evolution - Do ring species exist?

In trying to understand evolution better, I have been looking at examples of speciation, and have thus come across the topic of ring species. I have tried to find concrete examples of how these work, but have been unable to. This paper deals with one of the frequently quoted examples of ring species, but concludes:

In conclusion, although ring speciation is theoretically possible, the few well-studied examples suggest that it occurs infrequently, because the dynamics of species’ ranges are more likely to result in fragmentation, i.e. periods of allopatry, before the slow process of isolation by distance leads to sufficient divergence to allow for circular overlap.

The paper does, however, cite an article on a bird that appears to be a strong example of a ring species, but buying access to it is more expensive than a year´s supply of toilet paper.

Is there hard evidence that ring species exist? And if so, what is the evidence and what does it teach us about the nature of speciation?

undergraduate - Attending conferences as a first-year undergrad

I'm a first-year undergraduate student in physics. Since starting my studies I've tried to get involved in research as much as possible. Recently, the team I work with encouraged me to submit an abstract about my current project (which is the first serious one that I've taken on) for an upcoming conference. I did and I got accepted with a poster.

Now my question is: How should I approach this to benefit the most? Or maybe there isn't even a point in me going at all?

I'm under the impression that most of the typical advantages of attending a conference such as networking, or keeping up-to-date with recent advances aren't really applicable to me as I simply lack the necessary knowledge. So far I've only taken a basic mechanics course and I have some working knowledge that I've acquired while working at the lab but nothing beyond that.

Additional information: the conference is obviously not a high-tier one. Judging by previous editions, about 150 attendees are expected, around 1/3-1/2 of that international (this is all in Europe by the way). Travel funding is provided by our department [active participation, in form of a poster, was part of the requirements to get that funding].

job search - Should all voluntary self-identification forms for faculty positions be filled?

When applying for a faculty position, usually there will be an request to fill a self-identification form about things like race and disabilities. The request will mention that it is a “voluntary” form and will not affect the application. My question is whether applicants should spend some time and fill out all such requests or maybe just the ones for schools with which they have an interview?

Answer

You can fill them in if you want, you don't have to if you don't want to. That's why they are voluntary.

They are supposed to be either anonymous or confidential and not used to affect your file and/or hiring in any way. The reason they exist is so that if there is an allegation of bias in hiring at the school, they can have statistical data to prove that they were not biased at least in their solicitation for applications (e.g, "we had 300 applications: 48% were women and 12% were people of color"). This is a federal regulation for hiring, so they have to do it.

The school is obliged to send you the postcard. You aren't obliged to send it back. I usually did when I was on the job market, although I didn't if they didn't pre-stamp the postcard meaning I would have to pay for the stamp myself, which I wasn't about to do so for their benefit. Petty, yes, but the survey is for them, not for me.

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Addendum: There seems to be three types of forms and I am unclear how and why some HR department select between them:

1. Completely anonymous: No indication on them whatsoever as to which position is being applied to or who you (as the applicant) are.



2. Position identified: The position (job opening) identifier is given, but not the job applicant identifier.


3. Position and applicant identified: There appear to be coding for both the position and the specific applicant.

In my own job market experience (which is now 7-8 years old), I only remember getting types #1 and #2. I would have personally never responded to type #3 because of my own politics, but that would be a personal decision and you can decide yourself what to do.

Is there a more user-friendly way to download multiple articles from arXiv?

I am subscribed to the arXiv daily digests for my subject area. I find myself, every day, doing the following, when I get to work:

1) Browsing through the arXiv email and right-clicking on the articles of interest to me (to open each of the pages in a different tab in my browser)

2) For each of these pages, downloading the pdf by clicking on the link, re-naming it by .pdf, and saving the pdf in a directory on my PC

[3) the directory is then automatically synched to my tablet during the day]

4) Looking at the articles on my commute home on my tablet.

I am bored of doing (2). It only takes 10-20 seconds per article (depending on things like how many carriage returns or inappropriate characters I have to remove from the cut-and-pasted article title and author names -- e.g. math characters (I am a mathematician and symbols in titles do not cut and paste well)) but when I'm interested in 5 articles and one has a lengthy title with carriage returns and symbols in, my mind wanders and I start thinking about whether this has already been automated by someone, because it seems to me that there would be no obstruction to doing so in theory, but I would not be capable of doing it myself. Does such an automation exist?

publications - Mentioning that my paper extends my project X: compatible with double-blind review?

I am going to submit a paper to a conference that uses double-blind review. The paper extends my project X, which was published somewhere else last year. In order not to break the anonymity, in the paper shall I hide the fact that project X was mine? (If I don't they could simply look at the reference associated with project X to identify the authors.)

Answer

Yes, refer to Project X without stating that it is yours.

In my field, instructions to authors for conferences that are double-blind reviewed often say:

Do not omit references to provide anonymity, as this leaves the reviewer unable to grasp the context. Instead, a good solution is to reference your past work in the third person, just as you would any other piece of related work.

In reality, of course it is often obvious that the paper under review is likely to be an extension of the cited work by the same author. However, as an author, it is not your responsibility to make sure that the reviewers can never identify you. It is only your responsibility to

make a good-faith effort to preserve the anonymity of your submission, while at the same time allowing the reader to fully grasp the context of related past work, including your own.

Citing your own previous work in the third person is a good faith effort to preserve anonymity, and (at least in my field) that's all that's required.

university - How to comfortably interact with famous professors?

I know that they are "just as human as we are", but I feel somewhat uncomfortable to talk nonchalantly with the top-notch math researchers and professors in my department because of their social position, their extremely superior knowledge and talent, and also because of their age.

Still, I feel that it is like a waste to have such interesting mind-expanding people around and not to interact properly and talk about maths when I meet them in the department (outside the lecture hall).

So my question is: according to your experience, what is the best (where best means: most polite, appropriate, acceptable, but also profitable) way to interact and make the most of the presence of such awesome professors? Can I discuss "lower" [mathematical and non-mathematical] subjects with them even though their actual (research) interests lie in much more abstruse topics?

Any suggestion (even in the form of a comment) is really appreciated.

Answer

From a student's point of view, here is how I tackle the situation. You can break it down by the circumstances in which you meet, and thus guesstimate how much time the professor has for you.

Asking "may I talk to / email you later about...?" can be useful if it's not the right time and place for a useful discussion.

DTK's answer has good points about how you should approach a conversation.

Of course there will be some variations depending on the culture and environment of your department, and how well you know the prof you're talking to.

Hallway / elevator encounters

If they look busy or rushed, perhaps best save it till later. Otherwise, keep questions very brief, concisely answerable, and related to something you know they're interested in (i.e. their own research field).

Discussions at semi-social occasions, such as at a gathering after a seminar, or breaks at a conference

Here, the professor probably has no immediate obligations or things urgently pressing on his or her mind (or else they'd have disappeared by now). This is a better opportunity to ask broader or more complicated questions, or if they work in a related field you could ask for an opinion on a problem you've been thinking about.

Social occasions such as at lunchtime, conference dinner, etc.

As above, but they may even prefer to talk about something other than their own field of expertise -- sports, politics, an interesting paper from a completely unrelated discipline that you read whilst procrastinating, etc. If you don't know the professor very well, you might want to wait for him or her to initiate steering the conversation in that direction.

molecular genetics - Are mitochondrial genes decoded in the same way as nuclear genes?

Mammalian mitochondrial genomes contain only 22 tRNA-coding genes, which is an insufficient number to decode mRNAs under the standard wobble rules.

How is translation of mitochondrial mRNAs achieved with this number of tRNAs?

The possibilities that occur to me are that certain genes encode multiple tRNAs (but this appears unlikely as each gene has its own promoter) or that mitochondrial tRNAs can adopt alternative three-dimensional structures, each with a different anticodon loop and hence a different anticodon.

Answer

Answer Summary

Translation in the mitochondria of mammals differs markedly from that in the cytoplasm. Although it has more similarity to translation in prokaryotes, it also shows significant changes from the latter. A smaller repertoire of tRNAs is able to translate a ‘simplified’ genetic code through structural alterations and base modifications that allow their anticodons to decode groups of synonymous codons, not possible according to the standard wobble ‘rules’.

Relationship to the eubacterial translation system

One of the pieces of evidence for the endosymbiotic theory of the origin of mitochondria was the fact that their translation machinery was more similar to that of prokaryotes than to that in the eukaryotic cytoplasm. The similarities to prokaryotes included the (smaller) size of their ribosomes, the susceptibility of their ribosomes to antibiotics specific for bacterial ribosomes, and the formylation of their initiator tRNA — fmet-tRNA.

Although in no way rebutting the endosymbiotic theory (which is widely accepted), mitochondrial translation shows several differences from that in prokaryotes. These include there being a single tRNA to decode methionine in both initiation and elongation (discussed below), the lack of leader sequences preceding the initiation codon, hence precluding a Shine & Dalgarno type of recognition by the ribosome, and additional ribosomal proteins which are thought to “provide a specialized platform for the synthesis and membrane insertion of the highly hydrophobic protein components of the respiratory chain”.

Decoding with 22 mitochondrial tRNAs

General Review: Suzuki et al. (2011) Annual Review of Genetics 45, 299–329

As the question states, mammalian mitochondria encode 22 mitochondrial tRNAs, which would be insufficient to decode mRNAs using the standard genetic code and the wobble ‘rules’ that apply to translation in the eukaryotic cytoplasm and in prokaryotes.

One way out of the dilemma would be if some of the tRNAs were encoded in the nucleus and imported into the mitochondrion in a similar manner to that of nuclear-encoded mitochondrial proteins. Although this turns out to be true for certain organisms (although the import system is different from that for proteins), and important in some cases, this is not the answer for mammalian mitochondria. Thus, as reviewed in Current Genetics (2009), the mitochondrial tRNAs encoded in the nuclear genome of H.sapiens only duplicate the 22 mitochondrial tRNAs and their anticodons. (The one exception is an extra Gln(anticodon CUG) in addition to the Gln(anticodon UUG).)

Let us look more carefully at the problem. Although there are 61 codons specifying amino acids, because of wobble, fewer than this number of tRNAs are required to decode them. The left-hand frame of the figure below shows the standard genetic code, and the minimum number of tRNAs needed to decode it using the wobble ‘rules’ shown beneath, indicated by the colour-coded rectangles.

For those not familiar with the actual pattern of wobble (summarized in my answer to another question), in elongator tRNAs the 5′-position of the anticodon has some flexibility such that a G in that position can form base pairs with U or C in the 3′-position of the codon, an inosine (I) can pair with U,C or A, but an anticodon C can only pair with a codon G. The unmodified bases A and U are rarely found in anticodons, but a variety of different chemically modified Us are found (U* in the figure) which only pair with A. Thus, the minimum number of elongator tRNAs needed would be the number of coloured rectangles — 36 — and, as there are separate species of tRNA_met for initiation and elongation, the minimum number of tRNA species is 37.

When the human mitochondrial genome was sequenced, two anomalies stood together: the limited number of tRNA genes already mentioned and (more sensationally) changes from the standard genetic code (indicated in red on the right-hand side of the figure). It was immediately realized that these changes served to rationalize the code so that all synonymous codons were in groups of four or two. If it were assumed that the decoding specificity or wobble of mitochondrial tRNAs were different, then 22 tRNAs would be sufficient using the ‘wobble’ shown beneath the right-hand frame of the figure for groups of four amino acids (dark blue) and groups of two amino acids with codons ending in A or G (red).

One further requirement was that a single tRNA_met be involved in both elongation and initiation, a requirement the fulfilment of which has already been mentioned.

What features of the tRNAs could change the wobble ‘rules’ that have been conserved between prokaryotes and eukaryotic cytoplasm? There turn out to be two types of changes. The first, and most obvious, is the fact that certain (but not all) mitochondrial tRNAs have non-canonical cloverleaf structures, the most extreme being tRNA_ser in which the whole D-loop is missing. The second is the post-transcriptional modification of bases in the anticodon — just as is the case for tRNAs in the cytoplasm, this can markedly affect decoding specificity.

It is not yet possible to describe the codon–anticodon interaction in mitochondrial translation in the way that this has been done in for the cytoplasm or for prokaryotes. The problem would appear to be the difficulty of obtaining sufficient pure tRNAs. Whereas it is easy enough to clone and transcribe the tRNA genes, this is insufficient without the secondary chemical modifications of the bases which is key to the structure and function of the tRNAs.

Can a university revoke one's degree for his minor misconduct?

I don't mean misconduct that will make him get expelled or miss his academic requirement. He will have received sanction like making an apology or suspension for a month if the university finds it out earlier. But the student now has graduated and will not be back. Can the university still do something to him?

neurophysiology - Photoreceptors and light with mixed frequencies

I am interested in how the activation of a, say, blue cone depends on the incident light. Wikipedia tells me this:

, which describes how strong the activation of the blue cone is for light with a single wavelength and a given intensity. But what happens if the incident light has several frequencies?

My question is: given the intensity i(f) of the incident light at frequency f, what is the activation of the blue cone?

(A natural guess would be that if b(f) is the activation curve in the figure, then the activation of the blue cone should be the integral of b(f)*i(f) over f. But I have not found any confirmation of this guess. For example, in the reference for the picture above, only pure light was used in the experiments.)

Answer

Yes, current color models assume a linear response in the spectrum.

Given a light with mixed spectrum $\Phi(\lambda)$, the response of a cone with spectral sensitivity $\Psi_i(\lambda)$ is a (nonlinear) function of the L2 inner product:

This is how CIE XYZ color space is defined.

Reference:

mammals - What selective factors drove the evolution of lactose in lactation?

As far as I can determine, lactose, and the monosaccharide galactose have few biological uses outside of mammalian lactation. It not only required enzymes for its production, but enzymes in offspring for its digestion, suggesting that it serves some specific purpose. Yet intuitively, it seems like it would have been significantly easier to just concentrate glucose from the blood or generate a disaccharide readily found in the diet like sucrose, for which digestive enzymes already existed.

What drove the evolution of lactose in mammalian lactation?

Answer

As it happens someone has just published a theory about this. To save you following the link, I reproduce the abstract below.

I must admit that I had never realised that lactose is synthesised within the organelles of the secretory pathway (β4-galactosyltransferase is a Golgi enzyme and α-lactalbumin is, of course, a whey protein, so is in transit through the pathway). This may go part of the way to answering your question: by having a disaccharide that is made within the Golgi, the cells of the mammary gland will effectively partition their glucose metabolism between the cytoplasm and that destined for secretion as lactose (transported into the Golgi lumen).

Mammalian milk or colostrum contains up to 10% of carbohydrate, of which free lactose usually constitutes more than 80%. Lactose is synthesized within lactating mammary glands from uridine diphosphate galactose (UDP-Gal) and glucose by a transgalactosylation catalysed by a complex of β4-galactosyltransferase and α-lactalbumin (α-LA). α-LA is believed to have evolved from C-type lysozyme. Mammalian milk or colostrum usually contains a variety of oligosaccharides in addition to free lactose. Each oligosaccharide has a lactose unit at its reducing end; this unit acts as a precursor that is essential for its biosynthesis. It is generally believed that milk oligosaccharides act as prebiotics and also as receptor analogues that act as anti-infection factors. We propose the following hypothesis. The proto-lacteal secretions of the primitive mammary glands of the common ancestor of mammals contained fat and protein including lysozyme, but no lactose or oligosaccharides because of the absence of α-LA. When α-LA first appeared as a result of its evolution from lysozyme, its content within the lactating mammary glands was low and lactose was therefore synthesized at a slow rate. Because of the presence of glycosyltransferases, almost all of the nascent lactose was utilized for the biosynthesis of oligosaccharides. The predominant saccharides in the proto-lacteal secretions or primitive milk produced by this common ancestor were therefore oligosaccharides rather than free lactose. Subsequent to this initial period, the oligosaccharides began to serve as anti-infection factors. They were then recruited as a significant energy source for the neonate, which was achieved by an increase in the synthesis of α-LA. This produced a concomitant increase in the concentration of lactose in the milk, and lactose therefore became an important energy source for most eutherians, whereas oligosaccharides continued to serve mainly as anti-microbial agents. Lactose, in addition, began to act as an osmoregulatory molecule, controlling the milk volume. Studies on the chemical structures of the milk oligosaccharides of a variety of mammalian species suggest that human milk or colostrum is unique in that oligosaccharides containing lacto-N-biose I (LNB) (Gal(β1 → 3)GlcNAc, type I) predominate over those containing N-acetyllactosamine (Gal(β1 → 4)GlcNAc, type II), whereas in other species only type II oligosaccharides are found or else they predominate over type I oligosaccharides. It can be hypothesized that this feature may have a selective advantage in that it may promote the growth of beneficial colonic bacteria, Bifidobacteria, in the human infant colon.

evolution - Evolutionary chronology - if any, which species have evolved in the last 100 years

I heared somewhere, I cannot remember where, that there has not been an evolution observed in our lifetime. In life science class, right at the start, we was doing the usual MRSGREN (how to tell if something is a living organism), and the tutor said that you can also tell something is a living organism if it evolves. So I asked if there has been an observed evolution in our lifetime. She said that there had been many but could not recite any off the top of her head, so the next week she handed me a piece of paper with 8 or so websites that aparrently corroborated her claim. I have not got the paper anymore but I recall there been on there the peppered moth or something. So I set out to look for a chronological list of evolution but could not find an authoritative one. I could only find something on wikipedia that indicated that species have been dying out for the past thousand years, but nothing saying that any have evolved.

publications - Why do I have the "required reviews completed" status on my submission in Elsevier?

I had submitted my paper in an Elsevier journal one year back. Now, status update on the submission tracking says "Required reviews completed." However, for the last two weeks still there is no change in the status.

Should I ask the editor what is going on with my submission?

Answer

To expand on Dirk's comment: The status you see means that the reviewers have submitted their reports to the online system, and the handling editor has received an email about this. Now she has to read the comments (and likely look at your manuscript again to see if they comments are relevant), come to a decision, and write a corresponding letter to the author summarizing the comments and justifying the decision. This will in general not take more than an hour.

But you should keep in mind that yours is not the only manuscript (nor, in all likelihood, the only journal) the editor has to deal with. In addition, this is both the end of semester and conference season in many parts of the world, so it is reasonable to assume that the editor is just very busy with more urgent deadlines, or isn't even in office. (Remember, editors are unpaid, so this work is on top of the regular duties of teaching, advising and doing their own research.) In some cases, the final decision even involves two editors (associate/managing editor and editor-in-chief/communicating editor), which doubles the chance of other things getting in the way.

In light of that, I would say two weeks is definitely too early to worry and start contacting the editor; give it at least a month.

(Although I know how stressful the wait at this stage of the publication process is...)

translations - Translating academic CV - translate names of papers/thesis?

I have found links on academia-SE pertaining to translation of documents here and here, but those were not for a CV. Please tell me if my question is a duplicate.

I have just moved to France from an English-speaking country for a PhD. My French is not amazing currently; this is a work in progress and I'm going half-time on my research to take an intensive language course in May. However, in June I hope to attend a school which will be taught in French, and for this reason I need to translate my CV into French to apply.

Question:

When translating my CV from one language to another, should I:

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  translate the names of past works e.g. the name of my masters and bachelors dissertations? Or leave them in English, as they were submitted to my past university?

  
  


• 
  

  translate the names of publications (and leave the name of the journal as-is)?

  
  


• 
  
  

  leave the names of the university and the qualification as-is per link 1, or put in parentheses the French name equivalent of my prior qualification?

  
  

And mostly: Are the rules different between translating a CV and translating a publication/bibliography?

Answer

Things can be different in the humanities, but English is the language of science and, in a STEM field, you can reasonably expect whoever will read your CV to be able to understand the titles of your works (if they are in English).

However, if, as a courtesy to the reader, you wish to translate the titles anyway, don't eliminate the original titles, but put the two versions side-by-side.

Your last point is more critical:

leave the names of the university and the qualification as-is per link 1, or put in parentheses the French name equivalent of my prior qualification?

1. The name of the university should be absolutely left as-is, unless the university itself does not provide an official French translation, which I doubt (on the other side, universities from non-English speaking countries sometimes issue statements about official English translations of their names or department names).


2. It's not always easy to find equivalences among qualifications in different countries, and it's almost impossible for grades. Thus, if you want to provide a translation, leave the original qualifications and grades too, so that the application committee can employ their equivalence rules, if they have any.

publications - What is the point of listing 1000 authors for a single scientific paper?

I arrived at the printer room this afternoon to collect my printing and I happened to notice that someone was yet to collect a printout of the gravitational waves paper that has been all over the scientific news the last few days/weeks. Of course, I was curious, so I had a peek.

It struck me that there was only one author... until I saw the asterisk indicating a full list of authors could be found at the end of the article.

There I found three full pages of authors. I have no intention of counting the exact number, but a quick estimate by word count suggests there are over 1000 authors from 133 institutions.

You always need to give credit where credit is due, that is a given. But to put it in context, there are at most 7 words of article per author. In fact, I can think of a number of problems coming from so many authors (like who do you contact if you have a question - the list is alphabetical and there doesn't appear to be a designated contact person).

What is the value of listing so many authors and why should (or shouldn't) it happen?

Update: Thanks everyone for the thoughtful answers. As much as I want to choose an answer, I honestly cannot decide between the two most upvoted, so I'm going to abstain from choosing one.

united kingdom - Reputation of 1 Year Master's in Comp. Sc. in the UK

I'm currently studying for my Bachelor's degree in Computer Science in Germany. I've noticed that UK Master's programs, even at such prestigious universities as Oxford or Edinburgh, only offer 1 year Master's programs for full time study. In Germany, on the other hand, Master's are usually 2 years / 4 semesters.

I was wondering how this is perceived in academia. Say for a professor in the US offering a PhD position, would he expect people from the German two-year program to be better at their subject? (Assuming grades are similar).

Why have international branch campuses?

There are campuses in Malaysia belonging to the universities of Southampton, Nottingham and Reading. There is a Mauritius branch belonging to Aberystwyth University, whereas the University of Wolverhampton has shut down its Mauritius campus. Newcastle University has a Singapore campus. There are many more examples of UK universities with campuses in Asia or Africa.

Why do (some) universities based in the UK spend resources on establishing a campus on another continent? Is it a form of developmental aid, to bring UK expertise to a spot where existing universities may be perceived to have less quality? Or is there a different reason?

I don't know if this is exclusive to the UK or if it also occurs with universities in other countries — I have not seen it anywhere else.

The Wikipedia article International branch campus is not terribly informative.

Answer

So focusing on the UK to start. The universities seem to be attempting to provide UK standard university education, but in more 'exciting' locations, increasing the number of students who study with them and their global reach.

Branch university campuses are in many ways a win-win-win phenomenon. For the university, they mean more students and stronger ties with other countries. For the host nation, they’re a quick way of boosting higher education standards and attracting more students, both local and international. As for students, the prime attraction has already been mentioned: a degree at an internationally ranked university, in a location where this was not previously possible. (1, 2, 3)

Back to the question of why universities are doing it?/getting involved? It seems to be that these branch universities are risky and liable to fail.

This article is great and discusses many factors. It predominantly suggests that branches can be financially lucrative but they have a high risk of closure. As such, it concludes that prestige and a desire for international reach that are the main drivers, citing this report.

It is true that although financially risky, there are many sources of funding for these ventures, whether its tax breaks from the home country or incentives from the host region.

Nottingham's Malaysian campus has the benefit that it can apply for funding from more than one region. Doughty says: "EU funding is quite interesting because we are viewed as both a UK and an Asian institution so we can pitch to whichever suits us best." 5

However I think this thesis offers the best view, these campuses are seen as new opportunities for universities otherwise limited to their own country.

Multiple factors contributed to Texas A&M being poised and ready to accept the opportunity to open an international branch campus: an invitation from a host country sponsor willing to cover all expenses, existing international ambitions, and strong support from the central administration.

These campuses predominantly provide undergraduate and masters degrees because tuition fees can cover the costs, but some campuses can provide highly specialised research centres for PhDs but it is usually not worthwhile undertaking research outside of the main multi-disciplinary hub of the home university unless the research is local to the branch because of isolation and funding.

NB: Other countries have these branch campuses:

There are currently over 240 international branch campuses around the world; many of these are located in the Persian Gulf region as well as (and increasingly) in Asia ...

71 countries hosting branch campuses – up from 53 in 2012; 30 “home countries” (i.e., originating countries) for branch campuses, up from 24 in 2012.

evolution - Reasons why living fossils exist?

A living fossil is a living species (or clade) that appears to be similar to another species otherwise known only from fossils, typically with no close living relatives.

A living fossil is considered as a successful organism, which has made its way through many major extinction events. Also, the morphology of living fossils resemble some species of organisms which we know only through their fossil remains.

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  What is the reason for a particular type of species to become a living fossil; is the engineering of this particular species extraordinary, in that it can survive any selection process encountered thus far?

  
  


• 
  

  Is there not enough selection pressure exerted on this species in order to force it to change morphologically?

  
  
  


• 
  

  Have these organisms modified themselves, so that currently their morphology seems to be similar to a fossil organism?

  
  

Answer

One part of your question betrays a serious error:

• Is there not enough selection pressure exerted on this species in order to force it to change morphologically?

Actually the reverse is true; constancy of form can only be maintained in the presence of continuous selective pressure. It's just that this is stabilising selection that acts to maintain the existing form rather than push the organism to new morphologies. In fact, most selection acts in this manner. This shouldn't surprise you: organisms are typically well adapted to their environments so changes are more likely to reduce fitness than increase fitness.

It's also worth noting that although living fossils show little morphological change they can continue to show change at the molecular level at rates as high as, or higher than, other organisms - e.g. (May et al 2007; Cao et al 2013).

Is it worth self-funding a PhD to attend a top 10 university?

What should I opt for?

Option A) very well paid PhD, around €3000 per month at a respectable university or;

Option B) a non-paid PhD, where I have to pay €2000 per year at one of the top 10 universities of the world?

EDIT: Actually they are both UK universities, Option B is ranked between the top 10 in the world in engineering and tech, and I do get a scholarship that pays 18000 pounds which covers the difference between international student tuition and EU tuition. In Option A, I will be doing research in a good university and will be working alongside giants in the industry.

Answer

Congratulations on receiving these two offers from good universities, both of which offer at least some funding. I make it that the difference between your two options is about €114000 over the three-year period that UK PhDs are usually funded for. This is probably a very large difference and it might be worth trying to ask somebody within your field who knows both institutions and departments whether that would be worth it.

Certainly, self-funded students can survive PhDs in the UK, and your prospects of successfully completing are probably better than average if you are in engineering and tech. In addition, it may be a realistic prospect in the UK to receive payment for carrying out some teaching and demonstrating. I would advise asking about this possibility before you commit to option B. Look at the research council guidelines beforehand to try to gauge the best practices for salary and training.

However, there may be more important criteria than money. In one department I worked in I saw hoards of both funded and self-funding students abandoned by a particular supervisor before they quit. Don't let this be you. The (prestigious) department did nothing; it was absolutely buyer beware. So the usual advice applies: Talk to your supervisor's previous students, did they complete on time? What are they doing now? Did they see others around them succeed and being supported? Did they feel the supervisor, department and university helped them to succeed? Unfortunately, a top department is absolutely no guarantee of a non-toxic research culture in the group.

If option A is research council funded (or is funded by a high-profile UK body or another funder demanding results for their money), this would weigh heavily in my decision to take it, even if it is at a less prestigious university. There will be consequences for the group and department if a council-funded student fails to finish by the four-year deadline, and this means that both the supervisor and institution are absolutely committed to the student succeeding and solutions will have to be found if things start to go wrong.

application - Clarification needed: Job market paper

During my ongoing academic job search, I'm seeing that some universities require a job market paper as a part of application package. While I read a bit about the meaning of the term, I'm still somewhat confused about it and hope that more experienced people on this site will clarify that.

Question: What exactly is a job market paper? Is this term interpreted differently across disciplines and fields of study (and to what degree)? Is it closer to research statement or writing sample?

Note: my main discipline is information systems (a multi-disciplinary field of study with a focus on management science and other social sciences; in addition, my own current focus is computational social science, complex socio-technical systems and data science) and I do have both research statement and writing sample (a slightly abridged review of literature from my dissertation).

Answer

Elaboration on Above Comment

In economics and certain business school fields, a major part of junior academic hiring is the job market paper (JMP). The JMP is an original piece of research by the applicant that constitutes their best research to date. It is meant to serve as a signal of the candidate's potential for becoming a good researcher.

Bob Hall makes a number of nice points here, which I will condense and expand upon. Answers to the two questions posed by @Aleksandr Blekh after my comment are in bold below.

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  It should highlight the original contributions of the research.

  
  


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  Write "for a wide audience of highly trained economists" (replace "economists" with the appropriate noun).

  
  
  
  
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    Don't take this the wrong way, JMPs are a great place to showcase one's technical skills.

    
    
  
  
  
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    However, think very carefully about who might be on your committee.

    
    
  
  
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    Hall says to write for JPE or AER. More generally, think of the journal in your field that everybody at least skims through. Write as if you're submitting to them.

    
    
  
  
  
  


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  The JMP need not be published. (See also discussion in penultimate paragraph below.)

  
  
  
  
  
  • 
    

    If you get a flyout you will probably be asked to present the paper at what is essentially a working paper seminar. Participants will not expect that it is complete. You can always substitute out a work in progress but it is far better to have one close-to-publishable paper than one publication and a half-baked paper (this is when all of the faculty who aren't on the committee will see you).

    
    
  
  
  • 
    

    People are looking for good ideas, all of the finicky stuff that goes into a publication can be ironed out later (assuming your idea is sound!).

    
    
  
  
  
  


• 
  
  

  Hiring committees will probably only look at your JMP so that is what you should focus your efforts on.

  
  


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  Yes, do post your work to repositories where others in the profession will see it. This is probably a good way to gauge whether your paper is ready - are you willing to post it in a semi-official place like arXiv where you can't just take it down and post it back up willy-nilly?

  
  


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  For most people the JMP is their first publication. So, yes, do expect to publish the JMP in a traditional journal.

  
  

Some concluding notes about why economists bother with this JMP business in the first place (and a method to gauge how much this applies to your situation). Very few economists are coming out of grad school with publications. Ergo, hiring committees can't do the thing where they just scan down the list of previous publications and sum up the prestige (economists - of all people - would if they could). So instead candidates get one shot at wowing committees with their JMPs.

Therefore, if you can already signal to hiring committees that you're awesome (or not) in some other way (i.e. past publications), then the JMP may be something of a formality. This also motivates another reason for not using published work as a JMP: If you already published something in a good journal, the committee can easily incorporate that information into their deliberations. Using another paper gives them a second piece of information to go off of. I would also speculate that using a prior publication might be a negative signal in the sense that it suggests that the candidate is a one-hit wonder (of which there are many).

Best of luck! Let me know if anything needs to be clarified or amended.

publications - What does a "major revision" mean?

I recently received the reviews/comments for an article submitted few months back to a journal. All the reviewers overall appreciated the content and the usefulness, but also suggested corrections (varying from minor to major) : typos, better title and abstract, reorganizing the material, better exposition at certain places, adding more benchmarks; that need to be addressed before publications. All the reviewers recommended the paper for publication if the reviews were addressed satisfactorily.

The editor, looking at the reviews, mailed stating a major revision of the paper is needed before re-submitting the paper.

My question is, what does this mean, in terms of the chances that my article is accepted, when I re-submit it after making the corrections suggested by the reviewers?

In general, I would like to know what goes in the editor's mind when he suggests minor revision/ major revision etc. If an article needs major revision, will it be reviewed again? How do these translate into chances of the article being accepted?

publications - What should I do if my advisor insists on being first author, in violation of my field's conventions?

My advisor obligate me to put her name first author name in my publication. What are the possible pros and cons of this order? What should I do if my advisor insists on being first author, in violation of my field's conventions? My field is IT.

Answer

I have unfortunately seen these kinds of shenanigans before, so: know you are not alone, whatever cold comfort that may be.

This situation has no "pro," and has the following significant "con:" you are not getting the credit you deserve for your work. In fields where author lists are not ordered alphabetically, order is used to signify the author's contributions to the paper, and first-author papers are much more important for things like hiring and promotions.

I suggest the following steps.

1. Talk to your advisor

Maybe this is just a misunderstanding, or there are other variables in play you're not aware of (unlikely, but possible - see this question). Have a conversation with your advisor to see if you can clear this up.

Here's your opener:

I thought that in IT, usually the student who did most of the work is the first author and the advisor is the last - this is the case in all the papers I have read. Why do you propose a different order?

2. Run, don't walk

This behavior is typically an indication that either

• your advisor is completely unaware of conventions in your field (charitable interpretation), or


• your advisor is aware of the authorship conventions and is deliberately violating them to your disadvantage, which is extremely unethical behavior.

In either case, this means that your advisor is simply unsuitable to be an advisor, to anyone, and you should find another one as soon as humanly possible.

3. If all else fails

If you are stuck with this advisor for some reason¹, be prepared for a very bumpy ride. This is not likely to be the last stunt he/she pulls.

However, you can at least try to argue your case: there is some advice on the subject here, although that question does not specifically address the case where the advisor is demanding first authorship for him/herself.

---

¹This site is full of students who insist on staying with a completely unsuitable advisor, for one reason or another. I suspect Stockholm syndrome.

phd - Should I send reminder to a professor in a school I applied to, for an introduction email I sent two weeks ago?

I have applied to 4 PhD applications in Computer Science and I have sent an introduction email to a professor in each of the schools I have applied to. In this email I first introduced myself and then mentioned one of their papers I'm interested in, and at the end asked them for any time they can give me to meet them in person and talk to them about my future plans.

But, I just heard from one professor and the rest have not replied my email after two weeks. How could I write an email to remind them about my old email I sent them?

I googled and did not find a concise answer. Any help is appreciated.

Answer

As a busy professor myself, I personally appreciate getting a reminder email. I fully intend to reply to every email I get from a prospective student, even if only to say "Sorry, your research interests do not seem to be a good match for the work we are doing in my group." But in practice, life gets busy. I'm traveling. Or I'm booked solid with meetings and so I don't have time to immediate answer the 50 or so daily emails requiring responses. And so some emails fall through the cracks. Thus I appreciate receiving a single reminder email. Such emails help me do something I want to do: namely, be the kind of person who gives every serious inquiry the courtesy of a response. (A second reminder email is not necessary. If I haven't replied the first two times, there is likely a reason.)

As for what to write, anything short and sweet and non-accusatory should be fine. Personally, I prefer the polite fiction that perhaps I did not receive the original email. You know it's not true, I know you know it's not true, but in phrasing your note this way we agree to mutually overlook these facts. I'd suggest something very simple, such as the following.

Dear Prof. X,

I wrote you a letter a few weeks ago, but given the uncertainties of email I do not know whether you received it. Thus I am resending my note just in case.

With my best regards, Joe

[and then append the earlier letter here]

graduate admissions - What are the best question to ask a committee panel after a PhD interview?

I've a Skype interview for PhD application (it will make me miss one of my classes today.) I've been asked, in advance, to prepare a short presentation and then there would be some discussion with the panel (I guess.) I expect that they will ask if I have some questions so, I'm wondering what are the best (type of) questions one might consider?

human biology - How are our senses dimmed during sleep?

Our senses are not as sensitive during sleep compared to wake. There is an arousal threshold during sleep that only when it is overcome will it wake a person up. My question is how is this arousal threshold lowered as sleep progresses? And how it is raised again during the latter stages of sleep?

publications - How common is it for submitted papers to have minor errors?

I am going to submit a paper in these days. I dedicated to it a lot of time, and a lot of effort to check that all the theoretical results in it are correct. Anyway, I am still afraid of having written something wrong without even realizing it, as the deadline is very sharp.

So my question is: how common is in the academia to find submitted papers with minor errors? If there is a minor error that is not invalidating the results, will the paper be rejected, even if the content is considered interesting?

job - In practice, how secure is a tenured position in the US?

Coming from France, where any official academic position (i.e. associate professor or full professor, or equivalent positions at public research institutes) is a civil-servant one, and therefore automatically for life, I've been always intrigued by the "tenure" system in the US.

While reading the Wikipedia article, I spotted the following paragraph:

While tenure protects the occupant of an academic position, it does not protect against the elimination of that position. For example, a university that is under financial stress may take the drastic step of eliminating or downsizing some departments.

Does this kind of elimination/downsizing occur a lot in practice? Is it possible to "cheat" and to pretend to cut a position in order to save money just to get rid of a tenured professor? Are there some laws stating that if a position is cut, then another equivalent one cannot be created right after?

Answer

I haven't seen any statistics on how many tenure professors have been fired, but most articles on the topic treat tenure as though it's a lifetime position (e.g., this Science article, "Tenure and the Future of the University"). Anecdotally, you will likely never meet someone who knows someone else who was fired from a tenure position; it simply doesn't happen.

Note, however, that the number of tenure track positions made available over the past decade been trending downward fairly significantly (see the same article, and simply do a google search on the topic to see more).

research process - Is it possible for reviewers to mistakenly reject a quality paper?

If I am not wrong, turbo codes was submitted to the ICC conference and rejected but accepted later on.

I want to know if there are other similar works (strong works) that were rejected at first but then accepted and considered revolutionary.

Answer

Higgs's 1964 paper on the Higgs mechanism was rejected by Physics Letters (where his preliminary paper on the subject was published).

He was told that it was not suitable for rapid publication and that he should send it to another journal. However, he reportedly heard that the paper had been rejected because the editors felt that "it was of no obvious relevance to physics."

Apparently, Higgs acknowledged that the paper "had been short on sales talk," and after adding a couple of paragraphs it was accepted by Physical Review Letters.

Here is an early example of manuscript rejection, from 1842: Mayer came up with the theory of conservation of energy, and wrote an article explaining his idea that "energy is neither created nor destroyed." It was rejected by the leading physics journal of the time, ended up in an obscure chemistry journal, and was mostly ignored by physicists. When the physicists of the time rallied around Joule, who described conservation of energy later in the 1840s, Mayer suffered a mental breakdown. Towards the end of his life, he was finally given credit as a father of thermodynamics.

Nature declined to accept Krebs's paper on the "Krebs cycle" in 1937. The work later won a Nobel Prize. The letter from the editor regretfully informs Mr. Krebs that the editor already has "sufficient letters" for the next 7-8 weeks.

The seminal paper on quantum cryptography, Wiesner's “Conjugate Coding,” was rejected by the IEEE Transactions on Information Theory. (A surviving copy of the original typewritten manuscript says "Submitted to IEEE, Information Theory" on it.) It was published about a decade later.

In the same subfield, the original manuscript by Bennet, Brassard and Breidbart that introduced quantum key-recycle scheme (QKRS) was rejected several times by major CS conferences including STOC, and was never successfully published.

Ernst's work on nuclear magnetic resonance spectroscopy, which won the 1991 Nobel Prize in Chemistry, was rejected not once, but twice, by the Journal of Chemical Physics.

Binning and Rohrer's report on their first experiments in scanning tunneling microscopy, which earned them a Nobel Prize in Physics in 1986, was initially rejected on the grounds that it was "not interesting enough."

These are just a few examples. Many more have been compiled in various publications:

hematology - Does Blood Loss Shorten Telomeres?

If blood loss necessitates immediate cell division to replace lost cells, does the increase in cell division correlate to shortening of telomeres? Does it further cause the Hayflick Limit to be reached sooner? Does blood loss accelerate apoptosis?

professors - How do academics change their area of research in the middle of their academic career?

Often, I have come across profiles of tenured faculty members who are now doing research in completely different topics than what they had done in their PhD, postdoc or in the beginning of their academic career. For example, a professor in our department had done his PhD, postdoc and initial career in using molecular dynamics for nanomechanics. However, over the course of time he also added quantum mechanics (density functional theory) and continuum mechanics in his research. In other case, I have seen a faculty with an engineering-physics PhD related to thin films shift to working on 3D printing and developing aerospace materials.

My question is, how do academics change their area of research and what efforts goes into establishing oneself in a changed research area?

I have seen academics hire a PhD student to work on a new research area and learn as they guide the student. But, how can someone guide if the area of new research is very minutely related to their area of expertise.

genetics - What does min mean?

I read that

"trp operon is located at 27 min on E.coli chromosome."

What does "min" mean ?

Answer

Min means minutes. Minutes are counted for interruption points since onset of DNA transfer in F-pili-mediated conjugation. The point "0" is not associated with ori, but is close to thr. The total chromosome size is 100 min (time taken for conjugation).

See:

publications - Is it ethical to explicitly or implicitly bias against student papers unless co-authored with senior researcher(s)?

A few days ago I was browsing open-access social-science journals and I found one ‘author guideline’ explicitly saying that they are accepting student submissions if and only if the manuscript is co-authored with the academic advisor or a senior researcher.

I have acquaintances with several editors and editorial board members at various journals and I know from experience that some of us tends to be careful with manuscripts coming from PhD students. This manifests in practices that I find questionable (e.g., insisting on three unanimously positive specialist peer evaluations before acceptance, while a senior researcher’s manuscript may go with only two positives) and in other practices that I find to be biased (like an easier desk reject, or being less willing to deal with them, which results in longer peer evaluation cycles).

Is it justifiable for editors to restrict – formally or informally – the opportunities for PhD students to publish in their journals, like restricting them to submit only co-authored papers or subject their manuscript to more strict criteria than those of senior researchers before acceptance?

Answer

In my opinion, such a policy is absolutely unethical.

One of the key principles of science is that scientific work can be done by anybody. Good science can be done by people who aren't even in academia, let alone by students. A scientific paper should be evaluated on its merits, not an argument from authority based on its authors.

Now, humans being humans, reviewers will tend to bias towards known authorities and prejudice against unknowns, students, etc. But this journal's policy, rather than fighting against such a tendency, explicitly enshrines and adopts it. Likewise with the informal policies that you describe: anything that amplifies unfairness in judgement rather than de-amplifying it is highly suspect and likely scientifically unethical.

This doesn't mean that one should drop standards. Rather, it means that one should treat a paper coming from a well-known PI at an august institution with just as much suspicion as one from a student author from a developing-world university you've never heard of before. Being status-conscious primates, we're not very good at doing this, but such a condition is the goal towards which we should strive.

PS: Note that a policy the other way, i.e., student journals that don't accept papers without student authors, is not problematic because it is inverting the privilege gradient.

evolution - Why is chlorophyll green? Isn't there a more energetically favorable color?

Chlorophyll being green means it absorbs light in the red and blue area of the spectrum. Isn't this the high and low energy light? Wouldn't plants get more energy if they absorbed light in the green area of the spectrum instead of the red one?

zoology - Can the regeneration mechanism of lizards be used in humans?

Is there any mechanism or specific protein which helps lizards to regrow their tail? Can the mechanism of regeneration be used in humans to regenerate our limbs? Is there any other animal which has this kind of ability?

human biology - What are the most important factors influencing a person’s gut microbes?

You are your bacteria! The probiotics and the antibiotics...

There has been on going discussions about how our gut bacteria is important for a healthy lifestyle.

Figure 1: Schematic diagram illustrating potential or known mechanisms whereby probiotic bacteria might impact on the microbiota. These mechanisms include (1) competition for dietary ingredients as growth substrates, (2) bioconversion of, for example, sugars into fermentation products with inhibitory properties, (3) production of growth substrates, for example, EPS or vitamins, for other bacteria, (4) direct antagonism by bacteriocins, (5) competitive exclusion for binding sites, (6) improved barrier function, (7) reduction of inflammation, thus altering intestinal properties for colonization and persistence within, and (8) stimulation of innate immune response (by unknown mechanisms). IEC: epithelial cells, DC: dendritic cells, T:T-cells. For further details, see main text.

Also, an online search provides numerous articles about diet aspect that alters our gut bacteria.

e.g.

1.A New Diet Quickly Alters Gut Bacteria-(not sure about the credibility and relevance to humans as the study is on mice)

2.Artificial Sweeteners Change How Our Gut Bacteria Work, Paving The Way To Diabetes And Obesity

3.Changing gut bacteria through diet affects brain function

As far as the GIT is concerned, health, lifestyle, eating habits and the environment a person is living may be at large influence and affect one's gut microbes.

Are there day to day encounters, in-depth examples and references that can prove the factors which influence our gut microbes the most?

Answer

Our Unique Microbial Identity (Gilbert 2015) suggests that the gut microbiome is shaped and stablized during infancy and tends to restore equilibrium if it is disturbed later in life. Antibiotics temporarily change the composition of the gut microbiome (by suppressing the growth of certain groups of bacteria more than others), but it tends to drift back to resemble its original (stable) community after treatment is stopped, likely due to the interdependency of individual strains as producers/consumers of particular compounds (i.e., some bacteria will eventually arrive to serve a particular role in the microbial community). A recent study in antibiotic treatment provides some empirical evidence of the long term effects of antibiotic treatment on the human gut microbiome.

The American Gut Project is currently open to the public for participation, and it has the goal of identifying exactly the factors you describe. They are accepting samples from individuals across the country, along with lifestyle information, including dietary habits. A related publication by the group provides a summary of the common gut bacteria implicated in a variety of diseases.

H. pylori infections are a common gut microbiome health issue. This bacteria is present in about half of gut microbiomes and are not generally harmful unless the stomach lining is already compromised (e.g., due to medication or diet). In those cases, they can become opportunistic pathogens that can persist for decades and cause peptic ulcers which can lead to a variety of difficult to diagnose ailments such as arthritis.

publications - Should I include a paper with a low impact factor in my CV

I'm a Masters Student who has an old paper. I wrote a paper years ago with a research group in my old school. However, it's a really simple idea and was published in a not very reputed journal (Impact Factor 0.3). It was a long time ago, and honestly I would rather not be affiliated with it.

International Journal of Advanced Trends in Computer Science and Engineering

Should this be included in my CV?

http://www.warse.org/pdfs/2013/icetcsesp%2010.pdf

It's relevant to what I'm doing now but just not very important and I consider it a not very good use of my time

Answer

Yes, probably.

An academic CV should be a comprehensive record of your academic past. It is not like a professional resume where you include precisely the (true!) information that you think will be to your advantage. It is very likely that anyone reading your CV will assume that they are looking at the complete list of your publications. So omitting a paper because you think it will make the reader think worse of you is something that, if discovered, would be regarded as inappropriate by many. (And in many academic fields nowadays, such a discovery would be quite easy to make.) If it is a standard convention in your field to include only "selected publications" in your CV, you could do that...but of course it could make the reader curious as to what was not selected.

Let me also say that not wanting to include a publication because of the low impact factor of the journal it was published in is at least one step further along on the path to impact factor insanity than I had heretofore heard of. A paper is not good or bad because of some numerical measure of the journal it is published in. Further, not all papers are our best papers and this is so obvious that there should be no shame in it. However, if you really think that a paper is so weak that you might later regret publishing it: think harder, and if you're convinced then don't publish it.

Added: According to @ff524's comment, the impact factor may be the least of your worries. But I think my answer applies even if you're published in a "predatory" journal.

Further Added: People may be interested to know that I have a publication in a journal whose publishing company, SCIRP, is on Beall's list. I won't tell the full story of how I came to publish the paper there except to say that this is a journal in which one ostensibly has to pay to publish, I was curious what happens when one submits to this journal and is not willing to pay, and in the answer in my case is that they published the paper anyway. (Yes, this "experiment" was not well thought out nor necessarily ethical behavior on my part.) Moreover, my opinion of the journal has declined in the intervening years since I published the paper. Nevertheless I list the paper on my webpage and on my CV: on the one hand, I feel obligated to. On the other hand, despite the fact that the paper was published in a journal some of whose practices look pretty shady, the paper itself is a real (though rather modest) research contribution. In fact, from what I can tell (the subject of specialty of the journal lies outside of my core expertise) a good number of the papers published in this journal are solid. (So the journal is in some ways predatory and some ways legitimate. I find this very strange, wish I understood the situation better, and again, I wish I hadn't published there.) I would much rather have a line on my CV that shows that I made a naive, questionable choice of where to submit a paper than have a CV which is not intellectually honest.

Yet Further Added: I will record here what I found on the web concerning the question of whether an academic CV should list all publications.

1) This link from UC Berkeley's Guide to CV's as part of an academic job search says "List all the papers and presentations you have delivered or will deliver."

2) Our trusted friends at Elsevier weigh in on the subject and seem to come to the opposite conclusion:

It is advisable to list your most reputed publications in ranking of type, such as books, book chapters, peer-reviewed journal articles, non-peer-reviewed articles, articles presented as prestigious conferences, forthcoming publications, reports, patents, and so forth. Consider making an exhaustive list of all publications in an appendix.

Please direct further questions on this article to its author, "Elsevier Biggerbrains."

3) Caroline Eisner at academic coaching and writing says

When you list your publications, begin with the most recently published, or those out for review (list these in italics), and move down your list to the one published first. If there are early publications (or conferences) you are no longer proud to list, or you no longer care to publicize, leave them off the list. If you delivered a paper long ago, and it is not relevant to your current academic self, don’t include it.

4) This University of Washington guide to academic CVs writes

List your published works in reverse chronological order according to publication date. Use the reference style appropriate to your discipline. If you have multiple publications, consider dividing them by type such as articles and book chapters, or refereed and invited papers. If an article has been accepted for publication, indicate ‘in press’ or ‘forthcoming’ in lieu of the publication year. Consider bolding your name on each publication.

It seems to give the impression that all publications should be listed. (There is also the implication that there will not be so many.)

5) The University of Kent counsels structuring the CV so that the most relevant publications are highlighted, but the implication is that all should be included.

graduate school - Faculty or industry applications without phd advisor's letter

How is an application for an academic position seen if there is no reference letter from the graduate advisor? Are any of the potential issues for academic positions the same for industry positions? Do industry positions request letters of reference from phd advisors? I'm concerned I will not get a glowing letter from my phd advisor. Is a mediocre letter better than no letter?

How can I tell whether a mathematics journal seems reputable?

There are some general questions on this site about judging the reputability of journals in general:

I am interested in answers specific to mathematics, that may not have been raised in the other questions.

I received the following email from the "American Journal of Pure and Applied Mathematics" ten days after submitting a paper online. How can I tell whether this is a reputable journal? In general, how can I tell whether a mathematics journal is reputable?

Dear Authors,

On behalf of the Chief Editor of the “American Journal of Pure and Applied Mathematics” we are happy to inform you that your article entitled ‘A possible approach proof to proof the Riemann Hypothesis” is accepted for publication in (Jan-June 2015).

Please send DD/Cheque for US $ 250.00 payable to ‘ Vijay Kumar Jha ‘ to our address.

Our address: Vijay Kumar Jha Managing Editor c\o. ACADEMIC RESEARCH JOURNALS (INDIA)

4383/4A, Ansari Road, Darya Ganj, New Delhi-110002

(M) 08826561892

We thank you very much for your contribution and encourage you to continue submitting your future.

Yours sincerely,

Answer

For academic mathematicians, it's not so hard to avoid predatory journals. We have a sense of the journals that we "typically" publish in, and the journals we "aspire" to publish in, and we stick mostly to these journals. For journals we don't know yet, we can ask colleagues to get their opinion. One (possibly unfortunate) goal of publishing in academia is to build a vita and maintain/advance your career, and it doesn't help as much to publish in a journal that none of your colleagues or supervisors has heard about.

For people who don't have that kind of professional experience, there are several easier questions you can ask. The better answer to each of these is "Yes". On their own, none of these questions indicates that a journal is necessarily reputable or nonreputable. But, if the journal gets a "No" answer to many of them, then I would be very hesitant to submit a paper.

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  Does the journal publish with no cost to the author? Reputable mathematics journals almost never charge fees for publication. Some very good journals offer an open-access model as an option, but it is almost never the default at the moment.

  
  


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  Is the journal indexed by MathSciNet and/or Zentralblatt MATH? These sites aim to be very comprehensive for mathematics journals. Being indexed is not really a sign of quality, but not being indexed is a red flag.

  
  


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  Is the journal ranked on the Australian Mathematical Society Ranking? Even C-rated journals can be OK, but if a journal is completely omitted I would take that as a reason to be cautious.

  
  



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  Is the journal either published by a well-known publisher, or affiliated with a university or mathematical society? Most reputable math journals fall into these categories, but not all. Some journals run by professional publishers are still not very reputable, of course.

  
  


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  Does the journal have a professional looking website? Grammatical errors or parts of the website that seem to be entirely missing are a cause for concern.

  
  


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  Does the journal have a long history of publication (say, at least 20 years)? Most predatory journals are very young; most math journals are relatively old.

  
  

The "American Journal of Pure and Applied Mathematics" has a "No" answer to all of these questions. If they really did have a 10-day turn around between receiving a paper and accepting it, as described in comments, I am even more skeptical of the quality of the journal - that is an almost absurdly fast turn around time for a mathematics journal. I would not pay them anything to publish a paper of mine, nor would I recommend it to anyone else.

Of course, you can publish in a predatory journal, just as you can publish in a for-hire press. But if you are an amateur or "outsider" looking to publish in a math journal, you are likely doing it to get a sort of "seal of approval" on your paper. Journals that mathematicians view as unreputable will not give your paper that kind of recognition among mathematicians, just as degrees from unreputable colleges are unlikely to impress others.

If your goal is just to disseminate your mathematical work, and you don't require peer review, you can often use arXiv.org instead. Depending on the area, you may need to have a professional "sponsor", but the arXiv will keep your paper available for free for the indefinite future in a way that is widely accessible to the public.

grading - A student forgot to answer an exam question

A student in an undergrad class seems to have forgotten to answer the last few questions on a written essay.

This student has achieved an average of A+ so far (over the term)

The last few questions are not worth much, but is the difference between receiving an A and an A+

This student has also submitted a draft of this essay earlier in the term to get feedback (all students are allowed to do this once).

Should I give 0 because this student did not answer it, or part marks because this student knows how to answer it (as evidenced by the draft) but simply forgot?

publishability - Can I still try to publish my work if my algorithm's results are not as good as other algorithms'?

I've written a classification algorithm that does a pretty good job at classifying some datasets. However, I compared my algorithm to other classification methods, and their results exceed my results by a little. For instance, when classifying a dataset from a repository, my algorithm is getting 95% correct while another algorithm usually gets 99% correct.

Should I continue to publish my results although 1) my algorithm is a little slower, and 2) my algorithm's results are not as good as the other results.

I'm a little torn. I'm excited as my paper and results are a contribution to the classification field as the algorithm is novel. Also, I'm of the stance that you can't beat EVERY algorithm. If we only published algorithms that could (loosely) beat other algorithms either A.) we'd never have new innovations, or B.) eventually every dataset would be 100% classified each time, or C.) every algorithm could instantaneously classify a dataset (speed).

I hope that my algorithm will continue to grow and others will pick it up and extend it. I hope that one day -- with tweaks -- my algorithm can reach 99% too.

I'm afraid of being rejected by the journal again. Yes, my first submission was rejected. One of the reasons for the rejection was that my dataset was small. However, when the dataset was small I was beating the other algorithms. Now, as the dataset has grown, the other algorithms are now beating me. I'd like not to be rejected again.

phd - Is it true that a full Ph.D. is a disadvantage for technical positions in the private sector?

If you do work that requires a technical skillset (ex. programming, data science) and plan to work in the private sector. Is completing the Ph.D. degree a disadvantage in terms of what opportunities are available to you? Or, do the additional publications, work completed, and everything else that goes into a dissertation count as valuable experience? Is the degree viewed as valuable in and of itself? Additionally, is any increase in pay or job stability enough to offset the opportunity cost of making a graduate student stipend for 2-3 years?

I've wound up in a situation where I'll probably be financially unable to take a postdoc position upon graduation, and will likely be forced into the private sector anyway (which functionally closes me off from an academic career-track), so am considering the option of leaving my program after advancing to candidacy.

Answer

As someone with a PhD who did a regular postdoc and now works in the private sector, the answer is definitely probably not...maybe. As with all things, it depends on the job and your field.

I have a PhD in Computer Science. I did research for a couple of years as a postdoc. I enjoyed my postdoc, but a great offer came along for a private sector job. In my field (high performance computing), having a PhD is valuable whether you're in research or industry. In fact, we hire fresh PhDs as well as folks with experience.

That being said, if you were to go to a startup in NYC or Silicon Valley with a PhD in CS, I'd imagine that while you would probably have as much chance of getting the job as anyone else, you probably won't be getting what you might call "reimbursed" for your opportunity costs. The big companies will have research arms where they know what to do with PhDs while the small ones won't.

It all depends on what you want to do. If you want to get into research (or get back into it eventually), having a PhD will be a must, even if you take a few years in industry to shore up financially. However, if you don't get your PhD now, the chances of you finishing it later much smaller. There are plenty of people who do it, but if you look around your group right now, you can probably tell me how many you see.

The exception is getting a job where your employer will essentially pay for your PhD (not like an RA position where you make beans). There are some companies or research labs that will allow you to work on your PhD while you work for them, often using a project with your company as a part of your thesis if your interests align with those of your employers. You might be able to find a position like that.

ethics - Is it reasonable to report another student for cheating when it has no impact on me?

I currently am studying on an Undergraduate Maths course, in my third year. At my university there are various modules from which students can pick to make up the required number of credits for the year.

5/6 of my circle of friends take a particular (popular) module which I do not. Recently, they had a piece of coursework due for submission. They had about two weeks to do it, and the submission deadline has now passed.

One of the students, with whom I am friends, has informed me that she took pictures of her answers and gave them to another student (with whom I am not friends) three hours before the deadline, because that student had done little/no work and was going to fail. This was not a group piece of coursework, and she essentially gave the other student her answers.

I'm not entirely sure why I'm so upset about this, considering I don't take that module and it has nothing to do with me. I have my personal opinions about the student, but I feel like that shouldn't be relevant to the situation.

I do want to report this as cheating, but I'm also well aware that it's effectively hearsay. None of the others of my friends (who do take the module and who are also aware of this incident happening) has reported it.

I'm wondering whether it may even be out of line for me to report this incident, given that I have absolutely no evidence in my possession of what happened, and I do not take the module, and I wasn't involved in any way.

Is it appropriate in these circumstances to report what I've heard to the lecturer of the module?

Answer

As others have already mentioned, cheating is wrong and it's the right thing to speak up when someone commits a wrong. It may also indirectly affect you when someone cheats (eg. through grade inflation).

However, by reporting the cheater you are also implicating your friend who passed on the photos and facilitated the cheating. Your friend might feel upset (and perhaps rightly so) that you didn't put your friendship above some general (and perhaps minor) moral obligation. I caution that your obligation to report is not unconditional in the sense that you have to accept a disadvantage for yourself, such as a spoiled friendship. Moreover, I would argue that you also have an obligation of loyalty towards your friend; whether or not that 'trumps' your obligation to report depends on how close your relationship is.

How do some Ws on transcripts affect PhD admissions in mathematics?

I am a senior who is graduating in December with a Bachelor's Degree in Pure math. I would really love to apply to the PhD program. However, I have been really depressed because even though I have a good GPA (3.85), and I have gotten mostly A's in all of my math classes (I have taken math classes up to Topology, measure theory, and Algebra), I feel like this is not good enough since I have 8 W's [withdrawals--no grade given] on my transcript. The horrible part is that 6 of these W's are on math courses. All those W's occurred during my first year at my university. The second year up to now I haven't gotten any W's.

My question is: How horrible (by the Committee who selects candidates for the program) is a W seen on a transcript? Is there anything I can do about it?

I feel like I have a big hole on my transcript, and it has been chasing me throughout my undergrad years even though I managed to hide myself from this monster and continued to take a lot of math courses, earning A's (and two B's) in all of them.

Answer

Your situation doesn't sound so bad to me at all.

First of all, though perhaps I shouldn't, I will admit that many graduate admissions personnel do not thoroughly scour the transcripts. They look at the GPA and they look at the courses taken. Often this information is given separately on the application, so a look at the actual transcript may only be required if there is something missing there. So there's a tip for you: if you are asked for separate information about courses taken, definitely be sure to list it. (If on the other hand you are asked to list the courses taken together with the grades you got, it seems to me that you are ethically obligated to list the W's.)

More than this though, W's occupy a sort of nether region in academic grading. In my university we have WP (withdrew passing) and WF (withdrew failing). Only the latter affects your grade, and my understanding is that WP is not meant to be a stigmatic mark at all. (In fact undergraduate students are limited to 4 WP's over the course of their careers.) Unless the registrar puts an asterisk next to your 3.85 GPA and says warning: there were some W's! then in at least one very official sense the W's are not being counted.

More good news: all of the W's are in your first year. That is exactly the sort of localized difficulty followed by dramatic improvement that admissions committees are looking for.

I think it would be a good idea to use your personal statement to briefly address the W's. I'm thinking of one or two sentences which acknowledge that they exist, say a few vague words of excuse (e.g. "time to adjust to a new academic environment", "personal difficulties long since resolved"; nothing too specific or gory), and especially: point out how nicely you've moved on. If you feel like you can use the W's as part of a larger depiction of a crescendo of academic accomplishment, you might try that, but that's a more "advanced technique", so to speak.

I think it is quite likely that the average effect this will have on your application is little or none. Honestly, to me you sound significantly more guilty / apprehensive about a minor issue long since resolved than you need to be. I forgive you! Please don't hesitate to apply to all the PhD programs you're interested in. (If you like algebra/number theory/geometry/topology, please consider UGA.)

When applying to a Phd in Physics or Math , do grades in unrelated courses I took have any effect on my admission?

I'm currently studying (Undergraduate) Physics in a University where, regardless of their department, every student must take some English, Turkish and History courses, which I don't want to attend. Turkish and History courses are non-credit but not English, so it affects my GPA. Moreover, I will take violin, astrophysics and philosophy courses as non-included.

So here is my question: when I am applying for a PhD in Physics or Mathematics, does any of these courses have any effect on my admission?

Note: My main concern is whether having low grades in English ,which is not a non-credit course, affect my Phd admission ?

Answer

If you are applying to programs in the US, more important than your grades in English classes is your performance on the TOEFL. Many universities have a minimum TOEFL score required before the department can even consider your application, and these rules are often difficult or impossible for the department to bend, even for an exceptionally attractive candidate.

There is more information in the answers to this question. (For example, someone there mentions that the minimums at "Yale and Stanford are about 100, Harvard is 109" -- out of 120 points total.)

Given the quality of the English in your original question (before it was improved by helpful editors), I don't think you can afford to blow off your English classes if you have any hope of studying in the US.