physiology - Fast standing and the heart's insufficient accommodation of the increased venous return

Assume you are 45 minutes on the supine position. Furthermore: you stand all of a sudden and fast and without sympaticus activity. The venous return (smooth musculature of vessels) accommodates faster to the change (decrease of venous return) so returns blood to the heart before the sympaticus has accommodated for increased cardiac output. This creates a significant increase in the blood volume entering the heart. In pathological situation where systemic vasoconstriction not occurring normally, the heart is not capable of handling the overdistension; resulting in a pain during the second cardiac cycle.

I am interested in knowing which phase the heart is most vulnerable:

• filling,


• isovolumetric contraction


• ejection


• isovelumetric relaxation

or more explicitly (from my answer here)

• Atrial systole



• Isovolumetric ventricular contraction


• Rapid ventricular ejection


• Reduced ventricular ejection


• Isovolumetric ventricular relaxation


• Rapid ventricular filling

I think filling can happen normally, but not with the sudden isovolumetric contraction (most sympathetic innervations here, so therefore I think this is the weak link). When there is too much blood in the ventricles, some of the blood is reflected back from the ventricles into the atria causing a painful sensation and possibly tachycardia (as well as an possible increased risk of atrial fibrillation if such events happen regularly).

Is the isovolumetric contraction (systole of ventricles) of the cardiac cycle the possible weak link in accommodating a sudden increased venous return?

evolution - Identity By Descent vs Identity By State

Background

The concepts of Identity By Descent (IBD) vs Identity By State (IBS) are central in population genetics, yet I fail to fully wrap my head around the definitions.

You can find examples where my understanding of IBD vs IBS is quite poor in @DermotHarnett's answer here or in the comments with @PaulStaab here. @PaulStaab suggests that different authors have used different definitions of IBD and IBS.

What is unclear to me

From what I remember from Hartl and Clark (I don't have the book with me to quote), IBD depends on an arbitrary time threshold in the past beyond which if coalescent events occurred, then we still call the two alleles IBS (Identical by state) and not IBD. The idea that the concept of IBD depends on an arbitrary threshold bothers me though!

I suppose that two alleles can be IBD without being IBS in the case where a mutation or recombination event in the middle of the sequence of interest prior (looking backward in time; more recent) to their coalescence. I suppose two alleles can be IBS can not be IBD only if we use an arbitrary threshold that is older than their coalescent time or if convergent/parallel evolution happened.

Questions

• Does IBD depends on an arbitrary threshold?


• Are there several definitions of IBD and IBS in use?



• Does IBD implies IBS?


• Does IBS implies IBD?


• Can you please make a short review of these definitions to clear things up?

How to make thesis-writing feel less tedious?

I'm about to finish my master's thesis on a TCS topic (algorithms). I'm quite happy with my results; the most engaging part of the thesis was grappling with getting up to speed on the state of the art, then taking that and developing new and/or more efficient algorithms for the specific model I'm working on. Proving that the algorithms actually work has been very satisfying as well.

However, I'm having a hard time sitting down and TeXing it all; it feels very tedious. I did write out the most important bits very soon after I had them figured out so I could give them to my advisor. Yet for the better part of the past two weeks, every day I considered getting down to it and putting it all together into a presentable thesis, eventually deciding to put it off for another day. As I'm hoping to do a PhD afterwards, I thought I should nip this in the bud so I won't be wasting time like this for too long.

What are effective methods to motivate myself to do what is necessary in research as efficiently as possible so I can focus more on the actually interesting, creative parts?

(I could not figure out how to tag this; feel free to edit tags)

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There is a number of great answers speaking to organization and extrinsic motivation by now; I was wondering if anyone has had any success in finding/improving their intrinsic motivation with regard to writing? Possibly a change in attitude, maybe a point of view that may not have occurred to me that makes writing appear more useful?

Answer

tl;dr: Divide and conquer. – aeismail♦

The Balloon Analogy

I used to hate writing with a passion. Trying to squeeze a 5 page paper out of me was like trying to juice a rock.

Eventually, though, I figured out the root cause for my procrastination.

The biggest sense of daunting I found when writing a paper is that you start with nothing, and have to end up with a significant something.

So, let's look at what you have set up. You create a new Word/TeX document, and it's there. Page 1 of 1. A blank page with that blinking cursor.

Pretty intimidating and most likely the reason why we push it off till tomorrow until it's due next week and then we've wasted forever. This is basically like us trying to inflate a big weather balloon. You do a little work, and it doesn't seem inflated at all.

I eventually got over this intimidation by reducing the size of the problem to its individual parts. Imagine trying to fill up a dozen individual party balloons with the same amount of air as the weather balloon. Each bit of inflating goes a long way, and a fully inflated mylar balloon is much easier to achieve.

Transforming one Big Balloon into a Bunch of Smaller Balloons

A strategy that we all learned in K-12 is outlining, which actually helps more now than it did then. Now, it doesn't have to be a formal outline. However, the idea behind the outline is that it can transform into a full-sized paper much more easily than a blank slate, for little actual effort in.

Stub out each individual section of your paper. If you have a glossary, add that. If you have a bunch of subsections, create them, and add the titles. Don't be afraid to dedicate an entire page to a chapter with no content, if you feel that eventually you will need it.

For basically 12 or so lines of typing, you've turned a single blank sheet into perhaps 8 or so pages with a rudimentary summary of what you're going to talk about. Filling out a single page or two is much less daunting than that previous 20-page paper we were fretting about before. This dividing and conquering of pages has turned 1 very large paper into 8 relatively easy to populate short papers.

Inflating the Balloons

After that, pick a section, any section, that you want to write. It doesn't have to be the introduction if you're drawing a blank. That's perfectly normal. I rewrote my introduction all the way to the end of my paper because the rest of the paper was evolving to include additional topics. Some sections needed more meat or could be expanded, others could be shortened or removed.

Now, type away at the keyboard on the section you've assigned to yourself until you fill it up or have run out of ideas. Wanted to write Chapter 5: Potatoes in Artwork? Go for it! Chapters 1 to 4 can wait until you're sufficiently inspired to do them, or have enough information from Chapter 5 to help give substance to the other chapters.

When you're done with the small subsection you're working on, you should evaluate whether you feel you can do more. Sometimes, after doing a relatively easy section, I enjoy tackling a somewhat harder piece and getting that out of the way. Other times, I'll need a break, and take one.

Basically, my strategy is that one shouldn't plan to, or even reasonably expect to, write the paper front to back.

Breaking the paper into parts, giving them sufficient weight so that you can see the progress as you go, and slowly but steadily inflate and become a full paper.

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Author's Note: Yeah, for some reason now I write really long posts even when I don't mean to.

advisor - My supervisor doesn't believe in depression

This is perhaps less a question and more of a cautionary tale, but I've seen a few people asking how best to talk to their supervisor about mental health and I wanted to share my experience with this and perhaps get some advice for if I find myself in a similar situation further down the line.

So, to give a little context, I am a female student who has just completed her viva. I also suffer from anxiety and depression. For the most part, my PhD went well, I was happy to follow my supervisor's guidance and tried my best at everything she asked. As time went on though, depression and anxiety started creeping in. By the time I got close to handing in, I was seriously depressed, bordering on suicidal, and was having near daily panic attacks at the thought of facing my supervisor. It also took me a long time to get help, my supervisor was very much of the 'just work harder to get over it' mentality and I ended up adopting that for myself. I couldn't really be depressed; obviously I just needed to work harder.

Fast forward to having handed my thesis in. My supervisor was advertising a post doc position, built on the results from my PhD. She was very keen on me applying for this post, telling me multiple times that she was happy to hand it to me on a plate, as it were. I, however, couldn't face another three years of working with her. I had finally started getting help for my depression and, although I wanted to get better, I was very aware of the fact that remaining in my current situation would not be helpful. I didn't want to be rude, and simply not apply for this postdoc, so I sent my supervisor an email.

Dear {supervisor} I have decided not to apply for the postdoc you have advertised, but I felt I owed you an explanation for my decision. I understand that you need the best person possible to fill this role in order to do the project justice and to produce the best science possible, and at the present time I do not feel I can be that person. This has not been an easy decision to make as the project is both an interesting and exciting topic, which would allow me to develop all the work from my PhD. I have spent a lot of time weighing up the options, but I cannot honestly apply for the role and give it my best. My mental health has been deteriorating for some time now, and this combined with other stress-related problems means that I cannot commit to a long-term role at this point. I have seen a doctor and am currently having sessions with a therapist to help work through these issues, and I hope in time I will be able to return to a healthy state. At present, however, I do not feel that I can honestly apply for the role, and I hope you will accept my apologies for disappointing you.

I appreciate all the help and guidance you have provided during my PhD studies, and I am very thankful to you for providing me with this opportunity. Of course, I will still do my best in readying the remaining chapters for publication and in preparing for my viva. I just cannot commit to a future role at this point. In conclusion, although my current health problems prevent me from applying for the role, I wish you all the best with this project and hope you find an eminently suitable candidate.

In hindsight, this perhaps was not the best move. Since the subsequent meeting following this email the supervisor has been increasingly angry with me. She has told me that my behaviour is unacceptable, and that anyone else would have fired me. If I make mistakes, she accuses me of behaving maliciously towards her and tells me that I am unqualified for a career in science. She has also told me several times that she can't possibly write a reference for me, despite my good work for the majority of my PhD, because she doesn't know if that is the real me or whether instead I am a nasty manipulative person.

In some respects, very little of this matters. I have been offered a job outside of academia, which I am looking forward to starting, and have recently worked with a conservation organisation who are more than happy to give me a good reference. I have also passed my PhD, and have no corrections to make. I do, however, still have to interact with this supervisor, as she wants to publish work from my PhD and I am worried that, unless I am involved in the process, she will not include me as a co-author.

I would like to get some feedback, though, on how common this sort of reaction to mental health problems is in academia. I know that the percentage of the academic community with mental health problems is disproportionately high, and that it is important that more people are open about mental health. Is it something that is still viewed as a weakness in academia, though? I don't want to believe that is the case, but I do want to advise caution for anyone thinking about telling their supervisor something like this.

I also want to encourage anyone who is struggling with their mental health to seek help. It's really important that you don't try to deal with something like this alone. You can't fix your mental health just by working harder. Furthermore, it is not a weakness. It is an illness, a medical condition. Just like a broken bone or a fever, a mental health problem is not your fault.

Just to clarify, in case anyone is worried, K Grayson is a pseudonym.

formatting - Do all Elsevier journals require ONE column format for manuscripts to be reviewed?

I want to submit my paper to Elsevier Optics Communications, but I'm confused about the template of the journal. According to the guide for author, the manuscript can be in either Word or LaTex format.

It seems that there is no sample template for Word format, but they DO say that the Word template should be in ONE column.

This journal doesn't provide its own LaTex template but they provide the general template for all types journal in Elsevier. There is also a sample LaTex template which is in ONE column format. There are several options including "preprint", "review", "1p", "3p", and "5p". The default option in the sample template is "review" which has ONE column format.

What makes me confused is that the final format of Optics Communication (as can be seen in published paper) is TWO column. Does this journal (and maybe all Elsevier journals) require ONE column format for the manuscript to be reviewed? After the manuscript is accepted, the officer of the journal will turn the manuscript into TWO column.

Answer

In mathematics, usually authors aren't expected to format their paper according to the journal's template until after the paper is accepted. Even then, authors usually don't bother and leave it up to copyeditors. This is the case for Elsevier as well as other publishers. Although publishers' websites often "encourage" authors to format submissions in a certain way, these suggestions are typically ignored.

What is true for math might not be true for optics, so it is probably worthwhile to ask a scientist with firsthand knowledge of the journal (or at least the research field in general). Perhaps such a person will answer your question here. Otherwise, I would suggest that you only invest any effort into reformatting your paper if such a scientist (not an Elsevier employee) confirms that this is indeed important. If it's not practical to ask a colleague, you might e-mail a member of the journal's editorial board with this question.

postdocs - What questions should I ask when I visit labs for potential post-doc employment?

I am approaching the end of the tunnel and starting to look for my options beyond the PhD. The few contacts I have initiated have been positive so far and I will be visiting some labs in the coming months.

I am wondering which questions would be good ask during these visits. What insights would be valuable to acquire after these visits?

Regarding the talk with the group/lab leader, I am thinking of keeping the conversation/discussion around research interests for both parties, as well as his/her expectations from me and my responsibilities, if I start a post-doc there.

With respect to the group members, I intend on inquiring about the social environment, work ethics/common practices, different competencies that are in the group. Edit: a good advice I recently got from an ex-colleague who's doing post-doc in the US now, was to investigate whether or not there is a tradition of inter-group competition, i.e. will there be another post-doc working on the same project?

Any comments/suggestions based on personal experience?

Answer

Your list is a good start, but I would dig a little deeper into the "expectations" item than you may plan. "Postdoc" is maybe the least well-defined role in a research group, and what you are supposed to (and allowed to) do can vary greatly. You need to have a clear understanding in advance whether your vision of the position matches with the vision of your mentor. Concretely:

• Ask whether you are supposed to write papers without your mentor. If yes, try to get a feel whether the mentor means it (very few will outright say No to such a request). Try to get a feel for what percentage of joint vs. individual work your mentor expects.


• Ask whether you are supposed to write grant proposals. Ask whether you will be the PI of said proposals, or your mentor.


• Ask whether you will be responsible for your own PhD students.


• Ask whether it will be possible to work on topics that are of interest to you, but of less interest to your mentor.


• Try to get a feel for the mode of collaboration your mentor expects. Everything from "you do your thing and ask me for input when you need it" to "I'll tell you which problem to work on, and you report back your results to me" is possible, and you will want to know which one it is.

In addition to that, also ask what your mentor has in mind in terms of your career plan. When you apply for assistant professorships in a year, will he fully support you, or will he want to keep you around for longer? If the latter, what can he realistically offer you?

publications - Article-based PhD and advisor's (new) role?

My engineering university offers a relatively new option to do an article-based dissertation, where the primary research is submitted (and hopefully published) in several scientific journals (at my university it's 3). The dissertation is then shorter than a typical PhD, because it describes how the articles fit together to form the thesis, etc.

It's a relatively new idea (for engineering PhDs and for me), which I find interesting as an advisor because it engages PhD students more in the research experience (publishing). Also, it is theoretically more efficient for the advisor and student (as a co-author), since time and energy spent on revising could be more focused on getting publications, and not only on a big PhD dissertation that few people will ever read.

There are other advantages described here (not my university).

My question is not about whether it's good or bad, but how the role of an advisor on co-authored papers might change in such cases.

For example, when students write a traditional dissertation (masters or otherwise), they often struggle with communicating. Students grow and improve written communication and contents of the dissertation in an iterative and incremental process (draft revisions after feedback from the advisor).

In traditional grad-student co-authorship setting, I would take a more active role as an editor (as my advisor did when I was a PhD student) on a paper, mostly because of experience and to increase chances of getting an article published. Sometimes that role is minimal, if only a workshop or conference is targeted, since it might be easier to publish there.

But with an article-based PhD, it seems that the active approach in editing co-authored journal papers is essential, and in effect writing a big part of the dissertation for the student. I realize every case is different.

I'd be happy to know from experienced advisors in this setting to know if and how an advisor's role must change in article-based PhDs.

Answer

The system of article-based theses has been the norm in my field and university for as long as we have been in existence, although monographs are also accepted. We therefore lack experience with monographs, although I wrote my thesis as a monograph in the US system once upon a time.

The main differences, as I see it, between monograph and article writing is that with articles, you must reach a high level very early during your PhD study. With a monograph you can work on all of it until the very last moment. With an article-based thesis, articles must be planned and written up early on. I would say that it is both common and useful to have the first paper being mainly written by the advisor so that the student can learn from scratch in every part of the article write-up. Since the goal is to make independent researchers out of the PhD students it follows that the advisor involvement should gradually decrease over time. This is of course good in theory but difficult in practise. The point is, however, that it is important to get an early start with the writing and the structure of the work has to be such that it is clear that publishable results can emerge after the first or second year.

Article-based these need to be thought through so that papers can be produced. We let the advisor and student write up a time plan for the PhD work which also outlines the basic research work and the resulting papers. The plan is filed by the subject responsible. This plan is followed up annually so that changes can be discussed between advisor, student and subject responsible. This is useful since everyone needs to think things through on a regular basis.

phd - Maximizing opportunities to be admitted in top schools

I did a modest undergraduate in Information Systems (3/4) and good master's in CS (3.4/4). I've PhD acceptance from a good school in Canada. However, I still need to go to top school , or at least a well-known school, in US.

I am planning to apply to top schools in CS next year (since deadlines already passed). I have done some research and got some papers accepted at good conferences. Beside getting good scores in GRE, what should I do to be well-prepared for the next year?

I am fully sponsored student by my government, how will this affect the admit decision?

publications - "Awaiting AE decision" has lasted for nearly four months. What should I do?

The status of my manuscript is "Awaiting AE decision", and it has lasted for nearly four months. I have sent two pieces of mail to AE to inquire of the status, but I have not received any reply. What does this situation mean? What should I do? ..While, I am still waiting, no reply.

publications - What kind of design freedom can you permit yourself in academic writing?

In scholarly journals, or publicising in certain magazines you are expected to hold true to a certain design pattern and citation style. However, when publishing your own work independently you are free from those constraints, or are you?

I am a designer by heart and every couple of years I create a new template that I use for future academic papers, following contemporary design patterns. In my opinion, my templates look nice. Not too strict, though flirting with kittenish. I am convinced that a nice design leads to a fruitful first impression. However, I am aware that this might be very subjective.

My question is, then, do academics generally look down on "design hippies" and should all retain a strict - possibly even chippy - style? Or does all of this matter not as long as everything is legible and well-formatted?

I use hand-written, cursive fonts in informal paperwork all the time. That's why I posted this question: even though certain fonts are well-suited for distinguished forms of design and publicity (such as magazines or webdesign), how does a formal academic world react to such patterns. On a (possibly less formal) website, for instance, Pacifico would be used without question. Of course, an academic audience is an 'ole other bunch all together. That's where my inner designer and outer academic struggle with one another. Should we stick to the trusted, formal (and, let's be fair, boring) style, or can we go a little (just a tad!) crazy? Note that I'm not strictly talking about fonts. It can be anything, going from structure (column layout), to colours and highlights, to bold face and font families. Heck, maybe even illustrations!

Update: people in the comments seem to focus a lot on the fact that I mentioned Pacifico, a cursive font. First of all I should clarify that I only brought it up as an example. Secondly, I only considered that font as a candidate for large headings with a font size of 24pt or larger - which increases readability. I did not imply to use this particular font as the main typography for my text, but merely as a means for catching titles. I'd also like the emphasise - again - that I am aware that certain fonts are not formally applicable and would annoy rather than refresh an academic reader's mindset. But as said, I am a big fan of design trends (focusing on, but not restricted to, fonts) and innovation, and I am simply curious to know how academics think about this: how far can one go. How different is an academic design style from for instance web, advertising, magazines and newspapers.

Answer

I read papers, I don't hang them on my wall. That is the main objective, and your design should subdue to it. I enjoy a well crafted book, but I get extremely annoyed when some unnecessary decoration gets in the way of usage.

In your case, the font of the titles requires a mental effort from my part to read them, which I find unacceptable, and thus, annoying. When reading a paper, I usually skim through the sections to get a broad picture of it; with Pacifico, I need to waste neurons in deciphering it while constructing my mental idea. I also find that the numbers in the text stand out a lot, probably more than they should, as they are not information I would like to get while skimming.

On the other hand, I have encountered a few unique and very nicely crafted documents, and those made a more long lasting impression. If not for anything else, I remember the general image of the article.

Bottomline is, if your design is good, it will be welcomed; but if it has flaws, some picky people like me* may get displeased and cause a worse first impression. A standard template is a safer option; but more difficult to stand out.

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*To give you an idea of how much, I find several citation styles to be rather annoying because they are clearly inferior to others. For example, anything without DOI in the modern times.

career path - What are the main reasons why academics leave academia? (Looking for references, not personal opinions)

Is there any research/study/survey that looked at the main reasons why academics leave academia?

I did read a few articles explaining why some particular academics left academia, but I would like to have some statistics to see what are the most common reasons invoked.

I mostly interested in the computer science field (machine learning) in the US, but curious about other fields and locations as well.

phd - How not to lose confidence in front of supervisor?

I have been working on my doctoral thesis with a very well known professor in the field. I am going to finish 1 year of my study with him. As usual, we have been meeting every week at least once on the problem.

Problem: No matter how much I do prepare about the possible discussion on any topic, I have been losing confidence in front of him almost in every discussion. This is probably has something to do with me thinking that I am not capable of working with him. My standard is not that much. I don't know whether is this normal? How do I get over this problem? Sometimes, I can't even speak properly when he sends me to the whiteboard for any explanation. This is weird. I feel really bad after that. I keep messing up discussions. However, he gives me time. Can I get a few suggestion on this?

Note: English, which is not my native language, is the language of communication during these discussions.

Answer

I experienced something similar at the beginning of my PhD. It was mostly due to the fact that as I was verbalising my ideas, I'd realise their flaws, that they don't quite make sense, or that I hadn't it as figured out as I thought.

I suggest you try to verbally explain your ideas to someone else (if no one else, plushies are great listeners) before you talk to him, that'll give you extra confidence. It is important that you speak out loud, and from the beginning: don't skip right to the meat of the question, your problem may be in the fundamentals.

If this is your problem, once you get the hang of it, you'll quickly learn how to weed out some of these bad ideas, and gain confidence on your explanations.

Something I have seen my students struggle with (and probably myself too, but I don't notice it so much) is that when I ask them a question, they try to answer it as soon as possible, so they get stuck in suboptimal explanations, increase their confusion, get more stressed, and lastly blocked. He is giving you time, so take it, think carefully about what you are going to say, and explore different ways of expressing it before you start saying it. And furthermore, if you find a better way of explaining it, feel free to scratch what you just said and start all over again.

Another option is to set the the ground for a discussion by sending a long email taking your time to explain everything. And if you feel you didn't manage to get your point across, never hesitate to send it after the fact.

Lastly, for a few weeks I got the feeling that my supervisor wasn't really understanding what I am trying to do; but after I gave a 30 min presentation of my work in the department, from the bottom up, he got very excited, and now his comments are, I feel, much more spot on. The presentation included explaining my tools for people completely unfamiliar with them (to be specific, a specific technique built on deep learning for machine [but not deep] learning practitioners).

For your case, consider asking for some time, thinking on it on your own, and coming back with an explanation whenever you have it.

graduate admissions - Is it possible to be admitted to a Master's program after not completing Bachelor's degree due to academic dishonesty?

Is it possible to get admission to a master's program in economics without finishing up your undergrad?

I have completed 105 credits so far for my BA Honours in economics and math degree, and still need 15 credits to graduate (120 required for graduation). However, a case of academic dishonesty could lead to my suspension from my current university. I know that I made a mistake at such a crucial time in my undergrad, but I can only learn from it.

The problem also I'm having is that some universities will not even consider my application as result of academic dishonesty. Apart from this my application is quite strong in terms of doing well in economics courses, strong letter of recommendations, and GRE score..

I have already published an economics paper in an undergraduate journal and feel as if there isn't anything to learn about economics from my university.

I can study economics independently and work to get "food on the table" and have some real-world experience under my belt before embarking on a journey as an intellectual.

application - What are the key points in short descriptions of research experience?

When writing short descriptions of research experiences as a student (undergrad or postgrad), what are the key points that professors, potential collaborators and admission committees would like to see?

These might be very short descriptions in a space constrained academic CV, or slightly less short descriptions on an online profile or research statement. What are the key essentials (in the CV case) and the additional points (statement/website case)?

Answer

In a one-sentence statement, I want to state as precisely and concisely as possible as much relevant detail about the project I was working on. For instance

Analysis of Widget Manufacturing

doesn't tell me much about what you did. On the other hand

In-situ XYZ Experiments and Numerical Modeling of the Parametric Influence of Temperature, Humidity, and Cooling Time on the Strength of Widget X under Load-Bearing Conditions

tells me much more about the problem you're working on.

If you have perhaps a paragraph, then I went a short summary of your work. You should provide: a motivation for the problem, an overview of what you did, and a summary of the main methods, results, and conclusions of the work.

advisor - Does it amount to plagiarism by supervisor?

I have been working on an idea for last 2 years almost independently along with other research works. My advisor did not believe in my work much initilally, so I did not get an RA for two years even after requesting. Recently, I am getting encouraging results with some specific examples and scenarios with good hope for success to solve a complex problem using that idea. I have not published the work yet. Initially, my advisor was not interested in the idea partly because the work is not his area of expertise and insisted that I spend my time in other research projects with a senior colleague. I pursued it with my interest in spite of RA support, but with new results and potential benefits of the approach my advisor became extremely interested and even described the work as the next big idea in our lab meetings. I am happy about it or maybe he says it to make me happy. However, recently I encountered a situation which was difficult for me to comprehend. I found my advisor present a perspective paper along with many other renowned experts in the field, proposing and highlighting the approach I have been working on as the future direction and visionary in the field along with other important developments in a conference. Even though I was not a co-author in that paper and my work was not cited or even acknowledged, I consoled myself as my advisor was alluding me that he was promoting the idea; it was an advertisement of the work (of course with out any acknowledgement).

As he was not the first author of the perspective paper and there is a possibility that first/other authors can make claim of it, he asked me to file an updated technical report in the department before the paper is published. It looked to me like he wanted to promote himself among his colleagues with that idea with out acknowledging it to me before the audience and greater scientific public where it matters.

I happened to attend the conference as a PhD student, and found that the presenter of the perspective paper (whom I don't know) presented more than half of his talk on my idea with my slides that I shared with my advisor, and there was no acknowledgement or mention of my report or work. It was even worse to see that some of the terminology that I planed to use, was disclosed and few misinterpreted while explaining.

Even then, people really seemed to liked the idea and the approach and many are convinced that the idea is going to impact the field. While I saw a very drastic change in the way my advisor treated me recently, but what really made me sad was when my advisor asked me to refer to this perspective paper (to which I was not a co-author) in my impending submission (on the idea).

I feel like it was unfair but I don't know if research is done this way in academia or if it is perfectly legit to do something like that. I decided not to cite the perspective paper with possible consequences. I just wanted to know how other students handle such situations effectively and if such a thing is a common practice.

Edit: I do have all email traces and even a previous publication explaining part of the idea and a recent technical report submitted to the department with the complete idea.

UPDATES

June 2014: I have continued with the situation I described above honestly because as a student I hardly have any options and as suggested by many that it would be an academic suicide. But, it had impacted me severely, mostly because I believe that any good idea I will bring to the table will be stolen or misrepresented and there will be cleaver manipulations to take ownership of them. I will take two steps forward and three steps backward. I could hardly perform in my potential. I will let you know my ordeal soon and many thanks for your kind help and support.

graduate admissions - How much is expected to know before starting a PhD

I recently graduated with a BSc in applied mathematics and considering on applying for a PhD. In fact, I contacted a supervisor and he seems some what interested in my undergraduate academic performance. He also sent some articles to read so that I get an idea of what sort of problem is there to be analysed in the PhD, and of possible methods to follow. I read them, however I do not understand everything in those papers as I am not familiar with some of the methods used. However, as I have a basic background knowledge from undergraduate coursework, I believe, I can study those methods in depth and gain knowledge. But it would obviously take couple of months for me to learn the material. Although my PhD wouldn't start (if I get selected) for another 6 months, I have to tell the potential supervisor about what I read in the articles he sent and how much I understand.

So, if I say like I didn't understand all the details, but I intend to learn them before the start of the PhD, does it look negative? Does supervisors expect us to know everything before the commencement of the research?

Answer

The best way to respond to this specific question is to engage the potential supervisor about specific content in the articles. You are not expected to know everything at this stage. But it is important to show you are interested, can engage with the material, and (not least) actually took the time to read what they sent.

A response like "I read them but I didn't understand everything" doesn't give them any information about you.

Be specific, e.g.

• I found the way authors applied X method in this paper to be really interesting. I was familiar with this but didn't realize it could be used this way.


• The authors did X but why didn't they use alternative approach Y?


• I don't understand what this statement means...could you explain it?

Asking questions about things you don't understand can be one of the best ways to engage.

How do graduate schools evaluate GPA?

I am wondering how graduate schools like Stanford, Berkeley, Caltech, and MIT evaluate the GPA?

Because you can boost your GPA by taking easy classes and in the application it only says enter your GPA. Do they consider classes students have taken? Do they consider whether course are challenging or not?

Answer

As a filter.

The main purpose of asking for GPA in grad school admissions is to quickly weed out people (like me) who have actually low GPAs. Nobody is admitted to top PhD programs solely on the basis of their GPA, or even primarily on the basis of their GPA. Other factors, including which classes you took, are more important.

If you have a high GPA, but no evidence of research potential, you will not be admitted.

biochemistry - How do disulphide bonds in hair cause curling?

I understand that there are several characteristics of curly hair which differ from straight hair (such as an asymmetrical distribution of disulphide bonds in curly hair), but really am struggling to understand the root cause of inherent curl on the macroscopic level.

My current understanding of the hair structure is based mostly upon this website

The most relevant part of the hair for our discussion is the cortex, which is made up of many axially aligned macrofibrils, or macroscopic keratin fibers, which are in some filler essentially of lipids/proteins. Inside these macrofibrils are microfibrils. These are also aligned axially and in some filler of lipids/ proteins. Inside the microfibrils are the protofibrils, even smaller fibers which are twisted around each other like a yarn. These protofibrils are made up of 4 keratin chains which are essentially twisted together and connected by disulphide bonds and hydrogen bonds. While hydrogen bonds are easily broken, the disulphide bonds are not. In curled hair, the macrofibril isn't symmetrical but I am unsure as to how this, or what other effects, actually lead to the curling.

I had previously assumed that the reason for curling is that in an asymmetrical configuration of the hair(IE not cylindrical but more oval in cross section), some residual stresses are formed by the disulphide bonds between the keratin, If this is true, it would lead me to believe that it would cause increased buckling of the protofibrils. But, even with straight hair and more symmetrical disulphide bonds, you already have some curling and buckling of the protofibrils, but the hair doesn't curl on a macroscopic level.

As such, it doesnt seem like this buckling due to asymetrical disulphide bonds would necessarily lead to a curled or organized structure on the macroscale, with the macrofibrils. This leads me to believe I am missing something.

neuroscience - If the brain has no pain receptors, how come you can get a headache?

I've read many years ago in books, that the brain has no nerves on it, and if someone was touching your brain, you couldn't feel a thing.

Just two days before now, I had a very bad migraine, due to a cold. It's become better now, but when I had it I felt my head was going to literally split in half, as the pain was literally coming from my brain.

So it lead me to the question: How come people can get headaches if the brain has no nerves?

Answer

Brain, indeed, cannot feel pain, as it lacks pain receptors (nociceptors). However, what you feel when you have a headache is not your brain hurting -- there are plenty of other areas in your head and neck that do have nociceptors which can perceive pain, and they literally cause the headaches.

In especially, many types of headaches are generally thought to have a neurovascular background, and the responsible pain receptors are associated with blood vessels. However, the pathophysiology of migraines and headaches is still poorly understood.

mutations - Can cancer cells in the same person, organ, and origin have different DNA?

Is it possible for cells from the same tumor to have different genetic material, and if so, to what degree is it possible (how fast do they mutate) ?

Answer

Cancer cells and normal cells differ on the genetic basis but they share the same genetic background, so they have not different DNA in the sense of two different people. They have to be different, since cancer cells have to accumulate mutations on a number of genes to become a cancer cell, which can survive and will not be directed into apoptosis. These are genes which control the cell cycle, certain growth factors, tumor suppressor genes, cell signalling and so on. In all these genes there need to be either activating or deactivating mutations present. Most of these mutations are point mutations (single nucleotide polymorphisms, SNP), where only one base is altered to achieve a mutation. An example for such a mutation would be the mutation in the B-RAF kinase, which is involved in signaling and activating genes, where a point mutation exchanges Valine 600 to glutamic acid (V600E, for reference see here). These are relatively small differences between these two cells. The Cancer Genome Project aims to sequence cells from a cancer and also normal cells from the same individual and then do a comparison. Later stages tumors often tend to genetic instabilities where complete regions of the genome are duplicated, inverted or deleted, see here for a review. A more basic overview is given by the Ebook "Essentials of Cell Biology" by the Nature Group, which has an overview of cancer cells.

Regarding the mutation rate, this is hard to estimate. There are a few papers available here, but they focus on the mutation rate in germ cells, so these are mutations that are transmitted to the next generation. The estimates there are between 70 and 100 mutations per generation per individual, depending on the research method. You can find a nicely explained blog article here, which gives a number of original references, too.

The mutation rate in cancer is a different thing, since this depends on which genes are mutated. The mutation rate for cancer has to be higher for the cancer cells to allow to collect the necessary transformations into a cancer cell, but these mutations seem to occur only in a few hotspot regions of the genome (Further references can be found in this article called "The causes and consequences of genetic heterogeneity in cancer evolution" and in this called "Emerging patterns of somatic mutations in cancer"). There are two article called "The mutation rate and cancer" which are interesting in this context. They can be found here and here. As always, if you have problems with getting the articles, let me know, I can help there.

Forced to Quit PhD although the hard and proved work

I am a first year Ph. D student, and I have been working on a new topic of research. I worked day and night to prove something new and verified it. I began my Ph. D while my supervisor was on travel, but he returned before I had been here for long. When he returned, he told me we have to stop and not continue without any reasonable reasons.

After a few months he began treating me poorly---always belittling and underestimating---although I got two grants from a top conference, made videos and podcasts, and constantly received praise for my good work and personality.

It seems that I have been treated as a competitor, not a collaborator. Although agreeing with my approaches in private, my supervisor said false words to the committee to take the decision and stop my Ph. D work!

It is not surprising, as there was another former senior Ph. D student who I met on campus, who was not allowed to defend his Ph. D: this same supervisor claimed he was not able to finish his dissertation although he had published in a peer reviewed journal and having citation as well, it was scary and not familiar.

In front of committee, he lied, and said something without proving. I asked if he can make a detailed constructive criticism, but he could not. All I can say that they are a gang literally, and he said words that show that he is jealous and doesn't want to see me having self confidence in my self. I know no one will believe me, but this is the truth.

Honestly, I am distressed and I'm losing sleep. I had this dream where there were many people who saw me fail. All things considered, I don't know whether what happened is good or bad, and I definitely don't know what I should do next!

I would be grateful for your advice and whether there is someone has encountered any similar situation.

human biology - Athletes: nature vs. nurture?

Having watched a lot of olympians the last few weeks, I was struck by how many of them have actually spent their wholes lives/careers training for their one event (be in running a marathon, or throwing a javelin). This is of course unsurprising - a lot of people take their sport very seriously - but I wondered to what degree these athletes are predisposed to becoming atheletes, and to what degree they just 'happened' to end up doing it.

I've had a bit of a search around, but have been unable to find any studies (although there is an awful lot of media attention to the topic) that actually study the interaction between nature (genetics) and nurture (environment/training etc) in the context of top-end athletes.

It is quite clear to me that the answer is of course 'both', but to what degree? Have any common genetic variants/loci been identified, or is 'athleticism' a far too complex trait for this? Thanks.

Answer

For all types of athlete, their ability is determined by both genetic and environmental factors (nature and nurture). The degree to which each contributes ultimately depends on the demands of the sport.

As an example let's compare basketball and golf.

Basketball is likely to have a strong genetic component because players tend to be exceptionally tall (average is over 2 metres and there are only a handful who have played NBA under 1.75m). Because height is strongly genetically (but not entirely) determined by the genes, they have a big influence on whether someone can poses the physical qualities to play in the NBA. However, a large part of their technical capabilities are due to their environment. If you give a basketball to someone who has played 2 games a week their entire lives and ask them to take 10 shots it is likely they would score more than someone who has never seen a basketball!

Comparing basketball to golf, there are all sorts of body types within the PGA tour, and they is no/few obvious genetic traits which golfers tend to have over other people. This would suggest that golfing ability is more affected by environment.

So an easy way to get a rudimentary test of genetic contributions to sporting ability would be to compare frequency distributions of focal traits in the athletes to distributions of regular people. Obviously the phenotypic trait you measure has both genetic and environmental contributions (e.g. childhood diet) which could affect them but it would be a good starting indicator which could give some candidate traits to test.

As a scientist I would also consider sequencing some athletes and some non athletes and seeing which genes the athletes have more often then the regular person's genome. However, such studies are likely to be complex - linking phenotypes (in polygenic traits) to the single allele variants relies on large sample sizes. Generally it will be more difficult if:

1. There is large variance in the trait


2. The gene has a small effect (see major and minor effect genes)

Both of these problems going to be positively correlated with the number of genes affecting a trait (how polygenic is it?) which for athletic ability is probably quite a substantial amount of genes.

EDIT: Here are some possible studies for your further exploration of the topic-

Candidate genes for Specific Genetic Markers of Endurance Performance and o2max

Rowers have an excess of the ACE I allele

Elite Italian footballers with "explosive" leg strength also reveal ACE and other genetic markers

A precautionary tale about Genetic tests for athletic ability

advisor - How to teach "puzzling skills" (for coming up with examples) to PhD students?

Background: Some sub-areas of computer science are concerned with developing new methods to solve practically motivated problems of certain shapes (determined by the sub-area). While obviously using real practical problem instances would be best, few papers in these areas actually use them, because (1) it is hard to obtain these problem instances (from industry) without first giving them a method to solve them (chicken-egg problem) and (2) many of these problem instances have too many intricacies that need to be handled at the same time, so that to make progress in the area, most papers pick one particular challenge, show the challenge by means of a convincing but synthetic example and propose a novel method that gives some insight into how to solve the challenge.

Doing research in this area requires to identify the shortcomings of current techniques and to derive convincing examples that actually demonstrate the shortcomings of previous approaches. Coming up with such examples requires to marry (1) the understanding of previous techniques, (2) the basic idea of what the practical problems are about, and (3) conciseness of the example, so that it can be used as running examples for thinking session at the whiteboard and as running examples in papers.

Question: Coming up with such examples requires creativity and can be seen as a puzzling problem, as the requirements are somewhat contradictory. Now there are some PhD students who will excel at such tasks and solve them without any guidance, and others will not know how to start, despite having a working knowledge of all the involved concepts. So what are suitable strategies to teach such puzzling skills to PhD students? I find it highly difficult to give help in such situations, as vague hints such as "think about what happens in this situation in that application" are often insufficient for a PhD student who is not good at puzzling, but hints such as "start by doing this and that" yield no learning effect since "this and that" will typically contain all ideas for one particular solution. The strategies should help students who are already familiar with all formal definitions and basic concepts, but never looked at them in combination yet.

Example: To clarify the question, let me give a (made up) example that is at least understandable to computer scientists. Assume that there is some reason to believe that when translating a deterministic automaton over finite words (DFA) to a digital circuit, we can make the circuit smaller whenever there are two states s1 and s2 in the automaton such that the language accepted when starting the automaton from s1 is the complement of the language accepted from s2. We also have a reason to believe that this is relevant for some application that involves all possible kinds of computations with binary-encoded strings. The tasks is to find a DFA that has two such states s1 and s2, whose implemented language can be easily explained in a sentence or two, for which the DFA is non-trivial (i.e., no state accepts no words or all words), and that makes at least a little bit of sense from the application point of view (here: arbitrary operations over binary strings)

Example solution to the example: One solution is to take a binary alphabet and to encode the language containing all strings that have an even number of 1s. The minimal automaton will have two states that naturally have this property. Many other solutions are possible, though.

Notes: I'm posting this here as the problem may not be exclusive to computer science. The example description above can very likely be improved. But let's assume that the task is already crystal clear to the PhD student, including the motivation.

What is the difference between a PhD degree and a DSc degree?

Some universities that offer a DSc as the doctoral degree, while most of them also offer a PHD degree in science. What are the differences these degrees in terms of academic standing? What are the pros and cons?

Answer

It depends on the university and the country.

In England, a PhD is typically awarded for a thesis and oral examination of the thesis, usually followed by implementation of corrections to the thesis, the requirements for which are specified during or just after the oral exam. It's often done soon after a Masters, which is done soon after a Bachelors, so a fairly large proportion of PhDs are awarded at the start of one's academic career. Whereas a DSc is awarded for a portfolio of work, (in some cases submitted together with an over-arching critique of that portfolio), and thus is more likely to be awarded later in an academic's career.

Nominally, a PhD is a doctorate in philosophy, but is typically awarded for pretty much any subject. There are some who argue that philosophy of knowledge always form part of these studies, regardless of the subject. I occasionally use this line to try to inspire students, myself. A DSc is a doctorate in science, and is not awarded for literature, law, divinity, or music, each of which has its own dedicated higher doctorate.

The DSc is a higher doctorate than a PhD, in England. In some other countries, they're equivalent.

Both get the honorific title doctor.

productivity - Maintain scientific output after having a baby

I could have written this question in some other stack places, but prefer to do here because the affinity with the audience. I am the head of a research group, 38 years old, engaged in a lot of things and working on average 12 hours per day on research and all related stuff. My son (first one) was born last week and we really enjoy it. My only concern is: how will I be able to cope with my workload and scientific output after my paternity leave (in two weeks)? I really never thought about this and wonder whether other academics could give advice.

evolution - The falsifiability of natural selection

I was wondering if we could think about experiments to falsify natural selection . According to this wiki : we could invalidate natural selection

“...if it could be shown that selection or environmental pressures do not favor the reproductive success of better adapted individuals”.

So, to test this hypothesis we would have to:

• Have different individuals that are defined as more or less adapted to a given environment


• Put them in that environment


• See if the better adapted individuals have a better reproductive success. (I will avoid the word fitness because one can consider it already contains the principle of natural selection)

But is it possible to define a priori that an individual is more or less adapted? Of course, we could suppose a priori that because of some or other trait (higher longevity, higher stress tolerance, or whatever), an individual carrying that trait will be more adapted. But if we find out this individual does not have a better reproductive success in that environment, we could conclude it was just not the right trait to be better adapted and it would not invalidate natural selection.

Isn’t it, on the contrary, the fact that some individuals have a better reproductive success which allows defining them as better adapted a posteriori? There would then be some kind of a vicious circle.

Ok, so one could say that we do not need to define a priori better or less adapted individuals. We could just put individuals in an environment and see if at least some have a better reproductive success. That would mean that they are better adapted –and so that natural selection occurs-. But suppose we find no significant differences in individuals reproductive success: that could indeed mean that natural selection does not exist. But, well, that could also just mean that there was no selection pressure in that environment.

So if we want to test natural selection existence, we need either to get individuals that are a 100% sure better adapted than others; or environmental conditions that 100% sure exert selection pressures on organisms ; and we need to know this a priori. But, it seems to me that considering an individual as “adapted” or an environment as “selective” can only be done a posteriori if we already accept the idea of natural selection.

That’s why, to me, it is difficult to think of an experiment that would falsify natural selection. Is natural selection falsifiable ?

Answer

What is natural selection?

Natural Selection (NS) is an evolutionary process causing a directional change in both a phenotypic trait and the allele frequencies associated with particular values of this phenotypic trait whenever there is a trait that

1. Has a non-zero narrow-sense heritability $h_N^2$
   
   
   
   
   • See this post for the definition of heritability
   
   
   • Note that if $h_N^2 ≠ 0$, then it necessarily implies that the trait is variable in the population.
   
   
   
   


2. Correlate with fitness variance in the population
   
   

You may want to have a look at this post (maybe in particular Lewontin's recipe explained in this answer) or have a look at an intro course to evolution such as Understanding Evolution by UC Berkeley if this is unclear to you.

You may also want to have a look at the post How is “selection” best defined?

Note about the environment

Note that the genotype - fitness covariance does not necessarily need to be dependent or correlated with a specific environmental variable. Many selection pressures are indeed independent of the environment. If one specific genotype is associated to heart failure, then the environment may matter little. This genotype will always be associated with lower fitness.

In other words, you do not need environmental change, or environment specific adaptations in mind to test NS.

Would evidence that what is needed for natural selection to happen does not exist falsify NS?

Mutations

I don't think that an evidence that mutations do not occur would falsify NS because while NS needs genetic variation (fuelled by mutations), the process per say does not refer to the creation of new genetic variance via mutations. Showing that mutation do not occur would not per say falsify NS (I think) but it would make the point that NS cannot happen. A bit like, the absence of energy would not falsify the theory of gravity but it would prevents any gravity to ever happen.

The theory of evolution as whole would be falsified if one were to show mutations never occur (or occur at a much lower or much higher rate than currently observed) though.

Heritability

Similarly, if one could show that $h_N^2 = 0$ for all traits (nothing is heritable), then this would also prevent any NS to ever happen

Fitness variance

Similarly, if one could show that there is no fitness variance in population or even that fitness is always independent of the gentic variance (in other words, fitness itself is not heritable), then NS would never happen.

How to falsify natural selection?

You could show that for a phenotypic trait $h_N^2 > 0$ and show that genetic variance correlates with fitness variance (fitness can be measured as the number of offsprings) and yet repeatedly fail to see any change in the phenotypic trait values (or frequency of the loci explaining variance for this trait) over time. Such observations would falsify NS.

assessment - Advantages of second marking

In the UK a portion, and in some cases all, work is "second marked" where an independent marker also marks the work. In cases where the 1st and 2nd marker disagree, a 3rd marker may be used. Finally, the entire work of each student over the course of his/her studies is evaluated by an exam board with (sometimes) 2 additional independent markers. These exam board markers tend to only consider cases that are on the border of different degree classifications.

From my understanding of statistics, having all of these different markers will regress marks towards the mean. As I am currently faced with the daunting task of 2nd marking a large stack of off topic papers, I am curious what are the advantages of second marking?

Answer

Double marking has many roles, but mostly it is to ensure accuracy and fairness. The main way of achieving this, and avoiding the statistical anomalies alluded to in the comments is to produce an effective marking scheme, so that academics with sufficient background can grade the exam and produce virtually the same grades. Easier said than done.

More details can be found on the Internet, for example, on Swansea University's website.

terminology - Is it plagiarism to reference a fictitious source?

I'm dealing with a student essay that references three books in support of a claim. None of the books referenced have authors listed, and, based on the contents of the student's essay, I can't find any information on these books online. I'm fairly certain they don't exist, but I'm not sure what to call this beyond academic dishonesty.

I read this from the Nebraska Methodist College:

Other acts of plagiarism are more limited in scope, but are nonetheless cheating. If you decide to make up a quotation or other material and an associated in-text citation, this is plagiarism. If you change or invent the author of a quotation, an idea, or a statistic to make your paper appear to contain more numerous sources, this is plagiarism.

I've run into a few other university plagiarism guides that mention the citing of fictitious sources as plagiarism, but I'd like to know if this is standard, fair, or legitimate to label this practice plagiarism and not just academic dishonesty.

The conflict is this: the student isn't citing these presumably falsified texts directly, but they are referencing finer plot points and characters in them. That is, they are talking about the fictitious dilemmas of the fictitious characters as a way to support their thesis. To me that's dishonest and shows a lack of integrity. I'm grading students on a rubric that awards points for organization, analytical treatment, and language use. If I treat this as academic dishonesty maybe I knock the person's grade down in the rubric criteria related to analysis, but if I treat it as plagiarism I'd give the student a zero.

Answer

For example, Merriam–Webster defines plagiarism via to plagiarize, which it defines as:

: to steal and pass off (the ideas or words of another) as one's own
: use (another's production) without crediting the source intransitive verb

: to commit literary theft : present as new and original an idea or product derived from an existing source

This does not include inventing a quotation, which is in fact sort-of the opposite of plagiarism: passing off one’s own idea as somebody else’s. Other dictionaries agree on this and so does my understanding of the word plagiarism.

Moreover, defining plagiarism so broad makes the term rather useless and almost equivalent to the umbrella term academic misconduct. The reason why we have a word for plagiarism is to differentiate a specific kind of misconduct, not a specific severity.

The conflict is this: the student isn't citing these texts directly, but they are referencing finer plot points and characters. To me that's dishonest and shows a lack of integrity. I'm grading students on a rubric that awards points for organization, analytical treatment, and language use. If I treat this as academic dishonesty maybe I knock the person's grade down in the rubric criteria related to analysis, but if I treat it as plagiarism I'd give the student a zero.

I fail to see why you would be more lenient about academic dishonesty than about plagiarism. I don’t fully understand what you mean by “referencing finer plot points and characters”, but I would classify what you are describing as fabricating evidence, which is roughly as grave as plagiarism. I say roughly, because I see no point in ranking the severity of those misconducts in general and the severity distributions of individual instances of those misconducts strongly overlap.

What is important at the end of the day is whether you are reasonably convinced that the student in question did not just work sloppily, but intentionally deceived the reader (i.e., you). The aspect of intention alone suffices for awarding them zero points, in my opinion.

etiquette - Best way to politely remove someone from paper authorship who planned to contribute but did not?

(There is a similar question but not exactly.)

When you write a paper, you need various views. So you invite collaborators and it often works well. But assume that out of 5 invited, for example, one or two, don't contribute to the paper much but are kept on the email thread with updated versions of the manuscript.

How do you politely remove them from the author list (paper) and how do you say that politely in email. Do you just send them a separate email or a general "authorship rules" email to everybody?

publications - Rediscovery of calculus in 1994: what should have happened to that paper?

There's a well-known paper in academic circles that features a rediscovery of the trapezoidal rule for numerical integration by a medical researcher:

“A Mathematical Model for the Determination of Total Area Under Glucose Tolerance and Other Metabolic Curves”, Mary M. Tai, Diabetes Care, 1994, 17, 152–154.

I think the paper's only figure says it all:

               

You can find comments on many blogs about it, most of them along the lines of “turns out calculus was invented in 1994”. I think it truly is a bit sad that the paper made it past the researcher, her immediate colleagues and friends, a Yale professor of electrical engineering who is thanked for “his expert review”, and most importantly reviewers, without someone giving the author a hint.

In my opinion, the most optimistic view is to see it as an educational paper: the method is not new, but that particular medical community didn't know about it, so it was worth publishing. However, that is not what the paper states: the author clearly presents the method as new and names it after her.

---

Okay, I think I have explained the context. My question is: after that peer-review failure was exposed, what should have happened to the paper? What happened is that the same journal published a series of comments on the paper, and a reply by the author to the comments. Was that the correct/ethical way of handling the issue, as an editor? Or should the paper have been retracted?

Answer

The answer to this question depends on what we should term a peer-review failure. There are tons of journals in the academic market: some journals are happy to publish results as long as they are correct even if they do not push the boundary of innovation. There are some journals that are happy to publish unsound experimental work, and on the other hand, some that encourage theoretical models that are severely impractical and are essentially mathematical mumbo-jumbo.

Publishing something blindingly obvious even to a high-school student is ridiculous, but we could infer two things: one, the editor and the reviewers had not found this so obvious, and two, the journal did not (or does not?) have high standards on innovation anyway. Given it is a field that potentially could have practitioners who know not a thing about calculus, the publication should not come as a big surprise.

The reality is that publication of known facts is not all that uncommon in academia. The hoo-ha over this paper is basically because of the elementariness of the concept. One could expect apologies from journals for wrong results but not necessarily for stale ones.

career path - I want to leave my tenure track position before fall. I have great prospects but no new position "locked up": when should I break the news?

I am a relatively new tenure track faculty member at my school. For many reasons, I am certain I want to leave my current position. All of my reasons are professional reasons; there are no relocation issues or anything like that.

I do not have a new position lined up but I am being actively recruited and feel that having a new position by the fall is a near-lock. Regardless, my finances are strong and, outside of good personal relationships with a couple colleagues, I have absolutely no hesitation about leaving this position.

One issue for my department is that some of my future classes are "important" (required classes that, right now, only I am qualified to teach). I do not want to put them in an unnecessarily difficult position. Therefore, my main question is:

• 
  

  when should I break this news? Given my certainty about this decision, should I tell them ASAP?

  
  


• 
  

  Or, should I follow the general logic that one should never leave a position without a new job lined up? What if this means waiting two more months, REALLY leaving them in a tough spot for covering my "important" fall classes?

  
  
  

As a secondary question:

• any advice about how to break this news? Some of my reasons are related to the way the program is run and the behavior of some of my colleagues. Should I go into this, or should I simply say that the position turned out the be a poor fit and that I must move on?

Answer

Giving notice in 6 weeks time gives them the entire summer to replace you. Wait as long as you can to give your potential next department the time to make you a formal offer. As soon as you have accepted it, tell your current department chair. Don't do it before you have the offer in hand and have accepted. Unless you outright resign effective tomorrow, your current department may assume you are fishing for a counter offer, a raise, or early tenure. Without waiting until you have accepted the potential offer, you may end up burning even more bridges through this process even if you deny that you are trying to force your current department to upgrade you. If you don't walk out the door immediately, then you will have to spend the next several weeks being around your current colleagues. Wait until the semester is over and you have completed your obligations for the spring at the very least.

phd - How many students are typical for an advisor?

I am an undergraduate student in China, majoring in chemistry. I am now considering which advisors would be most suitable for my future research.

Actually, I have been working in a professor's lab since over a year at my university and I am interested in their research topics. What concerns me is that he recruits many students. He is the only professor in our group with over 10 graduate students, expected to increase to 14–16 students next year (depending on whether I join this lab). I am hesitant because I unsure whether he would have the time to provide me guidance with so many students.

How many students are typical for a professor?

[EDIT]

Our group typically hosts 1-2 undergraduates per year.

Answer

I have worked as a postdoctoral fellow in China for two years. My experience was mainly with two institutions -- CAS/Beijing and SCAU/Guangzhou --, but I have visited a few others informally. Thus I write here from my experience as a visiting scholar.

My impression is that the academia in China is strongly pressed to produce papers, and that all sorts of strategies are being employed by opportunistic PIs in face of the prospect of large short-term gains and fast career ascension. Most labs I have visited were crowded, and working 12/7, managed by 1-2 PIs only intermittently present. There is a growing interest in hiring external postdocs, where institutions are competing in salary conditions (often not met).

At the CAS I worked in a lab with many students, each working on different projects in diverse topics. Whilst the local PI had a strong physical presence and held constant meetings, all students complained they were being demanded for results without any actual support nor apprenticeship. The numerous students were also demanded to manage the PI's paperwork, post deliveries (most not work-related), peer-reviews, and paper submission steps. Often on Sundays. At one period that lab had 18 students sharing the same 2-room apartment, payed from their salary... to the PI.

I heard such lab situations are quite common currently, and that fitted with my witnessing of crowded labs. I do not think this local practice is academically nor scientifically healthy.

Therefore my main advice is that you search for a more balanced laboratory, perhaps considering a different culture / location towards a more solid, sane formation. If you find yourself in a bad place, don't play their game and leave it at once.

Good luck!

UPDATE:

I just realised I did not answer your question objectively. The best labs I have dealt with had ca. 3-5 students per professor, most of them are typically Master students. Postdocs are independent and may assist in tutoring students, writing papers; I have seen well-reputed labs with up to 4 postdocs under the same supervisor.

thesis - Some collection of students' theses or dissertations

I want to looking for information in graduating level. Is there any collection or library which provide students' theses or dissertations of many universities? Googling just find library for each university.

Answer

For British doctoral theses, check out the British Library archive. Many full texts are available.

As Ri49 says, you can see TEL for theses from France...they claim 42000 full texts so far....

Guide to learning about Population biology / ecology / dynamics for a non-Biologist

I'm an applied mathematician who works in the field of feedback control systems but has been becoming interested in looking at population biology (e.g. Lotka-Volterra, Mathusian growth,etc.) from a mathematical feedback and systems theory standpoint. Since I know almost nothing about biology save for a poor frog I nearly threw up on while trying to dissect in High School, I wanted to ask this community if anyone could provide me with some materials that give a good overview of the current state of this field.

human genetics - How do we know Neanderthals DNA?

According to this article, a small amount of Neanderthal DNA was introduced into the modern human gene pool. How do biologists even know what the Neanderthals' DNA look like?

The article doesn't mention how the science recognize what the Neanderthals' DNA actually is at the first place. So how do we know what the Neanderthals' DNA is if I'm guessing we never tested Neanderthals body cell samples?

If you say "From their bones/skull" but how do you know they are actually Neanderthals and not modern humans with some rare gene mutation or something else?

Answer

Neandertal DNA has been completely sequenced multiple times now, using DNA from bone and tooth samples found in cool or cold environments. The first Neanderthal genome sequence was described in 2010:

A Draft Sequence of the Neandertal Genome

Since then, as well as higher-quality sequence, more genomes have been completed; at least 6 individuals have been sequenced (perhaps more; I've lost track a little). As well, complete genome sequences from several Denisovans -- a Homo species that were approximately contemporary with Neandertals, but a distinct species -- have been recovered.

The science of recovering ancient DNA has advanced very rapidly in the last decade, and while it isn't routine to sequence 50,000-year-old DNA it isn't as magical as it used to be. The current record for sequencing ancient DNA is 700,000 years, which is earlier than the sapiens/neandertalis split.

neuroscience - How does Serotonergic (5-HT2A mediated) Psychedelia work?

How does serotonergic (5-HT2A specific) psychedelia work? I've read that there are some theories that it might involve the induction of a glutamate release in certain regions of the brain involved in perception.

Isn't heritability more important to genic capture than just genetic variance?

Rowe & Houle (1996) give two criteria for the selection of costly female choice:

1. Condition dependence of sexually selected traits


2. High genetic variance in condition

Regarding heritability, they wrote,

comparisons based on heritability are misleading, as Fisher's fundamental theorem of natural selection shows that the response of fitness to selection depends only on the additive genetic variance, and not on other components of variance.

However, the magnitude of environmental variance should matter for the selection of female choice for sexually selected traits, since the more environmental variance means the less likely offspring of fitter males will be fitter themselves and the less likely females should be to incur costs to mate with fitter males. Am I not correct? Is this an oversight on their part?

conference - Poster author added me as coauthor after abstract was submitted. Can I include it on CV?

Poster author added me as coauthor after its abstract has been submitted to a conference. As a result, on the conference website I'm not listed as an coauthor, but my name is on the actual poster.

Assuming that it's not possible to update poster authorship info on the conference website, should I still list this poster on my CV, or would it just create confusion or misunderstanding?

Answer

A poster of which you're not the first author is such a minor thing I wouldn't worry about it (even if it is listed on the conference website). I don't have a huge publication list but still only include posters I presented (aand only at major conferences). They don't have anything like the CV impact of a peer-reviewed paper.

Either:

• You were accidentally omitted and should be included. In this case the author should contact the conference organisers (but it's probably too late).


• Or your contribution was rather minor -- perhaps it only became apparent that your work made it onto the poster at all at the last minute. In this case while you're named as an author it's closer to an acknowledgement in practice.

Listing it as a publication, if the title can be searched for but you're not named, doesn't seem like a good idea. Realistically no one is ever going to look. But if you just happen to come up against someone who's interested in something very specific about the poster that you don't normally do, it isn't going to help you.

writing - Resources on how to overcome writer's block, especially for non-native English speakers?

One of the issues we have at my English-language institute is the problem of getting our doctoral students to write papers in English. For some, writing isn't a big challenge. For others, however, the process is about as pleasurable as pulling teeth or a lobotomy (without the benefit of anesthesia).

What we've found is that there are a few problems that tend to creep up:

• Students don't know how to commit their ideas into paper


• Students are afraid of writing poorly, so they don't write at all

What I'm wondering is if there are any resources available that can help—particularly international students—with overcoming the "academic" version of writer's block.

Answer

Of course there are plenty of resources about how to overcome writer's block, however for different people different techniques work. The advices I always found very useful as a PhD student (although I cannot find the original sources, it's been years) were these:

1. do not aim high at the beginning. Crappy and hasty first draft is perfectly fine, iterative improvement will come later: as the author here points out, inexperienced writers tend to have too high standard on themselves. Since I am in a formal field, I therefore refrained to start with the paper's motivation, but rather tried to work out the mathematical flesh first. That one is easier in terms of language since the form can be copied/learned from good papers of others. But this differs across disciplines.


2. 
   

   block time every day for writing and do nothing else at that time, even if you should stare at a blank wall: this is my way to kill the procrastinator in me. Simply three hours every day a week for writing. Even if during that time one would really just stare at a wall and write nothing, it's better than procrastinating. Eventually the boredom is so high that writing becomes welcomed activity. It is imperative not to do anything else, especially not to study, read or otherwise consult any literature, also get disconnected from Internet and colleagues, etc. The best for me was to go for this to the department's library where was no wifi connection. I read somewhere that this technique is used by some novel writers, but can't find any source of this advice.

   
   
   


3. 
   

   Another powerful technique is use public commitment wisely: that is, publicly commit to delivering an artifact at a precisely specified deadline. E.g., first draft of the paper next Friday. Tell to your boss, tell to your office-mate, whatever. The higher the authority you tell, the better. For many people this has a magic effect, because we tend to value our commitments, however painful it sometimes is to stand up to them.

   
   

But again, different techniques work for different people.

evolution - Why did the process of sleep evolve in many animals? What is its evolutionary advantage?

The process of sleep seems to be very disadvantageous to an organism as it is extremely vulnerable to predation for several hours at a time. Why is sleep necessary in so many animals? What advantage did it give the individuals that evolved to have it as an adaptation? When and how did it likely occur in the evolutionary path of animals?

united kingdom - How to negotiate the salary for a UK faculty position?

Following several interviews, I have been offered two faculty positions in the UK. Salary is among the factors I consider to choose one of the positions.

How can I reasonably negotiate the salary? Can I suggest the highest value in the range advertised? Or I shouldn't be greedy.

In general, how negotiable is salary in the UK universities?

Can I omit my undergraduate school from my CV?

I noticed some prominent academics omit where they got their undergraduate degrees from in a CV (I am sure it's not a case where they never earned an undergraduate degree at all; those people also exist).

My question: After earning a PhD degree, is it bad form to remove from your CV that you have also earned an undergraduate degree (possibly from a lower ranked place)?

academic life - Dealing with stereotypes and stigma while pursuing a career in academia

How do professors successfully cope with negative stereotypes and stigma while pursuing their research careers?

Specifically, some issues that come to mind are:

1. 
   
   

   Women scientists who are perceived as less capable, with their research ideas dismissed as "not so good" while others use the same ideas and get complimented with, "that's an amazing idea!" (true story, from my friend, at a top STEM department)

   
   


2. 
   

   Asian male scientists who are perceived as unattractive and boring and have trouble balancing a life in science with a social life outside of academia.

   
   


3. 
   

   Older scientists who are perceived as slower and having less research potential than their younger peers, and always having to work extra hard to prove themselves, and always having to climb a steeper mountain than others, it seems.

   
   

Do professors have mentors / advisors, like students would have? Do they go for professional therapy? Read books, blogs? What are some coping mechanisms?