mathematics - How are mathematicians paid to do research?

How are (pure) mathematicians paid to do research? Let's say my interests lie in the foundations of mathematics and I want to do research in that area. How am I going to get paid for that in the traditional context of academia?

teaching - What gets included for Continuing Professional Development?

When you are asked to list what continual professional development (CPD) you have completed in the previous 12 months, where do you draw the line on what gets included?

• I would think attending a seminar on teaching skills should be included.


• A new degree, diploma, certificate, etc. would certainly be included


• I would think that participating on this or any other website (Academia.se) would not be included.



• I would think that discussions, no matter how long or involved, would not be included.


• How about reading books?


• How about watching a video series specific to the position?


• How about audio books?


• How about reading articles?


• How about research for writing articles on the subject of teaching (if you are a teacher)?

I would also think as a general rule that things done to improve a teacher's teaching or subject knowledge would count.

Answer

Seconding Damien's answer - it depends on who you are reporting to, and it depends on what they want. Ask for guidelines.

I report to a committee of peers in my department who forward my report with recommendations to the dean. I am judged in several categories. Explicit guidelines on what counts (and what does not) in each category are provided. I would earn credit somewhere for everything on your list. Each category is weighted differently, so I do not received equal credit for all activities. I have taken your list of activities and placed them into the categories for which I would receive credit, and added some of my own.

Instructional Design and Development - Activities to improve the courses that I teach and the methods by which I teach them.

• Attending a seminar on teaching skills


• Video or webinar series on the position


• Experimentation in teaching methodology


• Developing new materials that better suit the needs of the course

Teaching Performance and Feedback to Students - Activities that improve my interacting with students in and out of the classroom.

• Nothing from your list fits here


• Reflecting on student evaluations and using them to improve your instruction


• Faithfully keeping office hours and responding to students in a timely fashion


• Advising students and writing letters of recommendation for them

Scholarly Activity / Professional Development - Activities to improve my knowledge of my discipline and which improve the discipline as a whole

• A new degree, diploma, or certificate


• Reading books, articles, letters, reviews, etc. in your field


• Conducting research in your field, even if specific to education in your field


• Attending, and especially presenting at, conferences


• Submitting grant requests, and especially receiving grants

Service - Activities which forward the mission and goals of the department, the institution, the profession, or the community.

• Participating in Stack Exchange


• Serving on committees at the department and institution level


• Serving as department chair


• Being active (and especially holding an officer position) in professional organizations


• Educational outreach to the community

Collegiality - Activities that improve my relationship with my colleagues and improves my colleagues' abilities to perform their jobs.

• Discussions with colleagues focusing on best practices


• Sharing of teaching materials with colleagues


• Mentoring younger colleagues

Again, the specific answer to your question is held by the authority to whom you are responsible - your supervisor, department, department chair, dean, provost, vice president, etc. Ask for guidelines. If your supervisor wants you to be productive in the desirable way, you should receive guidelines.

biochemistry - Histidine aromaticity

I understand that the imidazole ring in histidine is aromatic. I also realize that it retains it's aromaticity when protonated. I am wondering why it is not mentioned at all in basic text books such as Lehninger? Also, across the web there are a number of places claiming that histidine isn't aromatic in all cases. Another reason I am a little confused is, if protonation doesn't harm the aromatic nature, then why is histidine such a weak base? Am I missing something?

cell biology - Mechanisms of bone growth

The length of a bone is caused by growth of hyaline cartilage which is then replaced by bone tissue. How do cells know whether they should grow the hyaline cartilage? What are the key molecules that trigger the synthesis of hyaline cartilage?

Answer

How do cells know whether they should grow the hyaline cartilage?

Both growth factors and cytokines are involved but the trigger mechanism is unclear [1].

Bones grow in length at the level of epiphyseal plate where chondrocytes produce hyaline cartilage which by addition of calcium and phosphorus ions turns into hard bone [2].

It is believed that the growth process is under the regulation of local mediators like cytokines and growth factors:

In recent years, a large number of cytokines have been discovered and their molecular structures and biological activities described. A surprisingly large number of cytokines have been shown to affect skeletal tissues, at least experimentally, making this a complex topic, but one which is furthering knowledge of how the cellular events of bone growth may be so precisely regulated [3].

---

References

1. Ossification. (2014, July 3). In Wikipedia, The Free Encyclopedia. Retrieved 15:47, September 30, 2014, from http://en.wikipedia.org/w/index.php?title=Ossification&oldid=615387908


2. http://www.personal.psu.edu/staff/m/b/mbt102/bisci4online/bone/bone5.htm


3. J.S. Price, B.O. Oyajobi and R.G.G. Russell. The cell biology of bone growth. Available from http://archive.unu.edu/unupress/food2/UID06E/UID06E0U.HTM

publications - Can we submit our research paper for review at two IEEE conferences simultaneously?

Can we send our research paper to two IEEE conference simultaneously, and then after acceptance, decide which conference proceedings to publish it in?

publications - What to do if reviewers reject a paper without understanding the content?

One of my friends submitted a paper to a reputable communications journal and received some reviews a week back. The paper was rejected, but the review comments were abysmal:

• The language was so bad in one of them that it was difficult to understand what the reviewer was hinting at. Besides, the comments pertained to trivial things like naming of axes and there was no comment on (or understanding of) the overall work.


• The second of the three reviewers rejected the paper in one line saying it was impossible for him/her to understand what the paper aimed at.


• The third reviewer appreciated the paper and its results and made good suggestions for improving the results.

The editor-in-charge has rejected the paper since the vote was 2/3 in favour of that, but my friend feels hard done as he feels the two reviewers did not merit to review the work.

What recourse does an author have if his paper is rejected by a reputable journal, but the review comments indicate a serious lack of understanding of the paper's work? Should the author write his/her grievance to an editor higher in the hierarchy (an associate editor, for example)? Or is ditching the journal and submitting it to somewhere else the only solution?

Answer

F'x has ably covered one possible reason: that it's not you, it's them.

I'm going to cover the other side of things. That is, starting from the assumption that the editor has made a good decision.

The authors should consider rewriting the abstract and introduction. If two peer reviewers didn't understand the paper, the paper may just need a savage reworking.

The authors may also wish to try working with a freelance development editor.

Finally, the authors might want to bring on board a co-author who's been frequently published: I expect that many decent-sized, decent-quality departments have at least one person whose quality of writing leads to get manuscripts getting accepted first time, pretty much every time.

And then submit to a different journal. I don't know the field, but I'm willing to speculate that there are a few reputable journals where the article could be published.

application - How to write PIs asking for PhD position?

I have read here that the best way is to keep it simple, be short and ask for meetings, which is a bit generic way to ask for a job. I agree more with the discussion posted here by a student in a similar situation as mine (I still haven't started emailing people but I've already have a long unfinished list).

Speaking with some PhDs and postodcs I know, they told me that the best way is to know somebody in and maybe write them first in order to introduce you to the PI before you send your email. Another advantage of this is that you will know if there is a position available or if it's not a good idea to work there (the people who actually work there might have the best advice about that). Finally, they might also be "more reachable" than the PI who gets thousands of mails. On the other hand, I don't know the people who work where I want to go so it would feel as impersonal as this question feels to you.

Given the fact that I may have to write several (around 20) of these mails I want to have a good strategy. I know it's a debate that mostly depends on the area. My area of research is Neurobiology of Memory and Learning but I might also be interested to change a little bit, maybe to Addiction (Always within neurobiology).

I would also like to add that in order to write a detailed email about the PI's research history and future path one must be able to have the time for:

1. Read the publications = A large amount of time


2. Actually come out with an idea that meets with the PI's expectations AND research interest/approach/knowledge AND more important technique capacity

Of course, being a PhD student means that you have to suceed in both of them but not for every research we would be happy to do (if we were accepted) in advance.

journals - Is it ethical for an author to cite their own work with themselves as first author when they are not first author?

I was reading through a journal article by an author. Let's call him Author X. The author while referring to some of his own journal articles cite them as Author X et al., even though Author X is not the first author in the cited article. Is this allowed or should it be treated as academic dishonesty?

job search - Will self funding a PhD hurt employment chances?

I am thinking of self funding a PhD in Applied Mathematics at either the University of Oxford or Cambridge. Would employers, both for academic (postdoc etc) and industry (research) jobs think less of a PhD holder if he or she is self funded?

E.g. Would they feel that because I failed to secure funding for their PhD, I am inferior to students who did? Although I am planning to self fund to UK schools, it would be nice to hear about views from across the pond (USA) as well.

Answer

There's nothing on your CV that needs to indicate exactly how you were supported during your Ph.D. In fact, if you were self-funded, and managed to get an occasional fellowship or other form of support, that's a plus !

All a recruiting committee should (and does) care about post-PhD is the quality of your work (for faculty positions there are additional issues). No one cares about how you were paid to do that work.

Importance of undergraduate honors thesis vs. research published in undergraduate research journal, for graduate schools in the United States?

I have the option of graduating from my university (U.S.) a semester early. If I do so, I would not be able to complete my honors thesis and have it approved by the honors committee of my university. However, I would still complete the same research project, write up the manuscript, and probably submit it to my university's undergraduate research journal.

For admission to psychology PhD programs in the United States, how important is the actual "honors thesis" component?

writing - Present math for non-mathematicians

I am a graduate student in mathematics, and I recently got the question why there isn't a press release to the general public whenever we publish a paper (to advertise mathematics and increase interest).

Now, every paper is a bit extreme, but forced me to ask several questions:

Would arxiv be a good place to put math text aimed to the general public? (I am currently trying to explain an article in a very metaphorical, but accessible to non-mathematicians).

Would it be considered strange to explain research for non-mathematicians either in a separate abstract in a paper, or also writing a shorter non-math version? (I fear that this is considered slightly odd, and metaphors sometimes dumbs down the problem so that the question seems very silly. Also, will professors think it is a waste of time?).

A partial goal is to be able to explain what I've done the last five years to my family at the dissertation, but also get some experience in explaining math for grant applications. It would be nice if news from the world of mathematics appeared more often in the news, (local news for smaller achievements, explanations etc).

Answer

I would recommend blogging. This seems like the standard procedure for explaining your papers both to the lay audience and to other mathematicians (potentially ones that don't work on your specific problem). The blog format is preferable over arXiv or journal publications for reaching the lay audience because it is more accessible. Links to blogs are easier to share and faster to read than journals (which might be behind paywall!) or pdfs from arXiv. A blog setting also allows you to interact with your audience through the comments, this is the best way to help guide them through any confusion.

A blog setting can also be used to provide casual tours through proofs for experts and graduate students. This has recently started in TCS. Since this is aimed at the slightly technical audience, it is more appropriate to put on the ArXiv, although I would still advocate blogs.

application - Answer to "Will you be able to provide proof of your identity and employment eligibility if you are hired"?

I am an European citizen applying for some academic jobs in US.

I have some doubts on one question I have to answer during the application process

1) Are you presently legally authorized to work in the United States?

My answer to this question is NO

2) Will you be able to provide proof of your identity and employment eligibility if you are hired?

What should I reply here? Is it referred to my future or current eligibility?

human biology - Getting goosebumps at will

I can get goosebumps at will, regardless of the environment. Its mostly visible on my arms, and I can feel it on my head. It requires some level of concentration to achieve this.

My questions are : what biological mechanisms are involved in doing this ? Is it common ? Is it useful ?

Answer

Interesting! I haven't seen anyone able to do this deliberately.

Goose bumps are caused by the tiny muscles at the base of hair follicles contracting, and the hair stands up. The skin around it puckers. It's mediated by the sympathetic nervous system (the "fight-or-flight" aspect of the system). This is how animals' fur stands up when afraid or upset (think of a scared cat).

It's called the pilomotor reflex. It also helps them keep warm (fur insulates) - so it happens when we're cold too. But since we have so few hairs, it's not very useful to us. It's more of a vestigial reflex than anything.

It happens for other reasons too. See the wikipedia article, it's a good place to start. For more info, look at this article or a medical textbook.

If you can do it at will, you likely are in tune fairly well with your sympathetic nervous system. That's excellent. You may be able to make minor alterations in your pulse and blood pressure through breathing regulation - check out the concept of biofeedback. It is a way to help manage stress, keep yourself calm in terrible situations, manage anxiety or panic disorders, anger management.....

Being able to use physical self-awareness to affect physiological changes takes practice to develop as a skill. You've got a great start!

graduate school - Is it true that 'nice' professors fail to produce good students?

This is a very tough question to ask because there are so many advisors on this forum so I am expecting most inputs from the current grads. This question largely stemmed from a post I read online about picking advisors.

The top recommendation offered on a list of things about picking supervisor is to never pick someone who is nice, friendly and available. Specific examples being "nice associate professor ladies" and "prof emeritus".

This quote caught my attention the most

If you’ve never cried before, during, or after a meeting with your advisor, something is amiss.

But this is just one person's opinion. So my question is to what extent does this idea actually hold in academia? Is there any truth to nice profs are less capable than mean profs in producing good students?

Answer

That advice from the blog says to avoid an advisor who

1. Is nice, and friendly, and available.

And never gives you the fierce criticism and the tough pushback that forces you to confront your weaknesses, take risks, stop whining, cut the excuses, get over your fears, and make hard decisions about reputation, money, and jobs.

It's the part beginning with "and never" that describes a problematic advisor, not the "nice, friendly, and available" part.

An advisor who is unwilling to criticize a student and share harsh truths when necessary is certainly problematic for many students. But I wouldn't necessarily conflate that with being "nice." For most students, an advisor who is genuinely nice is a good thing.

As for

If you’ve never cried before, during, or after a meeting with your advisor, something is amiss.

Doing a PhD is difficult and sometimes discouraging for most people. My advisor is one of the nicest people I know, and I've walked out of his office on one or two occasions and gone off somewhere to cry. Not because he isn't nice, but because what I'm doing is difficult, and sometimes we have to have some very difficult and/or discouraging conversations.

publications - Suggesting connection to one's own paper in a referee report

When acting as a referee, I frequently find that some of my papers could be relevant to the paper I'm reviewing (let's say, in a tangential manner). Is it reasonable to suggest the author take a look at my paper, or should I avoid this at all costs due to the risk of revealing my identity and sounding that I'm shopping for a citation?

Answer

It happens quite often that as an expert asked to review a paper, your own work is relevant. But you are right to be concerned that it might seem gratuitous. So just like it is often the case that papers authored by any member of the Technical Program Committee (TPC) are held to a slightly higher bar at a conference than other papers, to try to avoid the appearance of nepotism, I try to recommend my own papers only if I'm really sure they deserve to be mentioned. Avoiding them at all costs would do a disservice to the publication because important work might be missed.

As an aside, I recently served on a TPC where I contemplated mentioning one of my papers and decided not to. A different reviewer went to great lengths to point out why my work was relevant, and I'm 95% sure the authors would conclude incorrectly that I was the reviewer in question. Meaning: just because you suggest a paper doesn't actually mean someone can be sure you're the one suggesting it!

You show a reasonable sense of caution in posing this question. That is certainly all that is required.

evolution - Why do we grow so much hair on our heads compared to our bodies?

I've been wondering about head hair, facial hair in particular. Human males can grow very extensive beards should they choose to not shave - however you do not really see this in our chimpanzee cousins! Yes, they have little pseudo-beards, but the difference being that they do not shave, that is just the length they reach. Whereas in humans we can grow to our hearts content (*this may not be the case, see this question).

I can't really see why this would have been selected, unless it's simply that (evolutionarily speaking) women like men with long beards?

So my question is: why can humans perpetually grow head hair, yet we have lost the majority of our body hair, in comparison to chimpanzees and other ape family members?

Answer

Wheeler (1992; and previous) discusses the evolutionary loss of "non-functional" hair in hominids from the perspective of water balance.

Wheeler's hypothesis is that naked, bipedal hominids could have tolerated higher ambient temperatures as well as elevated metabolic heat production. Naked skin would confer higher levels of evaporative cooling, but would have entailed more water loss.

Wheeler argues that bipedalism necessarily would have preceded loss of hair, which seems to agree with Carrier's (1984) hypothesis that early hominids were distinguished not by large brains but by upright, bipedal postures with striding gaits. Humans are unique among similarly sized mammals in their capacity for endurance running.

graduate school - Would getting a faster MSc instead of just BSc affect admission chances for PhD?

I will try to describe my situation briefly. The university I'm currently studying at offers a 4-year Bachelor program in mathematics.

I am currently in my 3rd year and the program for the 4th year consists only of optional courses (which I choose). As I have taken a rather high amount of optional courses so far, I can satisfy my ECTS requirements for the whole program in 3 years. The university, in this situation, would allow me to graduate at the end of my third year. Then, I could pursue an MSc. degree at the same university for a year and graduate with an MSc at the end of my 4th year of study in the university.

I would like to note that this has been done before by other students here and I'm not fantasizing.

My intention is to apply for a PhD at a university in the USA after the 4th year. (I am not a US citizen and I haven't studied there).

My question is: would getting an earlier BSc and MSc degree affect (negatively or positively) my chances for admission in a top university in the USA? Should I just graduate with a BSc. in math? I know that sometimes having a MSc. from the same university can be a negative sign. Should I be worried about that?

Some other background: My current university is not really "elite" of any sort; it barely enters the top 600 in the world. I have a few published articles and I have participated in conferences. I am also currently pursuing an internship in a research institute in the country.

Thank you.

Answer

(I'm on the admissions committee of a top-10 US computer science department; my advice may be way off base for mathematics PhD programs.)

All else being equal, getting a master's degree in one year would probably count against you. You're far better off taking some graduate-level courses, and possibly getting some research experience, while staying in the BSc progam.

At least in my department, PhD applicants who already have master's degrees are held to a significantly higher standard than applicants who only have bachelor's degrees. While having formal research experience is an advantage for undergraduate applicants, it's a de facto requirement for applicants with an master's degree. One year is not a lot of time to get some real (meaning publishable) research experience, especially since most one-year master's programs have heavy coursework requirements. And you'll be competing with other MS applicants who've already spent two years in graduate school.

My department steers PhD-oriented undergraduates away from our 5-year BS/MS program for this precise reason.

diet - Ultra Pasteurization and Pasteurization

What is the effect of pasteurization and ultra-pasteurization on proteins, enzymes, and nutrients found in milk and other dairy products?

human biology - How long do your eyes need to adapt to darkness and reach full contrast?

I heard you should wait some time until your eyes adapt to darkness and are able to see smallest luminosity differences, otherwise you might overlook faint objects in the ocular. Are there any rules of thumb here?

What about looking for 5 minutes on your bright laptop, do you have to wait again the same time or wear some sunglasses? ;)

Answer

Actually, the US Army and Air Force (and I assume the Navy) teach their life support troops about this (as well as the aviators), since so many missions are conducted at night. It is actually some very interesting physiology involved in this. This Army Instructional manual should be of help (PDF File).

On an average it takes 30 to 45 minutes for your rods to be fully dark adapted to night vision.

It also covers things such as Mesopic vision and Scotopic vision, eye health, and how to actually dark adapt. I suggest it as a good read. It's less than 14 pages.

publications - Sources to cover open-access fees

As this question mentions and as I know from my (limited) experience, some journals demand a high fee to make the articles you submit to be available as open-access. For example, a quote from JVSTB Info for contributors:

There are no page charges required for publishing. Authors have the option during submission to indicate if they would like the article to publish as open access. There is a $2200 fee for open access.

I can't imagine every researcher to pay this from his own pocket. I can see some universities are willing to cover these fees. However, I am pretty sure that my own university will not pay for this. What other sources to cover open-access fees I can look for?

Answer

Per the Scholarly Publishing and Academic Resources Coalition (SPARC)'s guide to open access income models:

According to one survey, article processing fees are wholly or partially subsidized, either by a research grant (34%), a foundation grant (5%), or by the author’s host department (8%) or institutional library (27%). The payment of such fees out of an author’s personal funds appears relatively low—about 5% across all open access journals.

The most common sources of funding for open access publication are research grants (that allow open access fees to be charged to the grant) and institutional library funds. PLOS has compiled a list of some institutions and funders from around the world who have Open Access funds or policies to support open access publishing charges. You can check that list to see if any of those are available to you.

If none of these options are available to you, find out if the publisher can offer a fee waiver. According to the SPARC guide:

Most publishers using the model make allowances for special situations (for example, individuals without a host institution or from less developed countries), assessing lower fees or waiving fees altogether when no institutional subsidy exists. Society publishers often discount article publication fees for members, or waive them entirely.

For example, PLOS waives fees for research from eligible low-income countries and offers fee assistance for authors who have no other source of funding that covers the open access publication charges. Similarly, Elsevier offers fee waivers "in cases of genuine need." Wiley offers an automatic waiver to authors in certain eligible low-income countries, and discount to authors from another group of countries. Springer has a similar automatic waiver, and also allows authors to submit individual waiver requests.

publications - How best to present long equations in two-column papers?

How best to present long equations in two-column papers?

I've tried splitting them in two or more lines along operators, but that still looks a bit weird to me, especially when parentheses have to be carried along across the lines. Also, I've considered stretching them across both columns, but that seems only an acceptable solution if the equation is of outstanding importance, e.g. the final result and not some middle section of a proof.

Answer

When I have had occasion to deal with obnoxiously large equations, I find that there are four strategies that do well for me. In order of readability, they are:

1. Shrink the font: if you are allowed (any many venues do allow this), you can usually shrink the font on an equation a few points without affecting readability.


2. Map separable terms of the equation to new variables, which can be given their own independent definition lines. This can really help readability in a complex equation as well.

--- The line of desperation ---

3. Break the equation across two lines: this works up to about 1.6 lines worth of smaller-font equation. When combined with adjusting font size, you can often adjust where the break occurs to make it look reasonable.


4. Move the equations to a full-width figure, where you can play all of the same games.

I have asked a professor if he were available for being my graduate thesis advisor, now my bachelor thesis advisor is angry with me

A couple days ago I was asked by my former bachelor degree advisor (let's call him X for short) if I were interested in doing a MD thesis with him. I have replied him that I wasn't sure yet about what I would like to do for my MD thesis and I told him I would have asked some other professor before deciding. He said he was perfectly okay with that.

I have therefore talked to several professor and, among them, to an ex collaborator of X, let's call him Y, who works in a different country. In the mail I wrote to Y, I did not put X in cc nor I have mentioned him.

Y replied to me, putting X in cc, and suggesting that I should ask him if he were available to be my internal advisor first.

Finally, X sent a mail to Y, with me and a friend of mine (who wrote the mail to Y with me, as he were interested too) where he said I was trying to "outmaneuver" him by writing directly to Y. He also reported a mail written before I wrote to Y where, among other personal opinions on me, he suggested I was a mental instable person and that I push around my girlfriend (X was the bachelor thesis advisor to my girlfriend as well).

Now, of course the reaction of my professor is beyond any acceptable boundary, but what I really want to know is whether I am wrong at all. Should I have asked him before writing to Y?

Also, how should I reply to X?

Beg your pardon for the Xs and Ys...

Answer

It sounds like you've found out the reason that Y is no longer a collaborator of X. Furthermore, you should thank your lucky stars that you found out now, before you committed to working with X.

Assuming there are no important missing pieces in what you report, the situation is pretty straight-forward: you were entirely reasonable in telling X that you wanted to talk to some other professors before deciding, and it is entirely reasonable for you to contact Y without reference to X (X has no claim over you and your interactions).

The email that you report X having sent is absolutely inappropriate, and also clearly disingenuous: if X thinks so badly of you, why would X have invited you to work for them? It seems clear that X is wanting to control you, and so you should definitely NOT work for X.

At this point, I would recommend writing an email to X, stating that you found the email both highly inappropriate and also confusing, particularly given that X was also asking you to work for him. State that because you find this inappropriate, you are no longer considering working for X. It is very important that this interaction be in email, and that after this point you restrict interaction to email, since X has proven to be manipulative and untrustworthy and you need a written record with which to defend yourself if necessary. I would also recommend continuing communication with Y, if this is possible despite the attempt of X to sabotage you.

research process - Is it formal to inform readers that a point will be discussed later in the chapter?

I mentioned an important idea in a section without developing it.

Is it formal to inform readers that the point will be discussed later in the chapter?

For example: This idea will be discussed in detail in a subsequent section.

If yes, should it be presented just like any sentence, maybe next to the idea? Or Does it require special treatment?

Thank you

Answer

There is nothing wrong with doing so. if you would not, the reader might start wondering. In cases where no other alternatives apply then signalling to the reader that more details will follow allows the reader to continue concentrating on the details at hand. If you end up with a situation like this, you should of course make sure that following such a structure is the best way forward. If it is not then restructuring the text is necessary. After all the goal of writing is to provide the reader with the easiest way to understand your writing (the way you want them to). If you find yourself using this form of signalling often, you should probably take a critical look at your writing and ask yourself why this happens. It might be that you are not structuring the text in a good way.

writing style - Are there general guidelines for including code in a research paper?

I'm a beginning researcher trying to write a research paper , so please bear with some of the really basic questions I might have. I've already looked around for some help online, but the websites I found were vague.

My program is written in perl. Should I include my code in the paper? If so, is there a maximum number of lines? Will people expect me to include all of it in the paper (either in the appendix or in the body) or can I just write out in text the general idea of what it does?

Answer

In general, I would never include code in the "main" paper outside of computer science or applied mathematics. There are very few cases where listing code explicitly would actually improve the quality and readability of the paper. If it is necessary to include the code, I would do so as part of the "Supporting Information" which many journals allow you to include alongside the main publication. I would then describe the features of the code as words in the main text.

Even in CS and math papers, I would still only put pseudocode in the main article, and would save any listings of actual code for the Supporting Information.

It's been one month since the graduate advisor (also the POI) said will get back to me regarding my grad application, should I send a follow up email?

It's been one month since the graduate advisor (also the POI) said will get back to me regarding my grad application, should I send a follow up email or should I just wait? He said in the last email that he is checking something for me and will get back to me as soon as possible, but it's towards the end of March, I am little nervous and worried. I don't want to sound too pushy and impatient since he already said he'll get back to me asap...should I still follow up? if yes, any advice to ask him about the status very politely?

plagiarism - How to protect your unpublished ideas?

My advisor introduced a new student in my work saying that I am doing X,Y,Z and he will be doing A,B,C. I was asked to explain X and share all the data, results, reports, all related publications etc to enable the student to do A,B,C. Once I have explained him X, Y, and shared my data and future plans, he changed/abandoned his directions and submits a paper with another lab collaborator and my advisor on my key idea X without even letting me know anything. After somehow finding it, I politely asked them about it. They were apologetic and both these students agreed through email exchanges that it was not their work and that they should have credited me. They also agreed that this should not have happened after a little confrontation.

I know, my advisor is fully aware of the whole situation, and this was done deliberately. I am not able get out of this whole situation for a long time. Taking a fight with my advisor or the students is not an option. How would you all handle this situation effectively? How can you protect your ideas that are unpublished but you have been asked /instructed to share with others? Even I have experienced situation where the supervisor himself misuse and steals student work without giving credit to the student who did it. So a tough question is, how do you protect your ideas from being stolen by your advisor?

funding - Can you contribute to Public Loan Forgiveness (US) while pursuing a funded Masters/PhD?

I think I can, if I'm understanding the rules right, but I was wondering if anyone had done this/could give advice.

I recently completed a JD. My dream in college was always to get a PhD in literature, but for several reasons, some good some bad, I chose to go for the JD instead (it isn't completely unrelated to my literature interests, so it isn't a total wash). I am working in the public sector after graduation, and will be paying down my JD loans using Public Loan Forgiveness, so when I sat down and thought about it I realized I might not have to abandon my PhD dream after all. After a year or two breather from school, I'd like to go back and start working towards a PhD, because if law school and working in the legal field has convinced me of one thing it is that literature (and hopefully a professorship) are where I will be truly happy.

As an overview of PLF: after 120 monthly payments made on my loans while working in the public sector (10 years) the government would forgive my federal loans (which make up 90% of my loans). I can pay income-based repayment while working towards PLF as well. I will never be able to pay my loans off on a gov salary otherwise, but 10 years and then they are forgiven is actually a pretty sweet deal.

Basically to qualify for PLF I have to be employed in a public sector job--generally government or a nonprofit--working full time, or two public sector jobs that combined mean at least 30 hours/wk. As most TA or RA positions for funded programs (MA or PhD) seem to be about 20 hours a week, doing 10 hours a week in another public position would, if I'm right, qualify me for public loan forgiveness. Probably I'd look at doing 10-15 hours of legal aid through a nonprofit or government agency to keep my legal skills up.

Has anyone done PLF while finishing a PhD? Is this dream possible, or am I crazy? I don't mind not making a lot of money--I never have, and am not making much $$ now. But I really want to go back to literature. I'm just hoping the JD won't have killed that dream for me. :/

terminology - What is the difference between muscle tension and muscle tightness?

Is there any difference between muscle tension and muscle tightness?

I want to study the relation between forearm muscles tightness/tension and tendinopathy (specifically, medial and lateral epicondylopathy) in humans. In that context, I wanted to understand whether muscle tension and muscle tightness are synonymous, and if not what the difference is.

phd - Priority of application materials for admission decision

As I've already saw, many people here are related to admission process. And I want to ask their opinion on what is priority of all stuff from application: what is the most important (letters of recommendation or personal statement, GPA or maybe test scores), what is less important for admission and what is the least important? Would admission committee prefer applicant with good scores, high GPA, but with not outstanding personal statement and without letters from famous or well-known professors (for example, my scientific advisor in undergraduate school get his PhD only a couple years ago), or student with less GPA, test scores, but with letter from university's prof?

Some graduate schools require General GRE (Graduate Record Examinations). Would it better to send GRE scores (general or subject or both) even if it's not required (in case of relatively good result), or them wouldn't be considered at all?

Answer

As aeismail says, what we are looking for is concrete evidence of research potential. So, in decreasing order of importance:

• 
  

  Decent grades and (if required) test scores; otherwise, no one will read your application at all. Here, "decent grades" means three-point-something from a good undergraduate program.

  
  


• 
  

  Research publications, if you have any.

  
  


• 
  

  Recommendation letters. You must have at least one (and preferably three) strong recommendation letter from a faculty member who praises your research potential in specific and credible detail. Letters that draw specific comparisons to other successful PhD students are best. Letters from junior faculty are perfectly fine; they can draw comparisons to their recent graduate school peers. Letters that say only "He got an A+ in my class" are useless; we can read your transcript.

  
  
  


• 
  

  Research statement. Your statement must discuss your research experience and interests in specific and credible detail. A statement that only describes your sources of inspiration ("Ever since man walked on the moon...") and/or brags about coursework is useless.

  
  


• 
  

  Other concrete evidence of independent research/scholarship/creativity.

  
  


• 
  

  No red flags. Potential red flags include low grades in classes central to your proposed research area, missing key classes entirely, abysmal test scores, negative (or overly delicate) recommendation letters, recommendation letters obviously written by the applicant, spelling and grammar mistakes in the research statement, any evidence of immaturity or personality issues, and any evidence that the applicant is not prepared/informed/serious about research.

  
  

Notice what's not listed.

molecular biology - How do DNA-binding proteins recognize the correct DNA base pairs?

My professor posed this question to the class today - "How do DNA binding proteins specifically bind to base pairs?"

He alluded to the different arrangements of hydrogen-bond donor and acceptors in A-T, T-A, C-G, and G-C base pairs. However, they are not always significantly different in some pairs (i.e. the minor groove of the C-G and G-C base pairs have the same acceptor - donor - acceptor pattern).

So how would a binding protein know the difference between C-G and G-C on the minor groove of a DNA base pair? How does a DNA binding protein know it's reached the right base pair, more generally?

Thank you!

Answer

There are different kinds of DNA binding domains; the ones involved in base identification in the major groove can differentiate between different base pairs of the same nucleotides i.e. AT vs TA because they bind to functional groups on a nucleotide and not the base-pair per se. The stereochemistry i.e. which nucleotide is in the major groove, is important. The location of the nucleotides in the major groove also is a factor (Figure 1).

Figure 1: DNA sequence identification by Helix-Turn-Helix transcription factor. This is the example case of the Engrailed protein in Drosophila. Reproduced from Paro and Sauer (1992) ^[1].

You can see that Adenine is recognised differently than Thymine. In many cases such as that of zinc finger proteins (ZF), sequence identification usually happens for dinucleotide pairs such that each finger (a modular unit) can identify a di/tri-nucleotide (Figure 2,3). An array of fingers in case of ZF and helices in case of Helix-Turn-Helix motifs can recognize a unique stretch of DNA sequence (which is certainly more unique than individual base pairs). Usually the binding of the fingers are co-operative which leads to increased affinity and specificity of the protein-DNA binding ^[2,3]. Analogous mechanism may exist for other kinds of DBD too (I haven't specifically looked for that). Moreover, many DNA motif binding proteins oligomerize, which is again co-operative. This increases the specificity and the overall binding kinetics becomes sigmoidal and thresholded (see Hill kinetics).

Binding mechanisms are best understood for ZF proteins that led to the development of zinc finger nucleases which was one of the first modern methods of targeted genome editing ^[4] (though they have now been obsoleted by CRISPR-Cas system).

Figure 2: DNA sequence identification by zinc finger proteins. This example considers the Zif268 protein. Reproduced from Paro and Sauer (1992) ^[1].

Figure 3: A more detailed depiction of Zif268-DNA interaction. Reproduced from Durai et al. (2005) ^[4].

---

References:

1. Pabo, Carl O., and Robert T. Sauer. "Transcription factors: structural families and principles of DNA recognition." Annual review of biochemistry 61.1 (1992): 1053-1095.


2. Krishna, S. Sri, Indraneel Majumdar, and Nick V. Grishin. "Structural classification of zinc fingers SURVEY AND SUMMARY." Nucleic acids research 31.2 (2003): 532-550.



3. Lee, Juyong, Jin-Soo Kim, and Chaok Seok. "Cooperativity and Specificity of Cys2His2 Zinc Finger Protein− DNA Interactions: A Molecular Dynamics Simulation Study." The Journal of Physical Chemistry B 114.22 (2010): 7662-7671.


4. Durai, Sundar, et al. "Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells." Nucleic acids research 33.18 (2005): 5978-5990.

graduate admissions - Choosing research ideas to include in a statement of purpose

The internet is littered with information on what makes a good SOP, but I would like to ask a specific question regarding mentioning one's research interests in SOP.

What points should a student keep in mind while writing her statement of purpose? If there is exactly one specific professor the student is targeting, it makes sense to talk of one of his recent papers and ideas for extending its results in the SOP.

• If 1) there are a couple of preferred professors or more, 2) each of them has multiple research interests and 3) the student is unable to zero in on a field or topic, how should the student tailor her SOP to make it appealing to more than one professor?


• Should the student worry about the feasibility of her ideas in the SOP? Is an extensive literature survey in the relevant field necessary before putting anything in the SOP?

Answer

Your research statement (not "statement of purpose" as university administrators strangely insist on calling it) should be a description of your research experience, interests, and goals, as a supporting case for your potential for independent research. If you were applying to work in my research area, I would much rather read about your research ideas than mine.

Here's what I like to see in research statements:

• 
  

  What have you already done? What problems have you solved, or at least worked on? What independent projects have you been part of? What were your key contributions? What did you learn? What did you teach the world? How do your results compare to what was already known? What original ideas are you most proud of? Be specific, technical, credible, and confident (but not arrogant). Refer the reader to your web page for more details. Have a web page with more details: preprints, project reports, source code, videos, etc.

  
  


• 
  

  What are you working on now? What problems are you currently trying to solve? What are you currently trying to build? What are the open research issues? What intellectual tools are you using, or learning to use? What are you reading? What prior results are you building on? How are you building on your own earlier work? What is your current favorite half-baked idea? Be specific, technical, credible, and confident (but not arrogant). If you have partial results, refer the reader to your web page for more details. Have a web page with more details.

  
  

You ask whether you should worry about the feasibility of your ideas. No more or less than if you were actually doing research. Ideally, I'd like to see both that you have good ideas and that you're not afraid to have bad ones.

• What might you want to work on in the future? What problems you would like to solve? What would you like to build? Do you want to push your existing projects further? If so, how? What new areas are you interested in exploring? What are your long-term career goals? Convince the reader that you are knowledgeable about your target area(s), but be honest about your ignorance. Be specific, credible, and confident (but not arrogant).

No one will hold you to your stated plans. You don't need to do an extensive literature survey (although it certainly can't hurt; put a copy on your web page), but at a minimum you should have had a strong undergraduate course on the topic.

• How does my department fit your research goals? (If the rest of your statement is well-written, the reader already knows the answer to this question, but you also need convince the reader that you know.)

A few sentences about motivation are worthwhile, but don't talk about how many programming languages you know, or about how you were a child prodigy, or how many contests you've won, or how many A+s you got, or how Alan Turing was your childhood hero, or how your research area will Change The World. Write in simple, direct, flawless English. Like Suresh, I have seen many phrases like "my first trembling steps", but never in successful applications.

The only credible reason to "target a particular professor" is if that professor's research interests already mirror your own. If you try to craft the bulk of your statements to different professors in different departments, the result will be much shallower, and therefore much less persuasive, than if you describe your own well-developed research interests.

Yes, that means you have to have well-developed research interests. That's the point.

publications - Referencing the reference?

Suppose I have a paper with the following text:

Roses are red, violets are blue, sugar is sweet, and so are you [3],[4].

As one can see, the author got the information from two other references.
If I want to add this information in my thesis, do I also have to reference [3] and [4] or can I just reference this particular paper, I got the information from?

Answer

If you need a reference that supports the factual information that roses are red etc., then you have to look up the original sources and cite those. If, however, you refer to a synthesis of the information that the author of your sample text has derived from the original sources (for example "flowers have different colors"), then you must cite the sample text.

Having said that, it is sometimes advisable to look up the references also in the latter case. First, because the information contained in them might be interpreted in different ways, and second, because you might learn something useful from them.

Only when you absolutely cannot access the original source, you may resort to a secondary citation, such as [3] as cited in [1].

titles - When I call a person doctor

If I call a person doctor, instead of Doctor XXX, will this person assumes that I forget his name?

When I talk with another person, I said:" I wish to study in doctor's lab." At that time, the doctor is just next to me.

Answer

It is not common in my experience (first-language English speaker in the US) to call anyone just "Doctor" unless they are a medical doctor. In non-medical settings, you should always use their surname after the title.

On the other hand, it is OK to use just "Professor", if you are speaking to the person.

So you could ask, "Professor, can I take the exam tomorrow?" But not "Doctor, can I take the exam tomorrow?"

If you are talking to someone else, you should always use the surname, don't just call the person "professor" or "doctor" as if that was a name.

graduate admissions - Can I submit application on the deadline?

If grad schools says the deadline is Jan. 15th, do I have to submit application before Jan. 15th? Or I can still submit on Jan. 15th?

Answer

Most commonly the deadline is inclusive, i.e., "January 15" means that the deadline is "at some moment during January 15". What does this mean can vary:

• 
  

  For online applications, it's usually 23:59:59.

  
  



• 
  

  For mailed applications, there are two options and exactly one of them is true:

  
  
  
  
  • either the poststamp has to be January 15;
  
  
  • or it has to arrive to the institution by January 15.
  
  
  
  


• 
  

  For applications you deliver in person, usually the opening hours of the office where you have to bring it apply.

  
  

In either case, it should be specified in the conditions.

And please remember that timezones can play a role here, and everything is in the timezone of the institution where you apply unless stated otherwise.

---

/From comments/
If you doubt the precise conditions, just call them or e-mail them and ask for clarification.
It will cost you less than solving any troubles afterwards.

cv - Avoiding confusion over the term "Research Assistant"

When applying for non-research related work in the commercial sector, how should confusion be avoided over the term "Research Assistant" being used in a CV?

Are human resources staff at companies, and recruiters, at risk of assuming "research" means market research, as opposed to scientific research, especially if they're skimming through the CV?

Is DNA replaced after organ donation?

If an organ from person A is transplanted to a new human body B, is it possible that we can detect A's DNA in B?

How long until the organ's DNA is replaced by B's DNA so that we are no longer able to detect any signature of A?

masters - Recommendation letter from a PhD-to-be?

I am applying for Master programs in Educational and Clinical Psychology. And I am in the process of choosing people for writing my recommendation letters. I have a BA in Psychology and I wasn't much involved in research - except when I did my year aboard, I participated in a research project launched by a teaching assistant who was then a PhD student at that college. We conducted the experiments together, collected and analyzed the results. In the end, he supervised my Research Project Thesis.

It was a valuable hands-on research experience for me. And I am thinking about asking him to write my recommendation letter. However, though he is still actively involved in several research, he hasn't yet obtained his PhD degree (he will in the coming year). So I am concerned that a recommendation letter written by him would look nice, but at the same time it would lack some sort of legitimacy and affect my chance of being shortlisted for further interviews.

So my question is - would a recommendation letter written by a non-PhD referee carry less weight and even not taken seriously? Should I ask this person to write the recommendation letter for me?

Thanks for viewing my question and I look forward to your answers. Thank you for your help!

phd - System for organising printed papers in folders?

For the people here who do not yet work entirely electronically, and still use printed papers & old school folders to organise their papers, do you guys have a system for organising these papers?

I have bought a few folders today and have made a few rough distinctions, but I am wondering how more advanced academics organise their papers once they've read hundreds to thousands of them (and also roughly on the same very specialised topic).

phd - How to nail a Ph.D. interview?

I have been asked for an selection interview by a Professor in Australia for Ph.D. position (cancer research group). This position is really important for me so I want to give my best. Can anyone suggest some tips or share his experience of success or failure so that I can get an idea how to prepare myself. Thanks a lot.

research process - Any pointers for reading articles digitally (on screen)?

First of all let me apologize for the title, as it is perhaps very vague. The issue is as follows; I have stopped printing my articles and instead starting reading them on screen via my library manager software (Papers2).

The problem is that I find it's MUCH harder to focus when I am reading on screen and thus takes much longer for me to read articles on a screen. It's almost like I get some sort of digital dyslexia... As possible reasons, I figure small things like new mail notifications, screen brightness, sitting/standing posture etc all weigh in somehow. But I suspect that the subliminal association of "how I normally read stuff on a screen" might have a larger effect. In other words since I am normally skimming through stuff when I am in front of the screen, my brain might try to take in information the same way when I am trying to read an article, which of course is a recipe for failure...

I wonder if it's just me or if this is a common phenomenon? Additionally I would appreciate if I could get some tips on how to tackle this problem. Obviously printing all papers is an option but it's neither elegant (creates a mess on/around my desk) nor is it environment-friendly.

Answer

I have terrible eyes and this is a very real problem for me. Although I'm not an eye care specialist I can say anecdotally that there are a few things that have really made all the difference for me.

First: if you wear glasses, get the computer lenses. Usually they are some kind of an off yellow to cut glare. These really help to reduce eye strain.

Second: look away from the screen every few minutes. Try to focus on objects away from the screen that let you change your focal distance. I find that doing this for just a few moments at the end of every paragraph really helps.

EDIT: Use natural light if you can. I've found that turning my desk so that the ambient light from the window illuminates my screen has also helped me a lot. You have to be careful of glare but when I finally got everything situated it made a notable difference.

Third: media counts a lot. If you're going to use a tablet or eReader look for something that has front/side lighting. Many people like the new Kindle paperwhite but I prefer the Kobo glo. If you're looking for a more stationary solution then I highly recommend a good projector. Prices have come down quite a bit and you can now get an 'OK' projector for just a couple of hundred dollars. It will take a little bit to acclimate yourself to the new reading format but once you do I think you'll find that you like it. I know that I do.

reference request - How much does it cost the publisher to publish a book?

I wonder how much it costs a publisher to publish a book (textbook or research book).

I'm looking for referenced numbers, not guesses. I am mostly interested in the fields of computer science and maths, and English-speaking venues, but I am curious about other fields and languages as well.

Answer

Here is one story on it from US News & World Report... Their example was a Calculus textbook selling for $289 at the bookstore.

Where does all that money go? According to figures from the National Association of College Stores, an average of 21.6 cents of every dollar spent on a new textbook will go to the bookstore, whether for personnel costs, operations, or income. For Kadue's $289 textbook, that's around $62. Another cent of every dollar pays for the freight of shipping a heavy book around, so subtract another $3 from her cost. That leaves around $224 that goes to the publisher, or around 77.4 cents for every dollar.

NACS no longer receives information from publishers about where textbook money goes, but as recently as 2008, they provided that cost breakdown. At that time, around 15.4 cents of every dollar went toward marketing the textbooks, 11.7 cents went to the authors, and the largest chunk—32.2 cents—went to the basics: paper, printing, and paying publishers' employees.

conference - Student Travel Grant = Volunteering; is it worth it?

I have a paper accepted to a conference and my adviser is willing to fully fund the trip.

However, I am also eligible to apply for a "Student Travel Grant" (being a student author).

Pros of getting the travel grant:

• 
  

  saves adviser grant money

  
  


• 
  
  

  goes on my resume

  
  

Cons:

• i would have to volunteer and possibly spend half of each day with tasks at hand

I am not sure whether it's worth applying for the travel grant and helping at the conference, as opposed to just going there.

For those of you who have been in this or similar situations before, what would you advise?

UPDATE: I learned that the grant covers almost half of my total trip cost, and that the volunteering time is around 1/4 of the total conference duration, which is good; Hence, I have applied for it. Thanks everyone for your help.

Answer

Based on my own experience, I would definitely recommend applying for the travel grant!

The pros you have mentioned are fairly substantial. Regarding the con: I have never found any conference volunteer job to be at all onerous*, and usually they have been fun and/or valuable.

For example, here are some volunteer jobs I have had:

Volunteering at the registration desk

If I have this job, I get to meet all the attendees as they come in. Usually, when I first sit down at the registration table, I flip through the badges to see who is registered, and make a plan for who I want to meet. Then, if those people come in while I am "on duty" and they are not in a rush, I can strike up a conversation.

By doing this, I've been able to have some really "spontaneous" talks with important people in my field who I wouldn't have had much of an opening to meet otherwise.

I've never been asked to do this job for more than a couple of hours at any given conference, so I didn't feel like I was missing out. If this is my volunteer job, I can usually arrange with the other volunteers so I am "on duty" during a time when there are no sessions I'm interested in anyways.

Taking minutes in meetings

Another time, I was a student volunteer at a conference that also hosts its sponsoring SIG's annual business meeting, and my job was to take minutes in this meeting. I got to listen in while all the big shots in the SIG talked about what they really think of the state of the subfield, the quality of the conference, the direction they'd like to see things go in, etc.

Also, the meeting was in the evening and there were no conference sessions going on, so I didn't miss anything while doing this (except maybe a nap).

Mic shuttler, running the 1-minute madness session

Some volunteer jobs take place inside the conference sessions themselves, so you don't miss out on anything while doing these jobs.

For example, I've been assigned to be the person that carries the mic around to people who have questions during the Q&A after each talk.

I've also been part of keeping the 1-minute madness session (where poster/demo presenters get up one after another and speak for one minute about their poster) on time. The student volunteer coordinator described this job as follows:

1 person in charge of lining up presenters in the correct order, 1 person in charge of advancing the presentations, and about 5 are responsible for throwing the presenter with crumpled paper balls at the 56th second to get her/him off the stage.

(I didn't have to throw any paper balls.)

* YMMV. At a large, well-organized conference there will be lots of volunteers, you can choose which task you prefer, and no one student has to do too much work. At a smaller conference, things may be different.

publications - What to do when you have two manuscripts under review where one cites the other, but the citing paper gets accepted before the cited paper?

I submitted an article around 11 months ago to a SCI journal and another article around 5 months ago in another SCI journal. The second article cited the first article which was under review for 6 months at the time of submission of second article. Recently, we got acceptance letter for 2nd article while 1st article is still under review. What action should we take? remove the citation in 2nd article and cite the 2nd article in 1st article or we stay with the current situation. but what if our 1st article got rejection?

genetics - What determines if an allele is dominant or recessive?

Going back to my high school days we were taught about dominant and recessive genes. We were taught how to calculate the geneotype and pheneotype of potential offspring using a small table (forgotten the actual table name). But it never occurred to me then what determines if a gene is dominant or recessive and how this is carried out biologically.

Take my example below, there is a 50% change that an offspring will carry both the tall (T) and short (t) genes. What determines that the tall gene T has a dominant effect over the short gene t.

Now, I know that there is going to be differences between the different genes (i.e. eye colour), but is there a general description any one and provide which states how a gene becomes dominant and how the dominant effect is carried out biologically.

Answer

Dominance is seldom complete. Owing to effects like co-dominance, incomplete dominance, collaborative (additive) effects of polygenes, our classical concept of dominance doesn't work. Having said that, there are certain ways in which a gene, if showing complete dominance can be analysed from the molecular level.

In an individual heterozygous for a certain trait, the following possibilities exist:

1. 
   

   Both the alleles, though different, code for a protein (which might be an enzyme or a regulatory protein) which is functional and is indistinguishable atleast in terms of its functions. In this case, no matter if the person is heterozygous or homozygous for either allele, the concerned protein will be in sufficient amounts and will always be functional. These alleles can be treated as the same allele while performing Mendelian analysis though their products might differ slightly, leading to formation of two (or more) functionally similar Alloenzymes (as opposed to Isozymes which are similar enzymes produced by genes at different loci).

   
   



2. 
   

   Haplosufficiency. In this case, one of the two alleles codes for a functional protein and the other either codes for a non-functional protein (or does not code at all). But, even in heterozygous condition where only one allele producing functional protein is present, the amount of protein produced is sufficient to show the phenotype and hence, even in heterozygous individuals, enough protein is coded for by the single functional allele exhibiting the normal phenotype. If the two non-functional alleles are present as a homozygous pair, no functional protein is synthesised and hence the phenotype is not shown (i.e a different phenotype is shown). Here, the functional allele is Haplosufficient (able to produce enough protein in heterozygous condition) and is called the dominant since it expresses its phenotype both in heterozygous and homozygous conditions. this is pretty common.

   
   


3. 
   

   Complete Haploinsufficiency. Here again one allele codes for a functional protein while the other does not. But this time, if the functional allele is present in heterozygous condition, then the amount of the protein produced is not at all sufficient and hence the phenotype is not exhibited. Here the non-functional allele is said to be dominant because heterozygous phenotype resembles the phenotype of homozygous non-functional allele (where no protein is synthesized) since the functional allele is completely haploinsufficient (unable to produce enough protein in heterozygous condition). This method is pretty rare.(e.g rare autosomal dominant dyskeratosis congenita)

   
   

If there is partial haplosufficiency /partial haploinsufficiency, the phenomenon of incomplete dominance can be explained. (heterozygous individual produces protein not sufficient for a full-blown phenotype but just a partial expression of the phenotype)

Here, "functional" refers to being actually "functional" as in case of flower colour (anthocyanin synthesis) or just performing certain kind of a conversion leading to a particular effect on thephenotype.

human biology - Can drinking caffeine, alcohol and other diuretics be part of a good drinking regime?

Tea, Coffee, Beer, Coke etc…

I wonder if the benefit from amount of fluid we get from them is bigger or smaller then the handicap of dehydration. In other words it is worth to drink them if we want to have a good drinking regime?

Opening on the recommendation from this question.

Answer

A PlOS One study notes drinking moderate amounts of coffee (aka moderate caffeine intake) doesn't necessarily lead to dehydration. They note coffee has hydrating qualities akin to water. Further empirical studies found no substantial fluid loss in caffeinated beverages.

EDIT: Make note we're talking normal doses and moderate intake, though source 2 goes into diminishing effect of caffeine-mediated fluid loss in heavy/prolonged uptake.

The issue therein is with alcohol, which tends to inhibit vasopressin and the kidneys are constantly permeable to fluids.

microbiology - Are single-celled organisms capable of learning?

I've read that the amoeba is capable of learning. Since these protists have no nervous system, it's safe to assume that even highly simplified learning mechanisms of the Aplysia are miles off in the evolutionary distance.

How does this species learn? I would presume that there is a complicated chain of receptor mediated transcription regulation, but what are the specifics? What types of receptors does an amoeba have to sense its environs?

Answer

I'd like to know what is the reference for amoebic learning. I cannot comment directly on this, but there is some evidence for "adaptive anticipation" in both prokaryotes and single-celled Eukaryotes which do not have a nervous system.

In the case of E. coli, it has been shown that the bacteria can anticipate the environment it is about to enter. E. coli in the digestive tracts of mammals will typically be exposed to initially a lactose, and then later to a maltose environment as the bacteria pass down through the animal tract. This suggests that upon encountering a lactose environment, maltose operons are induced. I.e., upon encountering lactose, maltose is anticipated. This suggests a "genetic memory" of the sequence of sugar types where lactose is always encountered before maltose.

Further cultures (500 generations) of E. coli in the absence of maltose but in the presence of lactose reduced the maltose operon activity to negligible levels, suggesting that this is an adaptive prediction of environmental changes.

Mitchell, A et al., Adaptive Prediction of environmental changes by microorganisms, 2009, 460, 1038

teaching - How to decide whether the amount of study material provided to students is enough?

Arguably the most time-consuming component of teaching is preparation of study material (especially when in comes to a fresh lecturer of a new module).

1. First of all, every presentation should have slides. Who takes a lecturer without slides seriously? (with the only exception of, perhaps, really senior professors). If one dares to use a black- or whiteboard, students will take pictures on their iPhones instead of following the lecture, pretending they will follow it at home, which they never do. And students who miss the lecture will complain, since the slides are not available.


2. Secondly, some question / exercise sheets are important to keep students entertained and busy in class / tutorial.


3. Question sheets imply answer sheets, with (some) of solutions worked out, to help students prepare to the assessments.


4. Lecture notes, to collect all relevant information in one place, and save students some trouble looking for it in various textbooks. Helps with those students who are hip enough to never use a library.


5. Practice instructions, to carry out lab classes.

This is just a basic list, which comes to my mind, and I'm sure that other types of study / supporting materials are used in teaching.

I've heard rumours about some loci amoeni universities in the US, which provide their lecturers with all (or most) of these materials, professionally prepared by academic publishers. Apparently, this is not the case in the UK, at least not at every university. And I can now appreciate, that preparation of all these materials to every lecture / tutorial class can take a very considerable time.

Question: How do we decide, which materials are the most important for the class, and which are not? How do we assess, that the amount of materials prepared is sufficient?

Specs (by popular request): I am teaching Maths at BSc and MSc level in the UK. However, I would appreciate answers regardless your discipline / profile.

Answer

Use backward design, start with what you'd like the students to become or to achieve at the end of the course. Then, according to each of these "wishes," determine the best way to collect evidence on learning, and according to each of these evidence, design the teaching/learning experience. Formats should not drive the contents; it's the experience you wish to achieve that drives the formats. If lecture with slides is the best way, then lecture with slides; do not add lecture with slides because it's your institute's status quo.

Here are some of my anecdotes addressing your points:

First of all, every presentation should have slides. Who takes a lecturer without slides seriously? (with the only exception of, perhaps, really senior professors).

Teaching in a US university, I have started to see students showing excitement because a certain lecturer does not use slides in the class as early as 2010. That got me start thinking if slides are still a viable teaching tool. After some thought, I made the decision to go slide-free and have complete done away with slides two years ago.

I like the format so far because slides had been acting as an invisible wall between me and the students. Just because I have clicked through them does not mean I have taught them. However, I felt safe behind the screen, and perhaps had grown to relish that false security too much.

I replaced the slides with what I call a "learner's package" (more details below) and I immediately felt a lot better. There are more discussions, questions, and interaction. The questions became a lot more spontaneous. In the beginning it can be daunting, but once I got into the rhythm I can never go back to the slides. As of now, four cycles into this new scheme, 80 students taught, and none of them complained the lack of slides in the evaluation.

If one dares to use a black- or whiteboard, students will take pictures on their iPhones instead of following the lecture, pretending they will follow it at home, which they never do.

It's not if they will or will not follow up; it's if you have structured the activities or evaluation exercises to make them follow up or not. If there is no reason, why would they be motivated to look at something they have already archived?

And students who miss the lecture will complain, since the slides are not available.

Many technological solutions here: e.g. First, make it clear in the syllabus that it's their responsibility to solicit notes from their peer if they miss a class. Second, consider video-taping your lecture. Third, consider using screen capture with audio recording if you will be using slides. Talk to your IT folks for possible supports.

Secondly, some question / exercise sheets are important to keep students entertained and busy in class / tutorial.

While I love the idea of enriching the types of formats and interactions, it should be based on the desirable outcomes of the course, and not based on entertainment (though I sense that your questions are portrayed with a bit of sarcasm). Different types of format have their pedagogical pros and cons and they should be used to best fit what you want to achieve.

Question sheets imply answer sheets, with (some) of solutions worked out, to help students prepare to the assessments.

I'd disagree with making it a routine to provide answers; this can cause them to rely on the eventually available right answers. Instead, I'd suggest base the questions on a defined set of skills (that you can point to at a section of the text, or on a certain page of the notes) with mild to moderate modification. That way, you can point them to the section to see how similar questions are solved, and encourage them to revise their answer.

If possible, base your answer scheme on instant feedback of the class's performance. E.g. if last week's quiz shows that only 35% of the class got question 6 correct, then consider making a detailed answer scheme for that.

Use your teaching assistants. Make them try your questions. They can i) find typos or errors, ii) give you a sense of how much time was needed to complete each question (multiply it with a factor of 1.5 to 3.0 to factor in the fact that the TAs probably can complete the exercise in a shorter time,) iii) draft the model answers.

Lecture notes, to collect all relevant information in one place, and save students some trouble looking for it in various textbooks. Helps with those students who are hip enough to never use a library.

I agree a one-stop reference point would be helpful. It can be a set of notes or a list of materials hosted on the online learning website (like Blackboard.)

In my "learner's package," I included the followings:

• List of learning objectives


• Learning resources, which include corresponding sections in the textbook, readings, videos, etc.


• Self-assessments. This section contains a list of activities and exercise with answers for students to test their own understanding. It's not graded.



• Lesson evaluation. This section details how the students will be evaluated formally. I often put the link to the weekly quiz here. And if appropriate I also suggest some mile stone that they should achieve in this week with their personal final project. (I provide rubrics and so, but this answer is long enough so I'll save it for another day.)


• All the notes, with citations.


• In-class exercise and activities.


• I use the Tufte LaTeX codes to compose the notes. I picked it because of its pleasant layout and ample amount of space for students to write.

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Lastly, here are some titles that have inspired me with trying different instructional designs (I'm not affiliated with these authors nor Amazon.com):

human biology - Can the dead be brought back to life by viruses?

Zombies have been a part of popular culture for decades. The living dead rising up to take over the world is a terrifying concept, worthy of Hollywood blockbusters and television hits. Some of those zombie fiction stories are based on infection by viruses or other organisms.

Is it possible to bring dead tissues back to life by virus infection?

evolution - What if $rB=C$ in Hamilton's rule?

Hamilton's rule states that if $rB>C$ then a gene giving altruistic behaviour will increase in frequency in the population. What would happen if $rB=C$? Will an individual perform the altruistic act?

Answer

I agree with @Amory in the sense that Hamilton's rule is not a rule that applies to each specific individual and explain their behavior (or other traits). The Hamilton's rule describe the direction (and not the dynamic) of how a social traits evolve. A social trait is any trait which does not only affect the fitness of its carrier but also affect the fitness of other individuals in the population. Theoretically, all (or almost) traits are actually somehow social traits.

$RB>C$ is a simplistic way of looking at Hamilton's rule which might bring you to some confusion. This formula makes more sense to me by replacing $B$ by $\frac{dw(x,y,z)}{dx}$ and $C$ by $\frac{dw(x,y,z)}{dy}$. $w(x,y,z)$ is the fitness function of a focal individual expressing trait $x$ and interacting with an individual drawn from a subpopulation expressing trait $y$ (expected value of the probability distribution of trait expression of individuals in the subpopulation) in a population expressing trait $z$ (expected value again). In the particular case where there is no population structure $y$ equals $z$. $\frac{dw(...)}{dx}$ describes the partial derivative of the fitness function according to the variable $x$.

Therefore the Hamilton's rule can be rewritten as:

$$R\cdot\frac{dw(x,y,z)}{dx}>\frac{dw(x,y,z)}{dy}$$ where $R$ is the coefficient of relatedness which can itself be expressed as a correlation between the variables $x$ and $y$.

Altruistic behavior evolves if (but not "if and only if") this rule is respected. Hope this reformulation of Hamilton's rule helps a bit understanding it.

In the special case where $R\cdot\frac{dw(x,y,z)}{dx}=\frac{dw(x,y,z)}{dy}$ then, the trait of interest is not selected (neither counter selected). Therefore the trait will evolve under genetic drift alone. While the allele frequencies are modified by drift, the Hamilton's rule might (or might not) differ from the equality and then the trait would not be neutral anymore.

publications - Is it ethical/legal to publish Master thesis manuscript as a journal paper?

I have submitted my Master thesis manuscript to the university library. It is completely new work (never published before to any journal or conference). Now, I want to submit my Master thesis to a journal (as a paper) without modifying it much/anything. Is it ethical/legal to publish your Master thesis manuscript as a journal paper? Should I mention this to the editor of the journal? Because, in the journal guidelines, it says: we accept the manuscript only if it is not published before to any journal or conference. It does not mention anything about other publication sources (like: Master or PhD thesis submitted to the university library). Will I face any problem in future if I do so?

PS: I am thinking to submit it in IEEE Transactions on Computers journal. I talked with the university librarians. They told me they do not have any problem if it is published elsewhere. They just keep a copy in the university library (including online library - which I can also keep 'private'). I am asking if the journal has any problem or not? For my university, it does not really matter (since I have already given the manuscript to them and they have accepted it). My university is in Republic of Korea.

Answer

It is perfectly Okay to make a paper out of a master's thesis. Many aspiring PhD candidates do.

However, an MSc thesis is typically 50-100 pages long. A paper is (in a dense journal format) typically 8-12 pages long. Let's make a generous estimate for 20 pages in the thesis layout.

So either your thesis is very thin, or the journal is very generous, both of which seems unlikely.

Next issue is that you write a thesis in a very different manner than a research paper.

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Hence, you would definitely need to rewrite the paper. And you have one issue less to worry about. The copyright might still be a concern for figures, for example, but from your comments I recon that this is not a problem. (It should not have been one, but it was proper to check before.)

publications - When picking a journal for my research should I value the publisher's reputation over the journal's impact factor?

I'm in the process of selecting an appropriate journal for my article. I short-listed a few journals based on topic coverage, IF and speed of the review process.

I am confused: should I select a journal with higher IF (2.3) published by a non-reputable publisher (MDPI) or should I publish in a journal with low IF (1.2) published by a reputable publisher (IEEE)?

By reputation I mean the reputable publisher (IEEE) is specialized in my area of research and non reputable (MDPI) is an Open Access publisher.

diet - Can a carnivorous animal consume plants with no adverse effects?

While I know that in nature, carnivorous animals are poorly suited to eat plants (largely due to having sharp teeth, not grinding teeth, as far as I know), I was wondering if, in an emergency situation such as imminent starvation, could a carnivorous animal such as a wolf survive solely on plant life, maybe requiring it to be ground up before hand? Could an herbivore survive on meat, if the meat was prepared in a manner that would allow the herbivore to eat it? Would a wild animal voluntarily consume food that it is not suited for if it would stave off certain death, or would it require force feeding or training?

Also, I am interested in the other side of this question: if an animal cannot safely consume food outside of its normal diet (carnivore eating plants, herbivores consuming meat), what negative effects would this action have on the animal?

Just a note, this is purely a hypothetical question, and I am only asking out of curiosity. I am in no way planning on doing this, nor do I advise anyone else doing this if there is a high chance of it harming the animal.

Answer

This is kind of a weird/trick question. How long do you want the animal to live? If the lifespan is shortened or compromised does that fit.... Obligate carnivores (cats, dogs) do eat plant material. In the wild cats mainly eat grass to get rid of hairballs. Cats are more impacted by phytotoxins than dogs. However, both, are extremely vulnerable to compounds that don't bother humans (xanthines like theobromine, caffine, compounds in garlic, onions, broccoli, mushrooms). Cats can't convert plant fats into what they need (we can) as a result they can go blind if they don't get the animal fats they need. Likewise, herbivores will suffer increased cancer, heart disease, renal failure from diets with animal fats / protein. Your mention of "wolf" is interesting because there is a South American wolf that supplements its diet with a tomato relative (called something like "fruit for wolves" in Spanish). This is probably only "good" for it in that it keeps the wolf from otherwise starving. I don't know that it has a strong deleterious effect (probably not, but it could be more sensitive to trace alkaloids in the fruit) but it could hurt it in a minor way.