to choose which ones to pick. Of course, I will select papers related to my research question as the first criteria. However, could I narrow the range of included papers more by

• publication date (e.g. only take papers published during the past five years),


• impact factor or citation count,


• type of publication (conference, journal),


• sample size (e.g. number of subjects)?

Or, if not these, what criteria are commonly used? I guess the answer is different for reviews and systematic reviews, so please cover both if possible. thank you!

EDIT: I'm considering this so that it would be possible to try publish my results.

genetics - (How) can a pink grasshopper exist?

I saw this foto on Reddit recently:

Is this possible? How can a grasshopper become like this? Is this just natural genetic mutation?

Answer

Pink individuals of the katydid species Amblycorypha oblongifolia are a relatively uncommon but natural phenomenon with a long history of research.

It looks from popular press accounts (Science Friday, Scientific American) that the pink coloration may be caused by a dominant allele, and is only rare because of a high selection pressure against pink individuals (i.e. they're much less good at hiding among leaves, and are eaten before they can reproduce).

---

Photo by Richard Whitby, via flickr.com/blueboat2 (cc-by-sa 2.0)

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citations - Is there a way to report to google scholar some systematic mistakes?

I've noticed, for citations, that some BibTeX files provided by google scholar are having regular errors (I believe these are errors).

For bib items, there is the "pages" field, in which we could input a range or a number of pages an article has. I've found at least two journals (in a short time span) whose articles have a wrong "pages" field. For instance

@article{baffou2009heat,

title={Heat generation in plasmonic nanostructures: Influence of                  morphology},
  author={Baffou, G and Quidant, R and Girard, C},
  journal={Applied Physics Letters},
  volume={94},
  number={15},
  pages={153109},
  year={2009},
  publisher={AIP}
}

or

@inproceedings{ammari2015super,
  title={Super-resolution in high-contrast media},
  author={Ammari, Habib and Zhang, Hai},
  booktitle={Proc. R. Soc. A},
  volume={471},
  number={2178},
  pages={20140946},
  year={2015},
  organization={The Royal Society}

}

Similarly, this last paper is not a proceeding, but an article from the journal "Proceedings of the Royal Society".

Probably there are some other mistakes around.

I know that these data are collected automatically, but, is there any way to report the errors to help google scholar to perfect their algorithms?

Answer

The obvious place to report it would be the Google Scholar "contact us" form. I suspect there is little chance of the problems being fixed (since scholar has been around for over a decade, and I'm sure others must have reported these problems over the years) but you have little to lose by trying.

job - tips for mathematics student giving interview for physics (quantum information)

As suggested by @PiotrMigdal I am putting a separate question regarding the title mentioned above.

I am a Mathematics PhD student doing work in functional analysis / operator theory aspects of quantum information. My basic training (up to masters) is in so called 'Pure Mathematics' ($C^*$ algebra, representation theory, elliptic curve etc.). I am about to complete my PhD and applying for post doctoral positions. It seems most of the jobs in this area are for experimentalists and a few for theorists. I do not have much knowledge about experiment. Moreover, my understanding about quantum measurements as very basic. These can be considered as negative points. Positive sides: I have a few published papers in some reputed physics journal, a few (in discrete mathematics) preprints, and a few works in the draft stage. However the published papers are not reviewed by math. review.

My question is, what a mathematics student, like me, should focus/emphasise if he/she go for a job (for me post doctoral) interview in front of physics faculties.

Also more general question can be regarding the job perspective of mathematics students in quantum information. Advanced thanks for any suggestion, answer etc. Feel free to edit and/or retag it, if you think it is necessary.

Answer

It may be too late for this, but I'd suggest giving a talk for physicists in a lower stakes setting (eg a seminar at a school that isn't interviewing you). Physicists often have different names for things and ways of talking about them, and it can be really nice to have some exposure to the kinds of questions you might get asked.

ethics - Is it okay to report classmates cheating on exams?

Is it acceptable or ok to report on students cheating? Many times during a test or an exam, I have seen students in front of me either passing notes, or otherwise collaborating whenever the professor isn't looking.

I don't want to get into trouble, and I don't know if it's "alright" to rat on fellow classmates. Part of me thinks they deserve being caught out, by virtue of trying to cheat their way through the course. However, I feel like I would get found out by other students if they were caught cheating.

What is the right course of action here? To be clear, I would never raise an accusation in the middle of an exam; it would only lead to me being ostracized by my peers.

Answer

Honor is doing what’s right when no one is looking. If your institution's Honor Code requires you to report cheating, I'd suggest you report the action to your professor or a higher authority. This is good for multiple reasons:

• You can prevent the cheating student from gaining an unfair advantage over his or her fellow students.


• If they're caught (and punished), they might realize their mistake. If you never report the cheating, this student might sail through the rest of the term repeating the same mistake.

However make sure the suspected cheater doesn't come to know who reported him/her. You can meet the professor after the exam and explain what happened. If you don't wish to reveal the person's name, don't. If you're not comfortable with talking to a professor about your classmates, you can send an unsigned letter, explaining in detail what happened during the exam and if possible, include some ideas on how to stop them next time.

Before you do anything, think of the consequences. What if the other student discovers you're the one who reported the cheating? How would you feel if you confronted the cheater directly? If you can't imagine any of these situations, I suggest you let it slide.

biochemistry - Can a human be made with ovum but without sperm?

This article says that scientists were successful in making a mouse using only a sperm and no egg (ovum). The article also states that this procedure could be applicable to humans.

However, I want to know why didn't they try with only an ovum?

Can a human be made only with an ovum, i.e. without sperm?

Answer

Nice question! It is actually very difficult to do so because humans, obviously, are far more complex than some animal species which naturally show parthenogenesis. Just to mention, there are female-only animals also present in nature, such as New Mexico whiptail, which reproduce only by parthenogenesis, meaning that it is not as impractical as one might think.

There have been many parthenogenesis tests on mice and monkeys, but they usually result in abnormal development. This is because mammals have imprinted genetic regions, where either the maternal or the paternal chromosome is inactivated in the offspring in order for development to proceed normally. A mammal created by parthenogenesis would have double doses of maternally imprinted genes and lack paternally imprinted genes, leading to developmental abnormalities. It has been suggested that defects in placental folding or interdigitation are one cause of swine parthenote abortive development.

During oocyte development, high metaphase promoting factor (MPF) activity causes it to arrest at the metaphase II stage until a sperm fertilizes it. The fertilization event causes intracellular calcium oscillations, and targeted degradation of cyclin B, a regulatory subunit of MPF, thus permitting the oocyte to proceed through meiosis. The most precise and exact mechanism is not known yet.

But this does not mean that it is not possible. Actually, it has been done quite a few times; once on June 26, 2007 by International Stem Cell Corporation (ISCC), and once (controversially) on August 2, 2007 by Hwang Woo-Suk. Even the procedure for parthenogenesis (in swine though) in lab is available. To initiate parthenogenesis of swine oocytes, various methods exist to induce an artificial activation that mimics sperm entry, such as calcium ionophore treatment, microinjection of calcium ions, or electrical stimulation. Treatment with cycloheximide, a non-specific protein synthesis inhibitor, enhances parthenote development in swine presumably by continual inhibition of MPF/cyclin B As meiosis proceeds, extrusion of the second polar is blocked by exposure to cytochalasin B. This treatment results in a diploid (2 maternal genomes) parthenote Parthenotes can be surgically transferred to a recipient oviduct for further development, but will succumb to developmental failure after ≈30 days of gestation.

The major problem with parthenogenesis in humans is the abnormal development of embryo. This has been accounted by a phenomenon known as genomic imprinting. Genomic imprinting is the epigenetic phenomenon by which certain genes are expressed in a parent-of-origin-specific manner. For example, if the allele inherited from the father is imprinted, it is thereby silenced, and only the allele from the mother is expressed. The death of diploid parthenogenetic or androgenetic mammalian embryos is determined by the absence of expression of the genes of imprinted loci of the maternal or paternal genome, which leads to significant defects in development of tissues and organs. How this exactly works is not known yet, but it is supposed that it evolved to prevent parthenogenesis. Bi-parental reproduction is necessary due to parent-specific epigenetic modification of the genome during gametogenesis, which leads to non-equivalent expression of imprinted genes from the maternal and paternal alleles. Thus, genomic imprinting seems to be ineffective during normal reproduction.

As a side note, in the article you refer to, the researchers did not just mix two sperms and produce diploid zygote or something like that. In the procedure, they injected a normal sperm to the above explained abnormal embryo, which later on proved to be viable. They, thus, showed that these kind of embryos can also become viable if they get fertilized by a sperm within time.

References:

• Abnormal development of embryonic and extraembryonic cell lineages in parthenogenetic mouse embryos; Karin S. Sturm, Margaret L. Flannery, Roger A. Pedersen


• Parthenogenesis - Wikipedia


• Patient-Specific Stem Cell Lines Derived from Human Parthenogenetic Blastocysts; E.S. Revazova, N.A. Turovets, O.D. Kochetkova, L.B. Kindarova, L.N. Kuzmichev, J.D. Janus, and M.V. Pryzhkova


• Genomic imprinting is a barrier to parthenogenesis in mammals; Kono T.


• Genomic Imprinting and Problem of Parthenogenesis in Mammals; E. S. Platonov


• Mice produced by mitotic reprogramming of sperm injected into haploid parthenogenotes; Toru Suzuki, Maki Asami, Martin Hoffmann, Xin Lu, Miodrag Gužvić, Christoph A. Klein & Anthony C. F. Perry


• Stem cell fraudster made 'virgin birth' breakthrough; Silver lining for Korean science scandal; 3 Aug 2007, Christopher Williams

evolution - How can homosexuality evolve despite natural selection?

I would imagine that the answer to this question would be population control, especially since even if one sibling is homosexual this does not necessarily mean that the other siblings will be too.

publications - Submitting the same research to multiple conferences

I'm aware that it's a violation of terms for most publishers to submit the same article to more than one journal, but I frequently see authors whose papers seem very similar, particularly papers released in a single year. In my field, neuroscience, this is particularly true about conference papers; one researcher will often have numerous posters/conference papers about seemingly the same topic. What are the guidelines for acceptability regarding this type of behavior?

Answer

1. 
   

   According to the Committee on Publication Ethics Guidelines on Good Publication Practice, the term "redundant publication" is defined this way:

   
   

   
   

   "Redundant publication occurs when two or more papers, without full cross reference, share the same hypothesis, data, discussion points, or conclusions." In addition, it states: "(1) Published studies do not need to be repeated unless further confirmation is required. (2) Previous publication of an abstract during the proceedings of meetings does not preclude subsequent submission for publication, but full disclosure should be made at the time of submission. (3) Re-publication of a paper in another language is acceptable, provided that there is full and prominent disclosure of its original source at the time of submission. (4) At the time of submission, authors should disclose details of related papers, even if in a different language, and similar papers in press." Note that (2) states that it is generally acceptable to present a paper in a conference and then later publish exactly the same paper in a journal, as long as you mention to the editor that the paper has been publicly presented.

   
   

   
   


2. 
   

   According to the paper Science journal editors’ views on publication ethics: Results of an international survey,

   
   

   
   

   "Breaches of publication ethics such as plagiarism, data fabrication and redundant publication are recognised as forms of research misconduct that can undermine the scientific literature." It also stated that redundant publication is an unethical practice. Of 16 ethical issues studied, redundant publication had the highest severity (that is, it caused editors the most concern---more than plagiarism or data fabrication).

   
   
   

   
   

publications - Is it acceptable to have a research paper with no references?

I (an undergrad) and 2 other profs from my department have been working on something and we were thinking of submitting our work to a conference (a pretty well known one) this week. The fact is there is no related work that has been done on the problem we are solving and therefore there is no paper which we can cite as a starting point for our work. The only existing things that we make use of are trivial definitions from mathematics (like Riemann Integral) and also definitions that are pretty well known in my area (CS). So again, we do not think there is a need to cite any particular papers for that.

Now my question as stated was - is it acceptable to have a paper with no references? Or do you think we should just mention some papers (we never had to use them) where those definitions were actually proposed?

PS: I'm sure some of you might suggest me to ask those profs. But quite frankly none of them have much experience as far as publishing papers is concerned. So it would be great if some one could give me a good advice and help me out.

Edit: Thanks everyone for the answers. Of course somewhere a little sarcastic and ridiculing, but I can understand since this is a little weird. Actually yes, I had the notion that a paper wasn't worth citing unless I use some results from it (say an algo or some theorem). But I guess that isn't the only reason why I should be referencing as many seem to suggest here. The fact is we had seen quite a few survey papers before we started this out and I was under the impression that there wasn't a need to cite them since anyone could find them. But now, things are bit more clear and I guess I should cite them and I will :)

Answer

Though I don't think there's any hard rule against having a paper with no reference, it seems pretty weird. Note that references are not only for citing other people's results (theorems, algorithms, etc.) which you have used, but more broadly to recognize other's scientific contribution. For example:

• Has the problem never been discussed before? Who first realized it was a problem, stated it, formalized it?


• You probably put the problem into the broader context of your field. And if you don't, you probably should. This sure requires citations on recent work on related problems, even if nothing was ever done on the one problem you're addressing.


• For example, is your problem a specific case of another problem, or does it have generalization?


• What are the consequences of your results/findings? They probably have some impact on other related problems, or practical consequences on real-life issues.


• Didn't you or your co-authors ever do any prior work on this issue?

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Finally, let's see it another way: you have solved a problem, that no one else has solved, worked on, or more generally discussed. And you did so using only elementary techniques, which have been known for so long that they do not require citation. Stated like that, it may sound like either you're a genius opening an entire field of mathematics, or you're working on a useless problem that nobody cares about. You probably don't want the reviewer to be thinking that way!

career path - Academic progression in Germany, what happens after a postdoc? What is the next step?

As a follow-up to this question, I am wondering whether or not there are intermediate positions between a postdoc and a tenure in the German academic system.

I was told that there isn't really a step up from postdoc (like an assistant professor) until you get a professorship (for which you have to do habilitation among other things). If I understand things correctly you can be a postdoc for 12 years (?!) in Germany, and if you're successful (and lucky) you can get a professorship.

Is this accurate? Or are there more intermediate positions? Specifically I noticed there is a "junior professor" position, which would seem to fit the bill. What are the differing qualifications of a junior prof (W1) and a senior postdoc (either E13 or E14)?

postdocs - 1.5 years later, how to make sure unprofessional behaviour by former mentor has consequences?

I was a post doc at a large US university for a year and after took another postdoc position in my home country. My mentor was a tenure track assistant professor. It pretty soon became clear that working together was going to be difficult due to different ideas on how to approach and manage projects. Furthermore, I might eventually not have been the best fit for that position given the somewhat different topic of my PhD work. This ended in a complicated work relationship, in which several requests on my side calling for meetings to discuss ways to improve the situation were ignored.

All the while, in my opinion, I was treated abusively: in group meetings in front of the whole lab, I felt humiliated by unconstructive discussions and was called out for the too little progress I made. In smaller meetings with up to two other lab members, I was shouted at by my mentor and told I didn't deserve my PhD etc. Sometimes, reasonable questions of mine were answered in a passive-aggressive way. Furthermore, the significant amount of time I spent in helping more junior lab members in their (very ambitious) projects was not appreciated.

At the time, I asked a university official in charge of postdoc affairs for advice. I was being told that a formal complaint at HR or the department head would most likely have no direct consequences. I furthermore feared retaliation, mostly because my J1 visa and housing depended on that position. For these reasons, I did not take any further action.

At one point, I decided to quit the lab after the initial agreed-upon one-year duration of my stay. Two and a half months before I wanted to inform my mentor in a one-to-one meeting about my decision, but two e-mail requests for that meeting ("to discuss the fact that my contract ends", which is how I worded it) were ignored. I eventually managed to get hold of my mentor after a group meeting and in the following conversation, after asking me why I think the whole thing didn't work out, they did not acknowledge any wrongdoing or unprofessional behavior on their part, even after I brought up several examples.

Other, more junior lab members (PhD and master students; I was the first and only postdoc) reported similar incidents of unprofessional behavior, but also didn't speak up. My guess is that they, too, were fearing retaliation and didn't want to jeopardize the relationship with their supervisor.

My question now is how to achieve the following (in decreasing order of importance):

• have my former mentor improve their behavior so that they treat future students and employees better


• if that doesn't happen, make sure their propensity for unprofessional behavior is known to the tenure committee


• be sure the other professors in the department know that both sides are to blame for what happened; that is, restore my reputation


• find closure: I'm going to leave academia for industry soon, but feel my academic career could have been more successful and my stay in the great city this lab is located in even greater had it not been for the terrible time at work (although this might possibly be hard to answer and / or worth of its own question)

While I am aware that there are several questions on this site about similar issues, I believe mine is different because I left that lab a year and a half ago. I fear that, after such a long time, simply contacting the department chair will come across as bitter and and as wanting to retaliate at the end of my academic career.

edit:

As per Dan Romik's suggestion: I'm not only interested in advice how to achieve the above goals, but also whether this is actually adviseable. Also, as the time span of 1.5 years indicates, this isn't a super urgent matter for me. But I've been thinking about this question for a long time and I really appreciate all of you answers, most of them taking very different point of views! I don't know which one to accept - a natural choice would be to follow the suggestions I find most promising and see how it works out. Although not being accepted, this wouldn't make the other answers less valuable.

What's the minimum distance of focus for the lens of a human eye to reach maximum flatness?

According to the Wikipedia article on eye accomodation, the range in which a human eye can focus is from 7 centimetres away up to essentially an infinite distance. Of course, people can't see things an infinite distance away, but at a certain point the light reflected off an object will come at the eye in effectively parallel paths.

As an eye focuses on objects progressively farther away, it seems to me there would be a point when the lens hits maximum flatness, after which it everything will be equally sharp in focus. Looking at an object 500 metres away or 1000 metres away probably doesn't require any change in the lens. However, going from one metre away to seven requires the ciliary muscles adjust to just the right amount.

My question is, what is a normal minimum distance from the eye at which the lens will reach maximum flatness? Everything else in this question is just for context, so an answer to this, stated in metres from the eye, is all I am seeking.

The article I linked to above mentioned the human eye seeing "13 dioptres", and I have tried to understand dioptres, but it's a little confusing for me. If I understand correctly, the higher the dioptre, the closer you focus, so the 13 dioptres refers to how close the human eye can see. If I have this backwards, please let me know.

In any case, my purpose in asking is to determine the range in which ciliary muscles would be required to do more nuanced work in order to hold the lens at in the right shape. Focusing on something 7 centimetres away, the ciliary muscles are at maximum exertion, and at a certain point and beyond the ciliary muscles are completely relaxed. To hold somewhere in between would require more subtly nuanced, and, I suspect, more difficult work on the part of the ciliary muscles.

At least, I assume that to be the case because I am hypothesizing that the act of contraction for the ciliary muscles would be similar to other muscles. For example, it is easier to do a bicep curl with weight when going from full resting position to maximum contraction, as opposed to stopping at a particular spot somewhere in the middle of the motion. To stop mid-motion requires more muscle control, and, depending on how fast you wanted to do it, can be difficult to be exact.

Answer

There are practical questions in ophthalmology and you've asked someone that has a common theoretical answer: 6 meters.

However, you should know that from the same theoretical point the far the object the less accommodation we need, so the second answer is - infinity.

What is the difference? From the practical point the accommodation between this two points is negligible and does not have to be taken into account when we correct the refraction error.

Small theory - to see an object placed at a distance of 1 meter we need 1D of accommodation power (1/1meter=1D), to see an object placed at a distance of 30cm we need 3D of accommodation power (1/0.3meter=3D), for an object at a distance of 10cm we need 10 diopters and finally for an object at the distance of a 6 meter we need accommodate 0.16 diopter.

Thus between 6 meter and infinity the accommodation is very low and this is why the distant visual acuity is checked at this distance. Consequently, the lens convexity difference between 6 meters gaze and infinity is negligible and this is why the answer to your question is between 6 meters and infinity (zero accommodation).

From this explanation you can calculate the dioptric add for any reading distance and understand how the reading spectacles correct the loss of accommodative power (=presbyopia, the vision of older people).

If you want to know how much the crystalline lens changes its dimensions during accommodation, the answer is near 7% for diameter and near 10% for thickness, so the lens as was convex, stays convex and the visible changes are minimal.