journals - Is the status of conference publications in Computer Science really absolutely unique?

It has been discussed and explained many times that in (at least some subdisciplines of) Computer Science, conference publications have a special status compared to many other fields - where in other fields, journals are the only way of publication, in Computer Science, many conferences allow publications with a comparable peer-review process as a journal, and consequently, reputable conferences in some subfields have a similar standing as reputable journals.

Some exemplary resources that outline this peculiarity:

While the perception of a special treatment of conferences in Computer Science appears to be evident, there are sometimes hints this can actually be observed in a few other fields, as well:

Daniel Standage writes in his question:

(...) whereas some of the more quantitative and technical fields (comp sci and engineering especially) seem to be focused on getting accepted to high-profile conferences with low acceptance rate (...)

Fomite responds:

(...) CS and related fields very heavily weight conference presentations and proceedings papers (...)

badroit cites from the Department of Computer Science & Engineering, University of Minnesota: Criteria for Promotion and Tenure:

A 1994 NRC Committee on Academic Careers for Experimental Computer Science stated “The requirements for good research and engineering in experimental computer science and engineering (ECSE) are different from those of many other academic disciplines” and then added “Because conferences are the vehicle of choice in ECSE for the dissemination of research, well-refereed conference proceedings (as well as work published in refereed private journals) should be given as much weight as archival journal articles

On the other hand, there is also the contrary claim, that Computer Science is an absolute exception with this. For instance, aeismail remarks in one of his answers:

(...) I would argue that the weighting of conference papers seems to be restricted to computer science (...)

Likewise, Lance Fortnow starts his article Viewpoint: Time for computer science to grow up by stating:

Unlike every other academic field, computer science uses conferences rather than journals as the main publication venue.

As it is notable that a rather unspecific "engineering" is consistently mentioned in the examples that imply a few other fields use conferences the same way as CS, I have tried to track down those fields, but could not come to any useful conclusions. In particular, I am not even sure what to look for, because "engineering" might mean various things:

• It might mean all of engineering, which I find improbable (that would probably mean peer-reviewed conference publications are not as unheard of in other fields as some CS people suggest).


• It might mean a few subfields in engineering. To find more information, knowing which subfields those are would probably be helpful.


• It might actually be a pleonasm for computer science, in a way that a department for "engineering and computer science" wants to highlight it does not only deal with theoretical aspects, but also investigates "technical", "practical" sides of computer science.

Thus, my question is: Are there any other fields beside Computer Science that use peer-reviewed conferences for publication, where such conference publications have a similar standing as journal publications? If so, what are some examples of such other fields?

Note: I consider this an answerable question, not an indefinite list question. One or a few verifiable examples for other fields that use conferences as described - or a sufficiently convincing statement or reference that shows there are no such other fields at all - are completely sufficient, I am not looking for an exhaustive list of fields.

phd - What kind of questions can I expect to see on a qualifying exam?

In mathematics, there are certain open questions which are the subject of current research (think of the newest papers in the top journals). I have also heard that some graduate programs ask questions such as these on their qualifying exam. How common is this practice? What kinds of questions can I expect to see on a qualifying exam? I know that a qualifying exam typically tests the knowledge gained in graduate school, but I'm not sure to what extent this knowledge is tested? How "advanced" should I expect these questions to be?

Answer

I think you shouldn't believe everything you hear. Mathematicians like to tell stories about posing various famous open problems to certain brilliant young students, the idea being that these students don't have the respect and fear for these problems that an adult mathematician would and that maybe, just maybe, they will innocently work on them and even solve them. And it seems to be true that every once in a great while a student solves a serious open problem this way. The vast majority of the time they don't, of course: a problem that the experts in the field want to solve but can't is not going to be accessible to a young student, however brilliant, 99.99% of the time.

So maybe every once in a while a faculty member decides to put a "ringer" problem on an exam. What do you think is going to happen? With probability very close to one, no one will solve the problem, and the writer will have to own up to the fact that the question was not an appropriate one and make sure the students were not in any way penalized by its appearance on the exam. How many times have I seen this happen on exams I have taken, written, or otherwise encountered? Zero.

In fact qualifying exams test a standard syllabus; they certainly do not test research level mathematics. Every department does their exams at least a little differently (a very few departments, like Princeton, don't even have written qualifying exams!) so I don't think there's much point in preparing / worrying about quals until you enroll in a specific graduate program.

Conversely, when you arrive in a graduate program, you should start asking for information about the qualifying exams. And you'll get it: most programs have posted syllabi for quals. Many programs, including those I've personally been involved with, have years and years of old quals for you to page through. Nowadays a lot of these are freely available online: in fact, please see Ohio State's webpage: not only do they do they have posted all of their own qualifying exams going back at least ten years, they helpfully post links to qualifying exams at almost 20 different departments.

Thus the way to study for and pass quals is to go through old quals learning the material and techniques that come up again and again until you can do most of the problems on a given qual in a reasonable amount of time. It's not really any more mysterious or romantic than that...

writing style - How to thank a teacher in a thesis?

Given that a student wants to thank you her teacher for her assistance to her project thesis, is it polite if she writes any of this at the end of her thesis:

1. Thanks to your assistance, my project was done under your supervision.


2. You have been my project's tutor. Now it is done successfully, thank you.

Answer

Well, what I wrote was partly humor, partly serious:

"I would like to thank: Prof. [my adviser] for his advice and support throughout the thesis work, Prof. [] for his patience as I mis-implemented his design, [] for his assistance in selecting components, the [lab and department] for computer time, [], whose Masters thesis provided the format I have adopted, the manufacturers of [caffeinated beverages] for their stimulating ideas, E. Gary Gygax for giving me something to kill, and the States of Alaska and Confusion."

I think you're overthinking this. Any polite statement crediting those who have made a significant contribution to the project will be fine.

Suggestion: see if your school maintains copies of past theses in their library, read through a few to see what other people have done, and adopt what seems useful from those.

graduate admissions - Why do potential supervisors not reply to my emails?

I have contacted so far 5 supervisors for my master program that I want to enroll in ( applications open late September and admission January 2017) .

I emailed various faculty in the most polite way possible. Introduced myself, showed that I am interested in pursuing a research career in their field, talked briefly about my achievements but only one supervisor replied. I am not sure why is this happening ? I have attached my transcript ( I am not a high GPA student but I received excellent grades for my thesis and seminar courses).

• I emailed them this week ( and one hardcore researcher last Friday)

what could be the reason ? note : I am intending to apply for the biomedical engineering program (one I really want to pursue) , most students have engineering undergrad however , I have a biotechnology degree. Could that be the reason? the department said my biotechnology degree is acceptable for that admission purposes.

job - Is it peculiar for a department not to have any of its own PhD graduates as professors?

I have been doing research into graduate programs and have noticed that some departments have a representation of their own PhD graduates as professors while others have an absence.

For example, a department I have looked at in a top university in Canada had a faculty completely composed of PhD graduates from top American schools, but none from its own.

I can see this as a signal of either two things -

1. That the department may not want to be seen favouring its own candidates.


2. That the department may not have as much faith in its own graduates as that from other schools.

I understand that this may differ from field to field.

But in general, what is the majority view-point on a department that has no representation of its own graduates on its faculty?

Answer

It's common in computer science for a university to have few if any of its own graduates as faculty, and should not be taken as a bad sign by itself. This low representation is for two main reasons:

1. 
   

   The best five or ten universities in the United States produce a disproportionately large number of strong academic candidates. In practice universities that have research departments at all (let alone the exceptionally strong ones) tend to be filled with professors with Ph.D.s from the elite few.

   
   


2. 
   

   Going somewhere else leads to cross-fertilization of academic thought. Presumably after 5+ years of graduate school one has spent a lot of time learning from the expertise available in their department. Going somewhere else allows a professor to transfer her knowledge to a different group of researchers, and to get fresh insight from them in return.

   
   

publications - Is Academia.edu useful?

I received a mail today from Academia.edu (a site I wasn't previously aware of), asking me to confirm that I co-authored a paper with a colleague.

Having looked into it a little it sounds like it might be a useful site - the idea of a "social network for scientists" is one I've seen the need for in the past. However, partly due to bad experiences with the seemingly similar ResearchGate, I'm also skeptical.* Without signing up for an academia.edu account the site doesn't offer much information, so I would like the following information:

1. 
   

   What specific features does academia.edu offer to its users?

   
   


2. 
   

   Is it genuinely useful for any of the following purposes (each of which seems genuinely needed)

   
   
   
   
   1. as a platform for networking with academics
   
   
   
   2. for discovering relevant research
   
   
   3. as an effective system for post-publication peer review
   
   
   4. for organising references among a small team of people working on a project
   
   
   
   


3. 
   

   Will it send out mails to my colleagues without my express and explicit permission? (I.e. are the mails I received today the result of a deliberate action by my colleague, who is aware that I will be emailed and wishes me to join the site; or are they essentially spam from a social networking site aggressively trying to expand its user base?)

   
   


4. 
   

   It's clear from its Wikipedia page that it's a private, venture-capital funded company. What is its business model?

   
   
   

In short, is this a site that has some genuine utility for academics, or should I just ignore it?

_{*I've never signed up for ResearchGate but I regularly receive spam from it purporting to be from my colleagues, who aren't aware that it's being sent on their behalf. I would be mortified if my senior colleagues received such mails claiming to be from me, so I won't touch it with a barge pole.}

Answer

I distrust it for an entirely different reason. I once wanted to download a paper, and could only do it if I signed up. I signed up by logging on with my facebook account... Well, academia.edu took my profile information, and, without me knowing it, created an academia profile. With my picture, publications it could find via search engines, and a list of interests that were half right and half ridiculous. I'm a neuroscientist; it listed me as being interested in marketing, among other things. I only discovered this profile about a month later.

Apart from it being entirely unprofessional, I simply do not trust information that is on there, as I have first-hand experience that information on me was wrong.

publications - Will I be regarded as academic dishonest if I submit one paper to a conference as well as a journal?

I finished and submitted one paper (journal version) several months ago. My mentor suggested to me to submit a shortened version of the original paper to a conference. The conference version is almost the same as the journal version, except that some detailed mathematical proofs are omitted. But we cross-cited these two papers and told the reviewers of the conference paper that the journal version was under review.

Now both the journal and the conference have accepted my paper. I wonder whether there will be any problem if I choose to publish these two papers in a journal and a conference at the same time.

Furthermore, now I am applying for a PhD degree. If I list these two papers on my resume, will I be regarded as academic dishonest and be rejected?

Answer

Publishing a shorter conference version and a longer journal version of the same article is common practice in at least one discipline I am familiar with (computer science) and maybe in others. So that by itself is not an offense. Keep in mind that conference and journal publications are philosophically different and serve somewhat different purposes:

• Publishing in a conference proceedings is a quick way to get your research published. And of course you also get to attend the conference and speak about your work to people working in your area. Hence in rapidly moving fields this is the standard venue for publishing exciting new research. However, proceedings papers have strict length limitations so one cannot include as many details as in a journal article. And most importantly, the review process for conference publications is faster and usually not as strict as for journal articles. Many people consider conference publications not to be proper peer-reviewed publications, and when citing a result from such a publication one must be aware of a very real possibility that the result has not undergone the fullest scrutiny as to its correctness and may be wrong. (Of course this possibility also exists in journal publications, but to a lesser extent.)


• Publishing in a journal takes a lot longer for the review and publication process, but there are fewer or no space limitations, and the review is a proper peer review that (ideally, though not always in practice) provides strict assurance that the results of your paper have been checked and are correct (or use proper scientific methodology and are likely to be replicable, in experimental sciences).

Because of these differences, in a field like CS one common practice is to submit a short and quick version of your paper to a conference to get the ideas out in front of their intended audience as quickly as possible, and then to follow up later with a longer, more detailed, version of the results, and to submit that to a journal for strict peer-review certification and the accompanying credibility and prestige.

With regards to your question, I think there are two potential pitfalls you need to beware of in your specific situation:

1. 
   

   It sounds like the journal editors are unaware that you concurrently submitted a short version of the paper to a conference. Since you made the conference submission after the journal submission (which is the opposite of the usual order of doing things, as someone else pointed out), there is a possibility that you are violating the journal's submission policy. I suggest making very sure that that is not the case, and if in doubt contacting the journal editors to inform them of what you did and ask if it's okay. There is nothing shameful or dishonorable about making such an inquiry - you are trying to do the right so it makes perfect sense to ask such questions.

   
   



2. 
   

   Even if you verify that with both submissions you did everything by the book and did not break any rules, NEVER claim or make a representation in your CV or publication list that the two versions are different publications. That in my opinion would expose you to serious criticism of dishonesty and resume-padding. Benoit Kloeckner's answer gives a good explanation of the proper way to cite the two versions by including both in the same entry in your publication list.

   
   

The bottom line is that in some areas it is acceptable to publish two versions of the same article, one in a journal and one in a conference proceedings. I should add that in my opinion doing so is also of questionable value, unless you are in a discipline where this is the standard practice for publishing for the reasons I listed above. You will not get, and should not try to get, double credit for publishing the same material twice.

publications - Should a PhD student be credited in supervisor’s article that is based on a book chapter by both?

Jane is doing a PhD and is supervised by Professor Mary. Mary asked Jane to put together a review article for a book based on a draft chapter from Jane’s thesis with additional suggestions from Mary. The book article was submitted with the authors listed as Jane and Mary (corresponding author). I am unsure whether this has actually been published, though it was submitted well before the now-published review by Mary.

Sometime later, Mary submitted a broader review article online which used large chunks of text and figures from the book article which were directly written/generated by Jane. Whole paragraphs were copied verbatim from the first article to Mary’s article, and many more paragraphs were slightly rewritten but contained exactly the same references and phrases from the first article. Mary’s paper did not cite the book review. Mary was listed as the sole author. Jane was not informed this review was being written, and was not asked for permission to include her figures or content from the book article, which were originally written by her for her thesis.

1. 
   

   Did Jane ‘hand over’ the rights to her written material to Mary by agreeing to submit the book article under both of their names?

   
   


2. 
   

   Should Mary have credited Jane in the article as a second author because she used exact sentences from the book article which were written by Jane?

   
   


3. 
   
   

   Will Jane still be able to use these (her) phrases and figures in her thesis despite not being credited on Mary’s online article?

   
   

professors - Why are recommendation letters highly relied upon?

For any kind of academic application (from graduate admission to professor position), recommendation letters have a major impact on the outcome. The basic idea is understandable: discovering what others think about the applicant. It can help the review committee to decide about the applicant.

However, recommendations letters cannot be statistically reliable. For instance, when all recommendation letters of an application are highly positive, this cannot guarantee that all colleagues think highly of the applicant. Instead, it can be the result of only a few friendships.

In a typical example, if someone has three socially close friends (including current colleagues, coworkers, past professors), then, his applications are always supported by strong recommendation letters. For example, one could have conflict with his entire university, but having close social connection with three persons who can recommend him.

So, why are recommendation letters relied upon so highly, given these limitations?

UPDATE: I do not mean friendly recommendation letters. I mean influence of friendship on a professional recommendation letter. As an another example, Applicant A who has good relationship with 20 professors of his department is an ideal academic with professional relationships at workplace. BUT applicant B who has serious conflicts with most of his colleagues (professors of his department), but having only three friends among his department professors will get better recommendation letters. Those three professors will write recommendation letters based on the applicant strengths by ignoring his weakness in the light of their friendship.

Answer

In a typical example, if someone has three socially close friends (including current colleagues, coworkers, past professors), then, his applications are always supported by strong recommendation letters.

No, that's not what "strong recommendation letter" means.

First, strong recommendation letters do not simply state the author's high personal regard for the student, but provide specific, personal, and credible detail supporting the applicant's potential for excellence. I don't just want to know that someone thinks you'll succeed—I assume they wouldn't write you a letter if they thought otherwise. I want to know why. I want compelling evidence, not mere opinion.

Second, recommendation letters have more weight if they come from credible sources. At a minimum, the author should work at a credible academic institution. The best letter writers are themselves experienced, visible, active researchers, with documented experience mentoring and/or selecting candidates for admission/hiring/promotion at departments similar to the candidate's target. For faculty promotion in my department, letters are essentially required to be from full professors, preferably in named/endowed positions, in top-10 computer science departments, and there is a strong preference for ACM/IEEE Fellows, NAE or NAS members, and major award winners (Turing, Gödel, Dijkstra, Gordon Bell, etc.).

The intersection of these two aspects of strong letters is direct comparisons with the applicant's peers. An ideal PhD recommendation letter for my department includes sentences like "Among the 13 undergraduates I have mentored who went on to top-10 PhD programs in computer science, I would rank [applicant] roughly 3rd, well below [famous person who proved P=NP], but on par with [successful person] at MIT, [successful person] at Stanford, and [successful person] at CMU."

What can the timing of human urination tell about the human's physical condition and circadian rhythms?

I've noticed a peculiar phenomenon. A subject drinks 400 ml of water, then observes time until the urge to urinate is felt. The time is 15 minutes. The subject releases water. 14 minutes later another urge to urinate is felt. The subject releases water again.

I'm particularly interested in what kinds of biological systems are involved in timing of such events. Does the time depend on how full the subject's stomach is? Does caffeine and other diuretics play a part? Is it time of day (circadian rhythm) sensitive? Does that predict anything about the suppression/release of diuretic hormones?

What I'm trying to understand is if the timing between human urges to urinate after water consumption can be used to make predictions about the human biological clock and the state of various systems within the body (for example the digestive system).

I will be conducting this experiment at different times of the day. My hypothesis is that at night, when diuretic hormones are suppressed, the timing would be longer for the same amount of water consumed. This is based on my limited research in the area. Update: I did perform the same experiment at night, the time was 75 minutes for the same amount of water. The experiment was performed at the end of one of sleep cycles, which makes me think that 75 minutes was the duration of the subsequent sleep cycle.

I appreciate your input on the subject, along with any keywords that can help me advance my research in this area. Thank you!

Answer

The fact that urine output (enuresis) and other kidney functions are circadian is well known, just search on pubmed 'circadian urine kidney'. This can be due both to the fact that liquid consumption is less during the night and to the fact that hormones regulating kidney function like aldosterone and plasma angiotensin II are circadian.

graduate admissions - Can I get into PhD in Physics with a high GRE score and an unrelated masters degree?

I recently completed my MBA and have worked in the IT field for the last 7 years. I have an undergraduate degree in mathematics, and have completed 3 physics graduate courses (mechanics, E&M, QM) as an open university student. Is it realistic for me to self study for the physics GRE, get a great score, and then have a chance to be admitted to a physics PhD program?

The physics graduate courses I took were from a master’s school, but I had to pay for these out of my pocket. I though about continuing in that masters program but it is just too expensive given my situation (I have a family and a mortgage).

I want to know if I have a shot at a PhD program without going for the masters and only with a great physics GRE score and a mathematics undergraduate degree.

species identification - What is this strange mantis-like coral reef dwelling creature?

On the first episode of BBC's Blue Planet II they visited a coral reef and showed some odd reef-dwelling creatures as part of their establishing shots, but did not name the creatures.

In particular creature that resembles a mantis:

I tried a Google reverse image search and it very 'helpfully' identified it as "Documentary film". So close, yet so far.

Answer

The specimen is indeed a mantis shrimp (to be specific, a peacock mantis shrimp).

These predators have highly sophisticated vision and, depending on the species, either spearlike limbs or clubs that move so fast the water can't keep up, causing dangerous cavitational effects that can even break glass.

graduate admissions - Where to find grad school acceptance rates?

I've been searching (without luck) for the kind of information that was very easy to find when I was applying to undergrad; namely, information such as acceptance rates and median GRE scores of accepted applicants. I'm planning on applying to pure math grad school. Is there some online resource for finding this information?

Update: I found one resource for this information, but I'm not sure how accurate it is. After clicking on the colleges it had acceptance rates for most of them; search filters are on the left. http://www.petersons.com/graduate-schools/SearchResults.aspx?id=MTRkODRkYWEtODEwZC00OWU3LTk3NDUtYjliNDdhZTYxZDk5

Answer

This may not directly answers you question but I found it useful when applied to grad schools in the past. GradCafe results shows different applications results for institutes. Applicants usually put their GRE scores and GPA along with the decision.

Most importantly, some applicants communicate with their school and write something really useful as a note (like # of application received/accepted/rejected).

genetics - How to find suitable qRTPCR reference gene for a inflammatory response experiment?

I have tried several housekeeping genes – Hprt, β-actin and GAPDH, to analyze the relative expression of a cytokine for measuring the inflammatory local response in mice ears. However, all these housekeeping genes show significant variation in both within and between different experimental conditions.

I really don't know how to solve this. I take the same amount of RNA (quantified by nanodrop) to make cDNA so I guess I have the same concentration in all the samples.

Any suggestion of what can happens and how to solve it? Could I use something different to measure the relative quantification? (My cytokine of interest is TNF).

conference - How does the acceptance rate affect papers decisions?

Some conferences do maintain a percentage for the number of accepted papers to the total number of submissions.
Does this mean some good papers will be inevitably rejected just to maintain the acceptance rate? How conference chairs deal with the acceptance rate? or it is not related at all to the acceptance/rejection process.

Answer

Yes.

But it would be more accurate to say that conferences have a fixed budget of papers that they can accept, due to scheduling constraints.

At most computer science conferences, every accepted paper is presented in a 20-minute talk; for a three-day conference with no parallel sessions, this practice imposes an upper bound of about 50 accepted papers. Of course larger conferences have parallel sessions, but program committees generally do not have complete freedom to add another parallel track, partly because of space constraints at the conference venue (which is planned long before the submission deadline), and partly because major changes to the conference organization usually require input from the community.

So inevitably, if a conference attracts a large number of strong submissions, it must reject some of them. This is generally considered better than the alternative, which is that the conference must necessarily accept some bad papers.

This answer is specific to computer science.

phd - Etiquette for an initial meeting with a prospective advisor: What is expected of the student?

Assuming that one has begun a PhD program at a university which allows a student to choose an advisor after his/her first year in the program and the student has narrowed down on a couple of potential advisors and has taken AT LEAST one course with each of his potential advisors:

What should the student take to the first meet? A rough research idea, summary of the professor's important papers or otherwise?

Note: I have made 5 separate questions as suggested (As opposed to the single one which I started off with)

Answer

For an initial meeting, I would take an general idea of the kinds of things you'd like to do in a particular advisor's group, a sense of what the advisor works on—you don't necessarily have to have read papers in advance, and an open mind. That said, you'll make a better impression if you have read a few recent papers, and have a few intelligent questions to ask. It will pique the advisor's interest, and show your sincerity.

As for coming in with ideas for a research project, this depends a lot on how the project will be funded. If you have your own fellowship and can design your own project, then you should definitely have an idea or two ready. On the other hand, if you will be funded by an existing research grant within the group, your choice of projects will be more constrained.

One final note—I would say that it's definitely not required that you take a course with an advisor before considering them as a research advisor. If that were the case, I would have been on a completely different career path than the one I'm on now, as I'd be working for my fourth-choice advisor (who was the only one I took a class with before choosing a research group!).

How does water move throughout plants?

I haven't yet found a decent explanation for how water moves throughout plants. It does seem to travel more efficiently upward than out or down. Why is that? How does it travel through the plant?

Answer

Most water moves up through the xylem by capillary action. Imagine dipping a pipette into a small pool of water; the water would rush up into the pipette. Or, imagine dipping the edge of a paper towel in water. The water "runs" up the paper towel. This is capillary action.

As water evaporates out of the leaves and such in higher regions of the plant, a capillary force pulls up more water. If for instance, you were to dry the top of your saturated paper towel, more water would be pulled up from the pool below to wet that top section.

As for a molecular explanation, Wikipedia has a good explanation of Cohesion-tension theory.

united states - Is consent required to record audio of a conference talk in the US?

Do I need a consent to record audio of a presentation at a scientific conference in USA (provided that the conference does not explicitly prohibit such recording)? I'm guessing since it is not a private conversation, it's okay to record it.

This question is out of curiosity. I do not actually have clear intentions of recording talks.

Answer

I don't know the relevant laws, which may vary between U.S. states, but I wouldn't focus on the legal question. Regardless of whether you have the legal right to make a recording, you should not do so without the speaker's permission. If someone asked me, I would probably give permission, but making a recording without asking feels creepy and inappropriate. If you go around doing this in academia, it's likely to be viewed as unprofessional, and some speakers will become angry.

Even if you ask, people may wonder why you want a recording. (Are you stalking the speaker? Are you going to scrutinize the recording to try to find misstatements? Are you working on competing research and trying to document exactly what was said in your competitor's talk?) If you have a compelling reason to make a recording, it's worth explaining why. For example, perhaps it could help accommodate certain disabilities. Otherwise, you can certainly ask, but it may come across as a weird request.

human genetics - What is a Mitochondrial Eve and Y-chromosomal Adam

I've read this question: What kind of event would cause the current Mitochondrial Eve to be replaced by a new one?

And the values in Wikipedia about Mitochondrial Eve and Y-chromosomal Adam and I am not sure I understand the concept behind them.

When talking about a maternal unbroken linage and a paternal unbroken linage, is the meaning that Mitochondrial Eve had a linage of only women reaching every person today, and the same with Y-chromosomal Adam and men? So that other humans that lived in their age, didn't have an unbroken line of linage consisting of only same sex descendants?

How is the specific "identity" or time period of those persons is known, assuming that researchers didn't check the Mitochondrial DNA or Y-chromosome of every single living human being today, how can they know for sure that there aren't some tribes in the Amazons, which have a direct female linage to Mitochondrial Eve's sister?

Answer

When talking about a maternal unbroken linage and a paternal unbroken linage, is the meaning that Mitochondrial Eve had a linage of only women reaching every person today, and the same with Y-chromosomal Adam and men?

Kind of, yes. The concept behind Mitochondrial Eve and Y-Chromosomal Adam has to due with cell replication and basic genetics.

The Mitochondria ("Power Generators" of the cell) are directly inherited from mother to daughter cell. That is, new cells do not start with 0 and are forced to make them de novo. Some Mitochondria are replicated before division and some are 'given' to the daughter cell to start with.

Because of the unique way that Mitochondria are inherited, when it comes to creating new humans it means that only the Mother's Mitochondria are given to any children she gives birth to regardless of the sex of the child. So I, being male, have my Mother's Mitochondria - which the same as my Grandmother's - and the same as my Great-Grandmother's - etc. etc. etc. until you can trace that line back to "Mitochondrial Evel" whose Mitochondria are the origin for all humans on the planet and are inherited Maternally.

In that sense it is an unbroken lineage of genetic information as inherited from mothers, though not exclusive to women.

"Y-Chromosomal Adam" is a similar concept - Women do not have a "Y"-Chromosome, so every Y-Chromosome men have today had to originate from somewhere. It's trickier to do than tracing Mitochondrial DNA because while Mitochondria are inherited exclusively from mother to child, there could have been multiple Fathers to Mitochondrial Eve's children and other similar complications that muck things up.

How is the specific "identity" or time period of those persons is known, assuming that researchers didn't check the Mitochondrial DNA or Y-chromosome of every single living human being today?

For "Y-Chromosome Adam" it's still more or less in the data-gathering phase as far as I was last aware. It's not as concrete as "Mitochondrial Eve", which has a very solid body of work supporting her.

The "identity" is known because the more in common a person's genes have with the genes of another, the more closely they are related. The researchers took a lot of genes from very divergent populations, and compared them. The researchers were then able to tell which portions were common among all of the Mitochondrial DNA, which had changed the most, and which had changed the least from each other. Using that data, you can construct a rough image of what the originator (or LCA - Last Common Ancestor) had for their own genetic makeup.

You can construe a time period because portions of your DNA (either Mitochondrial or Nuclear) acquire/tolerate mutations at an expected rate - say 1 mutation every 1.5 Million Years. So as long as you have a rough idea of what your LCA's genes looked like (see above), then a modern day sample with 5 mutations is 7.5 M.Y. away from the LCA.

how can they know for sure that there aren't some tribes in the Amazons, which have a direct female linage to Mitochondrial Eve's sister?

They didn't when they started testing. That's part of the fun of the project.

The "Out of Africa Hypothesis" rose in prominence partially due to the findings of the research. It basically posits that the ancestors of humans evolved once in Africa, and then spread from Africa to the rest of the world. Because the Mitochondrial Eve research concludes that "Eve" was around before we spread throughout the rest of the world, it implies that every ancestor already had Eve's legacy when they started migrating into Europe, Asia, the Philippines, etc. Thus every human on Earth, no matter where they are today, shares traits with Mitochondrial Eve.

For the Amazonian tribes, they would have inherited it from their ancestors in North America, which were ancestors of tribes in Asia who crossed an ice bridge into North America, and the tribes in Asia came out of Africa.

microbiology - How heavy are all foreign microorganisms in and on the human body?

I define "foreign microorganism" as a microorganism which is not produced by the human body (not antibodies or leukocytes) including bacteria, viruses, fungi, biofilm aggregates or small lifeforms independent if they are benign or hostile.

Let's say I have currently a weight of exactly 100 kg. How much of it consists of organisms not belonging to me?

Answer

Edit: Matters Arising

In this Nature News article, Scientists bust myth that our bodies have more bacteria than human cells, and in the bioRxiv pre-print article, Revised estimates for the number of human and bacteria cells in the body, a new estimate of the ratio of microbial cells on the human body to human cells that make up the body has been revised down to close to 1-to-1, with there being slightly more microbial cells to human cells.

It should be noted that near 90% of the human cells taken into account were red blood cells and platelets.

^{- Revised estimates for the number of human and bacteria cells in the body, Sender et.al. bioRxiv preprint.
doi: http://dx.doi.org/10.1101/036103}

Note: Preprint articles have not been refereed. The information in them is subject to change, may not pass review, and in the end my not be accepted for publication.

Readers should therefore be aware that articles on bioRxiv have not been finalized by authors, might contain errors, and report information that has not yet been accepted or endorsed in any way by the scientific or medical community.
^{- bioRxiv.org: What is an unrefereed preprint?}

---

Original Post

The human body contains trillions of microorganisms — outnumbering human cells by 10 to 1. Because of their small size, however, microorganisms make up only about 1 to 3 percent of the body's mass (in a 200-pound adult, that’s 2 to 6 pounds of bacteria), but play a vital role in human health.

From: NIH Human Microbiome Project defines normal bacterial makeup of the body

Additional Information on Microbiome and Obesity

From Cell

Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences

From The American Journal of Gastroenterology Supplements (a Nature Press Journal)

Disclaimer

This article was published as part of a supplement sponsored by the Gi Health Foundation, a nonprofit 501(c)(3) educational organization dedicated to increasing awareness of the effect of gastrointestinal disorders in the United States. The foundation's goal is to provide health professionals with the most current education and information on gastrointestinal health.

Impact of the Gut Microbiota on the Development of Obesity: Current Concepts

book recommendation - What are good sources of free-to-use images and diagrams

I am looking for good image repositories for biology teaching. Photos and textbook-like diagrams.

I am interested in images that can be used commercially without payment, or, at least, that require a small one-time payment. They would be used in videos, not only on lectures, hence the worry about copyright.

epidemiology - Where can I find a list of diseases and their incidence?

Say I am studying a particular disease and I know that its incidence is 0.8 per 100000 children below the age of 18, how would I find the incidence of a whole bunch of other pediatric diseases (or even not just limited to pediatrics)?

Essentially I want to find diseases that would be familiar to a medical audience and provide an example of a disease with an incidence of about 0.8 per 100000, another one that is one tenth the incidence and another one that is ten times the incidence.

publications - How to cite lecture notes? (and should I even do this?)

When learning a new subject, I would frequently use lecture notes found somewhere in the Internet. When writing a paper (or a master thesis, as in my case, but the rules should be similar, I believe) one should give some reference for used results which are not common knowledge, if I understand correctly. This make me wonder: what do I do if I want to reference a result I found in some notes?

The natural thing to do would be to just add these notes to bibliography. What format would be preferable for this? Note that there will generally not be much publishing information, perhaps not even a definite year and place. (A BibTeX template would be .)

Secondly, is it OK to cite such materials as a reference?

Answer

You should make a good-faith effort to find and cite original source of the results (to give proper credit). You should only cite the lecture notes if (1) they are the original source, or (2) the original source is inaccessible, either literally (out of print or unpublished) or figuratively (written in a foreign language, with excessive generality or formality, or just badly).

Finding the original source may require significantly more scholarly diligence on your part than the author of the lecture notes, since most lecture-note authors (including myself) are fairly sloppy with references. Such is life.

genetics - IBD-value in pedigree with inbreeding

I have a question about IBD. Please see the figure below. How many pairs of alleles are IBD for X and Y, or what is the IBD value for X and Y. Is it four (4)? I have seen it to be maximally 2, but then we assume that no inbreeding occurs, right?

Answer

An Identical-By-Descent (IBD) value is the number of alleles which are the same because of descent from a common ancestor. Since each (diploid) individual has two alleles for a given (autosomal) gene, the number of them that are IBD with another individual can only be 0, 1, or 2.

In your example, X and Y inherit each of their alleles from A₂, so their IBD value is 2. Inbreeding is just an extreme form of descent from a common ancestor; it causes on average greater probability of high IBD values than when comparing less-inbred individuals. See the passage here for more detail.

publications - Alphabetical Order for Authors in Computer Science

I was wondering, in the field of Computer Science, if there is a convention for acknowledging that author ordering for an academic paper is by alphabetical order, not contribution.

I know that in CS, alphabetical ordering, isn't all that common, however due to a lack of internal consensus, alphabetical ordering would be preferred in my situation.

Even in fields outside of CS, is there a convention for perhaps indicating in a footnote that the author list is alphabetical and NOT by contribution?

EDIT: To elaborate a bit more, after examining the question posted here, our field would likely be considered 'computer systems' (rather than theoretical computer science) where it is stated that the first author is usually the team lead. However in our situation, as I said, we are having internal disagreement over which person would be considered 'leader', and I was wondering what the best way to indicate equal contribution, or perhaps use alphabetical ordering to avoid the issue all together. We weren't really expecting to submit our work for publication (we're undergraduates), so this all has been rather unexpected.

etiquette - What does “Prof. Dr. ir.” mean?

I have a Belgian colleague who is “Prof. Dr. ir.”. What does it mean?

Answer

Ir. means a masters degree in Engineering.

source : Belgian Education :)

I added a "reference". This Prof. Dr. Ir. received a M.Sc. degree in electrical engineering and the Ph.D. degree in mechanical engineering from the Katholieke Universiteit Leuven (K.U.Leuven), Belgium

Also, from wikipedia: Belgium

In Belgium, there are two types of engineering degrees:

• "Burgerlijk Ingenieur" /"Ingénieur civil" or "Master of Science in Engineering" (abbrev. "ir.") - 5 years study (3 BSc. + 2 MSc.)


• "Bio-ingenieur"/ "Bioingénieur" or "Master of Science in Bioscience Engineering" (abbrev. "ir") - 5 years study (3 BSc. + 2 MSc.)


• "Industrieel Ingenieur" or "Master of Science in Industrial Sciences" (abbrev. "Ing.") - 4 years study (3 BSc. + 1 MSc.)(3 BSc. + 2 MSc. in 2013-future) (for the Flemish Region)


• "Ingénieur industriel" or "Master of Science in Industrial Sciences" (abbrev. "Ing.") - 5 years study (3 BSc. + 2 MSc.) (for the Walloon Region)

link

job search - What should I ask deans during my interview?

I managed to snag my first interview for a tenure-track assistant professor job. As I had heard, the itinerary seems somewhat gruelling. What caught my eye in particular are three 45min-1hr meetings with various higher-ups: The Dean of Science, the Associate Dean of Graduate Studies, and the Associate Vice-president (Academic).

While there is certainly no shortage of topics to discuss with people in my potential department, I have very little sense of what the above three meetings will be like. So my question is:

What kind of questions should I be thinking about asking deans/VPs during these meetings?

Answer

You want to be friendly, of course, and make a good impression. Depending on the school, these meetings are not usually too grueling; one purpose of the meetings is just to put a face with your name. There is a good chance these meetings will end up being shorter than the scheduled time.

• 
  

  Be prepared to give a very brief "elevator style" summary of your work.

  
  


• 
  

  The deans may ask you about grant funding. You may have a good sense, depending on your field, how important grants are to you getting the position. (Andy W mentioned this in the comments).

  
  

Some particular questions I would ask include:

• 
  

  I would ask all three: Where do you see the program/college/university going in another 10 years? This can help you tell whether your vision for a school fits with theirs.

  
  


• 
  

  I would ask the Dean of Science about tenure practices in the college. Do your homework and read the tenure policies before you arrive, of course. As long as you are polite and non-pushy, you can ask for clarifications for anything that isn't clear. You can ask about tenure rates in general, but don't ask anything that would require talking about individual candidates. If you are in a field where grants are important, you should also be sure you know the weight given to grants when they make tenure decisions.

  
  


• 
  
  

  If you will need anything unusual (e.g. large start-up equipment costs), you should mention that to a departmental representative first, and they can advise whether it needs to be mentioned to the dean.

  
  


• 
  

  If you are trying to arrange a second hire for a spouse, the dean may be able to discuss that. Again, you can talk with the department first. CAUTION: This bullet only applies to applicants who are also interested in finding a job for their spouse, and who have decided to bring up their spouse before getting an offer. There isn't room in this answer to get into the debate about whether it is preferable to wait until you have an offer to mention that your spouse is looking for a job, which is another commonly advocated strategy for applicants looking to find a job for their spouse at the same institution.

  
  

job search - How hard is it to get an academic position in Australia/New Zealand with a PhD from the US?

I am originally from India, currently a PhD student in Mathematics in the US. As such I don't have very many ties to the US and I was wondering whether it is common for PhDs from the US to get academic positions in Australia and New Zealand. I have seen some jobs postings on http://www.mathjobs.org/ advertising positions in Aus/NZ universities, but I am not sure how many US PhDs apply to them.

Are most faculty members in Aus/NZ universities 'homegrown', or is it fairly common to see PhD's from other countries? Is a US PhD the norm, an advantage, or a disadvantage when applying for an academic position in Aus/NZ?

Answer

The proportion of "homegrown" to "...imported?" PhDs varies depending on your discipline, but at the science end of things (I'm in computer science, but know plenty of mathematicians and also majored in chemistry as an undergraduate) it's quite international. Apart from pathological cases (known "bad" universities, or otherwise extremely dubious universities), where you got your PhD is not particularly important. As Jeromy says in another answer, international experience is definitely viewed favourably though. My having done my doctorate overseas has definitely been a boon.

The real criteria are performance based; publications, teaching (especially awards or other recognition) and ability to bring in the grant money! (That last one in quite important, for better or worse). As a recent Doctorate, you'll mainly need to show that you can conduct quality research.

Just for some completely non-statistically-significant stats, my Australian undergrad. chemistry department had about 50% overseas PhDs, my CS department had more like 90% overseas PhDs and my maths department had about 50% too. At my current (Australian) department (CS), it's probably about 70-80% overseas PhDs (though that's a guesstimate at the moment), including me.

Of course the caveat is, again, this will change from department to department and university to university. Some like to only hire their own graduates, others will never hire their own graduates. Your best course is really to contact the academics offering the jobs, establish a bit of an informal relationship and find out what each position is looking for.

biochemistry - How to form biological metallic tissue?

There are numerous popular articles claiming that the wasp Apocrypta Westwoodi Grandi features an ovipositor tipped with zinc. You can find such an article here. You can watch an impressive video here. Beyond that, I have found information on the genus to be sparse.

Yet my question is, how metallic tissue can be formed. The popular article claims actual zinc was detected. It seems unlikely to me, these creatures consistently find a source of zinc to feed from, so as to deposit zinc in their tissue. Even so, I don't understand how this zinc can be made to deposit at a specific point. The article clarifies:

With an x-ray detector and the electron microscope, they discovered the presence of zinc. It was only on the tips of the parasitic fig wasp’s ovipositors. Gundiah said, “We see it very consistently only at the tip and not anywhere else.”

I am no biologist, but, to my feeble understanding the only alternative is that the so called zinc is actually synthesised by the body as a protein normally is. Surely no atomic reactions could take place in the wasp! :-p Even teeth are mostly Ca5(PO4)3 OH, Calcium is found in plenty of our foods. Phosphorus is present in meats. But zinc? I totally don't understand it!

Answer

First and foremost, it looks like the original article is slightly less dramatic:

Parasitoid ovipositor tips have a higher content of the transition metal zinc compared with the cuticle elsewhere on the ovipositor

So a 'higher concentration' isn't quite the same as 'tipped with'. It looks like they are describing a higher numbers of metal ions, rather than pure metal:

The presence of transition metals in insect cuticle and mandible is hypothesized to increase material hardness to permit cutting through hard substrates with minimal wear

There are many examples of organisms using inorganic chemistry to make materials. The overall topic is called biomineralization and you even mention teeth - which is hydroxyapatite (not really organic chemistry!).

However, a pure metal like zinc is unusual, I think. There are examples such as the snail that has an iron pyrite 'armor' or even the iron nanocrystals in ferritin.

More spectacular examples include the bacteria that produce gold particles

As a result, Au detoxification is mediated by a combination of efflux, reduction, and possibly methylation of Au-complexes, leading to the formation of Au(I)-C-compounds and nanoparticulate Au⁰.

Where Au⁰ is pure gold. I don't know of any other examples of pure zinc in organisms, but there is a nice review here of zinc biochemistry.

When you say 'synthesise' I assume that you mean 'deposit'.

Why do we have nerves in our teeth?

Toothache is a useful signal to us as we can visit the dentist who can try to fix any problems with our teeth. But what is the natural biological role of toothache? Does toothache make animals take action that helps them to deal with their dental problem?

graduate admissions - Is it a plus point for my PhD application to mention that I am already a PhD candidate at some other university?

I have recently completed my MS and joined as a Ph.D. candidate in the same university. But I want to move out. I am filling the application for an other position where they have asked the following:

Please give the full contact details for you at your permanent institute.

If you do not have a permanent institute, you can use the Leave empty button to leave this page empty.

There are options to mention that I am currently a Ph.D. candidate. Is it a good idea to mention that I am currently a Ph.D. candidate? I am asking this because someone have told me that if you are currently a Ph.D. candidate, universities don't give much attention to your application.

Answer

I can't really see how it is a plus, but it could be a big negative.

The obvious question is going to be: why is this student leaving his current university? Doing a PhD involves a pretty hefty investment for both sides, and you're about to leave a university in an attempt to go to another. Universities want to be convinced that you will make it to graduation.

I would expect you to have a very good reason for this (trying to go to a better ranked school after starting at one isn't a good enough rationale to me).

application - What is a better point in an academic career to move to the U.S.: as an assistant professor or after tenure?

I am starting my second academic year as an assistant professor at a university in Europe. I'd like to move back to the US at some point in the near future. If I stay at my current university for 2 or 3 more years, it's likely that I will be offered tenure. Based on the openings I see in the US in my field, there are more assistant professor positions than associate professor positions.

• Will it be better for my career prospects to apply now for assistant professor jobs in the US? If so, should I expect a reduced tenure clock?


• Or should I wait a few more years and with tenure under my belt, apply for associate professor jobs?

teaching - Is it ethical to profit by having my students buy my textbook?

This question was suggested to me by How can I sell my text book to my students in e-book format? which asked about the practicalities, but attracted many comments about the ethics. So this question is to ask about the ethics directly.

Suppose I have written and published a textbook, and I want to use it as the text for a course I am teaching. I receive royalties from each copy of my book that is sold, so if my students are required to buy my textbook for the course, I will make some money. Is it ethical to do so?

Well-reasoned opinions would be useful answers, but even more useful would be pointers to institutional policies, professional codes of ethics, etc, that address this issue.

Of course, there are many ways to avoid profiting from the sale of my book to my students. If my contract with my publisher allows it, I could distribute PDFs to my students, or have the university bookstore print out copies and sell them at cost. Another approach I've heard of is to compute how much I earn in royalties on each copy, and refund that amount from my pocket to each student who buys a copy. Or, use my royalty earnings to buy pizza for the class. Certainly these are nice gestures, but I would like opinions on whether they are ethically required.

Edit: To address some questions that have arisen in the comments:

• 
  

  This question is hypothetical. I haven't published any textbooks myself and have no immediate plans to do so. In any case, my personal preference would be to make the book available to students for free, if at all possible. So I've phrased this question in the first person for rhetorical convenience only.

  
  


• 
  

  I had intended the question to be only about the potential financial conflict of interest that could arise if I make money by assigning my own book. Some of the answers feel that it is improper for me to assign my own textbook at all, whether I make money or not, but I don't think this point of view is prevalent within the academic community. If it happens that my book (as a pithy but now-deleted comment put it) "blows", I think most would agree that my decision to assign it is pedagogically unfortunate, but not unethical.

  
  


• 
  

  I don't literally mean that students would be required to buy the book, only that they'd be expected to have it. I might assign readings or homework problems from the book, so that the student needs access to the book in order to do them, but they could certainly achieve this by getting a used copy or borrowing from a friend. But probably most students would buy new copies anyway, since that is the most convenient way.

  
  
  

Is it a good practice to choose my undergraduate research topic on my own? Can I get enough help?

(This question is one of three correlated questions: How should I do it? (second part), What are the downsides? (third part).This is the first part)

I am an undergraduate student (in Computer Engineering) and I will be starting undergraduate research for my thesis. I have talked with many professors about possible projects and all the projects they proposed to me seemed interesting enough.

During summer, though, I read a paper and I was very interested and excited about it, but this paper was not for the projects that were proposed to me, but in a different area. I would like to do research in this area but I have some questions, because none of my professor is doing research in this particular field.

So, my questions are:

1. 
   

   Should I try to do a project in that area, even though my professors aren’t doing research in that particular topic (some do research in a close field) or choose one of the projects that were proposed to me?

   
   


2. 
   
   

   Will any professor be able to help/guide me through the project, even if he is not doing research in this topic exactly? (I will ask them if they are capable of helping me, but I want to know, how much can someone help me if he is in the same field but I am doing something different than his projects)

   
   

P.S. I want to understand whether it will be beneficial to do a project that I want to do because of some paper(s) that I read or it will be better to do a project that was proposed to me. Also, I would like to go for a Ph.D. after I graduate.

graduate admissions - Where can I find academic CV samples containing minor research projects for PhD applications without publications?

Context:

• 
  

  Prof messaged me, interested in my CV

  
  


• 
  

  During my master's in mathematical finance, I may have had one "publication" if a quasi-thesis, that wasn't exactly a thesis, counts.

  
  


• 
  

  While applying to (more) grad school (pure not applied), I'm currently working in the tutoring industry (I'm not teaching in a university) as I have been since grad school (tutoring industry is very serious in country A compared to country B), and my industry CVs/resumes consist mainly of tutoring jobs (I've never had a finance internship, but I did have a sort of statistics/economics research internship).

  
  
  

I do not believe I have formal pure math research experience, but I have a lot of applied math research experience in our "thesis" (or technical report as Nate Eldredge might suggest) and class projects.

I have so far not found academic CVs for PhD applications that include minor research projects in master's (I don't know the terms. They are "research" projects but are not published or as long as theses. They're simply class requirements that are not exams or "homework"/"problem sets") so please provide references.

Examples:

1. 
   

   UTexas - Ella Fitzsimmons

   
   
   
   
   • GOOD: has master's, no PhD
   
   
   
   • BAD: thesis only. no minor research projects in master's here.
   
   
   
   


2. 
   

   UCSF - Rembrandt Van Rijn

   
   
   
   
   • GOOD: mentions minor research projects pre-PhD
   
   
   • BAD: has PhD and so mentions minor research projects pre-PhD without further elaboration
   
   
   
   



3. 
   

   Academics - Anna Mustermann

   
   
   
   
   • GOOD: has master's no PhD
   
   
   • BAD: For master's: thesis only. no minor research projects in master's here. has publications
   
   
   
   


4. 
   

   Surrey - ROBERT BROADSTONE

   
   
   
   
   
   • BAD: No master's. Has PhD. Has publications
   
   
   
   


5. 
   

   Harvard - Anjan Lo Subramayan, Keisha Thomas

   
   
   
   
   • BAD: Has PhD/Is PhD candidate, No master's, Has publications
   
   
   
   

Answer

There is no need to follow a standard or template unless the specific job you apply for explicitly states that you should do so (which is rarely the case).

I am a biophysicist, not a mathematician, but from what I have seen you can put on your CV whatever you want, especially in academia: it is your CV. You should definitely include your minor research projects. You can have a look at templates for some inspiration but it is up to you how you organise your CV and which sections you include or not.

Publications usually only count if they are published in international peer-reviewed journals or books. You can possibly stretch this definition a little by including conference proceedings, abstracts, application notes, and so on, but it may be viewed as strange if you call these a "publication" (mathematicians, please correct me if this is different for you). In any case, this is the topic of your other question and is better discussed there.

species identification - Help identifying tiny jumping bug

I've found a few of these bugs hanging out on my desk. There aren't many. Maybe 5-10 at any given time. Are they a type of springtail? I couldn't find an image in searching that made me say, "That's it!"

Any help is appreciated!

Thanks!

Answer

Those are springtails. Order Collembola. You can find yours here on BugGuide. https://bugguide.net/node/view/258362

publications - Editor rejected my paper stating that reviewers had refused to review it long after submission; How can I understand what is wrong with my paper?

I am having very frustrated at the turn of events and review process. I had sent a paper to an International Journal. The paper was based on my work and well received by PhD committee of my Institute. The paper was submitted 3 years back. The paper was in status "Editor Assigned" for 6 months. After that its status changed to "Under Review". After 9 months in this status (15 months after submission date), I sent a polite mail to editor asking about how much time it will take to complete review? There was no response. After I month similar gentle mail was sent. There was no response. After month, I again sent query (18 months after submission). At that Editor replied saying that they could not review the paper as assigned reviewers either refuse to review or did not agree to review. The paper was rejected after 18 months without any review comment.

So how does one know where it requires improvement? If paper was not of required quality why they kept with them for so long?

I feel that it is wrongly rejected.

Is it correct answer?

How can it show status as Under Review and then Editor says no Reviewer did not accept or refuse. My understanding is that paper goes in "Under Review" state only after "Reviewer" accepts to review. So what would have happened? Why Editor requires 3 months just to tell the status and comes back with mail like this? Editor did not bother reply to mail. Is it that he got angry because of persistent queries.

I had even worst experience with next Journal. The paper was submitted and it remained in status "With Editor" for 9 months. Wiser by experience, I asked Editor about status? After persisting with it for about 2 more months, Chief Editor said that they rejected paper based on quick review as paper is not suitable to Journal as it does not meet its criteria like Originality, Depth etc. Again there no review comments about improvement.

It is not sour grape, I do feel that around 60% papers in that Journal do not possess these qualities and have been published in 6-8 months (after revision). If paper is not of required standard, they could have rejected in 2-3 months, why it took them such long time. If I would not have sent mail, probably it would have remained with them for long time. This work is now 3 years old not published anywhere and I even do not know what to do to improve. I am feeling very bad and really do not know what to do?

What would happened? Is it wrong to ask editors about status even after 9 months or year? Our University requires two Journal publication for PhD thesis submission and really do not what to do?

Many friends are suggesting that publish in Open Access Journals.

publications - Should a conference paper in a journal be considered a journal article?

I have recently been doing a revision in my CV. I organized my publications into "Peer-reviewed journal articles", "Peer-reviewed conference papers", "Other published papers" ...

My dilema is which section to choose for conference papers published in a journal (either regular or special issue). Which of these two criteria should be used for classification of publications: the paper origin or the publication type?

Assumed, I have chosen journal article section for some of my conference papers. Could omitting conference details be treated as misleading?

Answer

To the best of my understanding, the key reason why some conferences publish their proceedings as journal special issues is precisely to enable the papers to be listed as journal papers rather than conference papers. This is essentially a kludge to get around bureaucrats and people from fields with an "only journals count" prejudice.

As such, I think that it's entirely reasonable to list such papers in either the conference section or the journal section. The "technically-a-journal" form, however, typically has different citation information than the conference publication, so if you choose to list them in the journal section, be certain to list them with this alternate citation information, as reported by the journal archive site.

publications - Is typical ebook reader with pdf support enough to read scientific papers

I am considering buying either an e-book reader or a full tablet. My main motivation is to read books and scientific papers and I really don't need all the extra stuff tablets can give me.

My only concerns are

• whether e-book reader (that has pdf support) will handle many different layouts used in articles (how well will 2-column A4 page fit in an 800x600 e-ink display)


• whether it will display math properly

Do you have any thoughts and (more preferably) experience about this?

Answer

No. Not sufficient. Kindle DX, an almost full-sized page, was not big enough. Refresh rates are not fast enough for flipping back and forth. Zooming interface is terrible. E readers are good for simple flow text, one page after the next. That is not how I read papers. Tablets do much better.

teaching assistant - Time management as a TA in mathematics

I just started being a TA in mathematics at a university in continental Europe. My big problem is my time management: I feel like I don't have time for my own research. During a working time of 40h per week, I usually have the following duties (other than my research):

• Teaching duties 3h


• Attending two lectures (total of 3h) plus their exercise sessions (total of 2h)



• Attending a seminar of 2h


• Solve exercise sheets of the two lectures I attend


• Think about good exercises for the course I'm a TA of


• Write solutions to the current exercise sheet

If I include the last three points with a total of - say - 7h (which is probably too little time), my duties in the week take around 17h. Well, this does not sound too much. I do not have to attend these lectures and the exercise sessions, but my advisor strongly recommends attending, as their topics are very important in my field, although they are not at all related to my current work.

But, of course, there are some other things which prevent me from working on my stuff:

• 
  

  The two lectures I'm attending are right one after another. Between these two lectures, I have a break of 30 minutes. But in this short period of time, I cannot be productive. When I finally got started working on my research, I already have to attend the next lecture. This problem occurs a lot for me: during my teaching duties and another duty, I have only one hour to do something. But in this one hour, I mostly have to prepare for the next lecture/seminar/... - Basically, my whole Mondays and Tuesdays are blocked by problems like that (I cannot be productive in just one hour - it's just too little time to get started).

  
  
  


• 
  

  Prepare seminar talks for the seminar mentioned above. This is not a regular work to do, but nevertheless takes a lot of time.

  
  


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  As my two lectures are on the same day and there is only a 30min break between them, I usually feel very tired after the second lecture. This decreases my working efficiency by a lot. I do take some lunch break after the lectures, but I usually feel even more tired after the break.

  
  


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  Attend seminar talks which take place on a irregular basis.

  
  



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  The only day on which I don't have any duty is Friday. But on Friday, I'm usually really tired as a consequence of the stressful week. Therefore, I cannot be as productive as I should be, even on Fridays.

  
  


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  As I just started being a TA, there are many "small" things which have to be done. Set up a new computer, find out how to use SSH on this one, ... - those small things add up and end up costing a lot of precious time.

  
  

I also considered working on weekends, but this would be too much for me; there have to be some days spared for regeneration. Sometimes I think about the exercise sheets of the two lectures on weekends, but nothing else.

About the two lectures and the seminar: I really want to attend those to broaden my view of my field and learn new things which are (currently) not important for my work. One could think about not solving the exercise sheets of the two lectures, but then I won't learn a lot by attending these lectures.

So my question is the following:

How do I maximize my productivity as a TA (in mathematics)?

(Closely related: How can I stay being concentrated after two lectures/on Fridays/...? How do I maximize my productivity-to-time ratio?)

publications - What to do when you are suspicious about numerical results in a submitted manuscript that you are reviewing?

I am currently reviewing a paper and feel suspicious about their numerical results. I feel their results have been slightly modified to exhibit their superiority compare to other comparative methods.

I cannot give an exact mathematical reason why I think their numerical results have been manipulated, but it is so odd that in all 15 scenarios they have been better. Actually, I am pretty sure that their method is better than his benchmarks but not always. Maybe they modified some scenarios.

As I don't have a mathematical reason why I think some of their numbers are altered, should I ask for their computer code and run them myself?

Answer

Complementing the other answers, either in addition to, or apart from, asking for the codes and running them yourself, I don't think it is a bad idea to explicitly ask the authors, something like this:

The standard algorithms for executing (bla bla bla), e.g. as followed in the works of Refs. [1-3] (feed these in), are suggestive of a standard accuracy in typical algorithms. The current work appears to have bettered the same, which is a strong point in favor of publication. However, the authors should include a comment in the manuscript, mentioning what changes have they implemented to the typical algorithms so highly prevalent, which leads to this enhanced accuracy.

My jargon may have to be twisted a bit here, but I think I convey the point.

This being a query in the referee report, the authors shall be obligated to feed in the details, and if there is some manipulation involved, it may end up being exposed.

Hope that helps :)

publications - Name change during the course of PhD?

I am now working towards my PhD degree. In the very near future, I will have a citizenship change, which also leads to a name change. In detail, I am adding another given name to my current name with the original surname and given name untouched. So it's like going from

FirstName1 LastName

to

FirstName2 FirstName1 LastName

I already have some publications under my current name, FirstName1 LastName, which I do not wish to lose after my name change. At the very start of my PhD, my supervisor has advised me to stay consistent with the name for a better recognition in the field.

Is there a way to minimize my loss of recognition in the academia? Will the publication stats tools, such as Google Scholar, include my publications under my new profile?

Answer

I would recommend sticking with what you started using, since there is no real advantage not to. That said, if you really want to change I don't think a change in first name will affect you much. Depending on the citation style, the name change won't even be visible. I don't think this particular change is anywhere near a change of last name in terms of impact on your popularity.

With regards to Google Scholar: you can always add your new publications manually to your profile in the unlikely case that scholar borks, so that's not an issue.

bacteriology - What are the functions of magnetic bacteria?

I'm trying to understand why are bacteria "equipped" with magnetosomes ("intracellular organelles in magnetotactic bacteria that allow them to sense and align themselves along a magnetic field") and why and for what do they need such organelles.

Answer

You can find a detailed discussion of this topic here.

Magnetic bacteria contain chains of magnetic crystals (magnetite or greigite) which cause the cells to be oriented in a magnetic field.

It was originally proposed that magnetic bacteria use their magnetosomes to ensure that they swim downwards into the sediment (everywhere on earth, except at the equator, these lines of force have a downward component vector.) However, the current view is more complex than this: magnetic bacteria are microaerophilic and occur in stratified aquatic environments (i.e. ones where there are zones of oxygen concentration at different depths). In this view the magnetic "sense" is not a true taxis, but rather is used to keep the cells oriented in the magnetic field while they adjust their position by sensing oxygen (aerotaxis). As you may be aware, the standard way that Gram-negative bacteria operate is to perform a biassed random walk in three dimensions. The alignment of cells with the magetic field will reduce the dimensionality of the movement, which is more efficient.

interpersonal issues - How to survive the remaining 5 months of my postdoc in toxic environment?

I am international postdoc and 7 months into my 1 year postdoc. My PI is very young and the lab is relatively new. I chose this lab because after the interview I was convinced that the PI and I had similar research interests. I had also made sure the work would be experimental in nature since that is what I am an expert in.

The research direction proposed seemed interesting and I have enjoyed working on the project. But there is a major mismatch between our attitudes. I do appreciate him taking the time out to listen to my research plan and goals but I just cannot bear the abusive nature of the PI. In my 6 months time he has humiliated me in front of the whole group twice (both for journal clubs), saying my presentations should be much better than what it is. The theoretical aspect of my work is not of my interest and he expects me to know each and everything about it even though it's a new topic for me. There is zero tolerance for any mistake or unanswered question.

Long story short, I feel under-confident and bullied I am convinced that I need to look for a new position and have already started contacting some potential advisers (no luck yet).

My questions are the following:

1. How do I survive the remaining 5 months of my postdoc with an abusive mentor who has unreasonably high standards?


2. I have been so stressed since the past month that I feel unfit for any position. How do I regain my confidence?


3. How do I find a position without a reference letter from the current adviser?

age - I want to do research but I'm too old for a PHD

I really love research. I started a research project in graduate school for my M.A. in English. My research topic is a very viable and interesting topic for a dissertation. I'll be 60 on my next birthday and I know that many Ph.D programs are traditionally geared toward younger students.I was wondering are there any programs that I can continue this research in without facing the issues of ageism in academia?

evolution - Is there any evolutionary/physiological advantage to multi-lateral symmetry?

Just wondering ; I get the impression a large number of multicellular organisms are multi-lateral in their physical structure. Why would evolution/mutation have retained multi-lateral symmetry in an organism? What advantage/s does symmetry provide an organism?

EDIT: By multi-lateral symmetry I mean at-least bi-lateral symmetry (as in the case of many beings such as elephants, crabs and fishes), but perhaps more than bi-lateral too (starfish come to mind)

END EDIT:

publications - Why do universities tolerate uploading papers on their websites?

Lots of professors provide their full papers published by scholarly journals on their personal website (in the university official domain). PDF files of their final papers published by different publishers are available online. However, this is against the copyright transfer agreement, and the authors have no right to distribute their papers publicly. In other words, the authors have the same right as well as others to distribute their own papers publicly, as this is the marketing right of the publisher.

This is clear violation of the US copyright law, like distributing cracked software programs or movies without copyright. Why the university officials do not take action over this copyright violation?

One may say that this is their personal website and they are legally responsible, but if someone distribute an illegal item on his/her personal website, the university will not allow this because it is part of the university domain.

I think universities ignore this because it seems to be less criminal, but why? as it is still illegal. So much the worse, it is even common in top universities where considering legal issues in different aspects is quite serious.

Answer

Why the university officials do not take action over this copyright violation?

Because they can't. There is no way to tell whether a given electronic preprint violates the publisher's copyright-transfer agreement or not. Different publishers place different restrictions on authors' rights to redistribute their papers. Some allow posting pre-edited versions; some allow posting the official camera-ready version; some allow neither; some only require an exclusive publication license and leave copyright in the author's hands. These restrictions change over time, and may depend on whether the author paid an open access fee to the publisher. The only way to determine whether an electronic (p)reprint is posted illegally is to read the actual copyright-transfer/publication contract. But this contract is directly between the authors and the publishers; universities have no record of these agreements.

Because they don't have to. At least within the US, university web sites generally fall under the "safe harbor" provisions of the Digital Millennium Copyright Act, which requires copyright holder to request removal of the specific items to which they claim copyright.

Because the publishers don't care. Scary legal language notwithstanding, academic publishers in many fields have zero interest in pursuing legal action against individual researchers for posting copies of their own papers in violation of copyright transfer agreements. (I have heard this said specifically about ACM, IEEE, SIAM, and Springer, by people with connections inside each of those organizations.)

Because it's not in their best interest. Both universities and the public benefit materially from the public availability of research by their faculty, students, postdocs, and other researchers. Universities have no incentive—aside from a potential legal threat that they know will never materialize—to proactively censor that research. Many universities, and more recently many governments, have adopted open-access policies that either encourage or require their members to amend publication agreements and make their work publicly available.

Because researchers would revolt. Even if academic publishers started sending DMCA notices to universities, and even if universities required their members to take down copies of their papers, in violation of research community expectations, the people whose research is being censored would simply take their business elsewhere. Those publishers would receive fewer papers, and those universities would receive fewer graduate school and faculty applicants.