mathematics - Can I apply to graduate school twice?

I'm currently a second year undergraduate student in mathematics and I'll have finished all my degree requirements two years early, but I'm at an absolutely great department so I don't want to graduate ASAP because I have a lot of opportunities here.

However, out of curiosity, I want to know if in a year or so if I could apply to graduate school and see if I can get in, and if I do, go, since I will have the option to graduate, or otherwise try again the year after. Is this frowned upon? Especially if I'll be applying to some of the same places twice? I'll probably be taking prelim courses anyway, so the course load isn't something I'd be missing out on, but the department is.

Answer

If I interpreted your question correctly, you're asking if you can apply for graduate school one year, and, if rejected, re-apply the following year. Unless there are some field-specific norms that I am unaware of, the answer is almost definitely yes. Of course, for you to stand a chance of not being rejected a second time, your application should be significantly improved. In your case, that seems likely, as you'll have had an extra year of schooling, possibly stronger references, perhaps some research experience. Good luck in any case!

genetics - Neanderthal and Sapiens DNA

From WIKI:

Modern humans and Neanderthals share 99.7% of their DNA

and

1–4% of the DNA of living non-African humans are found by the Max Planck Institute to likely come from Neanderthals, a result confirmed in 2012, and refined to 1.5–2.1% in 2014

What do they mean? If it is similar for 99.7, how it could be that 1.5%-2% is unique genes from Neanderthals? The Africans do not have them, so African different from European in 1.5-2% ? But that's not true.

Is it a good idea to submit a recommendation letter from a friend who is doing PhD at the university I am going to apply?

I got a friend who is doing PhD at one of the prestigious universities. Two and half years back we were classmates in graduate studies. I have good relations with him. I started working for industry and he is doing PhD. He has good credentials as far his research and academic records are concerned. There is PhD vacancy at the same university but in different department. I need to submit two recommendation letters. Is it a good idea to take recommendation letter from him? Will it increase the chance of getting selected for that position?

Answer

No, it is not a good idea to ask your friend to write a letter for you.

Recommendation letters for graduate admissions should be written by people experienced within the field, who know you well enough to form a clear opinion of your preparation and potential for graduate work in your chosen field. In almost all cases, they should be faculty members with whom you have worked closely, or at a minimum, taken classes with.

Having your friend write the letter would be useless:

• 
  
  

  He is working in a different field and would not know what skills are needed in your field.

  
  


• 
  

  He presumably has little or no experience of research of his own, so will not have as good a sense of the attributes that are needed for success in research in his own field, much less yours.

  
  


• 
  

  He is your personal friend and there would be doubts about his objectivity. (Ethically, if he were to write a letter for you, he should disclose that relationship.)

  
  

The fact that he is currently attending the same institution where you want to apply is irrelevant. That doesn't give his opinion any extra weight.

Beyond being useless, submitting a letter from your friend would lead an admissions committee to think one of two things:

• 
  

  You cannot find two faculty members who have a good opinion of your abilities, so you asked your friend instead. This would suggest that your preparation is extremely poor and your application should be rejected.

  
  


• 
  

  You are completely confused about how the application process works and did not understand that a letter from your friend would not be helpful. You have not done your research and probably don't really know what grad school would be like or why you want to go. They are not likely to accept such an application, either.

  
  

publications - Is Obama's JAMA paper OK?

As some of you may have heard, Barack Obama recently published a paper in JAMA describing the US health care reforms (link). First of all, I am not trying to start a discussion on the validity of the content of the paper.

Maybe I am overreacting, but as an academic, that specific publication raises a number of concerns. Within scientific research and publishing we have a number of ethical principles that should always be adhered to (e.g., authorship, conflicts of interest, plagiarism, ...). When I look at that publication, I can't help but wonder about a number of things, such as:

1. 
   

   Authorship: Obama is listed as sole author on the manuscript. I personally highly doubt that he has done all of the research and writing himself. That constitutes a problem in publication ethics, as is often discussed at length on this site. He does name a couple of people in the acknowledgements, but in my opinion these people should have been authors while Obama should've been in the acknowledgements. Quoting the acknowledgements:

   
   

   
   

   I thank Matthew Fiedler, PhD, and Jeanne Lambrew, PhD, who assisted with planning, writing, and data analysis. I also thank Kristie Canegallo, MA; Katie Hill, BA; Cody Keenan, MPP; Jesse Lee, BA; and Shailagh Murray, MS, who assisted with editing the manuscript. All of the individuals who assisted with the preparation of the manuscript are employed by the Executive Office of the President.

   
   

   
   


2. 
   
   

   Conflicts of interest: the paper essentially "finds" that the reforms done by the Obama administration are a good thing. Of course Obama will say his reforms are good, yet this was not explicitly disclosed in the conflict of interest statement.

   
   


3. 
   

   Political papers: the article is published as a special communications, which requires prior inquiry before submission. I feel that this type of paper does not fit into a scientific journal. It's fine to do politics, but I feel it should be done elsewhere.

   
   

I am genuinely left wondering whether papers like this one are good or not. While I applaud the idea of scientific papers coming from policymakers, the above mentioned issues (and others) are significant.

My question: are such papers in scientific venues OK or not?

etiquette - How to react to a student proselytising during office hours?

A few weeks ago, a student asked me during my office hours whether I was religious or not. More specifically, he asked whether I believed in his religion, and was visibly disappointed when I replied negatively.

How should I react to a question such as this? Religion is a bit of a touchy subject, and even if I am a TA (i.e., not the instructor of the course - and more importantly, also a student), I don't want to be put in a similar situation again.

More generally speaking, how do I react to a situation in which I have to answer a question in a way that I know is likely to upset a student, without lying or making the situation worse?

edit: Some comments have pointed out that the student was never actually preaching, and I understand and somewhat agree. The reason I chose this phrasing over anything else was because he did try to make the conversation into something along the lines of "Do you want to learn about the ways of [religious figure]? There's always time, you know".

edit 2: I'm in computer science; there is no link whatsoever between religion and the contents of the class (or the whole program, really).

Answer

You address this by stating directly

"I would prefer not to discuss this topic during office hours. Can I help you with any questions you have on the homework?"

If the issue persists, I would speak with the professor and perhaps also your dean of students (or something similar).

human biology - Does a bigger breast give creamier milk?

It is fairly common for a woman to have one breast larger than the other. I have also heard that, for a breast feeding mother it is common for one of the breasts to yield a creamier milk whilst the other is more watery/less nutritional value.

My question: Is there any correlation between the larger of the two breasts and the one which yields the fattier milk?

Answer

Because mammary glands define us (mammals), the genetics of the ability to make milk has been of interest.^[1] Because we consume milk, we have a dairy industry. Because the industry places a monetary value to certain milk constituents, the genetics of milk component production has been a viable area of study^[2]. Since you are talking of cream production, we'll stick to that.

The effect of nutrition and the environment (e.g. temperature) on milk fat production has long been known, and the ability to selectively breed for higher fat content has been exercised for decades if not longer^[3][4], But the molecular genetics of milk fat production is only recently starting to be understood.

Mammals with the highest fat content are those in cold environments where an insulating layer of fat is required, such as gray seal milk (53.2% fat), whale milk (34.8%), and polar bear (31%). Humans and cows have approximately the same milk fat percentage (~4.5% fat).^[5] The gene most studied to date is the DTAG1 allele^[6] on chromosome 14.^[7]

It is very clear that genetically milkfat production is under the governance of part of chromosome 14.^[7][8] Since this chromosome is identical in both breasts, genetically one breast cannot make milk with a higher fat content than the other. Environmental and nutritional factors affect both breasts equally, so those can be ruled out as a source of fat percentage differences. The only factors left that can be variables are 1) fat content of one breast over the other, and 2) demand from one breast over the other.

In cows, more frequent milking increased milk production but decreased fat percentage; in the end, the effect on fat in milk was the least influenced by frequency of milking (significance questionable).^[9]

Triglycerides in milk are synthesized in the smooth endoplasmic reticulum of the mammary alveolar cell from precursor fatty acids and glycerol (obtained from blood nutrients), and while other cell types are involved in milk let down, etc., there is no known function of interstitial adipocytes (fat cells).^[10]

That was the long answer. The short answer is: no^[11].

<sub>[1] The origin and evolution of lactation
[2] Milk Components: Understanding the Causes and Importance of Milk Fat and Protein Variation in Your Dairy Herd
[3] A review of nutritional and physiological factors affecting goat milk lipid synthesis and lipolysis
[4] Factors affecting milk composition
[5] The Highest Percentage of Fat in the Milk of an Animal
[6] Evidence for multiple alleles at the DGAT1 locus better explains a quantitative trait locus with major effect on milk fat content in cattle.
[7] Identification of novel single nucleotide polymorphisms in the DGAT1 gene of buffaloes by PCR-SSCP

[8] Scientists pinpoint gene linked to fat in cow’s milk
[9] Covariance among milking frequency, milk yield, and milk composition from automatically milked cows
[10] MILK SECRETION: AN OVERVIEW
[11] Does a bigger breast give creamier milk?</sub>

entomology - Species Identification - small insect: is this a bed bug?

I found this bug in my apartment in Chicago. We had bed bugs in our house the previous year (but we thought we got rid of them). This bug was very small - maybe 2 millimeters in length. These photos are all of the very same bug (just different lighting).

Answer

This is a really old thread but just in case someone happens upon it, this isn't a bed bug.

I am not an expert but it looks like it's likely a book louse or psocid. See comparison photos of unfed first instar bed bug nymphs vs. psocids/booklice here: http://bedbugger.com/2008/03/04/booklice/ It's all about the shape of the head and body.

How to manage publications on a local computer

I would like to find a better way of naming publications which I store on my local computer as PDFs. So far I have been doing something like this:

Albano R., Sole A., Adamowski J., Mancusi L. (2014) - A GIS-based model to estimate flood consequences and the degree of accessibility and operability of strategic emergency response structures in urban areas.pdf

This presents a couple of disadvantages:

• Titles can be extremely long. This causes problems in certain operating systems or software such as OneDrive. You can only have so many characters in a filename...


• Not all publications can follow this format. The above is OK for journal papers and theses, but not so much for books or other kinds of publications.

I would like to have a consistent way to manage such a database. I thought of keeping the publication metadata such as authors, date of publication, type of publication and type in a separate text or excel file and naming the PDF files by ID, like 1.pdf, 2.pdf, etc. This could work, but it would require referring to and managing a spreadsheet which would contain all the meta data.

Is there a simple method or perhaps lightweight software that I can use which can help me with this sort of task?

EDIT

I didn't really like the way @Jonas Stein's script is set up, though I do owe him the inspiration and indication to use JabRef. Here's my alternative script:

import bibtexparser
import os
from shutil import copyfile


filename = 'db.bib'
out_folder = 'out'

with open(filename) as bibtex_file:
    db = bibtexparser.load(bibtex_file)

for entry in db.entries:
    print(entry['file'])
    id = entry['ID']

    file = entry['file'].split(':')[1]

    copyfile(file, os.path.join(out_folder, id)+'.pdf')


print('done')

It's much more compact and does the job.

Answer

I manage publications with JabRef in a bibtex database. It is possible to add a link to the filename with JabRef in the bibtex database.

A python script pybibtexcleaner transcribes the special characters in the title and moves all sorted files to one folder with file names in the format

bibkey-title.pdf

The script will generate from a bib entry

@Article{Stein2017a,
  author    = {J. Stein and M. Baum and S. Holbein and T. Finger and T. Cronert and C. Tölzer and T. Fröhlich and S. Biesenkamp and K. Schmalzl and P. Steffens and C.H. Lee and M. Braden},
  title     = {Control of Chiral Magnetism Through Electric Fields in Multiferroic Compounds above the Long-Range Multiferroic Transition},
  journal   = {Physical Review Letters},
  year      = {2017},
  volume    = {119},

  number    = {17},
  doi       = {10.1103/physrevlett.119.177201},
  file      = {:../included/119.177201.pdf},
  publisher = {American Physical Society ({APS})}
}

the new filename

Stein2017a-Control_of_Chiral_Magnetism_Through_Electric_Fields_in_Multiferroic_Compounds_above_the_Long-Range_Multiferroic_Transition.pdf`

and copy the file to ../articles/ and also adjust the path in the .bib file.

It is very useful if the filenames start with the bibkey. You should always use all digits of the year.

The script can also transcribe chemical formulas in a readable way, if they are introduced with \ce as in \ce{H2O}.

You can keep track of your work with git and you can restore old versions or synchronize the literature database on your different systems.

ps: I use the old stable 3.8.2 version of JabRef, because the new versions 4.x were less stable when I tried them. The user has better control on the rename process with the short python script and can easily adjust it to the needs, but recent JabRef versions are shipped with similar functionality.

job search - Translating British faculty titles into American equivalents

A recent job posting at a British university has specified available openings at multiple levels: lecturer, senior lecturer, reader, and professor. However, it's not clear how to map these titles to American equivalents. For instance, where would someone who has finished up several years of an assistant professorship and is interested in moving into such a position be classified? Would it be as a senior lecturer or reader?

Answer

Usually, lecturer is the lowest open-ended position (although there are exceptions), and professor is the highest one, everything in between can be quite specific. For instance, Swansea University is considering four different grades from 2013:

• Lecturer (replacing Lecturer Grade 8 and Tutor)


• Senior Lecturer (replacing Lecturer Grade 9, Senior Professional Tutor and Research Fellow)


• Associate Professor (replacing Senior Lecturer and Reader)


• Professor (that one at least is unchanged!).

Each title comes with a set of expected criteria. In addition, a concept I've seen several times in the UK is the notion of academic pathway, which can characterise further the criteria for the positions. For instance, at Newcastle University, where I'm currently working, we have three main academic pathways, with the corresponding positions. In order to illustrate the different expectations based on the pathways, I included the expectations w.r.t. the UK Professional Standards Framework (UKPSF). I also include the grade (positions above G are usually open-ended, although there are exceptions).

• 
  

  Teaching & Scholarship Pathway (the "standard" pathway):

  
  
  
  
  • Grade E: Teaching Assistant (encouraged to become recognised at UKPSF Descriptor 1)
  
  
  • Grade F: Teaching Fellow (be recognised at or be working towards UKPSF Descriptor 2)
  
  
  • Grade G: Lecturer (likely to be working commensurate with the achievement of Descriptor 3 and are encouraged to work towards it)
  
  
  • Grade H: Senior Lecturer (expected to be recognised at or be working towards UK PSF Descriptor 3)
  
  
  • Grade H: Reader (be recognised at or be working towards UKPSF Descriptor 3 or 4)
  
  
  • Grade I: Professor (be recognised at or be working towards UKPSF Descriptor 3 or 4)
  
  
  
  
  


• 
  

  Teaching & Research Pathway:

  
  
  
  
  • Grade F: Lecturer (should be recognised at UKPSF Descriptor 1 and be working towards Descriptor 2)
  
  
  • Grade G: Lecturer (should be recognised at UKPSF Descriptor 1 and be working towards Descriptor 2)
  
  
  • Grade H: Senior Lecturer (should be working towards UKPSF Descriptor 2 or 3)
  
  
  • Grade H: Reader (should be working towards UKPSF Descriptor 3)
  
  
  • Grade I: Professor (should be working towards UKPSF Descriptor 3)
  
  
  
  
  


• 
  

  Research & Innovation Pathway (since there is no teaching expected, UKPSF is not relevant):

  
  
  
  
  • Grade E: Research Assistant
  
  
  • Grade F: Research Associate
  
  
  • Grade G: Senior Research Associate
  
  
  • Grade H: Principal Research Associate & Reader
  
  
  • Grade I: Professor.
  
  
  
  
  

In other words, you should not try to translate the title, but instead understand where do you fit within the academic pathways of the university offering the positions. When it comes to teaching, it can be particularly useful to understand where one fits within the UKPSF, in order to match the corresponding title with the scheme used at the university. For instance, showing that you are working towards obtaining Descriptor 4 could be helpful to get a Reader position instead of a Senior Lecturer.

evolution - How does Natural Selection shape Genetic Variation?

Background

Importance of the additive genetic variance

As stated here, the fundamental theorem of Natural Selection (NS) by Fisher says:

The rate of increase in the mean fitness of any organism at any time ascribable to NS acting through changes in gene frequencies is exactly equal to its genetic variance in fitness at that time.

NS reduces the additive genetic variance

On the other hand, NS reduces additive genetic variance (discussion about the origin of this knowledge can be found here). The genetic variance of a population for multiple traits is best described by the G-matrix (here is a post on the subject).

What is a G-matrix

A G-matrix is a matrix where additive genetic variance of trait $i$ can be found at position $m_{ii}$. In other words, the diagonal contains the additive genetic variance for all traits. The other positions $m_{ij}$, where $i≠j$ contains the additive genetic covariance between the traits $i$ and $j$.

Question

How can one model how the G-matrix changes over time because of selection (assuming no mutation)?

Answer

First of all, here is a program which simulates the evolution of the G-matrix over multiple generations, it's a few years old (they seem to have stopped developing it) and I've only played with it briefly. This could solve how to model the evolution of the G-matrix.

Fisher's fundamental theorem is a great place to start off with the theory of this:

The rate of increase in fitness of any organism at any time is equal to its genetic variance in fitness at that time.

What this means (as I am sure you realise but I will put in so the answer can help others too) is that evolution by selection depends not only on the strength and form of selection, but the genetic variation underlying the selected trait. This is captured in the breeders equation $\Delta \bar z = G \beta$ where $\Delta \bar z$ is the response (in a multivariate space), $G$ is a matrix of the genetic variance within traits covariance between traits (different traits, the same traits in either sex, or the same traits in multiple environments) and $\beta$ is the vector of selection gradients on all of those contexts. It seems reasonable to expect that given enough time selection will erode variation because standing genetic variance is a finite resource and selection removes polymorphism while not adding any new variants (that's for mutation & migration).

This paper discusses the effects of both selection and drift on the G-matrix, they also deal with some modelling to support their results. More specific to simulation, this article by Arnold et al (a number of the big players in the G-matrix circle). It reviews "empirical, analytical, and simulation studies of the G-matrix with a focus on its stability and evolution." It would be a really good read for you on this subject.

This paragraph captures the essence of your question:

Focusing on a longer time scale, we find that the G-matrix evolves in expected ways to the AL [adaptive landscape] and the pattern of mutation. In the absence of correlational selection (rω = 0) and mutational correlation (rμ = 0), the average G-ellipse is nearly circular, although the ellipse fluctuates wildly about this average (first row in Fig. 6). At the opposite extreme, when the leading eigenvectors of the AL and the M-matrix [mutation matrix] are both inclined at an angel of 45°, the leading eigenvector of G is pitched at the same angle (last row in Fig. 6). Between these two extremes, G tends to evolve to a shape and orientation that represents an intermediate compromise between the AL and M. In other words, the simulation results confirm our intuition and theoretical expectations (Lande 1980b) that G should evolve toward alignment with the AL and M.

Simulation studies of the G-matrix:

• Bürger R, Wagner GP, Stettinger J. How much heritable variation can be maintained in finite populations by mutation-selection balance. Evolution. 1989;43:1748–1766.


• Multivariate mutation-selection balance with constrained pleiotropic effects. Wagner GP Genetics. 1989 May; 122(1):223-34.


• On the distribution of the mean and variance of a quantitative trait under mutation-selection-drift balance. Bürger R, Lande R Genetics. 1994 Nov; 138(3):901-12.


• Predicting long-term response to selection. Reeve JP Genet Res. 2000 Feb; 75(1):83-94.

The last article there by Reeve is probably the best paper for your question because it describes in some detail the simulation model they use and how it is all set up. Briefly they simulate a population of 4000 diploid individuals with three genetically correlated traits with separate but identical sexes, random mating, and discrete generations. 20000 generations are simulated to allow mutation-selection-drift equilibrium (almost like a burn-in time on an MCMC chain). They then shift the optimum for one trait by 10 standard deviations and simulate 1500 generations in five replicates. There are 100 unlinked loci underlying the traits, with 50 loci affecting each trait (randomly assigned) meaning there is likely some degree of genetic correlation though it is not perfectly correlated (for some reading on genetic correlations and the evolution of differences you can read Bonduriansky & Rowe 2005, Poissant et al 2010, and Griffin et al 2013). The model then assigns phenotypic values to individuals, and fitness is derived. Figure two shows how the mean, skew, and kurtosis of the variance distributions changed for those 1500 generations.

---

Addition

Roff 2012:

"While the mean trait values change under selection, so also will the G matrix, its orientation tending to shift in the direction of selection. ... Genetic drift may also play a role in changing the G matrix, but in this case the change will be random though on average producing a proportional change in the constituent variances and covariances."

What should I do if my professor changes the question mid-exam?

I was writing a 3-question examination today (undergrad) with 1200 other students when our professor comes in after ~2/3 of the exam and changes a question to make it solvable. This was a 1.5 hour exam where each question was designed to take 30 minutes so unless you did the other two questions knowing that question was impossible to solve and waited for an announcement on instructions of how to solve, you would not be able to finish. When I walked out of the exam, you could tell that everyone was mad that this changed question could have impacted their overall mark by 15-20%. What should I do to help out myself and my fellow classmates who were screwed over by this change? Has anyone ever had a similar situation?

graduate school - As a teaching assistant, how important are student evaluations?

I have seen a number of résumés of doctoral students, but only a few of them listed their evaluation scores when presenting their teaching experience.

• How important are these scores in evaluating the teaching capabilities of a student?


• How does one ensure that the students are sincere in their evaluations?

In case a professor does a slipshod work of a course, not teaching in depth or cramming a lot of syllabus in a short time, there is only so much a TA could do to salvage the course for the students.

• How does the TA make the best of a bad job in such a situation?


• Apart from holding weekly office hours and lenient grading(!), what is the maximum a TA can do, after all?

Answer

This is an excellent question, for faculty as well as students!

• How important are these points in evaluating the teaching capabilities of a student?

Obviously this varies significantly in different departments and institutions, but in my experience, the scores themselves are not that important.

My department does pay attention to these numbers when allocating future TAships, but definitely not in isolation. Narrative reviews from the instructors carry significant weight. The people doing the assignments also know which courses are unpopular, and which instructors are irresponsible, and adjust the evaluation accordingly, at least in principle. In practice, there are only three evaluations: (1) truly outstanding TAs, who are considered for teaching awards; (2) truly abysmal TAs, who are not rehired, at least without retraining (and since we have a TAship requirement, this has teeth); and (3) everyone else.

When we evaluate tenure-track faculty candidates, teaching ability is usually a second-order concern, but it is a concern. Poor evaluations on an applicant's CV are a red flag—why didn't they just omit them? Good evaluations are mostly a signal to look further. Teaching awards carry more weight. Recommendation letters that directly praise the applicant's teaching ability — with concrete and credible details — are even better. Similar issues arise when evaluating faculty for tenure, with one big difference: omitting the teaching scores is not an option.

• How does one ensure that the students are sincere in their evaluation?

You can't. Sorry.

However, I believe you can increase the fraction of sincere (and positive) responses by consistently treating your students with respect. Make your expectations clear from day one, and enforce them consistently. Invite feedback throughout the semester, and respond to it quickly and appropriately. Apologize quickly for mistakes, thank students publicly for useful suggestions, but do not buckle on high standards. Give timely, consistent, and useful feedback on coursework. Above all, do not waste your students' time; the correlation between hard work and low evaluations is much higher if the students don't see any benefit to doing the work.

• How does the TA make the best of a bad job [if the instructor is irresponsible]?

First, do your own job as best as you can.

Second, raise your concerns with the instructor; be respectful but brutally honest. If the instructor is unresponsive, raise your concerns with your instructor's boss; be respectful but brutally honest. (Note: Disagreement is not the same as being unresponsive.) If your instructor's boss is also unresponsive, your department doesn't really care about poor teaching; they're likely to ignore your evaluations, even if they are low.

• Apart from holding weekly office hours and lenient grading(!), what is the maximum a TA can do, after all?

There are many more things that TAs can do. At a minimum, hold office hours that the students actually find useful; don't just show up. Distribute practice problems, and offer feedback on the students' solutions. Hold weekly review/discussion/problem-solving sessions. As aeismail suggests, write review notes. If the instructor covered too much, distill down their main points; if the instructor didn't cover enough, expand on the key ideas they missed. Offer to give a few guest lectures, and then give fantastic guest lectures.

More self-servingly: Make sure the students see you working to overcome your instructor's shortcomings. If the students don't see you fighting on their behalf (even if you are), they'll write you off as yet another useless academic, like your instructor. But if you can make them believe you're on their side, they'll reward you. I think this is why students often reward "lenient grading"; if the students think the coursework is a waste of time, they'll see lenient graders as their allies.

Obviously this all takes time. As aeismail says, TAs usually have many other responsibilities, especially to their own classes, projects, research, families, and sanity. It is frighteningly easy for committed and caring TAs to find themselves being abused by less committed instructors (or even departments). Set limits.

Showing research experience in graduate applications

As an undergraduate, I have heard this term a lot. I have not graduated but will graduate soon.

When applying to graduate programs, research experience is what everyone tells.

Research Experience is used rather recklessly. Many students, even if they had to just type in data for professors/researchers, check some test tubes in laboratory or whatever depending on discipline mention they had research experience.

Last year, I had an internship at a renowned research organisation. The only thing they do is research and development. As an intern, I did not specifically join saying, I wanted a "Research Experience". I were involved in their project which was a research project. My task consisted of API development, working with Matlab and various stuff important for the project.

Yet, I did not come up with something new. Well, they did.

So, this is far better than what many students mention as research experience. But, is it worth calling this a research experience in my CV or applications? Shall I call this reaserch?

Making the question specific, what does a "Standard Research Experience" consist of? When graduate schools say undergraduate research experience, what kind of activities are they expected to have been involved in?

Answer

You're expected to describe research experience. It sounds like you've had some. You should describe it in your application. Talk about what role you had, what sort of things you actually did ("various stuff important for the project" and "working with Matlab" aren't very good descriptions). What was your role? Did you make decisions or did you just assist? What sort of products did you produce and what skills did those products require? How did you solve problems you encountered?

The idea behind these application questions is to try to differentiate people with no experience from some minimal experience (cleaning instruments in a lab and feeding rats) to moderate experience (sounds like what you have) and people who engaged in truly independent research (which is pretty rare, depending on where you did your bachelor degree and in what field). Be honest and detailed, that's all that's expected. Of course people will play up what they did, but if you made substantive contributions that demonstrate your abilities and experience, that will show through in your write-up.

job search - I graduated last year and my advisor passed away unexpectedly soon after. What should I do now for subsequent academic job searches?

I received a PhD in mathematics last May. Last December, my advisor passed away quite unexpectedly.

My advisor was an extraordinary person; in addition to being a fantastic advisor mathematically, he was a wonderful mentor who I always thought of as a friend – this is very much a personal loss for me. My initial emotional response was that I should clearly leave mathematics forever. Rationally, that seems uncalled for. Before all of this, I had been aiming for academic jobs in mathematics. However, I expect that a recommendation (as well as other help) from one's advisor is a significant part of an academic job application (for example, this recent answer states that the letter from one's advisor is read first even when applying for a tenure-track job after a postdoc).

How does one go about an academic job search when one's advisor has passed away?

For example, my advisor wrote a letter for me for my job search out of grad school. Does one try to use that letter (via perhaps my graduate department) for subsequent job applications? Do I mention in every cover letter from now on end that my advisor has died (that seems horrifying, since I like my vague sense of denial)?

I am in the first year of a (3-year) postdoc, so I won't be on the job market for a while (in fact, it seems simultaneously very soon and too far away). Of course I can tell that my productivity and motivation have slumped in the last few months, and I know that I should try to get back into gear as soon as possible.

PS: It’s entirely possibly that there’s no ‘practical’ difference between this situation and other situations where one doesn't have a letter from an advisor (as commentor Sumyrda has said), in which case that would be a perfectly reasonable answer that I would happily accept.

---

Related questions:

While in more of a 'denial' stage, I asked this question to try to get at this.

The analogous question for current graduate students was asked here and here.

There are several questions about dealing with not having a letter from one's PhD advisor on this site, such as this one, or this one, or this one.

Answer

This is a very difficult situation. As per the comment by Andy Putman, let your other letter writers explain the situation. Considering you got the Postdoc job, your current supervisor must have been impressed with what your advisor said in his letter. Your current supervisor can include a personal story about something your advisor said about you or even include a few of his favorite verbatim quotes about you from the letter of recommendation for your current postdoc. Anyone on a hiring committee will understand, and will possibly even be personally touched. This will not count against you.

I wouldn't send a copy of your postdoc letter in your application materials If your postdoc supervisor highlighted the strongest quotes from the advisor's letter. If he chooses not to do this or if your advisor's letter in its entirety is much stronger than the best few quotes from it and your postdoc supervisor still has the letter he could send it along with his letter.(note that in other fields this letter may be a bit inappropriate because it could contain a lot of detailed information about how you are a great fit for the particular postdoc position but as Pete points out this usually is not true in pure math).

Unfortunately this does not heal any wounds caused by the unfortunate passing away of your advisor and life long friend, but you should not worry about the letter writing situation. I can't say that I even begin to imagine the emotional pain of losing an advisor so close to graduation, but as someone who lost a parent while in college I greatly sympathize with you and I can think of no greater honor to your advisor than to continue in academia and continue doing great work.

species identification - Identify this smooth-cocoon worm from Southern India

I couldn't identify which species these worms belong to. I believe they're insect larvae. They measure approximately 5 to 10 mm in length, and are common in the southern states of India. They carry cocoons, open at both ends, which the worms can wriggle inside and alternate their direction of movement. These cocoons are perfectly smooth except for the openings. Another post shows something similar, but the cocoon of that worm looks more woven, while this one doesn't.

citations - How should I cite presentation slides?

A friend has made some nice slides that I could reuse (similar topics). He sent me the slides and commented that if I use them and could cite him that would be nice, I asked him how should I cite the slides but he said that whatever suits better to me he said "Just add my surname in some place where it's not very intrusive".

I'm not sure if he doesn't care or he doesn't want to be too picky, but I'd like to cite him, to each one his own.

AFAIK, they are related to a paper (but not in the paper) and to his thesis, where they could be as a diagram but definitively not animated. The slides (as such) may be available at some URL, he said they will be but they are not available yet (so I don't have the URL yet). If citing by the URL I guess I could use this: "How to cite a website URL?"

Should I cite slides? If yes, how?

Answer

There are two practical purposes to scholarly citations:

1. acknowledging scientific contribution of others, the borrowing of ideas (mainly) and content (sometimes, in the form of quotes)


2. helping people find relevant content if they want to read it


3. bookkeeping, for scientometric/bibliometric purposes

In your particular case, you cannot fulfill #2 and #3, because your friend's slides are not available for others to read, and even if they were, random documents on the internet are not really used for bibliometric purposes.

So, you want a solution that will achieve #1, i.e. make sure his contributions are recognized by people who will read your slides. To do so, you don't need to give your citation any specific format. I suggest you simply write, at the bottom of slides you borrowed from him:

Slide courtesy of John Doe

or

Slide modified from John Doe, with permission

In addition, you can thank him in your acknowledgements at the end of your talk.

evolution - Why is the probability of fixation of an allele equal to its frequency?

Introduction

In a panmictic population, the probability of fixation of an allele at a neutral locus is equal to its frequency at that time. I will refer to this probability of fixation as calculated at time $t$ as $P_{fix,t}$.

If $p_t$ is the frequency of the allele $A_1$ at time $t$, then the probability of the allele $A_1$ to reach fixation (rather than disappearing) is $P_{fix,t}=p_t$. Typically, the generation when the mutation occurred, the probability of the new allele to get fixed is $P_{fix,0}=p_0=\frac{1}{2N}$, where $N$ is the population size.

Question

This simple and classic result makes very good intuitive sense to me. However, I would fail to provide a mathematical proof.

Can you please demonstrate that $P_{fix,t}=p_t$?

Answer

Several proofs are given here (p. 9). My favorite comes from the genealogical argument:

Consider the situation where there are $2N$ alleles: $A_1$, $A_2$, $A_3$ ... $A_{2N}$.

By the genealogical argument, we may state that at $t = \infty$, all alleles at this locus will be direct descendants of one particular allele present at $t = 0$.

Allelic variants at this locus are selectively neutral, so $Pr(A_{1fix})$ $=$ $Pr(A_{2fix})$ $=$ $Pr(A_{3fix})$ $= ... =$ $Pr(A_{2Nfix})$. For any given allele present at $t = 0$, the probability of fixation is therefore $\frac{1}{2N}$.

Now define allelic variants $A$ and a as complementary, non-overlapping groups of the initial alleles, such that $n_A$ + $n_a$ $=$ $2N$. From the above, the probability of fixation of an allele within group $A$ is $n_A * \frac{1}{2N} = \frac{n_A}{2N} = p_0$.

advisor - I'm a PhD student, my supervisor is a complete bully. Should I take legal action?

If a PhD student has been bullied by their supervisor, should they take legal action and sue for damages? Taking legal action could prevent the supervisor from subjecting others to this treatment in the future. But could it also damage the students reputation and chances of pursuing further in academia? This is an edit to an original post that is a personal account relating to this question:

Original post: "She made a lot of false allegations and claims to defame me, the university is not firing her and has been protecting her which was why she could continuously making untrue events. Can I sue her?

I actually filed an appeal where she failed me without any solid evidence; I won my appeal. I filed informal and formal complaint with substantial evidences. She also filed a complaint but full of untrue events.

If you have not been bullied and in this situation, I appreciate it you move along. I considered to sue her so that she has less chances to continue to ruin the other students' life!

During the process of my formal complaint, she also made a complaint after me which the Student Union considers mischievous and inappropriate. In the complaint and many other meetings, she said so many untrue events, examples: I made the lab instruments dysfunctional; I said I want to publish papers with only my own name; the external advisor is very surprised that I didn't send the data to him however on the supervision log it clearly stated he was very aware of my tasks; I said her comments on something I wrote were not useful and not helpful; I made offensive languages etc etc...just so many so many! She also tampered my email in her complaint.

I have supervision log, email communications, recordings to support that she's made many untrue and inconsistent comments. I was following everything discussed and logged in supervision log, she completely ignores all communications and she uses her own law randomly.

It's her topic. No, I'm not considering to continue anything related to her."

biochemistry - Where is the H+ ion in this step of glycolysis coming from?

(from Fundamentals of Biochemistry by Voet, 5th ed.)

In this step of glycolysis, I'm not seeing where the $\ce{H+}$ ion on the product side is coming from. It seems to me that the G3P's aldehydic H is replaced by phosphate, and that H is given to $\ce{NAD+}$ to make NADH. So where is the extra $\ce{H+}$ coming from?

Answer

Although texts such as Berg et al. tend to refer to inorganic phosphate, $\ce{P_i}$, as orthophosphate ($\ce{PO4^{3-}}$), the term inorganic phosphate is used because in aqueous solution at pH 7.6 several phosphate species exist, the predominant one being $\ce{HPO4^{2-}}$. If this is regarded as $\ce{P_i}$, then it is the source of the $\ce{H^{+}}$, and the equation balances.

Note added by David:

On checking I find, in contrast to Berg, Lehninger’s book defines $\ce{P_i}$ as monohydrogen phosphate ($\ce{HPO4^{2-}}$), and Fersht actually writes the equation of the reaction (16-1) with $\ce{HPO4^{2-}}$ rather than $\ce{P_i}$.

metabolism - Can animals make their own unsaturated fatty acids?

I know that animals can't make poly-unsaturated fatty acids (PUFA) and so require them from dietary sources. For eg.Omega -3 and Omega 6 fatty acids.

My questions : Can animals synthesize other unsaturated fatty acids from scratch? If not, does the unsaturated fatty acids in the phospholipids of plasma membrane of animals come only from dietary sources?

bioinformatics - What could I call such nucleic-acid-Sequence? A sort of palindromic sequence? is there any term called mirror repeat?

5'... ATGCC|CCGTA ...3'

3'... TACGG|GGCAT ...5'

or say

5'... AAGT|TGAA ...3'

3'... TTCA|ACTT ...5'

or in generalised way; on each strand;

ABCDEF|FEDCBA

Is there any terminology for such-sort of repeat? A sort of palindromic sequence? A sort of inverted repeat? or mirror-repeat? Does they really exist in nature? (I could not yet found any helpful answer in web, including wikipedia.)

UPDATE

I asked this question because the term "palindromic sequence" is not like the situation in OP but "palindromic sequence" is like this:

5'... ATGCTTTC|GAAAGCAT ...3'

3'... TACGAAAG|CTTTCGTA ...5'

or in general;

5'... A B C D E F | M N P Q R S ...3'

3'... S R Q P N M | F E D C B A ...5'

Where on single-strand there is no symmetry when read (3'---> 5') and (5' ---> 3').

BUT I'm not telling like that. i'm telling about a situation where a reflection-symmetry present in each single strand when read (3'---> 5') or (5' ---> 3').

like

5'... A B C D E F | F E D C B A ...3'

3'... S R Q P N M | M N P Q R S ...5'

From no angle it is a palindromic-sequence because the symmetry is not between 2 opposite strand.

This question came to my mind when for first- time I'd taught about palindromic sequence. I was unable to "literally" match it with verbal palindromes like "AND MADAM DNA" . Rather it was looking to me like

I EAT CAKE

EKAC TAE I

So I thought, if really there exist any sequence literally like "AND MADAM DNA"... whatever if there is any terminology for it or not.

---

One other Q/A site mentions about a term "mirror repeat", with exact same situation as OP, but gave no reference and further biological importance.

http://www.answers.com/Q/Mirror_repeats_in_DNA

Latest revision of Wikipedia also mentions a term mirror repeat and everted repeat, but no further explanation and hyperlink is given.

Another result from google search.

URL: https://s3.amazonaws.com/classconnection/27/flashcards/2952027/jpg/mirror_repeat-14FB21C6EBF540D2120.jpg

Answer

It's simply called a palindromic sequence. As you can see here, these sequences are called inverted repeats when random nucleotides are found between the initial sequence and its reverse complement (e.g. TTACGnnnnnnCGTAA), while when there are no nucleotides between them they're called palindromes.

UPDATE
Sorry for my previous answer, I must've missed the point.
I think the situation you showed should be called mirror-everted repeats: to my knowledge, it's a very rare occurring, and I only found some reference in this and this articles, even though no graphic explanation is provided.
P.S. Should you not be able to access the full text of the second article, just let me know.

human biology - Blood pressure during exercise

What happens to blood pressure when we exercise? Does it increase, decrease, or remain the same? If it does increase, why are patients with high blood pressure recommended to exercise?

Answer

As pointed out in the answers above, your blood pressure increases transiently as you exercise because more oxygen and nutrients are consumed by your muscles. However, regular exercise increases your "cardiovascular reserve"-this means your body will be able to function well at lower blood pressures. However, caution must be taken in hypertensive patients whose blood pressures are already up the roof. In these patients, gentle exercise and life style modifications (diet, stopping smoking, weight loss etc) may reduce their blood pressures over time. This will also reduce their risk of cardiovascular catastrophes in the future.

So whilst exercise will reduce blood pressure, it is not recommended as a first line of life style modification in hypertensive patients because exercise itself is stressful initially and stress is also bad for a hypertensive patient. Hence, exercise is good but gentle exercise is recommended for hypertensive patients. But again I doubt gentle exercise will do maximum good to your cardiovascular system because the type of exercise that helps lower your blood pressure is one that makes you sweat (e.g tread mill, etc). But once the blood pressure of a hypertensive patient is under control, then they can safely exercise and this should help lower their blood pressure long term. I hope this makes sense.

teaching - What to do when students bring me questions related to other courses and subjects?

I teach all of the writing courses for one of my college's STEM department. Occasionally, students bring me questions related to their field, e.g. they are doing some project for another course and they want to know what tools I used for a similar real-world project I did before.

• If I help the students (which would amount to suggesting some books, tools, Web sites), perhaps the department will feel I am interfering in matters where I should not, as this is not my teaching area.


• If I turn away the students, perhaps the department or (students themselves) will feel I am not committed to serving the students.

What is the accepted procedure for such a situation?

teaching - What are the pros and cons of giving students assignments to write Wikipedia articles?

The Wikimedia Foundation initiated an education program at U.S. universities that in 2010 encouraged government, law, and public policy students from 33 classes at 22 programs to contribute to Wikipedia (https://outreach.wikimedia.org/wiki/Education). Surveying 463 students in the public policy program revealed that they were motivated to work on Wikipedia articles that could reach a larger audience and could impact the society more than traditional class paper. In addition, classroom characteristics, and level of class engagement were strong motives to engage students to contribute in the future. You can find more information about this research at:

Roth, A. Student contributions to wikipedia. Tech. rep., Wikimedia Foundation, 2011. Lampe, Cliff, et al. "Classroom Wikipedia participation effects on future intentions to contribute." Proceedings of the ACM 2012 conference on Computer Supported Cooperative Work. ACM, 2012.

In addition, the following paper shows that researchers in collaboration with the Association for Psychological Science (APS) involved 640 students from 36 courses in editing scientific articles on Wikipedia. As a result, students improved the content of over 800 articles and both students and faculty endorsed the benefits of the writing experience that would be read by a large number of people.

Farzan, Rosta, and Robert E. Kraut. "Wikipedia classroom experiment: bidirectional benefits of students' engagement in online production communities." Proceedings of the SIGCHI Conference on Human Factors in Computing Systems. ACM, 2013.

Before relying on these studies and defining Wikipedia based assignments for my students, I want to consult with you about pros and cons of this idea.

For which types of courses does it work and for which it doesn't?

For which types of assignments does it work and for which it doesn't?

Will it improve students' motivation to learn?

How can one define a rubric for this type of assignment?

More importantly, I was thinking asking students to contribute to Wikipedia for credit, might mitigate the altruistic nature of contribution to the public good.

Is there any study investigating the behavior of these student accounts on Wikipedia after the end of the semester? Does in absence of the personal incentive, the contribution decrease?

Answer

I have on several occasions given students assignments (in math classes I was teaching) to contribute to Wikipedia, either for bonus credit or in lieu of a traditional final paper. Both I and the students were very happy with the results and with the fact that our efforts (which included fairly substantial involvement on my part, see below) resulted in the creation of a valuable resource for the community. I am therefore inclined to view this idea very positively.

That being said, in my experience this type of project would definitely not be suitable for all students and in all circumstances, so one should consider carefully (as you are indeed doing by asking the question) the various implications and factors involved.

For which types of courses does it work and for which it doesn't?

The idea is suitable for advanced classes where you cover topics that are not currently well-covered on Wikipedia. E.g., something like a calculus class is a bad idea, but a graduate class on differentiable manifolds would almost certainly involve several topics that Wikipedia needs help with.

For which types of assignments does it work and for which it doesn't?

The first rule should be "do no harm". What I mean is that some students do not have the writing skills to make a positive contribution to Wikipedia with a reasonable effort of the sort that a course assignment should involve, and we certainly don't want them making negative contributions. Thus, my philosophy is that a Wikipedia assignment should be elective - i.e. either being for extra credit or being an option the student can choose instead of a traditional paper/essay.

Another reason for this rule is that some students would feel self-conscious about writing material for public consumption, and I think it's wrong to force them to do it, even if the contribution is anonymous. Finally, submission to Wikipedia requires agreeing to its Creative Commons license which means giving up certain rights to your creative work. For legal and ethical reasons I think it's untenable to make this a grade requirement unless specifically agreed to by the student who prefers this over alternative assignments.

Will it improve students' motivation to learn?

I've definitely seen students who became very enthusiastic about the writing project and after creating a page on a new topic continued to expand it, which ended with them adding quite a bit more material than was the minimum I required. I'd also like to hope (but don't know if it's the case) that some of them might have caught the Wikipedia bug and continued contributing "for free" later.

On the other hand, some students were clearly just doing it for the grade and didn't do any more than the minimum, so I guess for them there wasn't any improvement to their motivation.

How can one define a rubric for this type of assignment?

Good question. I was using my own subjective judgment to assign grades. Those were small graduate classes and in practice almost everyone got an A or A-, so that wasn't too much of an issue, but for a larger-scale project one might have to give this question some more careful thought.

---

Let me add a few thoughts about things you didn't ask about. A key thing to keep in mind is that writing for Wikipedia is very different than writing other kinds of content, both technically, stylistically and philosophically (in particular the collaborative aspects). Good Wikipedia content has to be extremely neutral, unopinionated, well-referenced, and written in clear and error-free language. Frankly, in my experience very few students would be capable of producing by themselves a draft for a new Wikipedia article that would not be either outright deleted or heavily modified (possibly to the point of becoming unrecognizable) very soon afterwards by other Wikipedia users/editors -- needless to say that would be quite bad for motivation... For this reason, in the projects I assigned I ended up taking on a fairly substantial role of reviewing and helping polish up the original article drafts before they were officially submitted. This was done in a sandbox page. It was practical for me to help out in this way, first of all because I was happy to do it, and second of all because only a small number of students were involved (4-5 in each of the courses I tried this at). At the same time, there is an obvious problem of scalability here, and I would be very reluctant to attempt such a project in a large class. The bottom line is be prepared to put in quite a bit of work yourself if you want the project to be a success.

A final thought (sorry for the long answer) to consider is that it would be wise for you as the instructor to propose to the students a list of possible contributions they can make (in the form of either new articles or new sections in existing articles). Some students can also come up with their own ideas for what to write about, but I feel that most would prefer being offered a list to choose from. Good luck!

Edit: as @Thunderforge helpfully pointed out in the comments, Wikipedia has a dedicated page with guidelines to students and instructors for Wikipedia-editing course assignments.

human biology - Why is rabies incurable?

I'm still not sure about the mechanics that lead to rabies being incurable. I know that it can be treated before any symptoms show up, but why is it that once symptoms show the person is a dead man walking?

Answer

This is because rabies is a viral infection of nervous tissue that propagates through peripheral nerves into the brain and causes brain tissue inflammation (encephalitis).

As long as the virus is in the brain there is no way to get rid of it. The main trade-off here is that everything that would kill the virus will be as (or even more) aggressive against the brain tissue, and impairment of the latter will lead to really heavy deficits in vital functions like breathing and thermoregulation.

The first manifestations of rabies are those due to brain damage. This means, the virus is already there and the brain is already fatally damaged.

cv - Does membership of academic honour societies carry any professional weight / recognition?

I understand honour societies have been around for years and it is a tradition more prevalent in the western world to recognise outstanding academic talent.

The largest honour society is perhaps the Golden Key which operates worldwide and has over 2 million members. It provides a range of services to members, including leadership training, networking and the opportunity to do good. Membership is by invitation only and only those who are in the top 15% of their class or high performing graduate students are eligible. The eligibility is based solely on academic performance.

I presume being invited to join a honour society is an 'honour' in itself, as the mere mention of this affiliation on the CV would indicate that you are a top achiever.

Question 1: Does membership of honour society carry any professional weight?

(i.e. does it give any additional advantages?)

Note: Honour society is not the same as professional society. The latter, as I understand it, is open to all persons in a particular field (irrespective of their academic achievement but as long as certain criteria are met, e.g. successful registration as a teacher to join a teacher's union).

Question 2: Are there other honour societies in addition to the Golden Key (which seems to be the most dominant one)?

PS: I am unsure of the tag, so putting CV. Please update!

Disclaimer: I am not associated with Golden Key.

Answer

Does membership of honour society carry any professional weight?

No, not in general. At a very early stage in your career, for example when applying to graduate school, it may be useful as a quick indication that you have received high grades. However, the grades themselves are more meaningful than the honor society membership, and in any case grades only matter so much. It's worth mentioning the honor society on your CV, but it won't make a big difference.

Once you are more than a few years past undergraduate studies, neither grades nor honor societies matter.

conference - What to do when no one speaks English around you?

Often when I attend conferences and meetings, there are some social activities sometimes specifically for graduate students to mix with each other and get to know other students and build possible future collaborations and contacts. Once in a while I end up with a group of let's say all Chinese foreign students. I am not Chinese and I don't know any Mandarin/Cantonese. But it is a little frustrating and in my opinion quite rude when everyone carries on their conversation in Mandarin sometimes bypassing me directly and I have no clue what's going on and I stand there looking like a complete idiot.

If the gathering is something like a cocktail party, I would move on pretty quickly. But if it happens to be a formal dinner then I am stuck at that table and the entire evening might go by with me hardly talking to anyone. My question is, what can I do or say which will make them realize this and to consider other people around who may not know Mandarin?

Just to clarify, this is in the USA and the students I am talking about are all foreign students attending American universities so it isn't a question of them not knowing English. Sometimes I know a friend or two and I would jokingly tell them only English which works for a couple of minutes and then everyone reverts to Mandarin again.

Any ideas?

Answer

This is a very relevant and interesting question. I agree with all answers so far that the problem can only be solved by being (pro)active, perhaps more than many young PhD students are comfortable with.

Anyway, what I can add to the discussion is a bit of insight from the "other" side. See, I am Austrian (mother tongue is german), and in my line of research Germany is pretty well-established. Hence, when there is a conference in Europe, german speakers (Germans, Austrians, Swiss) often form about a third or so of all participants. In these conferences, random chatter (not so much technical discussion, which people are used to doing in english anyway) often starts in english when a non-german speaker is present, but usually changes to german when the non-german speaker moves away or seems to be not interested in the conversation (e.g., he/she is turning away, or does not contribute at all to the conversation). Of course this means that it is hard for a non-german speaker to join in on a conversation after it started. Usually, if a non-german approaches the group, chatter will turn to english again, but this usually does not happen unless this person is already good friends with one of the people in the group (or would you approach a group of strangers talking in an unknown language?).

However, I don't think there is much to be done about this - it is just natural that a group of people converses in their joint language that they are all most comfortable with. People are not actively trying to be rude - but, sometimes, what comes naturally is not what is appreciated by the largest group of people in the conference.

Some concret suggestions:

• 
  

  When at a formal dinner, and you don't know anybody, try to not be seated surrounded by larger groups of people who are clearly friends or come from the same university / country. This can make for awkward dinners, even independently of language issues, but it is easy to spot already when sitting down. For networking, it is much easier to get into conversation with other people in your situation (more or less alone currently).

  
  


• 
  

  At receptions or conference breaks, as you say yourself, I would usually just move away from people who are excluding me by speaking a different language. If you are actually interested in what they are saying, but can't contribute for language issues, rocinante's suggestion is best - just tell them.

  
  

advisor - Problem with undergraduate research supervisor, how to proceed?

Setting

I am currently an undergraduate student in chemistry and I have recently started working on an undergraduate research project in a known laboratory in the US. I am very passionate about the topic, however I have problems with my supervisor, who is a PhD student.

Problem description

When I came to the lab asking for a topic to work on, the Professor assigned me to one of their students, which appears to be common practice, so I did not question this. However, I found out later that my supervisor (the student) was the only person in the lab working on the topic, and that she herself had only started working on it not long ago. After several days in the lab, my supervisor has not revealed what the eventual goal of my project will be, and from the way she behaves (stressed out, impatient towards me asking questions, which is an additional problem), I suspect that she might not know herself (quote: "we'll figure out along the way"). This is severely frustrating. I am aware that research is an open-ended endeavour that might be changed as new situations arise, but I thought that undergraduate research should be something self-contained, with a clear goal and time-frame, and usually well-thought out by an experienced researcher? I am aware that one possibility to resolve these issues could be to simply talk to my supervisor. However, there appear to be some barriers, which leads me to my question.

Question

How can I approach the situation without ruining my standing in the laboratory and appearing like a complicated student, even though I am not? I would love to continue on this or a similar topic in this lab, but the current situation is very unpleasant for me.

I feel like I cannot talk to my supervisor directly as she seems impatient and stressed out, and at the same time inexperienced with supervising undergraduate students. I fear that this could make the experience even worse, with my supervisor getting angry at my criticism.

The other option I can conceive of would be to talk to my supervisor's supervisor, and ask for some kind of intervention from above. But this could also backfire in many ways, possibly making me look complicated and unwanted in the lab altogether.

Answer

I'll be honest with you, remarking that this is only my opinion, by no means I'm right.

Undergrads are a pain to supervise.

Mostly because, in general, undergrads require a lot of "hand-holding" and training (proper research procedure and writing are not usually covered before that), which takes time (even worse if it is a good student that challenges you.... rewarding, but takes even more time).

You are right in thinking that undergrad research should be simple, self-contained, and well planned out. Properly planning stuff takes time, professors never have it. And simple means that the research is unlikely to have high impact.

I know several professors that don't accept undergrads simply because they think it is not worth the effort. The ones that do accept, pin them to a Ph.D. student (or a postdoc) and that's it. The Ph.D. students usually are busy, worried about their own things, and do not have the experience to deal with "underlings".

Yes, your project should be well defined, with clear goals and schedule. That never happens. Not as an undergrad, MS, Ph.D., postdoc, or professor. There might be a few unicorns around, but, usually, you have no idea where you are going. Ideally, you could use this opportunity to train the most important trait in a researcher: independence.

Instead of expecting to be handed goals and schedule, create them. It will be challenging for you, but you would learn how to do it, and get familiar with the field. Then you could go to the Ph.D. student and ask "Do you think this is a reasonable plan?" instead of "what should I do?". Worst case scenario, that plan can be a starting point for a better one. Bonus points if you include solutions to tangential problems of her research (stuff that would be cool/easy to do, but isn't a priority, so she would never do it herself).

Quoting a far better man, and professor, than myself:

"Be honest, be kind, be useful, be responsible, work hard, treat everybody with respect."

I'd advise you to go around the Ph.D. student only as last resort.

human biology - The gender of offspring of Twins?

Given identical twin males, Michael and Douglas, Douglas and his wife have four children, all of whom are girls. Michael and his wife have only one child, a boy, and are expecting another. What are the chances it will be another boy? If Michael and his wife have more children, what are the chances they will all be boys? Is there any support/evidence for, or a study about, one twin of an identical pair will have children all of the same gender and the other twin will have children all of the same (or opposite) gender?

citations - Is it ethical to obtain journal articles from places other than the publisher's official sites?

When I am at home and looking for journal articles I often find article PDFs through google that have been uploaded to various websites (e.g., universities, institutions, arbitrary websites, etc...).

I am worried that using these files may infringe copyright since these articles may be bought by these universities (for example) and (by mistake?) were freely uploaded to their domain name like: www.university.edu.lb/journal_article1.pdf (probably for their own students?).

• Is it ethical to use these downloaded PDFs during my research without going back to my own university elibrary to use them?


• When, if ever, would I be breaching copyright or breaching professional ethics if I accessed these files?

EDIT: my question also covers books as, sometimes, these are entirely available on some sites (whether they are institutional sites or not).

Answer

Yes, it is absolutely ethical to use these files during your research. Many publishers allow academic authors to upload a so-called "preprint" version of a paper to their own institutional websites or put them in repositories, and of course these can be used by others in research.

There's maybe just two minor things to be careful about:

1. You should try to verify that the preprint version is mostly up to date with the published version, comparing e.g. publication dates.


2. It is common practice to put the "official" publication source, i.e., the journal version, into your reference list. Nevertheless, if you can't make sure that the versions are equivalent regarding what you're citing them for, it may be necessary to state that you were using a preprint version.

In some cases, authors may put papers online even though it's technically a breach of copyright. But since you don't know the author's agreement with the publisher, you have no way of checking that, and in any case, it would be the author or institution that violates copyright, but not you.

Grading schemes to encourage effort

I'll be teaching a graduate-level mathematically oriented class with probably less than 20 students. I have to grade the students (our system doesn't allow for pass-fail grading), and while I don't want to be overly fussy about the grades (this is after all advanced level material and mostly Ph.D students), I would like to provide some incentive structure so students will do the classwork and hopefully learn something in the process.

One possibility is "coarse-resolution" grading where in each homework, the possible grades are +, 0, -, where + denotes having done about 75% or more of the work, 0 is between 50 and 75%, and - is below 50%.

At the end of the semester, the number of +/0/- determines the grade, with "mostly +" getting an A, "mostly 0" getting a B, and mostly - getting a C.

Is this likely to be effective ? Is there something else I should do ? I'm open to the idea of not grading at all and giving out dummy grades, but I do think that people who put in effort should be rewarded in some way.

genetics - Lac operon: How can lactose enter the cell in the absence of lactose permease?

My textbook states that

lactose permease...transports lactose into the cell

and

When lactose is added to the growth medium, the lactose molecules bind to the other site on the repressor protein

My question is, how can lactose enter the cell to bind to the repressor protein to allow beta galactosidase and lactose permease to be synthesised if there is no lactose permease present to transport the lactose into the cell?

Answer

Introductory textbooks will not get into the details of the lac operon.

Basically, the operon is expressed constitutively at a low level that means that Beta Galactosidase and Lactose Permease are expressed at low levels by the bacterium. This is because it takes a little bit of time to build up the concentration of LacI in the cell before it can start to bind the operator.

The LacI repressor only binds the operator in the absence of Lactose in the cell's environment due to the fact that allolactose allosterically binds the LacI repressor and affects that molecule's ability to bind the operator. So RNA polymerase can bind the promoter of the Lac operon at some low rate and continue to produce the protein.

When the cell no longer has glucose, it generates cyclic AMP, which induces the CAP protein to bind to the CAP site, just upstream of the promoter of the Lac Operon. CAP associates with RNA Polymerase, and this makes the promoter very active. Beta Galactosidase and Lactose Permease levels increase rapidly.

Where you see the full effects of the LacI repressor is when neither Glucose nor Lactose are present in the environment of the cell. At this point the repressor binds to the operator and blocks transcription by DNA Polymerase.

I hope this helps. I have an entire book that covers the Lac Operon, so even though this is a bit expanded of an explanation from a basic textbook, it is still a summary.

funding - Why do researchers need universities?

This is a follow-up question to How are junior professors evaluated for promotion? and probably an even more naive question. If I'm understanding the answer correct, professors need funding to do research, but once they get it, the university takes some of the grant as overheads (to pay for office space, electricity, etc), and the cut the university takes is substantial.

Given that then, why do professors need universities? One could just apply for the grant as per normal, and once one gets it, buy a slightly bigger house and convert one of the rooms into a lab. One loses nothing to overheads, gets to work from home, has zero teaching duties, can choose to settle anywhere (no two-body problem!), and can even monitor an experiment 24/7. This gets even easier if one works in a field that doesn't need a physical lab. Further, presumably the grant covers postdoc salaries, so one would still be able to pay for postdocs (although probably not PhD students since a professor without a university will not be able to award a degree).

The obvious answer is that one cannot apply for a grant without a university, but Google indicates that's not the case, e.g. NSA grants in mathematics only looks at one's previous accomplishments & potential applications of the research result, both of which are independent of the university. I suppose one could lose journal access, but there's always stuff like arXiv / ResearchGate, emailing the authors of the desired paper, or even Scihub (oops). It's conceivable that not working for a university loses one some prestige, since one can no longer claim to be a professor. However even then I'd expect at least some academics to choose this path, valuing the convenience & extra research funding over prestige.

If the answer to this varies from field to field, I'm most interested in the sciences.

Answer

If I'm understanding the answer correct, professors need funding to do research, but once they get it, the university takes some of the grant as overheads (to pay for office space, electricity, etc), and the cut the university takes is substantial

The number of services provided by a university is substantial, of which space and electricity are the least of them.

Maintenance, janitorial, and IT services - machines break, rooms get dirty, and technology has inexplicable problems. Universities have infrastructure in place to deal with all of this.

Access to literature - Universities maintain subscriptions to the journals, standards, and other references a researcher needs.

Laboratory equipment and specialists - Most scientific research requires specialized equipment, which can cost anywhere from a few hundred dollars to several million. Universities can afford to maintain such equipment, and the expert technicians needed to run the equipment at maximum efficiency.

Other researchers - A university department provides ready access to and familiarity with other experts in your field for potential collaboration. Additionally, it provides a way to find potential collaborators from other fields for the times when you find your research leaving the bounds of your expertise.

Students - an unfortunate amount of research is tedious. A university provides a ready framework for delegating simple but time-consuming work to students so that a researcher can focus on the parts of the research that only they can do.

Contacts - Universities maintain contacts with businesses, governments, and other research institutions that can open more doors than any one researcher could do on their own.

Reputation - Being a member of a respected university means that people who trust that university will afford some measure of that trust as well.

Legal services and other expertise - While it would be nice if research could exist completely separate from the outside world, this is not the case. Universities have systems set up to support and advise their researchers when problems arise during their research.

Many of these things could be aquired by a solo researcher, of course. But doing so would cost time and money, likely amounting to more than a university takes in overhead. And things like contacts and reputation are difficult to purchase.

publications - Should I explicitly remind people to include my name in the acknowledgement?

I am a research assistant. I've helped a PhD student from another department throughout her studies by providing and maintaining human cells for her project. She's now about to published, and I'm not sure she would acknowledge my contribution in her papers. Is it acceptable to remind her to acknowledge me?

Including my name would be good for my future graduate school applications and interviews.

Answer

My suggestion is that you could let her know that you would appreciate an explicit ack and that it would help your future, just as you have done here. Don't state it as a duty (which it probably is) but as a professional curtesy and "boost", which it also is.

You could even write a suggestion of the form of the ack you would like if you would like it to include anything specific rather than just a general statement of thanks. (... who maintained the human cells...).

publications - Is it possible to download paper from academia.edu without being registered there?

Based answers to Is Academia.edu useful? it seems that there are some legitimate reason why many people would prefer not to have academia.edu account.

On the other hand, it might happen that you see a paper there which is interesting for you and which might be difficult to obtain in a different way.

I have noticed that when I find some paper on academia.edu using Google Scholar, I will also have a direct link to download. To give one random example, when searching for ultrafilter site:academia.edu you can see that I get direct download link to this paper. (The link contains the string "expires", so it is probably only temporary.) On the other hand, when I try to find the same paper on academia.edu and try to download it, I am asked to login/sign up.

Is there some way to get the url for download from academia.edu website without being logged in? (This could be useful if neither Google Scholar nor some other searches give me a direct download link to the article.)

EDIT: To clarify (since I received an answer copying parts of the above paper). When I made this post, I was able to download it via the direct download link I have mentioned above. And this particular paper is also available on another website. So this is not a request for a paper. (Requesting papers would clearly be an incorrect use of academia.SE.) It is a question whether the annoying restriction to be registered before downloading something from academia.edu can be somehow bypassed. I have simply chosen a random paper as an illustration.

collaboration - How to integrate partial version control, data exchange and research assistants?

Currently, my coauthors and I use GitHub to collaborate in coding and writing but also in data exchange. We have a lot of data, often not in text format (e.g. pdf). Most of this is collected by research assistants, which which we don't share our Git repo.

More specifically, we use python, shell, R, Stata and Latex and most of it is fully integrated. That is, python and shell scripts generate the data that is used by R and Stata whose output is directly compiled in Latex.

We don't want to deviate from this high level of automatization, but our approach has two major shortcomings:

1. Research assistants can and may not upload their data directly into our repo. Instead, they send us their data and files via another git repo. This puts additional workload on me but we want to make them use git for it's fascinating issue tracker. However, there is too much additional work for us and git is often to complicated for young research assitants (even the GUIs).



2. Because of the data, which eventually changes, our repo is very large (>1,5GB) and internet is sometimes restricted. Getting the repo on a new computer is very time-consuming and often not working. Although the raw data changes from time to time, git, which was not made for the data exchange, keeps track of these changes. But that's useless for our purpose.

Can you suggest to me other software(s) or approaches, which combine the integration we have achieved so far where we can easily exchange data?

Answer

I've run into similar problems in collaboration with biologists, and found that a two-technology approach is best.

• Large-scale experimental data is shared via one or more BitTorrent Sync folders. The experimentalists can just drop their files into the appropriate place in the folder, and they get synchronized with the server and everybody else's copy (like DropBox, but private, free, and unlimited size).


• The analytical tool-chain, research products, write-ups, etc. are maintained in your preferred version system (e.g., git). This is then integrated with the experimental data just by giving a pointer to the appropriate directories.

This has the advantage of maintaining the data separation that you need, keeping the scary version control software away from the experimentalists, and also avoiding juggling massive globs of data in a version control system that was never intended to support this.