neuroscience - Relationship between nerves and axons

I just wanted to get a realistic viewpoint of our nervous system. I understand arteries and veins, but I wanted to know how similar our nervous system is to that?

I understand we have neurons (please correct me if I am wrong) all over the surface of body. Whenever we feel a touch a neuron fires a response, and that response travels through axons (myelin sheath).

My main question is what a nerve exactly is. Is it a long axon? How many axons (same thing as neuron body?) are in a nerve? I am sure it depends on different nerves.

Answer

I will go through your list of questions below:

• 
  

  I wanted to know how similar is our nervous system to [the circulatory system]?
  They are very different, but as in every comparison of very complex systems, there is some overlap. The circulatory system carries fluids, the nervous system electrical signals so they are functionally not alike. However, both systems run throughout the body and have a more or less central control unit (the brain and heart respectively). So there is a structural similarity. I reckon they are as much alike as a city's sewer system and electricity grid.

  
  


• 
  
  

  I understand we have neurons (please correct me if I am wrong) all over the surface of body.
  That is correct

  
  


• 
  

  Whenever we feel a touch (stimulus arises) a neuron fires a response, and that response travels through axons (myelin sheath).
  Tactile stimulation may result in firing of one or more neurons, dependent on the intensity of the stimulus. Larger stimuli will, obviously, recruit more fibers. Stronger stimuli will evoke stronger responses (increased firing). Axons indeed conduct the neuronal responses, like an electrical wire conducts electrical current. Longer axons are often myelinated (insulated). Not all neurons related to touch are myelinated, however.

  
  


• 
  

  So my main question is that what exactly is a nerve?
  A nerve is a bundle of axons that carry related functional information. Typically, nerves conduct information originating from locations closely located together in the body, and generally they convey this information to a localized spot in the body as well. For example, the optic nerve carries information from the photoreceptors (related information) from the retina (localized source) to the brainstem (localized target).

  
  
  


• 
  

  Is [a nerve] a long axon?
  A nerve contains many axons. 'Long' or 'short' is rather subjective.

  
  


• 
  

  How many axons (same thing as neuron body?) are in a nerve? I am sure it depends on different nerves.
  Neuronal cell bodies are typically located outside a nerve. Nerves contain varying numbers of fibers. For example, the auditory nerve harbors the axons of the spiral ganglion cells that transmit auditory information from the inner ear to the brain. It contains between 31k - 32k (myelinated) fibers in normal-hearing humans (Spoendlin & Schrott, 1989). In contrast, the optic nerve, which carries visual information from the retina to the brain, contains some 1.3 million (myelinated) fibers in young human adults (Jonas et al., 1992)

  
  

<sup>References
- Jonas et al., IOVS 1992;33:2012-8
- Spoendlin & Schrott, Hear Res 1989;43:25-38</sup>

Is it a bad idea to send an article under review as a writing sample? (faculty job application)

I have a manuscript that is under review in a major journal which is a main result out of a few recent years of my research. When applying for faculty positions, I would like to send the draft as a part of my writing sample. But since the material is not yet published, I am not sure if it is a good idea.

What are the foreseeable disadvantages of sending an article in review to the faculty search committee?

My area is neuroscience / biomedical engineering.

Update: The paper got into a high-profile journal, and I got a job at a different place which did not require a writing sample.

Answer

First, From a legal point of view I do not think you will have any problems sending out a pre-review version of your manuscript since your have the intellectual rights to your own work. Usually most publishers' copyrights start when they have processed the material in some way but even then, if you are not using the material for any commercial purpose or for being reproduced publically, I cannot see any problem.

Then, I cannot really see any problems sending a pre-reveiw manuscript to a search committee unless it is of poor quality. Sending your work allows people to see what you are doing and a manuscript (in very good shape) will allow people to see your latest work in detail. Naturally a manuscript will not carry as much merit as a published paper since it has not been through peer review. But, if it is interesting, well written and in impeccable order you will be showing your skills in some way.

So it could provide a slight positive in a search situation if good but be very negative if bad and your judgement is what will be at stake.

human biology - Do tenocytes move around in a healthy tendon or do they stay at the same location?

The 2018 study {1} mentions that:

The healing process of injured tendons includes tenocyte migration which occurs from intact regions of tendon into the wound site.

Do tenocytes move around in a healthy tendon or do they stay at the same location?

---

References:

• {1} Dursun, Gözde, Mersedeh Tohidnezhad, Bernd Markert, and Marcus Stoffel. "Effects of uniaxial stretching on tenocyte migration behaviour." Current Directions in Biomedical Engineering 4, no. 1 (2018): 313-317. https://doi.org/10.1515/cdbme-2018-0076

species identification - What kind of insect can this be? This appears to be just a shell after and insect went through a metamorphosis process

What kind of insect can this be? This appears to be just a shell after an insect went through a metamorphosis process.

journals - Submitting a subset of my work to ArXiv

I've been thinking of publishing a subset of my work in fluid dynamics to arXiv. I realize the following about arXiv:

1. ArXiv isn't a journal


2. I would need to be endorsed to submit an article on arXiv

The reasons I would like to submit a subset of my work to arXiv are:

1. It would only be a subset of my work thereby NOT negating my chances of publishing work in a regular journal.



2. I would like to disseminate information to the society as soon as possible.

Does anyone have any thoughts or comments about this? Is there something that I'd need to feel uneasy about?

I realize that there has been another question regarding submission of work to arXiv and I read it here.

Answer

Opinions on when to submit things to arXiv vary both between and within fields. See

for lots of opinions. You should talk to your advisor/colleagues who can give you a better sense of how people in your field think about this.

mathematics - Should I apply to tenure-track positions if I'm fairly certain I won't be staying?

I hope to receive my PhD in Mathematics in May of 2015, so I am currently applying for jobs. Due to life circumstances, I'm fairly certain that I will only be staying at my next position for about 2 years. Does this mean I shouldn't even try to apply for tenure-track positions? Will a hiring committee not even consider me for the position if I'm not willing to commit to staying with them for a certain amount of time?

I would love to get a teaching/lecturing position at any institute of higher education (4-year research university, liberal arts school, community college), but as I look for openings, a lot of them are tenure-track assistant professor positions. Should I go through the effort of sending in an application, or will that be a waste of my, and the committee's, time?

Thanks for any advice you have!

Edit (to address Nate's comment):

My wife is currently applying for 2 year graduate degree programs in various cities in the US, so I'm applying for jobs in the same cities. When she finishes her program, we plan to move outside of the US (Africa or Southeast Asia), where I do hope to remain in academia, teaching mathematics to college-aged students.

Answer

Apply.

If you accept a position, you are committed for the following year. Leaving after two years will disappoint people, but it happens fairly often, and the potential consequences of you not applying to these jobs are perhaps more serious than the potential consequences to the departments if you leave after two years.

Besides, I don't know what your circumstances are, but you are presumably not completely sure you won't stay.

career path - Job market after PhD in Human Computer Interaction (HCI)

Do people in the industry consider HCI a non-technical field? Do they expect an HCI researcher to have more design and social science skills than technical ones?

funding - Is it lawful for a fellowship linked to a permanent faculty position at a British university in the STEM field to only be available to females?

The internally funded Anne McLaren Fellowships at The University of Nottingham state in their eligibility that "Candidates for the Anne McLaren Fellowships must be female and pursuing a career in a STEM subject". (link) One of the benefits of the fellowship is

The linking of the Fellowship to an indefinite academic post, subject to performance against a high-quality threshold and the continued right to work in the UK

What this means is that fellows will be presented 2 contracts. The first is a 3-year fixed term research only contract with a start date mutually agreed upon by the university and fellow. The second contract is a permanent research and teaching contract with a start date immediately following the end of the first contract. The second contract has stipulations regarding if you get terminated during the first contract (e.g., due to a loss of the right to work in the UK or performance issues) then the second contract is also terminated. There is no hiring process at the time of the second contract.

The Equality Act 2010 protects people from being treated less favourably because of their gender during recruitment. Section 159 of the Act does allow positive action (e.g. favouring an underrepresented group in a tie-break) but as those not classed as female are completely excluded from applying then this appears to be unlawful discrimination not positive action.

It could be that The University of Nottingham has a general exception due to being a charity. But then it would need to be included in the aim of the charity and the University's Charter of Incorporation contains "16. The University shall treat students, staff and other people solely on the basis of their merits, abilities and potential, regardless of gender".

phd - How is a student perceived if he took more time to graduate?

Suppose, a student completed his MSc in 4 years, instead of 2 years, but has a CGPA of A.

Would he have any disadvantage as a Ph.D. applicant?

Edit:
I can think of two possible reasons:
1. financial difficulty.
2. took some time to develop the necessary knowledge to cope with some courses. For instance, he has to complete a course X (e.g. Stochastic Process) but found that he doesn't have the necessary background knowledge (e.g. Probability and Statistics) to obtain a good score. So, he took some time studied at home and then came back, and he scored an A or A+.

publications - Choosing my name as an author when publishing a scientific paper, can I use my "unofficial" first name?

I have one official first name which appears on my ID card. I have another first name which friends call me by. Is it possible to use my unofficial first name and official family name to publish scientific papers? How can I prove to someone that I am one of the authors?

Answer

It depends on the field, and in particular on the venue in which you are publishing. It's possible that some journals and conferences might have policies about this, which would of course override anything you read here. But in general: nobody checks (or cares) whether the name you put on a published paper matches your official name. So if you use an informal variant of your name, e.g. if your name is "Stephen" but you publish as "Steve", nobody will bat an eyelid. If you use a nickname or publish under a pseudonym, it would be a little odd if the nickname is something that sounds very informal, but still, it probably won't cause problems.

What people do care about is building a record of your work, and putting a face to the name if they know your face. So you should (1) be consistent with the name you use to publish, and (2) make sure other people in the field know that it refers to you.

titles - PhD candidate vs PhD student

I see researchers working on their PhD calling themselves PhD Candidates, other call themselves PhD students. What's the difference between a PhD Candidate and a PhD Student?

According to two posters on the WordReferences forums:

This terms vary from university to university, usually a PhD student is granted the candidate status after completion of a “comprehensive examination”, which occurs sometime after the first year.

and

Here in the U.S., a “Ph.D. Candidate” is a student who has completed all of the academic requirements for their degree, except their dissertation.

So this works in the USA and Canada I presume, because they have structured PhD programs where you attend courses as part of your PhD. Unlike most of the universities in Europe where a PhD student starts off directly with his/her PhD thesis. (Europe does have structured programs as well, but they are not as widely spread yet).

human biology - X-recessive disorders and genetic markers

Please observe the following pedigree of a family with a x-recessive disease (bleeder disease).

The A's are genetic markers so close to the disease gene that recombination is negligible.

I understand it like this: They place markers that cut the DNA at the locus of the diseased gene. If you have the disease, your gene snip will be different in size than someone who does NOT have the disease and this will be visible on a gel. So if A1 is the disease marker, how come II:1 is not affected? He only has 1 X-chromosome and has the A1 marker?

EDIT: Another problem:

Is the coming child affected? Here I don't understand how the mother A1,A1 is NOT affected when the child A1 is?! Obviously A1 is the diseased marker and the mother has two of them...So she should be sick? Unless it's spontaneous?

Am I misunderstanding something fundamentally?

Answer

Genetic markers don't cut the DNA. They're simply regions of DNA sequence that happen to be variable between individuals (see my answer to your previous question). They might be measured using restriction enzymes (i.e. RFLP) to identify the exact difference, but it's not the marker that's cutting DNA. Furthermore, they don't necessarily cause disease. They're used in pedigree analysis to find regions that are linked with various phenotypes, among which is disease. However, linkage does not imply causation, especially with so few individuals.

To answer your first question II:1 isn't in the affected family - he married into it. In the affected family, A1 has become linked with the disease mutation. It is not necessarily linked with the disease in other families.

This is also the answer to your second question. I:2 has A1 marker on one chromosome associated with the disease allele, and one that's not. II:3 presumably inherited an X chromosome with the disease allele.

email - What is behind the "Indian Undergrad Research Experience"-spam?

Every now and then I receive an email claiming to be from some undergrad student in Math or Computer Science at an Indian university asking for a summer research experience in "my research group" (there is no such thing).

These emails all have a very formulaic structure. There always is a claim that the student read and very much enjoyed some paper of mine, but never any indication that this actually happened (ie no reference to stuff in the paper). In particular, these emails look like they could have been sent to dozens of people with a little bit of copy&paste. Attached are real-looking CV's.

Are these real students or this is some elaborate scam? If these are from real students, why do they think this could potentially work? Why India?

Edit: While I have only received emails like this from India, in the comments Tom Curch mentions having received some from China, too.

Answer

I graduated from a premier Indian university more than a decade ago and have sent out such emails. Let me try to put this practice in context.

Like many universities around the world, Indian universities have a semester system and a three to four month summer break in-between. Many Indian universities (but not the IITs) have a compulsory summer internship that must be completed in the summer before the final year. These internships can be done either in industry or academia. Therefore, it is common for Indian students to apply for internships. Until the late 1990s, most students used to apply for such internships within India.

The situation changed in the late 1990s because a couple of European universities (EPFL for sure, but I think that there were others as well) started a summer internship program for Indian students (almost exclusively from the IITs). The primary reason was to attract Indian students for graduate studies; at that time most Indian students went to English speaking countries. I participated in such a program in the early 2000s.

These programs did not result in any mass emails. The department of the Indian university used to send a list of student CVs, and the department at the European school would select from that list.

However, once students realized that European universities accept students for internships, they started applying en mass. And most, if not all, of them got offers, typically from universities in Switzerland, Germany, Austria, Spain, and Singapore; but also occasionally from the US and UK. (At least, this was the situation at my time). Initially, only IIT students were doing this; slowly everyone else also started applying.

At our time, some of us applied because we wanted to experience the research environment in Europe, others applied because they wanted a paid vacation. Some were meticulous in their search and wrote personalized letters; others simply sent out a form letter to everyone. My understanding is that most students (at least from IITs) still get such internships, so the practice continues.

Note that the universities which started this practice to attract Indian students were successful. They saw an increase in the number of students from IITs who applied for graduate studies. I have friends who went to study in a non-anglophone European country because someone had gone to the same university for an internship and had had a positive experience.

I don't know if more European universities have started this practice or not; but I know that recently Canadian universities (rather a Canadian funding agency) started a university internship program for international students from India, China, and Brazil.

phd - Good questions for a student-advisor compatibility test

There are online a good amount of tests aimed to assess "compatibility" between two persons in a given life or work commitment situation; for instance, between coworkers, roommates, lovers, dungeons'n'dragons players.

Basically, the idea is asking questions to which there is no true correct answer, but different possible viewpoints based on personality, opinions and general attitude. Two people can check easily if they are on the same page on a number of controversial points, and early discussion helps identifying possible reasons for disagreement.

It would be interesting to come up with similar questions for the phd student/advisor relationship. For example,

A good advisor should:

a. provide detailed guidance and tell their student what to investigate in great detail, even on a day-by-day basis.

b. leave their student free to choose their work agenda, but arrange regular meetings to check on their status and make sure they don't go astray.

c. give their student a problem and tell them to come back when they have an interesting result, even if it is months later.

I would like to gather several specific questions of this kind as answers to a community wiki question.

How is a research direction determined between a graduate student and their advisor?

My question applies to Science, Technology, Engineering, and Math disciplines (STEM).

Q: By what process does a graduate student determine his or her research direction?

(Assume that the graduate student is in the first year and has no previous publications with this supervisor.)

I can imagine several scenarios:

• 
  

  The graduate student proposes a research topic and then their supervisor evaluates it for originality and feasibility. In this scenario, the graduate student has the foresight to know what research directions are promising and appropriate.

  
  


• 
  

  The graduate student performs an extensive literature review. In this process, the student finds a challenging and/or interesting problem. (I am not sure how much effort this requires. I also don't know how to identify a problem as "interesting" or "challenging".)

  
  


• 
  

  The supervisor comes up with an interesting research problem or question and then presents it to the graduate student. (This appears to be a common pattern, given the plethora of complaints that I see on-line about uninteresting research.)

  
  
  

I would especially like to see responses from professors who are supervisors and also from graduate students.

Answer

Any of the scenarios you describe can happen, in practice. (I am in the United States; this may differ in other countries.) It depends on the student's interests and abilities, the advisor's interests and advising style, how broad advisor's interests are, whether the advisor has funding for a particular project and needs a student to work on that problem, and many other factors.

All three have happened within my own research group. (Another possibility that happened in my research group that you haven't mentioned: student initiates a collaboration with another researcher, who proposes a topic, and involves the advisor in the project as well.)

Actually, the scenarios you describe are not discrete scenarios, but a spectrum from "most student-driven" to "most advisor-driven." Some points on the spectrum include:

• Student enters grad school with a topic in mind that's judged acceptable by advisor, and proceeds with that topic.


• Student enters grad school with a topic in mind, that evolves and changes following advice from advisor.



• Student enters grad school with a general idea and, together with guidance from advisor and extensive reading of literature, shapes it into a topic.


• Student enters grad school without idea, advisor suggests general direction, and upon extensive reading and with guidance from advisor, student shapes it into a topic.


• Advisor hands student idea, and student proceeds to execute idea. Of course, this is a PhD, so as student works on the topic, the student's mastery of the specific research will most probably come to exceed the advisor's, even though advisor originally proposed the idea.

Other scenarios include: student enters grad school with idea in mind and then changes directions completely in middle, student enters grad school with idea and changes advisors in middle but keeps idea, and many more..

publications - Why would my former colleagues acknowledge me for a nonexistent contribution?

I spent a postdoctoral period in China, where I faced number of issues with the administration and supervisor. In short, I felt exploited in many ways, from payment and funding restrictions to being constantly asked to provide unfair “favours” and contributions.

During my stay, I was constantly asked to revise manuscripts for language and suggestions. I am a critical person, and the local culture is refractory to open criticism. Still, whilst my suggestions seemed to be typically ignored and made others uneasy, my lab mates would continuously ask for my opinion on manuscripts under preparation. They usually acknowledged my contributions in the acknowledgments section. Exactly why they would ask me for suggestions when they didn’t seem to appreciate them had always puzzled me.

However, since my departure they have published three papers I have never seen whilst acknowledging me for suggestions. For example, this is the latest of these papers they wrote:

We thank Dr. [other researcher], United States; and Dr. [Scientist], ZZZ, China, for critical reviews of this manuscript.

Awkwardly enough, these are papers directly within my area of expertise, which were surely under preparation during my presence, and first-authored by close colleagues. (Meaning they certainly refrained from mentioning these projects around me, at least in English).

Why would someone acknowledge a nonexistent contribution from a close colleague? Especially on a project that was apparently kept secret? It feels very awkward.

Answer

I see two possible reasons for their behaviour. Others options are possible.

1. They are using your name to reduce the chances of desk-rejection. I have heard that a well-known expert in the acknowledgements can be seen as a positive point for some editors.


2. They copy-paste the acknowledgements of a previous manuscript and forgot to delete you.

genetics - How can co-dominant alleles work in flower petals?

I am studying gene inheritance, and I understand complete dominance/co-dominance and incomplete dominant penetrance in flowers. I know how to recognize each case.

However, how does co-dominance work? If I understand correctly: when a gene is transcribed, both alleles are transcribed. Hence, for flower petals, if I have a "red" allele and "white" allele, and there is incomplete dominant penetrance, I get rose petals. However, if both alleles are co-dominant, why are petals either red or white? Aren't both alleles transcribed? Or perhaps, in the case of co-dominance, heterochromatin is responsible for shutting down one allele in lineage cells?

I hope that I am expressing myself correctly. Thank you very much for your time!

publications - Research paper feedback: "interesting idea but does not add scientific value"

Where is the border line between a novel, creative work and work that is of scientific value? I have received reviewer comments like:

the ideas are creative and interesting but work adds little scientific value.

What do reviewers look for when making such comments/judgements? They often do not clearly state what was missing in the paper. My field is computer science.

Answer

Let me describe two extremes, though they come from very different fields.

In mathematics, if you re-prove an old well-known theorem with a new technique that might be applied elsewhere it will be very interesting, whereas if you prove a new theorem with only old standard techniques it may have much less interest.

Similarly, in Computer Science, a boring and straightforward program might answer an interesting question. If the question isn't about CS itself, this might not be considered "scientifically interesting", whereas if it were a longstanding CS question it would be. On the other hand an interesting and creative program might answer a question of no significance. This might be judged either way.

In many of the sciences (chemistry, psychology, ...), you can, and many do, use very standard statistical techniques to answer questions. But to be interesting, the questions themselves have to be significant since the technique isn't. However, what is significant to you might seem trivial to others and vice versa. Even if you use a "creative" technique to answer an insignificant question it might not have much scientific merit unless someone can conceive of using that technique to answer other, more significant questions.

So, the variables are, at least, (a) the question attacked (b) the techniques used. I'm guessing (only) that the comments you got imply that you are strong on (b) but not so strong on (a) and the reader didn't extrapolate. But it depends on the field.

writing - Should supervisors read acknowledgments before the printed version of the thesis?

I'm finishing my M.Sc. thesis and I sent it to my supervisors so that they can read it.

In the final version, I would like to insert an acknowledgements page where I thank them. Should I include it in the last draft that I will send them, so they can read it? Or should it be included in only the final version, without their knowledge?

Answer

There is no need to remove the acknowledgement in the final version. I know students have done so and for very different reasons, they want to "surprise" someone, they are not on friendly terms with an advisor and does not want the advisor to see it before it is printed. etc. The "surprise" aspect is, I would argue, greatly overrated. To not provide it because of a conflict is not likely to help the conflict. So, even if the reason is non-controversial, not including it might raise an eyebrow of a sensitive advisor. In the end, this is something that should not matter but some people are overly sensitive so ask yourself, are you confident that you will reach your intended effect by doing what you suggest, then go ahead, but if you do not feel so, avoid it. You will sometimes be surprised how much is read into a benign text such as an acknowledgement.

What is the point of a non-confidential reference letter?

In this question, it seems that most people think it is acceptable for candidates to see their references. I find this very strange, as in the vast majority of case I have come across it is expected or required that all references are confidential.

What is the point of having a reference that the candidate is able to see?

The person reading such a reference has no way of telling whether any praise is genuine or simply included to please the candidate. Likewise, the chances of negative points being included are minimal, even if they are very important. Thus the reference becomes little more than a vague sign of support. I understand that in business that is generally sufficient, but in my experience academic references are relied on much more heavily to discriminate between candidates.

research process - How can a researcher improve his contribution to society?

As an academic researcher in a theoretical field at a public institution, I am sensitive to the social value of my work (my own contribution to society). I do some teaching, whose contribution to society is easy to identify, but not much. Try to increase that aspect of my job, I have listed some things I can do (some of which I already do, some of which I don’t):

• Engage in collaborations with industrial partners (favoring transfer of knowledge to practical applications).


• Orientate one’s research goals to match an area of societal importance (green gas reduction, nuclear waste storage, you name it).


• Communicate science to a wide public, whether it is my own research or the knowledge of my field in general (popular science). This includes writing articles in magazines, writing a blog, developing educational software, …


• Get involved in education science: contribute to my national society of physics and chemistry teachers, for example. Offer some software for high-school and university teachers to demonstrate concepts.


• Register as an expert with the nearest court of law.

What other suggestions do you have to improve one’s social value? (Or should I stop worrying and love the bomb?) I mean, in the short term. I know that I (and my colleagues) contribute to the advancement of mankind in the very long term, but sometimes it doesn't help feel useful.

Answer

Have you considered contributing to political life? I refer not to upholding one political view or another, but rather to ensuring that there is informed scientific input on major issues when they are being debated in political circles.

I do not know in which country you live, but I am aware that there are far too many "first-world" countries in which the policy and decision makers are poorly informed at best, willfully ignorant - seemingly - at worst.

One of the best descriptions of a university that I have come across is that it should - must - act as the "critic and conscience of society". In my view this would include taking part in ensuring those that lead us are well informed.

One way this could be done is by taking an interest in the advisory process used in how policy is formed in your country. See if you can offer your specialist views via your professional association.

A related activity is to take part in advising courts when they are considering issues based on scientific topics. This would include contributing to amicus curiae briefs, for instance. This goes beyond acting as an expert witness in court. An amicus curiae brief presents a reasoned argument using a balanced analysis of facts, reaching a conclusion. A court expert, in contrast, offers answers on specific questions from the court.

career path - Possible pitfalls of taking a year off to travel following a PhD instead of immediately starting with a post-doc position?

If a student, soon to complete a PhD, is not ready to enter academia is a year of travel a good option? Assuming that academic route is still interesting after the year will post-doc positions (leading to tenure-track) still be a viable option?

graduate admissions - What to write in email to potential PhD advisor?

I would like to apply for following PhD studies in the Nordic countries, particularly in the field of Computer Science. The problem that I found is that it says in the admission procedure that "before applying one should get a Professor or Researcher that agrees to supervise the applicant".

I have checked up the personal webpages of the Professors and I have found their topics of interests, publications and so on. I like a lot of the topics in which they make research, but I do not really know how to address an email to them asking if they would agree to supervise me. Particularly I have the following doubts:

• 
  

  Should I make a small research article putting my ideas about one research interest of them? The problem here is that I believe I would not have the enough time to go through a lot of papers made on their reseach groups. What can I do if do not have the enough background? Time is running fast for submitting the application and I do not believe I would have enough time to study in deep their research.

  
  


• 
  

  Should I send my CV and ask to a specific Professor that I have interest in following PhD studies under their supervision, and if it would be possible if he or she to send me some open question or open research task so that they could see that I will manage to do it well on his or her research group?

  
  
  

I will transcribe what the ad specifically says:

1. 
   

   You must do your best to find a suitable supervisor at the department who agrees to supervise you. Please see the research pages of the department, and especially the descriptions of the research groups.

   
   


2. 
   

   You must agree on a study plan, a research plan and a financing plan together with your (found) supervisor, and submit an application to the steering committee of the department's doctoral programme.

   
   
   

also about the supervisor it says:

A student who wants to become a PhD student should start the application process by finding a supervisor at the department, who works in the field of interest of the student and who is willing to supervise the student. If the student is unsure of which supervisor to contact, he or she may first contact the research coordinator of the department who will steer the student in the right direction. Generally, a supervisor is a professor and/or principal investigator employed by the department.

For what I read it seems, at least to me, that one should really have in mind a good research proposal before applying, am I wrong? or only with an email will suffice to contact the potential supervisor?

What should I do in this situation?

Thanks

time off - What is the perception of students who take a gap year between their graduation and starting graduate school?

I am an undergraduate mathematics major, entering my fourth year. I plan on applying to graduate school, but I have not yet taken the GRE exams, and there a few key courses (Topology and Algebra in particular) that I have not taken yet, so I am hesitant to take the Advanced Math GRE too soon. (If you're wondering why I haven't taken Topology and Algebra yet, it's because I was trying to secure a CS degree, which sidetracked my mathematical studies last year. It was a healthy branching out experience, and one that helped me realize my true academic passion.)

My main question: what is the perception of students who take a gap year between their graduation and starting graduate school?

I think I will take the GRE tests this fall, a) for practice and b) if I score high, then I might as well apply sooner rather than later. However, I ask this question to gauge how much energy I should put into preparing for the tests this fall. If I hear, "You should really do your best to avoid any gap in your education," then I will work my butt off in preparation for the tests. But if I hear, "It's totally okay take a gap year before going into graduate school," then I would give myself more freedom in terms of my non-standardized-exam studies, extracurriculars, and in general social activities. I figure the answer to this question won't be as cut-and-dry as I hope, but any advice would be appreciated!

Just to clarify, my gap year would not consist of me sitting at my desk taking practice GRE exams all day... That would be a pitiful use of my time. I definitely plan working either as an intern or a research assistant at a successful organization. It seems like the general consensus is that taking time off is okay, and potentially beneficial, assuming you actually do something in that gap.

botany - Mating types in fungi (and somatogamy)

I would have some related questions about the mating types of fungi.

1. 
   

   Does a single spore generate a mycelium possessing only one mating type? If it does not in general, do Ascomycota and Basidiomycota possess only one mating type per individual mycelium?

   
   


2. 
   

   Are homothallism and heterothallism properties of the individual mycelium or of the species? The definitions that I find in my book and on line confuse me. I understand that homothallism is the property of a mycelium (possessing only one mating type or can it possess many mating types in a similar way to hermaphrodite animals? cfr. question 1) that can mate with itself (if it can possess many mating types and it can mate with itself only by using gametes of different mating types, is it still homothallic?) and heterothallism is the property of a mycelium that is not homothallic, but I am not sure I understand, because I read of homothallic and heterothallic species too: is a homothallic species a species where at least some individual is homothallic, where all individuals are homothallic or something else?

   
   


3. 
   
   

   I am sure that mating type is a property characterising at least gametes, but is it a property of indiviual cells too? As an example, I know that it is necessary, among many species of fungi, for two gametes to belong to two different mating types in order to produce a zygote. Some fungi, as it is the rule among Basidiomycota, reproduce by somatogamy, i.e. the nuclei generating the zygote are from somatic cells, other than gametes. In such cases, are there species where it is necessary for the somatic cells of a homothallic mycelium to belong to a different type than the type with which they are undergoing plasmogamy? Thank you very much for any answer!

   
   

publications - When should a supervisor be an author?

I understand that in a lot of big-lab fields it is common for the principal investigator to append their name to a paper even if they did not write the paper, design the experiment, or collect data since they spend energy securing funding, and managing the whole lab. What about for small labs?

What are the requirements for a supervisor to be included as an author on a paper, as opposed to just appearing in the acknowledgements? If you are working on your own projects independently of your supervisor, but using funding provided by your supervisor (how does this change when the funding provides resources versus just your salary), are you suppose to add them as authors or just acknowledge the source of funding?

Answer

Allow me to strongly disagree with eykanal's answer. There is no universal standard. You must ask your advisor in advance what her coauthorship policy is.

In theoretical computer science (and mathematics), it is generally considered unethical to list someone as a co-author who has not made a novel and significant intellectual contribution to the paper. In particular, merely funding the research is not considered an intellectual contribution. Adding a supervisor's name to a paper to which they have not directly, intellectually contributed is lying.

In practice, writing a good grant proposal requires at least as much intellectual novelty as writing a good paper. Most of the good ideas that PIs pour into their proposals also appear in papers; as long as those ideas constitute novel intellectual contributions, the PI merits co-authorship. But that only works once per idea; once an idea has been published, it's no longer novel, by definition.

To be specific and personal:

• 
  

  I am not a coauthor on all of my PhD students' papers. (Of course, I still report my students' independent work back to NSF as outcomes on whatever grants supported them. So I still get credit from NSF for having the foresight to fund the student.) The same is true of all the other theoretical computer science faculty in my department.

  
  


• 
  
  

  My PhD advisor is a co-author on only one of the papers I published as a PhD student.

  
  


• 
  

  My PhD advisor doesn't have a single co-authored paper with his advisor.

  
  

job search - Should I use my university's letterhead for a cover letter for a job application?

I currently teach at University X and am applying for a job at University Y. Should I write my cover letter on University X's letterhead, or use a blank page?

Answer

No. It is you as a person who is applying, not you as a representative for your university. Univ. Y would probably look very negatively on an application on such lerterhead, as would Univ. X. Letterheads are intended for your official business of your position at X as teacher, researcher etc. Applying for a job or for example writing somewhere for your private business is just that, private. You can, however, create your own private letterhead to use for such instances but this should reflect your private standing and show only private address, phone and e-mail.

So keep the official business separate from your private. As alluded to this also applies to e-mail, something most people forget about. It is good to have your own private e-mail for instances such as this.

Ethics of publishing received peer reviews

What are the ethics of publishing (on the web, etc.) peer reviews received for a paper? Does your answer change if the paper was accepted or rejected?

I am specifically interested in the "one-shot" case typical of computing science conferences, without rebuttals, where there is no or limited dialogue between an author and the reviewers.

This is quite distinct from Can I publish the reviews I write? as here I am talking about reviews I have received, not those I have written - the reviews' authors retain their anonymity, and presumably the paper would be included alongside those reviews.

Vijay's response below includes a summary of much of the other responses and my comments on those.

Answer

Let me add some data points to this discussion. Some items below are about discussing reviews and editors in a public forum and not about publishing reviews.

• Jens Teubner makes available the reviews to his papers online. I do not know him but I have heard from someone who does that he said he has not received negative feedback about doing this. Maybe you can ask him for more information.


• Doron Zeilberger has published reviews in Opinion 87 and for his paper Automatic CounTiling.


• Doron Zeilberger's Opinion 61 is about rejections and accountability (it has a response from Luca Trevisan) and his Opinion 81 is about rejection and snobbery.


• Peter Clark's mail to Doron Zeilberger about some material Zeilberger published online. This is only tangential to your question, but I think it's good to keep in mind that when you go down the road of open publication, you should be ready for others publishing material about you or your reviews.


• The Writings of Leslie Lamport chronicles in very direct terms the stories behind his papers including some notes about editors and reviewers (for example papers 62, 122,129, ).



• In The Writings of Leslie Lamport Paper 132 he talks about having written an 'unkind review'.

I have been meaning to publish my reviews for multiple reasons and I am glad to see that other people have been thinking the same and some have done it. I do not think the result or answer should depend on whether the paper is accepted or rejected. If reviews are published, I believe that one should also publish the version of the article that was used to make the reviews. Otherwise, the reviews are like quotations taken out of context. If there are coauthors, one should obtain their permission first, or at least include a disclaimer that you are publishing your reviews on your behalf only. As an example of a disclaimer, see Lamport's page:

Some of the stories read like complaints of unfair treatment by editors or referees. Such cases are bound to arise in any activity based on human judgment. On the whole, I have had little trouble getting my papers published. In fact, I have profited from the natural tendency of editors and referees to be less critical of the work of established scientists. But I think it's worth mentioning the cases where the system didn't work as it should.

The notification of acceptance is usually signed by the editor of the venue, even in the case of anonymous review, so one should ideally obtain their permission if you will reveal who the editor is. The same applies for reviewer permission in signed reviews. I cannot tell whether people in the links I give above obtained editor permission first so there may be precedent for not doing so. Publishing reviews intended for private circulation still takes them out of context. I would add a disclaimer that the reviews and notification letter were written as private communication and if published without permission of named entities, I would note that too. The latter is in case your intention is to protest the status quo by subverting standard conventions.

I haven't answered your question because I don't have a clear answer. Publishing reviews is not conventional academic behaviour. Doing so can be construed as unprofessional depending on how you publish them and what additional commentary you add. Calling it "unethical" seems a rather heavy handed judgement to make. There are things an anonymous reviewer can do that are clearly unethical (steal research, suppress publication, circulate the manuscript) or questionable depending on context (force citations, comparisons, reject without reading, write ad hominem reviews etc.). There is very little an author can do to wrong a reviewer that is remotely comparable and publishing a review does not seem remotely on that scale to me.

There are multiple reasons to publish reviews including accountability for all parties involved (including authors) and as a form of protest. I believe this intent is important to consider because forms of protest do subvert what may be considered acceptable behaviour. A useful thought exercise might be to put yourself in the reviewer seat and ask if you would be fine with similar treatment. I would not have an issue if the reviews I have written were made public (even if I knew that stylometric techniques could be used to identify me). I do not think all reviewers feel that way.

Finally, let me point again to Jens Teubner's page, which comes across to me as a model of how to publish reviews while retaining professionalism and dignity.

graduate admissions - Would it be okay to provide a template when asking reference?

I am applying for grad school this year and I am considering sending an email to ask a professor to write me a reference. He had previously agreed to write me a letter because I took one of his advanced courses.

I am not sure if it'd be okay for me to offer to provide a template to him for the letter. The reason I want to do this is I will be applying for a PhD in a different, though quite related, field, and I want to make sure that he knows what the advisory committee will be specifically looking for in his letter, and make sure that his letter corresponds well with my statement of purpose.

Is this an acceptable practice between professors and students? Or would they consider it offending since he is supposed to provide his independent opinion? And if it is okay, how can I offer it in an appropriate way?

Answer

Personally, I would be somewhat offended if a student gave me a template for a letter, and I wouldn't use it. (Unless I had asked for one, which personally I would not.)

However, it is perfectly appropriate to say, "I believe that the committee will probably be interested in my ability to dangle participles and reticulate splines; it would help if your letter could address this." It is also fine to include a list or resume of your other activities that he may not be aware of, but leave it up to him how to use this list.

It's quite possible that your professor has written letters for students in this different field before and already knows what is expected. Also, for letters which are submitted online, the writer normally gets a message from the requesting institution explaining what issues should be addressed.

sensation - What's the frequency resolution of the human ear?

I was thinking about audio compression (namely mp3), that "filters" out sound that we would not likely hear.

The MP3 lossy audio data compression algorithm takes advantage of a perceptual limitation of human hearing called auditory masking. from: http://en.wikipedia.org/wiki/MP3

I've also checked the wiki entry for auditory masking, and found this:

If two sounds of two different frequencies are played at the same time, two separate sounds can often be heard rather than a combination tone. The ability to hear frequencies separately is known as frequency resolution or frequency selectivity. When signals are perceived as a combination tone, they are said to reside in the same critical bandwidth.

My question is how much is this critical bandwidth or what's the smallest frequency difference we can perceive as two different tones, if you wish. Let's assume that both tones are equally loud, are coming from the same direction and distance and we are in a quiet room - so basically we eliminate as much noise and affecting phenomenons as possible.

As @ sanchises pointed out (thank you again!) in the comment section the frequency resolution is 3.6Hz between 1 and 2kHz. But since perception threshold is a function of the pitch of the sound I'd assume that the ability to resolve two tones would change with pitch too. Does anybody have any data on that? For example resolution X pitch graph.

Answer

The frequency limen, or frequency resolution can be determined in various ways using psychophysical measures. You refer to a simultaneous method, in which two (or more) frequencies are presented at the same time. This has consequences for the test as different frequencies are perceived with different perceived loudness under constant sound pressure levels, meaning that additional cues are present besides pitch cues.

One carefully controlled study Zwicker et al (1957) in this regard defined the critical band basically as "those frequencies where no intensity summation occurs", meaning that adding those frequencies (below or above the center frequency) do not result in differences in loudness perception (as expressed in acoustic threshold of the center frequency). This method nicely prevents loudness summation cues by deploying them in the criterion. This article shows the following picture (after Zwicker et al. (1957)):

The critical band (upper graph) is dependent on frequency, and ranges from 0.1 kHz to >2 kHz.

The markedly lower difference limen of 3.6 Hz as touched upon in the comments may have been obtained using an alternative psychophysical test where the test frequency is modulated by another frequency (bottom graph). This procedure is based on adding a frequency to a certain sinusoidal stimulus, basically resulting in a single stimulus instead of two (or more). This procedure is technically not defined as a critical band and indeed results in a difference limen of ~3.5 hz and up. The other graph plotted in the figure is a masking procedure (middle plot), which basically determines the physiological overlap between frequencies in the cochlea in the intensity domain by determining the amount of masking from one frequency by another.

NB: The authors worked with headphones so no effects of direction.

Reference
Zwicker et al. JASA 1957; 29: 548-57

phd - How to deal with constant pressure given by advisor

I am a third-year PhD student in mathematics from a very reputed institute in my country. I have one problem to share and discuss that is related with my guide. He is a senior professor in our department. The day I joined that institute he gave me one research problem and asked me to study about that and present. I did as much as I can and presented. In return, instead of appreciation I was being scolded for small mistakes. And it has continued for the last two years. Seniors say it is his way of working. I have lost my happiness. Sometime I cry for joining this course. My prof is not impressed with my good academic record and my hard work.

Second thing that worries me is that he is not much aware of my research problem. I feel like I know much more than him. He has no paper on that topic, although he has a good number of papers in other topics. I never got help from him in solving research papers. I have to study papers on my own and then have to present to him. And again for small mistake I have to suffer his taunts. I am scared whether I would be able to finish my degree in such an environment or not? Is this normal? Does every PhD student suffer such mental trauma?

I need advice. Thanks.

Answer

Every PhD student suffers mental trauma. You say your advisor "scolds" and "taunts" you. I think of scolding and taunting as personal attacks, and hence unacceptable. That said, your English makes me unsure if he is attacking you or your work. Attacking someones work is a common occurrence in academia. We tend to get one sentence notifications about our successes and pages and pages of feedback about our failures. Even the best researchers fail more often then they succeed. The key thing to remember is that, in general, it is not personal. You need to identify if your advisor is attacking you or your work.

You say your advisor "is not impressed with my good academic record and my hard work". Successful academics tend not to be impressed by academic records and hard work since it is par for the course. This doesn't mean they do not respect you. The best way to find out what your advisor thinks about you is to ask. Ask what you are doing well and what you can work on. Also say that you are feeling unsure of yourself and looking for reassurance. Some advisors will give you reassurance and a shoulder to cry on, others will simply tell you that you are not failing. Not failing is another word for a major success.

gene expression - which exact mechanism triggers the first cell differentiation after n divisions?

I would like to understand which mechanism triggers the first cell differentiation after n divisions.

I read previous articles on SE and Wikipedia articles on cellular differentiation and embryogenesis but still fail to understand what exactly makes it so that starting from a given division cells suddenly start to be different.

Wikipedia claims that

In the first hours after fertilization, this cell divides into identical cells. In humans, approximately four days after fertilization and after several cycles of cell division, these cells begin to specialize, forming a hollow sphere of cells, called a blastocyst

but do not explain why they begin to specialize.

I could imagine

• that a cell has a "counter" on the number of divisions which triggers differentiation after a given amount of divisions


• or a chemical substance (either cell-borne or external) forces a change in the division

but why some cells would become "cell A" and some others "cell B"?

I am fairly sure that the biochemical mechanisms which regulate the life of a grown up mechanism can explain cellular differentiation (through hormones for instance) -- I am however interested by this specific moment, this n-th division where identical cells become differentiated.

Answer

The first differentiation in human embryogenesis is from early blastomeres into trophoblast, which forms the outer layer of the blastocyst, and inner cell mass (ICM). It may be unsurprising then that cells on the inside of the 8-16 cell stage morula differentiate into ICM whereas those on the outside differentiate into trophoblast. However it is currently unclear whether this is a causal relationship (the inside-outside model) or whether blastocyst patterning is set-up earlier in cleavage (such as in the apicobasal polarity model) or if it is some combination of the two.

You were correct in imagining that tissue patterning is determined by chemical substances: a very broad class called morphogens. Cells don't necessarily count how many times they have divided but cell division can certainly affect morphogen concentration and localisation. I suppose in some sense you could describe this as a clock. I wouldn't though, especially because mammalian cleavage is asynchronous.

One line of studies showed that a transcription factor called Tead4 specifies trophoblast$^{ref}$. It was then shown that Tead4 can be regulated by cell-cell contact (mediated by Hippo signalling) $^{ref}$. They hypothesised that the magnitude of cell-cell contact could provide a mechanism by which Tead4 localisation could be controlled in presumptive trophoblast and ICM. This could explain why the cells have different fates because inner cells are completely surrounded (more cell junctions) whereas outer cells are largely exposed to the medium. Note that I only provided that as an example of a possible mechanism. It is not confirmed and, as with any model, the real picture is incredibly more complex and likely involves many factors.

I'm reluctant to go into too much detail on this because you're asking about a complex process that is still under active study and I'm unclear as to how much information you actually want. A book could be written on this subject alone, and many review papers have been published. Here's a recent one:

Development: Do Mouse Embryos Play Dice?

I suggest you read that and then if you have further, more specific questions, we can try and answer them for you.

taxonomy - What is difference between breed, variant, subspecies and species?

What is the difference between breed, variant, sub-species and species? Are there any similarities between sub-species and sub-population of a region?

theoretical biology - Stochastic parameters in population growth equations

I'm more of a mathematician than a biologist, so I had a question about an application of the population growth equation to real-life models, and thus would like to ask biologists for their insights. The equation I'm looking at is the following (in reality, I have n-species but it's just an extension of this two dimensional problem):

$$ \frac{dx_1}{dt} =x_1\Big(b_1-a_{11}x_1-a_{12}x_2 \Big) $$ $$ \frac{dx_2}{dt} =x_2\Big(b_2-a_{21}x_1-a_{22}x_2 \Big) $$

where the $b$ are growth parameters, and the $a$'s are all parameters describing interactions among the species (and carrying capacity). The papers I've looked at for stochastic perturbations with these equations have primarily dealt with stochastically perturbing either the $b$ parameters while holding the others constant, or perturbing the $a$ parameters while holding $b$'s constant. However, these papers are written by mathematicians with no biological experience, so the decision on which sets of parameters to perturb are somewhat arbitrarily decided without any biological basis.

For the biologists, can someone suggest some cases for where it would be more biologically reasonable to perturb the growth parameters and some cases were it would make more biological sense to perturb the interacting parameters? I ask because I'm a part of some interdisciplinary neuroscience project which is using equations of this form to study interacting neuron clusters, but since I'm a math person and not a biologist, I am trying to understand reasonable explanations for what stochastic perturbations mean biologically for these parameters.

job - How can I transition from industry to academia without having a college degree?

I've been working in the "private sector" since my late teens. I've gathered good web-development experience to be able to find work quite easily thankfully. I was never really interested in getting a degree, I only have a high-school diploma. I was passionate enough to study for myself and learn new things from colleagues and friends.

Web-development is still my passion, however recently I've been thinking about the actual work that I've been producing over the years for the companies I've worked for. It seems as though that even if the work is fun and challenging, I still get very little recognition for it: once the work is produced, my name is barely ever mentioned. I've been asking myself if all these things I'm building are really going to change someone's life.

Then I look at academia and research. Here people are doing things they actually love and study those subjects deeply with passion and generate new knowledge to help others within a specific field.

Has anybody ever switched from an industry job to an academic job? I'm wondering if it's possible to do research without a degree. What suggestions might you have for someone in my situation that wants to get a glimpse of the life of an academic where you can build and study something you actually love and not always do what "the company" wants.

Answer

If recognition is your key desire, academia will only be marginally better for you than your current situation. Just because your name is on a paper, doesn't mean anyone is going to care about your work.

I feel like there's a couple of threads in your question outside of recognition though. I'll make some comments where I can.

• 
  

  To transition into academia and start working on your own ideas you'll need to probably start a degree program. Masters and PhD programs, more than anything, are training programs on "how to work on stuff".

  
  

  It seems obvious right now that you have hundreds of ideas and the skills to pursue them -- but the academic context is a bit different. Research typically fits into a larger context than a single project, and you'll need to be able to sell your ideas to people who are experts in the area; most research projects that aren't 'consumer' oriented produce papers, not projects, so you'll need to learn how to write papers. The requirement for evidence is (or at least ought to be) high, which means that you'll need to learn what kind of evidence you have for your hypothesis, how to gather it, how to present it. All of this, the politics, the nitty-gritty of putting together a paper, is what you ought to get from a degree program. You can try to do some of this on your own to be sure, but it's not an easy ride.

  
  
  


• 
  

  If you want to get a feeling for what working in academia is like, without getting the degree, I'd seriously look into the possibility of becoming a programmer for a university. This helps you get a feel for what the work, environment, people are like. It could be that if you find the right project, your influence will be sufficient that you can get the recognition you want, without having to get the degree.

  
  


• 
  

  Reading your question, I get the feeling of a grass-is-greener illusion. One thing that might be worth considering is: How much of the problem just your job? Could you find work at another company, in another niche, doing some other kind of programming that could be better for you? I feel like you could get 99% of your desired outcome not from academia, but from a job change. Maybe you need to go deeper into the stack; work with a company that builds the web technology you use. Maybe you need to go higher in the stack; start building client applications to the web technology you use. Maybe you need to get away from the web... perhaps start looking at transitioning into games, or hardware, or.... the list is endless.

  
  

What title to put on a professional business card, for a person with a PhD

Is there a correct or preferred format for indicating 'Dr' or 'PhD' (or both) on a professional business card.

Background: I am employed in the industry and I have just earned my PhD (in social science). My company wants to update my business card.

The following are two options:

• Dr Name, PhD, University Name


• Name, PhD, University Name

I am told that it may be a sign of arrogance but I am also told that if you have earned it, you deserve it.

Answer

"Dr Name, PhD" is redundant, so this usage is often discouraged. If you are going to indicate the degree, I'd recommend "Name, PhD" rather than "Dr Name" since it's more informative (at the very least it will keep anyone from thinking you are a medical doctor). In the U.S. it's not common to indicate the university, but I think I've seen it more often in other countries.

I'd suggest thinking carefully before indicating your degree on a business card. Some people without PhDs may respond bitterly, like you are bragging about your accomplishments or implying that your expertise is more valuable than theirs. At the same time, some people with PhDs will look down on it as well, in a status hierarchy:

1. 
   

   Some insecure people without PhDs feel resentful and don't want to be distinguished from PhD holders.

   
   


2. 
   

   Some insecure people with PhDs try hard not to be confused with group 1, thereby irritating those people all the more.

   
   


3. 
   

   Some better-established PhD holders aren't worried about being confused with group 1, but now they don't want to be confused with group 2, so they pointedly denounce emphasizing your degree as being tacky and in poor taste.

   
   

As a rule of thumb, I would omit the degree from your business card unless it's important for your credibility (i.e., the skills from your PhD are professionally important and people would otherwise assume you don't have them).

The one situation in which you should absolutely not indicate a degree is if it's irrelevant. For example, if you're an accountant with a PhD in literature, then your business card should not read "Name, PhD."

terminology - What is the difference between these two depictions of chromosome?

I understand that this is a single chromatid, but would this be considered a chromosome? Also before mitosis, the chromosomes appear as single chromatids but during interphase they replicate to form sister chromatids which are attached by a centromere and are also collectively known as a chromosome. I do not understand the difference between the two of them. Are they both to be termed chromosomes?

administration - What is a "graduate school"?

Specifically, why do some universities have a defined "graduate school" and associated "graduate faculty," with separate appointment process, and some do not, even when they offer many graduate programs? What is the organizational and administrative thinking behind this?

phd - Why do universities fund Ph.D. students in the sciences?

I was recently accepted into an applied math Ph.D. here in the U.S., and being the 1st in my family to graduate from university, I had a hard time explaining to them why my university will be spending close to 50k on me per year (stipend, tuition, health insurance, fees).

I know that I will be working for the university as a TA, and that perhaps that will go towards covering some of the costs outlined previously, however, it hardly seems to justify the full expenditure.

Answer

A good question. Why would the school make this investment (which could be closer to $100K/year)?

1. As pointed out, if you are TAing/grading/teaching, you are providing services that the school charges undergraduates for.


2. The funding of a university is not entirely like that of a business. Some of the money is a direct investment in purely academic pursuits, especially that from grants. Educating people and doing basic research is part of what that money is allocated for.


3. Averaged over all the graduate students, the direct value that they provide to the university in terms of research which goes on to get grants/prestige/donations/patents is substantial.


4. There is a non-trivial chance that you will become a wealthy donor to the school.

professors - Are salaries for academic jobs in New Zealand negotiable?

The academic salaries and compensations in new zealand universities seem tobe fairly low compared to most other countries such as US, UK, Australia, etc. Is it however possible to negotiate the starting point in the prescribed academic levels (read: salary levels)? Are the salary levels also related to the No of years post phd?

graduate admissions - Is it necessary to double major with math to be considered for theor. physics grad school?

So here is my situation.

I'm an undergraduate physics major right now (second-year) at a moderately-good university. I've experienced a bit of analysis and algebra (and almost nothing in topology, which I should change), and I like it (I do study maths on my own time - I like [complex] analysis best). However, my style and preference gears me more towards physics than anything. I've experienced working under an experimental nuclear physics group for some time now, and I love it, but it has shown me that I'm probably better suited with theoretical physics. I'm not saying that because I've proven to some people to be a genius at mathematical physics [maybe I could become one :-) ], but rather because that's where my interests seem to lie.

But I've noticed something. A lot of smart students here and theoretical physics professors at various universities come from a double math & physics backgrounds (a few just from math), and I was wondering whether I should go down that same path. I've avoided it so far because I felt that with the topics I've learned on my own, I've gone more in depth and personal as compared with my classmates, and so I feel that it is in my best interest to continue to do so with my math courses. Also, I feel that getting the math degree will only take up time and my full-attention from my normally planned physics track.

On the other hand, I feel that I could probably learn quite a few things from my math classes that I wouldn't learn otherwise. Professors already know the material they're teaching, so they typically know what to teach you. On top of that, if I wanted to enter a theoretical physics program for graduate school, I might have more of a chance of being considered with that extra degree.

Does getting a double degree in mathematics and physics better increase your chances of being admitted to a graduate program in theoretical/mathematical physics?

Answer

Obtaining a double major is helpful but not necessary. In making your decision, consider what you would do instead of obtaining the double major. Research experience will count for more than a double major.

teaching - Good questions for post-class survey

In order to get feedback more quickly, I've seen some teachers run a quick (certainly no more than 5 minutes), entirely optional, anonymous survey for students at the end of each of each class, meeting, or session. The idea is to get feedback on what is working and what isn't on a per-week basis before mid-term or end-of-term evaluations. What are good questions or prompts to use on a survey like this?

For example, I am currently planning to ask something like:

Any feedback on the BLANK? (e.g., was it rewarding, challenging, about the right about, etc.)"

Where BLANK will be the readings, lecture, and discussion for the class session. I will also ask a general question like:

"Any other feedback or things you think I should know?"

Answer

My class sessions each had a lecture and a period of time devoted to discussion. As a result, I ended up using a Google form with the the following four questions each followed by a text box:

• Any feedback on the readings? (e.g., was it rewarding, challenging, about right, etc.)


• Any feedback about the case and/or the other class discussion?


• Any feedback on the lecture? (e.g., about the right length, too dense, etc)


• Any other comments, ideas, questions, concerns, or reflections?

I sent a link to the survey every week after class and kept it online so that students could fill it whenever they liked. All answers were anonymous.

About half the class filled it out the first week and there was decreasing numbers who did so in subsequent weeks. Since I used feedback to make adjustments to the class over the quarter, this worked out just fine. I felt that the survey was successful enough that I plan to ask it again, in exactly this form, in my class this quarter.

genetics - What is heteroduplex?

I fail to understand the what exactly is heteroduplex due to unavailability of a suitable diagram. According to wikipidea:

A heteroduplex is a double-stranded (duplex) molecule of nucleic acid originated through the genetic recombination of single complementary strands derived from different sources, such as from different homologous chromosomes or even from different organisms.

Should the following highlighted structure be called heteroduplex?

Answer

What you've circled is not a heteroduplex. A better name for it would be "crossover" or "junction". Instead, the two duplexes at the bottom of your diagram are what should be labeled heteroduplexes. Your diagram shows one process by which you could generate heteroduplexes starting from homoduplexes.

Here's a better picture from the NCI Dictionary of Genetics Terms that more clearly shows the difference between homo- and heteroduplexes:

The two strands in a heteroduplex still have to have a high degree of sequence identity or they won't be able to form into a duplex in the first place. However, because they come from different sources there's likely to be many short subsequences in which one or more base pair is mismatched, causing a deformation as shown.

publications - Why do some individuals who are productive PhD students at leading Western institutions, then publish infrequently as faculty in their home country?

I am a computer science student from Turkey. While I was checking the websites and publications of various CS Professors in Turkey for my future studies, I noticed a strange trend. (Excluding minor exceptions)

Usually, these professors hold a Ph.D from leading western institutions, and during their Ph.D they have published papers at extremely competitive top venues, like ICCV, ICDM, ICML and other places depending on their research interests. But, after returning back to Turkey and starting in an academic position, they can't even get their papers published in second tier venues.

So, what might be the reason for this ? If these people can publish during their Ph.D then why can't they do now ? Also, CS is not a field where extremely expensive lab equipment is required. So why are these people unsuccesful at publishing in top conferences/journals ?

phd - Why is novelty mandatory for a Ph.D. degree?

The institute I am studying at has added the following requirement recently:

A PhD scholar must publish two papers in his/her corresponding field in SCI journals.

This means that a student cannot get PhD without two SCI rated papers. To the best of my knowledge, novelty is a mandate for such journals; hence, novelty has became mandatory for a student to get PhD in my institute.

In this context, I have the following query: Why is novelty mandatory for a PhD degree?

Consider a scenario in which a student is ambitious and wants to do research on an open problem or famous unsolved problem in his/her field. The student cannot attempt to research such a topic since research may be locally saturated, and he/she cannot come up with a novel idea. Does the rule not restrict the research on such problems? I can see the alternatives like tutorial papers, survey papers, etc., but some of these require only highly experienced geeks.

Note: Assume that neither the PhD student nor the PhD supervisor is an extraordinary person in that particular field.

writing style - How to handle swear words in quote / transcription?

In my research, I interview practitioners/real users. One of them, a native english speaker, used a lot a swear words (basically the f-word).

Question: how to deal with curse words in content you need to quote?

Since I use transcripts for a content (and not formal) analysis, I sometime 'smooth' interviewee wordings (like removing "hum", "well", "you know", and other recurring verbal tics). In some case, I could remove the f-word:

it's just super f*cking slow, and really f *cking annoying

However, in some cases it is less harmless, because it more deeply changes the perceived meaning:

if you don't want to do things, just don't f*cking do it

oh f *ck, we'll just go back to do, as we were doing

and in some other, I simply cannot change interviewee's words:

[...] he really tried and wanted to build up, but he completely f*cked up every single part of every single thing.

---

Since I am not a native speaker, I don't know how "bad" would using the f-word be perceived (which is why I tried to be careful here.)

In some cases, I could do a cut quote, e.g. "it's just super [...] slow, and really [...] annoying", but it looks like I'm not accurately depicting the wordings.

I've also seen on the internet people using 'f*ck' standing for the f-word. Could this be a solution? (I personally find this solution a bit prudish.)

Otherwise, could I simply quote them? Should I put a warning somewhere?

Answer

If you're quoting someone, quote them as they said it. We're all adults. In the literature world, we quote swear words and other potentially offensive things all the time and no one bats an eye. I've no doubt other fields are the same.

Personally, if I saw an asterisk or similar, I would presume you interviewed them via chat or email, and they actually self-censored. If it were a printed text, I'd think it a part of the edition you used.

publications - When should I begin publishing?

I am finishing my Master's degree in Mathematics and will be enrolled in a PhD program in the U.S. starting from fall. In my country (Russia) we have thesis as a mandatory requirement for all degrees (including BSc and MSc, not just PhD). I hoped that my Master's thesis would be good enough to be published, but my advisor says it is not (I derived some new results, but they aren't very generic and groundbreaking). My Bachelor's thesis was not published too.

My question -- is it bad to have no publications prior to PhD or is it normal to begin publishing only during PhD years? In my view no publications is understandable for BSc students, but I'm not sure about MSc. The question is not about admission (I was admitted to a couple of decent programs this year), but about general timeline and expectations from students in sciences, especially from Master's degree holders.

Answer

In mathematics in the US, it is normal to have no publications prior to beginning your PhD. In my experience, hiring committees will even tend to discount publications from before your PhD program, unless there is evidence that they are significantly more substantial than the typical REU fare. Most US mathematics PhDs never do a master's degree, and most who do don't produce a publishable master's thesis, so people also won't generally notice if your master's thesis wasn't published.

As you imply, though, you absolutely should begin publishing during your PhD program.

mathematics - How to overcome a mistake you make in your proof and regain motivation?

I am an undergraduate student in computer science, and I have been working as an undergraduate researcher in theoretical computer science for 7 months. There was this problem that my supervisor mentioned, and I worked on it for a while. But I only managed to solve a sub-case of the problem, which didn't interest my supervisor at that time. However, he wanted me to write a manuscript about it anyway. I put a lot of effort into writing it, but he didn't bother to read it. And we have moved on to other things.

A week ago, my supervisor called me, and he said that he found an interpretation of the sub-case of I've solved, that economists are interested in. And he said that we can publish it in a journal. So, I was really hyped. We met the next day, to review my proof. But when I arrived, I learned that a friend of my supervisor found an implicit assumption at the beginning of my proof which was clearly wrong.

As you can imagine, I was devastated. I've tried to find a workaround, and fix my solution, but I've just found another thing that I've overlooked. So I've lost my enthusiasm and self-confidence.

However, my supervisor claims he found a completely different idea to solve the problem. He explained it to me, however it has some parts to be completed. So he wants me to write a manuscript about it and fill the gaps. However, I cannot find any motivation to do so. I am overwhelmed by the feelings of failure and anger.

I know that I should be working on my supervisor's idea, but I'm so distracted with the mistake I've made. How can I overcome my mistake, and start to work again?

UPDATE: A month later, we solved the problem :)

Answer

As an early-career mathematician, I have had this experience, more or less exactly, several times. I think I've solved a problem (or made good progress toward doing so) and I become proud and emotionally invested, only to show it to a mentor (first my PhD advisor, then my postdoc supervisor) who quickly points out a fatal flaw in my reasoning. Sometimes, he will propose a different and much better method. I completely get how demotivating this can be. After all, I would think, why am I even working on this project if my mentor could do it himself more quickly?

But you have to overcome these feelings. Here are some points of view that helped me do so:

• 
  

  Trying things and failing is how we learn. There's a mathematical lesson here about why my techniques failed and my mentor's succeeded. There's also a lesson about how to do research: how to do sanity checks, how to avoid "premature optimization," etc.

  
  


• 
  

  My mentor is a professional researcher with decades of experience. Of course he can solve things more quickly than me. Even if it feels like my role is to work out the details of his ideas, I'm learning a lot by doing that. And these "brilliant ideas" are usually adapted from previously existing techniques anyway--it's more an experience gap than an intelligence gap.

  
  


• 
  

  Experiences like this keep me humble, which comes in very handy when teaching people who understand less than I do.

  
  

I would encourage you to try to power through these feelings of inadequacy. Part of being a mature researcher is not being afraid of being wrong.

Having said all that, a good way to avoid situations like this is to keep the person you're working under more in the loop while you're doing the work, so that they can steer you away from dead ends. In your case, it wasn't necessarily your fault that your supervisor didn't devote much time to your project, but in the future you should try to get high-level feedback earlier in the process.

graduate admissions - How to cite future conference poster session on CV?

How would you go about listing a conference/symposium poster presentation that will happen in the future on your CV if the title or abstract haven't been decided yet?

For instance, the future conference/symposium for my case is university run so it is certain that the proposal submission will get approved for presenting. However, I have not yet collected all the data so I do not have an abstract or title prepared.

I have seen some people put,

Last name, first initial. (year, estimated month). Title of presentation. Poster session presented at [location]. (Planned)

I thought about preparing a tentative title since I know the general topic, but wanted more opinions or answers from those that had a better idea about this.

I've looked around a bit on the internet and found some information on this topic but it was primarily on invited talks rather than planned presentations. Thank you in advance to those who answer!

*This is for the CV I will be turning in as supplemental material for Psychology PhD application.

Answer

With a future event so tenuous, I would recommend against putting it in your CV at all.

Even if you think your CV is thin, it will not be improved by putting in an abstract that might or might not get presented and that you haven't even started to prepare.