publications - How can my organisation's published reports get indexed by Google Scholar?

My organisation (i.e. my employer) publishes peer-reviewed research reports in the form of a journal series via its website. The organisation alone publishes the reports and they are not published in conjunction with any publishing agency or academic body. The research reports are written and peer reviewed by academics and the research activity funding is managed by my organisation.

The research reports are in PDF form (with metadata attached), and are listed on a web page containing metadata in the form of the fields required by Google Scholar. The Google Scholar submission process was completed ten months ago in March 2016. There was one issue identified: there is not a volume/issue listing of the reports, they are discoverable via the website search engine.

The website has been submitted to Google Scholar with example URLs, but to date, the body of research that is made available via the organisation's website is not included in the Google Scholar index.

Where the research reports are also stored and published by university databases, these do appear in the index.

Additionally, citations to the research reports do often appear in the index without any link to the location of the report. Ideally, we would like to enable these citations to also show links to the online reports.

I had thought that the form and structure of the research report publication was suitable, but our organisation's website has not been included in Google Scholar indexing.

Some suggestions on the Google Scholar website are to use a journal publishing service (established journal hosting services) or recommended software such as Open Journal Systems.

What process should I follow to investigate or progress this issue further?

I suspect that I'm not looking in the right place in my investigations, so I need some direction.

Answer

We found that by submitting our content to SSRN we were able to see the content (once approved and distributed by SSRN) subsequently indexed by Google Scholar. This method is, therefore, an appropriate solution in our situation for this problem, without the need to restructure our website.

How is the Energy Systems Language used in ecology?

Is the Energy Systems Language useful in systems ecology? It is developed by Howard T. Odum, "the father of system ecology", to make analogies between ecological systems and electronic circuits. But how far this analogy remains correct? What important results have been found from it? Is it widely used by ecologists in other subfields? If yes, then why isn't it applied to other fields?

^{Related: What are the branches of system ecology?}

Answer

Energy systems language is definitely still used in systems ecology, ecosystems ecology, and ecological engineering. It can be used in other aspects of ecology depending on the approach of the ecologist, some ecologists appreciate it more than others. For a broad snapshot of how science is currently building upon Odum's 1983 Intro to Systems Ecology, check out a Google Scholar search for the latest papers citing that text by Odum.

In my experience with it, energy systems language and energy flow diagrams introduced by Odum are used as helpful conceptual tools: understanding and organizing complex systems qualitatively and then potentially quantitatively; putting useful constraints and guidelines on brainstorming the effects of adjustments to complex systems; etc. This can be done in a teaching context, helping students understand systems and bridging the fields of engineering and ecology. It can also be done in a high-level professional context, sorting out the intricacies and potential solutions of very complex environmental problems.

I find that energy systems language is used most wherever the study of complexity and ecology intersect. This is especially true in the study of ecological complex adaptive systems and in studying agro-ecology. Even in those cases it depends on the ecologist in question: those with more of an engineering background tend to appreciate Odum's framework, whereas those without an engineering background may rely on other frameworks.

Does a informative and clear professor webpage often increase the number of prospective PhD students who apply to work for the professor?

Here is what I would call a particularly informative and clear professor webpage.

Of course, it's not the most important thing (for me, personally, I mostly discovered professors through asking current professors whom to contact). But a lot of PhD students do discover professors to contact through Internet searches, which may be especially relevant for PhD students who might not have as many connections (especially international ones). And maybe a strong professor webpage could also increase the "fit" of the applicants who do decide to contact the professor.

Answer

As an international student who is (was?) looking for potential advisors, I'd say yes (As far as I know)!

The algorithm for me worked as follows:

1. Contact the obvious ones. These were authors of papers I read recently (& liked), editors of journals etc. Basically, the ones with good "academic presence".


2. Look at professors who have written textbooks or survey papers.


3. Look at strong departments for professors. (By strong I mean : Reputation, Rankings and Star Power/Infrastructure)


4. If a professor has a good webpage (Updated recently with list of current/past projects, list of graduate students and alumni), Shoof! Time saved!


5. If a professor has a bad webpage (Last updated in 2001 or with minimal content or whatever), then run him on google scholar. Read his papers and try to find out what his students are upto.


6. Once a professor has been selected, run youtube and ratemyprofessor on him. This is usually worthless but it did yield some awesome results once in a while. It did help get a virtual lab tour at times.

In conclusion:

• Maintaining a good website does help students (especially international) get to know the professor better.



• It does save us a lot of time by having access to all relevant information at one place


• What is most irritating is webpages with very old content. I would prefer limited recent content to old obsolete content.

evolution - How is "selection" best defined?

There is natural selection but there is also sexual selection which some regard as a category of natural selection. There is also artificial selection (by humans). The question is, what is a most appropriate for selection? What criteria does a force have to meet in order to be considered to have acted selectively?

epigenetics - How does CpG island methylation lead to gene silencing?

I see often the blanket statement that CpG island methylation can lead to gene silencing. However, I have been unable to find a straightforward explanation of the mechanism by this.

Is it a purely physical block of binding for transcription factors? Does the methylation create a tertiary structure that is compacting the DNA? Does it recruit histone modification factors that compact the chromatin?

Please feel free to cite literature so I can go read the papers.

Answer

CG methylation has long been associated with gene silencing due to the generally negative correlation between gene promoter methylation and transcription levels.

When CG methylation occurs in the promoter or enhancer region of animals (where these 'CpG islands' tend to be), methylation seems to impede (to some extent) transcription factor (TF) binding. That is the baseline mechanism for gene repression. The altered chemical properties of the DNA make it less favorable binding site for its cognate TF.

In some cases, methylation clearly prevents TF binding. For instance, some TFs bind DNA to block methylation, which facilitates access of another TF or set of TFs to the bound DNA (for instance, this paper by the Schubeler lab about NRF1). In the case of other TFs, their binding is less reliant on methylation state, possibly due to the strength and breadth of the binding site (for instance this work from the John Stam. lab about CTCF).

Methylation also can affect nucleosome positioning and stability in some contexts; the nucleosome effects are poorly understood currently because nucleosomes and methylation likely feedback on one another. See this work from the Zilberman lab for an example.

The role of a higher-order repressive structure forming is arguably not obvious yet; for instance, histone H1 bining does not appear to be heavily influenced by methylation state (although this is somewhat contentious because there is often a positive but weak correlation at repressed elements in the genome between H1 and methylation--for instance just pubmed 'h1 chip' with reviews and read a recent one). More certain is the relative change in location of methylated promoters within the nucleus to a place of transcriptional 'silence' (inactivity). These repositioning phenomena are under intense investigation; you can learn more about this by googling for 'nuclear topology and gene repression' or something like that.

hope this helps

ethics - Writing someone else's master's thesis: Unethical and illegal?

It is really difficult for me to decide on this situation: when someone calls me and asks for work-for-hire for his/her thesis. I don't know what to do. I want to help and earn money but I think this way of earning money is unethical. I think that receiving the title of thesis and giving back prepared manuscript is the intention that some people have, when asking for their thesis to be written. There are plenty of websites offering such services!

The question is that: Is it legal and or ethical to write someone else's master's thesis as work-for-hire?

Answer

As a former academic editor, I agree. You are absolutely right!

Whether or not the act is legal, writing someone else's thesis is helping them commit fraud. You would be helping him or her to obtain a degree that he or she has not earned. The question is, do you wish to participate in that kind of activity? I think you have answered your own question.

Yes, there are (depressingly) many, many, thesis "services" out there. There are many people doing dishonest things in the world. That doesn't make them less dishonest.

It sounds a bit as if someone is pressuring you to do this. If this is true, then for me, dealing with such a person involves finding the wording with which I am comfortable making my stand. Sometimes setting the individual decision in a larger context helps to de-personalize it - I might say that I had considered it, but have decided not to take on full thesis projects as a rule. Or, maybe, I would say that I am going to stick with editing projects for now. Both of these statements relate what my decision is. That is not arguable. I get to say what my decision is. If the person continued to try to argue, I simply repeat what I said, until s/he got it that I was serious. A friend of mine is great at saying, very politely, in many kinds of situations, "I'm sorry, that is not going to work for me," and then offering an alternative. She is voicing a personal preference, against which others can have no legitimate or polite argument. However, every situation is different - each person has to say what reflects his or her thoughts and boundaries.

If this person is desperate because they "have to graduate in May" or whatever, being a former advisor, I would recommend they send see their advisor and confess the truth. Then, try to figure out some options. The world doesn't usually end if students have to finish a course or two over the summer, perhaps you could offer your services for that time. Many students struggle with a large project without supervison. Having a writing coach to keep them on track (you) can help a lot.

If you are an editor struggling for money, that is a familiar problem! More marketing may be necessary, and/or check if your rates are what they should be. If no one ever hesitates when you quote, you may be undercharging. Also, making sure all of your friends know what you are doing, giving them business cards or a flyer, (relatively inexpensive) can help because if you have thirty friends/acquaintances, and they each have thirty, then someone in that 900 must need some editing. This is actually a useful way to search for "regular" jobs too. When I was editing I did find it did take time for marketing to pay off - it seemed like people would file my name away, and when the time came (like six months later) suddenly I would get a bunch of calls.

Hope some of this is helpful; please disregard the rest! And please excuse any typos - I am edited out for today!

Good luck.

publications - How can one prevent a co-author from publishing without consent?

I have been reading about several cases in which a co-author submitted a paper without the consent of another author (for example in What to do after I was named as co-author on a paper, without my consent?).

Consider a situation where one co-author goes on to publish without my consent when I am the first author.

I know the rule for most publishers would legally prevent a co-author from doing this as the submitting author requires consent from all authors. However, it seems that in practice many journals have no practical processes in place to prevent this. The co-author would likely submit to an Elsevier journal. It seems that the Elsevier submission system (EES) would allow them to submit and go through the whole process by themselves without informing me if they wanted to.

Moreover, it seems that for Elsevier journals, only the submitting author is informed of advancements through the process, so that the co-author could indeed go through the whole process without other authors knowing.

If I only find out when it is published, it also seems that I have nothing to do about it. It seems that a retraction would only do more damage to my career as the paper will just stay online with my name and also be tagged as retracted. There seems to be no way if disassociating yourself with a published paper.

I am a bit worried to see that in fact there seems to be no real barriers to a co-author doing something like that. Note again that I am referring to the Elsevier process, though there may be other publishers with a similar process (and potentially the process is not like this for all Elsevier journals).

To summarize, it seems that, at least for certain journals:

• A co-author could submit a paper without the consent of other authors and the journal would not inform or ask explicitly for consent from other authors.


• The co-author could go through the entire process, even up to publication, without any other author explicitly being asked for confirmation.



• Other authors in such a case would not even be informed of the submission or status changes of the paper


• If eventually the paper is published, the only option unaware authors have is retraction, which is likely to do even more damage to their career than the fact that the paper has been published prematurely.

Am I correct in my assessment? it seems like if this is true for even some journals, then the publishing process for such journals has been designed quite poorly.

I would like to know how, as an author, I could prevent such a thing from occurring to me. How can I prevent a co-author from publishing without my consent?

I am aware that the best means is having a good relationship and communication with the co-author in the first place and I will do the best I can in this regard. But I would like to know what other practical means I have of preventing this.

cell biology - Why are certain aneuploidies more common?

Certain aneuploidies such as trisomy-21 (Downs syndrome), trisomy-18 (Edward syndrome), Turner syndrome (XO) etc are more common than others.

I had a vague thought that it is related to chromosome size: the chromosomes which are towards the extremes of size will be affected in an improper segregation event.

Chromosomes 13, 18, 21 and Y are among the smaller chromosomes in humans, and are commonly associated with aneuploidy (but 22 which is also small is not affected). The larger ones are unaffected (X is an anomaly).

I thought that longer ones should be more affected because more cohesin bridges have to be broken, but it seems that is not the case.

• Is there any association of chromosome size and frequency of aneuploidy?

EDIT

• If the difference is because of differential lethalities then does the length correlation still hold true? Smaller the chromosomes, lesser the genes and hence lesser would be the effect of extra copy on the cellular biochemical networks.

Answer

I thought it was just that the other aneuploidies were fatal. They occur as often but miscarry earlier in the term therefore you don't see them. So basically there are only three that are viable 21,18 and the sex chromosome with a number of combinations: XO, XXY, XYY and XXX.

More information here: http://www.nature.com/scitable/topicpage/chromosomal-abnormalities-aneuploidies-290

With regard to the frequency for each chromosome:

For males (i.e., sperm; source):

The mean disomy frequency is 0.15% for each of the autosomes and 0.26% for the sex chromosomes. Most chromosomes analyzed have an equal distribution of disomy with the exception of chromosomes 14, 21, 22 and the sex chromosomes, which display significantly higher disomy frequencies.

Size of the chromosome is frequently reported as a factor in the frequency.

For females (i.e., eggs; source):

The data is obviously harder to attain. One study from IVF treatments show differences in the frequency of different chromosomes at different stages in meiosis.

Is there any chance for a person with BSc in mathematics to get into good graduate level theoretical physics program?

I am a mathematics major without any undergraduate level courses in physics. I am lately interested in physics. Is there any chance for me to go into good theoretical physics graduate program without any background in physics?

I am not sure if this kind of question is acceptable here, though.

ADDED My concern is do Universities even accept students with math majors into physics department without physics courses?

Answer

There are students with math major (and other major) go to physics graduate school, but I think all of them have taken physics courses. The first question you should ask yourself is that why you are interested in theoretical physics. If you were the admission committee and see an applicant said that they are interested in physics but taken no physics courses, what do you think? You must explain it in somewhere in your personal statement.

The first thing you should do is to take physics courses and get good grade on all of them. Also, you should try taking few graduate courses. There are no need to take courses on all topics, you should only have strong interest in few topics such as QM, EM, SM, QFT and string theory. Some of them are very mathematical (that good for you). Doing so can demonstrate your interest in physics.

Second, you might try to apply for master program in physics. It is easier to get in and after 1 or 2 years you can apply for PhD in physics to continue your study.

One more options is to apply for math department, in particular, you should look for applied math. There are usually few professors studying mathematical physics. It is particular true for some countries that the theoretical physicists stay in the math department and experimental physicists stay in physics department. Assuming you have good background in mathematics, it should be the easiest option for you to get in those school and start studying theoretical physics.

job search - Reply ‘no position’ while the job posting is still there (‘HiWi’ position in Germany)

I am third year undergraduate and I am not studying in Europe. I plan to apply for a master at a German institute by the end of this year which is the time for application.

This institute advertised a ‘Hiwi’ (student assistant) position on their website. They link to a PDF file which provides more detail, and in this file they refer to the job as ‘student assistant position’.

I wrote them an email asking about this position. But the group leader replied to me: ‘I could not offer you a position at this point’. This makes me a little confused. I know group leaders face many quite complex situations, but I don’t know how to interpret this. Is it just because he think I am not good enough at the first read of my email and make a polite refusal?

I did not mention that I intend to apply at this university and also that my main motivation is to get research experience (i.e., I am okay with not being paid). Should I mention these two points?

Answer

Student assistant positions in Germany are usually open only to students enrolled at a local university (often where the position is offered, but always in Germany). This is for reasons of social insurance and labour regulation.

You are not enrolled at a local university. In fact, you are studying outside Europe.

physiology - Are human fetuses more likely to be male?

Question: From a physiological point of view, when sex is determined in a human fetus, is it equally likely to be male or female?

Studies in this area typically measure age at birth, where the data would have already been biased. There's a slight imbalance in the human sex ratio, in that there's an overall tendency towards males. However, this could be accounted for in numerous ways, such as abortion.

Fisher's principle suggests there would be an evolutionary tendency towards 50:50 chance.

Answer

The Fisher's principle is not applicable to the fetuses because it has been formulated for parental expenditure and basically states that the ratio of male to female parents (implying that both parties have reached the age of fertility) will tend to 1:1.

There are several mechanisms that we can use and that are mentioned in the canonical paper by James (2007):

(a) there are equal numbers of X and Y chromosomes in mammalian sperms
(b) X and Y stand equal chance of achieving conception
(c) therefore equal number of male and female zygotes are formed, and that

(d) therefore any variation of sex ratio at birth is due to sex selection between conception and birth.

James brings much evidence that none of these conventional beliefs is true. Rather, they are dependent upon many factors: exposure to stress during pregnancy, glucose level etc. He reports that there is an excess of males at birth in almost all human populations, and the natural sex ratio at birth is usually between 1.02 and 1.08. However, the ratio may deviate significantly from this range for natural reasons. (I really recommend reading the paper I linked, it is available for free).

Branum et al (2009) analyze birth statistics in the US taking into account many factors like ethnicity, gestational age and plurality and show that the ratio can increase even more with growing gestational age and has different values among different races.

So, taking everything together, I can say thay YES, the chances for human fetuses to be male are indeed higher.

masters - Can it hurt to put my GRE score on my resume?

If my score is good and if I'm applying for an MS program in Europe, can it give me any kind of edge? The university I'm applying to requires GRE scores for certain programs but not the one I'm applying for. And if it won't be advantageous, can it hurt my prospects in anyway?

authorship - Can I make an exam question for graduate & undergraduate students to find an idea in making a breakthrough in my research?

This question comes in two parts.

1. If I am a lecturer in a field (say, Data Mining) and quite stuck in my research, am I allowed to make exam questions (for undergraduate & graduate students) related to my research hoping that some answers may give me ideas?


2. If I am allowed to do that and supposing that I did, what could I do if a student actually answers my question with a method (s)he is currently working on in his/her own research but has not published yet (which I don't have the means to know of)?

Should I give an announcement or some kind of encouragement to the students who actually give such an answer to finish their research as fast as they can so that I can cite their papers to avoid potential copyright infringements and plagiarism?

Answer

I think you can do it in a homework exercise, but only as a bonus question that is not part of the ordinarily graded questions. Adding it to an exam is not fair, for reasons mentioned in other answers. But rather than using it to find a breakthrough in your own research, use it to find hidden geniuses among the students. Make it very clear that those questions are completely optional and harder than the main homework questions; you may or may not state that they are actually open problems.

There are historical examples of students who solved open problems in homework exercises. For example, George Dantzig:

An event in Dantzig's life became the origin of a famous story in 1939 while he was a graduate student at UC Berkeley. Near the beginning of a class for which Dantzig was late, professor Jerzy Neyman wrote two examples of famously unsolved statistics problems on the blackboard. When Dantzig arrived, he assumed that the two problems were a homework assignment and wrote them down. According to Dantzig, the problems "seemed to be a little harder than usual", but a few days later he handed in completed solutions for the two problems, still believing that they were an assignment that was overdue.

Six weeks later, Dantzig received a visit from an excited professor Neyman, who was eager to tell him that the homework problems he had solved were two of the most famous unsolved problems in statistics.

Of course, when you do against all odds find a hidden genius this way, you can offer to supervise him or her in writing a publication, which should land you co-authorship on the paper.

ethics - Is it ethical to seek a PhD program if you suspect you may want only a Masters?

I'm considering a PhD or Master's in engineering in the US, and I haven't really decided which makes the most sense for me. There are many questions and answers here that mention leaving a PhD program with a Master's and how it's not a "failure" or "dropping out", but it occurs to me: what effect does this have on a person's adviser/professors?

What about references, future relationships, etc? Is it taken negatively or as an insult, or cutting ties, to bow out with the lower degree?

What prompted this question is that a few programs that most interest me state explicitly that there is very little funding available for Masters students (so you are mostly expected to pay your own way), but full funding and additional opportunities are available for those admitted to a PhD program. The way they are worded, they seem extremely interested in good PhD candidates, and not at all interested in Masters students.

I'm not considering seeking a PhD solely to get a Masters/funding, because that's just outright dishonest and I wouldn't stomach such deceit. But, what might the ethics be of not being certain whether you want a PhD or a Masters, but applying for a PhD program?

If one's adviser and/or program and/or professors are explicitly harmed by having someone complete their Masters requirements, then I'd be much more hesitant to even consider a PhD application unless I was certain that's what I wanted. If being unsure is considered normal and the "harm" caused by bowing out of the program with a Masters not so great, then that would certainly ease things the other direction.

To be clear, these departments also specifically suggest you pick Masters OR PhD, and generally discourage you from applying to both. Thus my quandary!

taxonomy - Is there a downloadable list of all species along with their traditional classification?

I'm looking for a downloadable list of all known (or better said, online documented) species in this straightforward format, as an example the European Frog:

Kingdom: Animalia
Division: Chordata
Class: Amphibia

Order: Anura
Family: Ranidae
Genus: Rana
Species: Rana temporaria

I'd like to have this list offline in a structured text or database format that I can parse. If such a list has other useful attributes (credits, distribution, common names), it is welcome, but the above is the absolute minimum I need. I know there are more taxonomy levels in the above system (Species 2000 & ITIS Catalogue of Life: April 2013 ), but I only need these basic 6.

I have been looking at several collections and am having difficulty getting the data that I need. Either the database is incomplete, not accessible as a database, has complicated data structures, or has poorly described and slow web APIs that I cannot rely on.

Conceptually, it seems to me that http://www.catalogueoflife.org comes closest to my needs, yet their download is a tool, not a database. I do see the download has a MySQL folder containing lots of files, but I don't know how to reconstruct it into a database. It seems also that they pulled the page to describe the database download.

As simple as my question seems (I'm not a biologist, so I assumed it was simple), I have wasted several hours coming up empty. I was wondering if anybody has done the work to provide basic species info in an understandable format as requested?

As for species completeness, the 1.3m of Catalogue of Life sounds really good, as I'm currently basing my system on Wikipedia, which only has 180k species.

human biology - Why do mammalian red blood cells lack a nucleus?

How did the red blood cell in humans get to lose its nucleus (and other organelles)? Does the bone marrow just not put the nucleus in, or is it stripped out at some stage in the construction of the cell?

Answer

Red blood cells are initially produced in the bone marrow with a nucleus. They then undergo a process known as enucleation in which their nucleus is removed. Enucleation occurs roughly when the cell has reached maturity. According to one research (Ji, et al., 2008), the way this occurs in mice is that a ring of actin filaments surrounds the cell, and then contracts. This cuts off a segment of the cell containing the nucleus, which is then swallowed by a macrophage. Enucleation in humans most likely follows a very similar mechanism.

The absence of a nucleus is an adaptation of the red blood cell for its role. It allows the red blood cell to contain more hemoglobin and, therefore, carry more oxygen molecules. It also allows the cell to have its distinctive bi-concave shape which aids diffusion. This shape would not be possible if the cell had a nucleus in the way. Because of the advantages it gives, it is easy to see why evolution would cause this to occur. However, since little is known about the genes the control enucleation, it is still not a fully understood process.

salary - Why is it that adjunct faculty positions pay so little?

There's been a series of articles recently [1,2,3,4,5] that basically decry the dismal working conditions of adjunct faculty.

I would like to ask: Why do these positions pay so little? Is it because there is a vast amount of oversupply of teachers? Is it because the Universities have such a diverse range of topics to cover that they cannot afford to hire full-time instructors to cover these courses? Is it because there is decreasing income and funding for academic institutions?

I am curious about what conditions led to this situation where adjunct professors are paid so little.

Answer

The adjunct model seems to be predicated on an assumption that most adjunct faculty are presumed to be employed somewhere else. It's supposed to be a win-win: the institution gets a qualified expert with current, out-of-the-ivory-tower experience; the adjunct gets a chance to scratch a teaching itch, or to work with the university. All this happens for a modest compensation – which turns out to be a bargain for the university, and a little extra pocket money for the adjunct.

I didn't read all five of the articles you linked to in your question, but I did look through three of them. They seemed to be focusing on the depressing conditions for those who are trying to make a full-time living through a collection of part-time teaching assignments. I don't think that's the way the system was ever intended to operate.

Where I teach, I'm an adjunct, and I love the perks. I get to use the campus gym, and I get access to campus library resources. I have a passion for teaching, but I don't get to do much teaching at my full-time job. The extra money hasn't made me wealthy, but it's led to a few lifestyle improvements and splurges for my family. $9,000 isn't enough to live off of, but it goes a long way when you want to renovate a kitchen, take a vacation, or help pay for a wedding.

Moreover, where I teach (a state university in the U.S.), the adjunct rates are not set by the department. The going rate is the going rate, take it or leave it.

My brother once asked me how much my adjunct job paid per hour, if I factored in prep time and grading time. I told him that I never bothered to calculate that, but it didn't matter, because I enjoyed my duties too much to give it up. I'm fortunate in that I'm not doing this for the money, so even the relatively low pay is very much appreciated. I enjoy the challenges of teaching, the chance to experiment with new pedagogies, and the chance to make an impact on the future.

Let me put it this way: Teaching two nights a week for fifteen weeks? $3,000. Staying up until midnight grading final exams? Zero extra dollars. Getting an email from a student from two years ago, telling you about how she's using stuff from your class at her new job? Priceless.

publications - Can we get a PhD in mathematics without publishing?

Do many universities allow students to get a PhD in mathematics without publishing a paper?

publications - How to withdraw ones name from an already published paper

I am having the following trouble. Within a collaboration I was asked to prepare and pre-characterize some samples. I did so and sent the samples along with a report on the characterization results.

A year later I received a first draft of a paper: some paragraphs related to the collaborators experimental technique some copy paste of older papers of his. I thought I could safely ignore this as it was just meant to signal "we are working on this!".

Next thing I get (four months later): Mail from the submitting author

Congratulations, paper accepted!

I asked him to send me the draft: Nothing!

Six weeks later, after having met one of his PhD students at a conference the submitting author sends me the proof from the publisher for proofreading. I come up with six pages of corrections (ranging from basic logical errors in argumentation to manipulative data representation), sent it to all coauthors (I assumed the others also might not have seen the manuscript before) and received zero feedback.

Paper was published two weeks later with most of my grammatical and semantical corrections incorporated.

I asked my boss (also co-author on the paper) how to deal with it. His answer: "Take it as one more paper and forget it!".

However, I do agree with this attitude. Now the tricky part: I never agreed on the authorship nor explicitly disagreed (hoping to bring the paper in a decent shape and considering the amount of work already put in). Should I adress the editor asking to withdraw my name arguing that I basically had not seen the paper? Or should I also point out the obvious flaws which might lead to a complete rejection?

evolution - The Origin of Mitochondria

For a long time I've just accepted, because it is just what everyone told me, that mitochondria became organelles in the cell when they were "engulfed" by another cell which acted like it's host. This is the endosymbiotic hypothesis.

"The endosymbiotic hypothesis suggests mitochondria were originally prokaryotic cells, capable of implementing oxidative mechanisms that were not possible to eukaryotic cells; they became endosymbionts living inside the eukaryote."

However, recently I looked at the wiki entry on mitochondria and saw there that it lists two main hypothesis, endosymbiotic and autogenous.

"In the autogenous hypothesis, mitochondria were born by splitting off a portion of DNA from the nucleus of the eukaryotic cell at the time of divergence with the prokaryotes; this DNA portion would have been enclosed by membranes, which could not be crossed by proteins."

It also states that, given that mitochondria have some striking similarities to bacteria, the most parsimonious hypothesis for mitochondrial evolution is that of endosymbiosis. (This question here deals with some aspects of multiple-occurence/convergent endosymbiosis).

My questions are;

1. 
   

   How strong is the evidence for either of these leading hypotheses (perhaps there is a review article)? Is there evidence that is overwhelmingly in favour of endosymbiosis?

   
   


2. 
   

   Further, are there any other (plausible) hypotheses to explain the origins of mitochondria (with or without supporting evidence)?

   
   

Answer

This is one of the most intriguing questions of eukaryotic evolution. As far as I know and have read, the autogenous theory is not accepted. There are quite some reviews on this topic. Also there is a wonderful book by Nick Lane on mitochondria called Power Sex and Suicide. You would be interested to read it.

There are no sufficient evidences for the evolutionary transition from prokaryotes to eukaryotes which somewhat suggests that this was some kind of quantum jump. For example:

• There are no microfossil records for the evolutionary intermediates


• Almost all eukaryotic features including organelles, syngamy, nucleus etc emerged simultaneously

So to answer how it exactly happened is quite difficult.

As for the autogenous theory; it would have been impossible for the huge eukaryotic cell (the precursor of mitochondria) to meet its energy demands without an organelle like mitochondria i.e. a prokaryote as large as a eukayotic cell wouldn't survive. You may check this post.

There are eukaryotic cells that lack mitochondria (eg. Entamoeba histolytica ) or have one with reduced functionality. However, these are not intermediates in evolution but have lost the functionality in a retrograde manner.

There is one more evidence to support the endosymbiosis theory: There is this observation that organelles that are less numerous in a cell have retained more of their genome compared to those with the organelles that are surplus numbers (eg. plastids vs mitochondria). This is called the Limited Transfer Window Hypothesis which reasons that the organelle to nuclear gene translocation would have happened because of organellar injury and the likelihood of a cell tolerating one is higher if there are more number of organelles.

This article suggests an alternative view that predatory bacteria like Bdellovibrio could have settled in a prokaryotic host. There are other cases of bacterial endosymbiont in a larger bacteria (I need some time to mine up the reference. Read it a while back) but these are not the the ancestors of eukaryotes.

How do I pick good keywords for literature alerts?

F'x has made a very informative post here about staying up to date with current research.

My question concerns the "publication alert" part of it. To be clear: I am asking about setting up an online service, such NCBI PubMed, to send you a notification (for instance, email) whenever a paper matching certain search criteria is published.

The objective is to get a decent number of notifications, but not so many that you are swamped and unable to actually pay attention to them. Also, the notifications that you do get should be prioritized the most important papers.

The biggest problem I am having is coming up with effective keywords. If I try to make myself come up with general keywords (such as those that might be given in the article's own "keywords" section), it seems that I end up with keywords so general that I would get thousands of notifications every week.

Alternatively, I could try to come up with very specific keywords, but how do I select those? What if they are too specific, and an important paper gets published without using my particular obscure keyword?

Surely people are not born with a natural talent for thinking of good keywords. So how can I train this skill?

Furthermore, is there a systematic method to deduce good keywords given a body of "gold standard" relevant literature? (I mean things such as statistical analysis of the text)

I know that it can be worthwhile to focus on certain "big player" authors. But if in a field with thousands of authors (eg. cancer), how does a new researcher map out who is important and who is not? Furthermore, the biggest players are probably PIs of huge labs, who already publish a very large volume of papers, so we are again at odds with the "not too many notifications" problem.

Another possibility is looking at citation metrics to identify the most important papers, as Google Scholar does. But clearly, this is not effective for new papers - who will cite a paper published last week?

Answer

One of the biggest problems is that there are, in fact, waaay to many relevant papers coming out; that's because there are lots of articles published each month in many different fields.

The approach I found most useful was threefold:

• Set up author-specific alerts for the big names in your field. Read both those articles and the citations. They know the literature and will cite stuff you should be familiar with.


• Set up alerts to see when someone cites a seminal paper. In my research, there were certain seminal papers that everyone participating in my tiny subfield would always quote. Find those and set up alerts when someone cites that.


• Read the most popular article(s) of the month (most downloaded/shared/read in your journal of choice) to stay on top of interesting stuff that's going on.

publications - I forgot to add preprint submission (BioRxiv) before the actual journal submission, what can I do now?

I was entrusted to do the entire submission process on my own (previously done by the PI) as a learning process, so I am learning by trial and error.

I was supposed to initiate and complete all the bits in the submission portal of the journal, submit the manuscript to BioRxiv, and then submit to the journal. At least that was the order I was advised to follow.

In the rush of getting things done, and done right, I forgot to submit to the preprint server, before submitting to the journal. Now that I check the author guidelines of the journal (ACS publishing), they advise:

... authors are allowed to deposit an initial draft of their manuscript in a preprint service such as or including these specific preprint servers, ChemRxiv, bioRxiv, arXiv, or the applicable repository for their discipline prior to submission. Please note any use of a preprint server in the cover letter and include a link to the preprint, and as appropriate, state how the manuscript has been adjusted/updated between deposition and submission.

Electronic posting of conference presentations or posters secured by subscription or institutional logins are not considered prior publication works. All other prior/redundant publication is forbidden.

Upon publication in [journal X], authors are advised to add a link from the preprint to the published paper via the Digital Object Identifier (DOI). ChemRxiv and bioRxiv add this link for authors automatically after publication. For further details, contact the Editorial Office.

Since you are supposed to mention the DOI from the preprint server in the cover letter to the editor (which is already written, signed and submitted) I'm thinking that I should not just submit the manuscript to BioRxiv without somehow notifying the editorial office.

The question is how to do that in a nice way. Should I send a mail to the editor-in-chief? the managing editor? I don't want to negatively effect my chances by annoying the editors unnecessarily, but I also don't want to assume anything and make a mistake along the way.

graphics - Software for extracting data from a graph without having to click on every single point?

There are many times when I am faced with the task of extracting data from a published graph (usually a bitmap image in an paper). For example, a scatter plot from which I would like to get a list of individual (x, y) coordinates for the points.

One option is to ask the contact author for raw data. Most will do it, sometimes in nice ASCII format, sometimes in Excel files, sometimes in formats that I cannot open (chemists are fond of software like Origin or Igor Pro). Some authors never reply, or ask questions like “what do you want to do with it?”. In all cases, it takes time. Sometime, it's not even possible (I can hardly email the author of a 1936 paper!).

The other option is to extract the data. I currently use g3data to do that, but for large scatter plots having to click on every single point is tedious. Thus, I am looking for a data extraction software that could recognize individual points automagically, and possibly filter them by point color or symbol used. Is that even something that exists? What other tools can you recommend to work around this issue?

^{I don't think it'd be appropriate to have extra requirements on the software, so I'm happy with free or commercial solutions, running on any OS. Of course, if given the choice, I'd prefer open source software running on Linux and Mac OS.}

Answer

A colleague suggested I use GraphClick, a Mac OS software that includes (according to its website):

• Automatic detection of curves (solid, dotted or dashed), symbols, bar charts, or perimeters of areas


• Frame-by-frame digitization of QuickTime movies

The later is something I had not thought about, but might actually be useful for some teaching needs (analysis of motion from a video). My first experiences are good: the software is easy to use, includes a nice magnification UI, and automatic curve detection works fine if the graph is “clean”.

---

And here's a list of other possible software from this answer on Cross Validated (link thanks to @AndyW and @Paresh):

• Engauge Digitizer (free software, GPL license) auto point / line recognition. Available in Ubuntu repository (engauge-digitizer)


• Get Data (shareware, free trial version, $30 for personal license) has zoom window, auto point / line recognition


• DigitizeIt (shareware, free trial version, $49 for personal license) auto point / line recognition

community - When is it appropriate to decline a review request?

There are some clear reasons to decline a review request, such as conflict-of-interests or not enough free time (e.g., going on a vacation..). But what if you are just not interested in the paper you got (i.e., it is loosely related to what you do, but not entirely irrelevant)?

On which occasions is it appropriate to decline a review request? Does it matter if the review is for conference vs journal?

Answer

There are a few clear reasons to decline a review request, although in complete honesty, I've never actually declined to review a paper yet, so these are all at least "in theory" for me. Some of them are one's you've mentioned, but there are some others:

1. Conflict of interest. This one's pretty clear, though with the way some reviews are handled - based on recommendations, closely related expertise, etc. what actually constitutes a conflict of interest can get a little vague.


2. Lack of time. This is one that people seem to ignore or discount, but it's a big one. If you can't give a paper the attention it deserves, or your review is going to be late (predictably, not because of unforeseen things), then you should probably decline to review it. You're not doing you, the authors, or the editor any favors by making them chase you down for months to get a review.


3. Lack of expertise. If you read the methods section of a paper and your primary thought is "Huh?" not because the paper is unclear, but because its far afield from your expertise, I'd strongly consider contacting the editor for advice and asking not to be a reviewer.

I wouldn't necessarily not be a reviewer due to a failure to find the paper sufficiently interesting. If your expertise is indeed appropriate and the work is not of sufficiently compelling interest, that is a review finding all its own. Additionally, one would hope that you can evaluate the scientific merit of things that - while you are capable of understanding - you might not find directly interesting.

Whether or not it matters if its a conference or a paper likely depends on your field (how important are conferences?) and the particular conference or paper. For example, I might make a special effort to "find the time" for a journal I submit to (or would like to submit to) or a conference I frequently attend, but might not for a journal or conference I've never heard of.

speciation - Evolution in 37 years, is it possible?

I am confused, can evolution ( speciation ) really occur in such a short time ?

In 1971, biologists moved five adult pairs of Italian wall lizards from their home island of Pod Kopiste, in the South Adriatic Sea, to the neighboring island of Pod Mrcaru. Now, an international team of researchers has shown that introducing these small, green-backed lizards, Podarcis sicula, to a new environment caused them to undergo rapid and large-scale evolutionary changes."

Here is a short video featuring the scientist.

Two related articles:

Edit: I asked a similar question previously about two people having 44 chromosomes and their possibility of creating a new species. You might like to read/answer that as well:

Can two humans with 44 chromosomes produce viable offspring?

Answer

I am confused, can evolution ( speciation ) really occur in such a short time?

Well, Evolution and Speciation are not the same. Evolution is the adaptation of an existing species to an environment over generations. Speciation is the development of a new species, and the definition of "species" can vary depending on who you talk to - but a very commonly accepted one is that two individuals cannot produce fertile offspring.

However, the answer is still Yes. Evolution can occur in as little as two generations because that's all the time it takes for a change in the DNA to be exhibited in the newest generation. For instance, Lactase Persistence - which allows the bearers to ingest dairy products without digestive stress into adulthood - has evolved at least twice in humans in separate groups. Both are the result of either one or two point mutations (single changes in a Nucleotide within the DNA). The result is that at one point in time for each appearance of lactase persistence, a child was born that could drink milk into adulthood while their parents and cousins could not.

That is evolution; the child was better adapted to the resources available, and because lactase persistence either...

• Provided a significant advantage over their kin in the environment (which is likely, as being able to digest milk in an agrarian society opens up a new source of energy)...

or

• Didn't hinder the child's ability to grow and produce fertile offspring of their own...

...it has persisted in the populations where it initially evolved.

Speciation is a little trickier, but that's because there isn't a known qualitative way to differentiate species at the genetic level quite yet. It could be a few key gene changes, it could be a whole genome difference of 10%, or a million other factors. Practically speaking, though, Speciation is simply the result of accumulated genome changes that at some point prevent the members of one group from producing fertile offspring with their ancestral group.

Because we simply don't know how much of or where the genome has to change, it's certainly possible that speciation could occur in the same time period as it takes to evolve: Two generations.

Since I'm doubting the wall lizards have a generational time of >37 years (don't mistake it for lifespan, humans can reproduce in our teens - even if we live into our 80's), it's definitely possible that the wall lizards could evolve (and potentially speciate) in such a short amount of time.

With organisms that have a very, very short generational time - like E. coli or other bacteria - you can observe the Evolution of populations in days or hours.

Why do so many publication venues have their own citation styles?

I have noticed that it seems like every other conference has it's own citation style; even in the same field, or subfield. Or at least each provide their own bibtex style (.BST) file.

• Are they actually different styles?


• Is there a historical reason for this?



• Is there a ongoing practical reason for it today?

(I am in Computer Science. I am not sure if this is field dependent)

skin - If cells regularly renew, why do we have scars?

Question may sound bit poetic but I have a pretty basic question here: Often we get a minor wound and cells renew and quickly "cover" it. But when we have deeper wounds, often they leave behind scars. Why does it happen?

I was researching around and saw this comment on a related question:

That's not true - some cells turn over quite quickly, others take months or years, others never replicate.

But how come we get some wounds "completely filled", while others leave scars on almost the same skin/body part? And ok, if a deeper cut has resulted in inner (different type of cells) being damaged, why do we find the scar on epidermis?

Thanks a lot for your guidance.

Answer

Scar tissue formation is part of the normal healing process in which fibrous material braces and pulls the wound together, in other organisms (and young mammals) this process is mild and just serves to temporarily reinforce the damaged tissue as new cells migrate in to begin replacing the missing tissue, sometimes to the point of replacing missing limbs in lizards and amphibians. However in adult mammals and birds the process of fibrous tissue is far more exaggerated, creating longer lasting or even permanent scars, Here the wound keeps filling in with more and more fibrous tissue instead of moving on to regenerating what was there originally. This dense fibrous tissue often prevents new cells from easily migrate into the tissue, essentially stalling the healing process. It seals the wound much faster than the more mild deposition of other animals but can often prevents replacement of the fibrous tissue which would otherwise happen as the missing tissues is regenerated. This mass of fibrous tissue is what we call a Hypertrophic scar. this is why scars can also fade, as cells often can migrate in and slowly replace the the matrix but this is severely limited by the dense packing.

Note there is a second rarer form of scar tissue that can form, called keloid scarring. This form of scar spreads beyond the original wound area and seems to be caused by some form of runaway extracellular matrix deposition. It should also be noted adult mammals sometimes do regenerate decent portions of tissue, albeit not well, possibly because some of the controlling cellular signalling machinery has be lost or reappropriated. All the factors that affect this are not understood and are a main focus researched. We do know it varies quite a bit from tissue to tissue and is not terribly consistent.

It is believed that mammals and birds develop this stronger matrix deposition which leads to permanent scar tissue becasue healing fast is more important for them than healing completely since their metabolism runs so much higher. They can't wait around for it to heal they need to get moving as soon as possible or risk starvation,additionally a stable body temp makes for a more inviting environment for bacteria so sealing the wound is paramount. Thus sealing and mechanically reinforcing the wound is more important than regeneration. As you can imagine the worse the injury the more important it is to plug it fast which is why minor injuries are less likely to scar. This is also why lizards and amphibians end up with less permanent scars they can take the time to better regenerate the tissue. Of course this is difficult hypothesis to test, however there has been some success in getting mammalian tissue to regenerate more by removing scar tissue as it forms or just preventing collagen production.

Evolution is one lang story of "good enough" and scar tissue is good enough functionally that the speed at which it can seal a wound favors it over slower regeneration.

What happens if someone publishes a paper on your current PhD thesis topic

This is not in any way relevant to me, I'm just interested. What would happen if you chose a PhD thesis to work on, and halfway through someone somewhere in the world who was also doing a PhD in the same field published their thesis, which just happened to be the same research that you were doing. Would your research still be considered since it was done independently? Does this happen often? Are there safeguards to prevent this from happening, like would you normally search the academic field to see if anyone else is working on the same topic? Surely that would be almost impossible to do?

Answer

A lot of it depends on how far along you are, your institution, your career goals, and to some extent whether its your fault or not. That is, you DEFINITELY need to search the literature to see if your topic was already studied. But sometimes, someone might just have the same idea because they are thinking about the same issues and reading the same existing literature as you are.

If someone scoops you, it's likely a lot of your work won't be publishable anymore. In some fields it might be possible to publish as a replication (with low impact) or it may be that if you look carefully there is some areas of non-overlap that you can run with. The issue of publication will matter a lot more if you want a career in academia: you need a strong publication record to move on to the next phase of your career. In that circumstance, it might actually be better to delay your PhD just to get some publications, unless you expect you can get a good post doc regardless.

If you are early in your work, even halfway, it may be possible to switch topics. It's also possible all you need is a minor shift. I got scooped. Twice. Both times it hurt, but both times I also realized that there wasn't anywhere near 100% overlap, and my work was still publishable, it just took some extra time to rework things, reemphasize novelty, etc.

Overall, though, your PhD should be awarded for the work you do, not necessarily whether the work pans out. Your institution shouldn't prevent you from getting a PhD if you have been scooped. Negotiating all these issues should be the role of your thesis committee. The thesis committee should be comprised of at least some relatively unbiased professors who can judge whether or not your work is acceptable. The point of the PhD should be to train to be a researcher. Sometimes being scooped is part of the learning experience.

(note: I am answering this mostly from the perspective of biological sciences in the US - of course there may be differences by field and location)

quotation - Quoting a typo: Do I really have to do "sic", or can I just fix the sentence?

I've got an upcoming work in which I quote a couple sentences from a scholar's book. There's an unambiguous typo in it; the author just switched a few words around.

Do I really have to quote him verbatim, adding "sic" to point out the error? Or can I just "quote" him, with the typo fixed?

graduate school - How do I plan for my PhD now that I have graduated with a Masters degree without thesis?

A bit of background: I am an Indian citizen with an undergraduate degree in Electronics from India and a Masters degree in Electrical Engineering with a minor in Computer Science (Funny, it is called a minor, given that 60% of my credits are from Computer Science Dept.).

I am currently working as a software developer with a company in Boston, MA. I was involved in some research work during my grad school, but however, nothing materialized and I decided to graduate with a coursework only option (with many projects as a part of coursework). Needless to say, I burnt a lot of bridges along the way which eliminated even the minutest chance for a strong letter of recommendation.

I wish to, however, apply for a PhD in Machine Learning and/or Algorithms, at least 2 to 3 years from now. The job I am at currently is not a research oriented job. I am doing a bit of research by myself with the data sets available online.

Given that all of the PhD applications in the US, most in Europe need strong letters of recommendations, if not publications, how can I now set things straight in the coming years. What should be an ideal line of action and is a PhD with a good adviser, possible, at all?

Note: I am currently working on some Machine Learning related open problems on large data sets, but I am not sure how much can I get done, while working full time in a non academic environment. Also, I do not have any reputable papers as yet.

publications - What are the challenges to publishing a paper when you have a huge number of collaborators?

Following on from this question, I'm really curious to know about the logistics of large scale collaborations when it comes to publishing a paper that everyone has some contribution to.

To summarise, the recently published paper on the detection of gravitational waves had an author list with over 1000 names and 133 institutions. The sheer number of people involved would make publishing a single paper somewhat less straightforward than, say, a small research group based at a single institution.

So, to my questions:

• 
  

  What were the logistical challenges of having over 1000 authors/collaborators when it came to publishing a single paper?

  
  


• 
  

  How were these challenges overcome?

  
  

I want to make this question as specific and answerable as possible, so please edit this question as appropriate.

human biology - Does an allergic reaction kill body cells?

I have wondered what actually happens in an allergic reaction that causes the symptoms such as pain, rash etc.

Is it possible that the human body actually kills its own cells in the process?

Answer

Is it possible that the human body actually kills its own cells in the process?

Yes it is. It is happens not only as a result of allergic reactions (see comment of @terdon). But in case of allergy our body have 3 methods for killing own cells.

• Cytotoxic, antibody-dependent (Type 2 hypersensitivity) The antibodies produced by the immune response bind to antigens on the patient's own cell surfaces.These cells are recognized by macrophages or dendritic cells, which act as antigen-presenting cells. This causes a B cell response, wherein antibodies are produced against the foreign antigen.


• Immune complex (Type 3 hypersensitivity) Occurs when antigen-antibody complexes that are not adequately cleared by innate immune cells accumulate, giving rise to an inflammatory response and attraction of leukocytes



• Cell-mediated immune memory response (Type 4 hypersensitivity) is an immune response that does not involve antibodies, but rather involves the activation of phagocytes, natural killer cells (NK), antigen-specific cytotoxic T-lymphocytes, and the release of various cytokines in response to an antigen.

See Wiki about types and diseases and about Hypersensitivity

Is PhD worth it when considering your career in industry

I'm a beginning doctoral student in the field of Machine Learning and I've been given several contradicting opinions on whether a PhD is worth it or not. I don't want to spend the rest of my life in front of a desk doing research, but I would like to deepen my understanding on my field. I am interested for a career on industry. Some people say I'm wasting my time for doing the PhD and some people say it is worth it. My plan at the moment is to finish PhD as fast as possible and then continue my career in industry when I'm still young. Any opinions or recommendations on what I should do? :)

P.S.

I want to add to this that I have already 2,5 years of work experience on industry (IT) already. For example I designed and implemented an online language skill tester for my university and have worked as a software engineer. So I wouldn't be entirely newbie in programming after I finish my PhD...

My subject is about applying the techniques of Machine Learning on Big Data.

Thank you for any suggestions and guidelines :)

Answer

You haven't really defined what you mean by "...when considering your career" in the subject of this post. On the one hand, you say,

I would like to deepen my understanding on my field.

If your goal is to deepen your understanding, one way to do that is to get a PhD. You can also do this on your own, without getting a PhD, but you'll find a more structured path and (possibly) more resources if you go down the PhD route.

On the other hand, you say,

I am interested for a career on industry.

Are you interested in industry because of the money? If that is the case, you're most likely better off earning a full income and "moving up the ladder" during the time you would spend in graduate school, which means you should forego getting a PhD to concentrate on the money.

If you're interested in a career in industry because of reasons outside of financial considerations, then you have to think about what kinds of jobs you're looking to take in industry. If you're satisfied that your current skills and educational level will make you competitive for the jobs you want, you should probably reconsider the PhD, and to "deepen your understanding" in a different way. Then again, a certain percentage of people want to get a PhD for the challenge and for strictly personal reasons, removed from the job details themselves.

If the jobs you want to get are generally given to PhDs, then you have your answer already -- get the PhD to make yourself competitive for those positions.

I suggest writing down all of your long-term goals, and then weighing them against the time and cost (and opportunity costs) of getting your PhD. If after all that you still don't have a good answer, you might consider continuing with your program for another year and just postponing the decision until then. Eventually, either you will get your PhD, or you will be convinced that it is better off that you stop the program (but the decision may get harder the closer you are to finishing).

united kingdom - Student comments from meetings frequently overreacted to by senior 'management'

I've worked at several UK institutions over the past 10 years and one aspect that consistently raises my eyebrows is the reaction to student-staff liaison meetings* from senior members of the team. Often, these meetings are merely an opportunity for the 'representative' to voice their own concerns and are clearly, obviously, not representative. Yet, time after time, when a far fetched and often untrue complaint/comment is made in one of these meetings, senior staff go into full meltdown and start firing off perplexing and demotivating e-mails asking for things to be fixed because the students are unhappy. The simple matter is, as previously stated, these are often not representative views and the sample size is one: the person who said it.

In any other context, a sample size of one would be immediately disregarded by those with only rudimentary scientific knowledge. No sound conclusion could ever be drawn from that sample. Yet, if this sample happens to be one student in the context of a 'staff-student liaison' meeting then it appears to be absolute fact to senior 'management'.

My question is for fellow academics from across the world, do you have this nonsense to deal with? What do you tell 'management' if they ask you to change based on comments from a single source? Am I being too touchy about it?

I am a lecturer at a UK institution.

*These meetings are usually bi-yearly where student 'representatives' voice any matters arising on their degree

---

For the those thinking "Jeez, this guy gets a lot of bad comments". I have not once been on the receiving end of this but I know good colleagues lose sleep over it.

I also see the benefits of these meetings, I do not wish for them to be scrapped.

Why do humans lose subcutaneous fat tissue with age?

Why exactly do humans lose subcutaneous fat tissue with age? It appears that we either lose fat cell volume or we might actually be losing the number of fat cells with age.

One hypothesis is that as the vascular system weakens with age, the fat cells on the perimeter of the body shrink and die because they don't have enough blood flow to sustain them. The problem with this hypothesis is that subcutaneous fat loss is very gradual and starts during young adulthood and continues. It also happens in very fit individuals too.

Another hypothesis I read before was that subcutaneous fat is loss because of a drop in estrogen levels after menopause. This hypothesis doesn't explain why men lose subcutaneous fat with age. Also, women start to lose fat on their hands and upper cheeks long before menopause starts.

physiology - If targeting a certain daily water intake, do you have to compensate for beverages that promote diuresis?

Please forgive my ignorance on the topic and I hope this is a "on topic" question here. It was a toss up between this SE and Physical Fitness SE but I want a more scientific answer.

---

I came at a impasse in a conversation with another fitness enthusiast. They stated that if you are targeting your water intake during the day then drinks with a diuretic effect (tea/coffee) count negatively towards that water intake total.

So, is it true that one should over-compensate if drinking these diuretics? Or does the water content of drinks like coffee and tea balance out or even positively hydrate you?

Answer

The notion that tea and coffee are diuretic and don't count in your daily waterbalance, is an urban myth. At most, both are mildly diuretic (if any).

The assumption is based from an old study from 1928 with only three participants. While the small number of participants alone is a good reason to reject the study (it would never get published today) because the findings would lack any statistical power, the design is also questionable. You can find this story in reference 1 if you want to read it.

It is known that large amounts of caffeine indeed have a diuretic effect by increasing the blood flow to the kidneys and inhibiting the reabsorption of sodium. This leads to the outflow of water and an increased production of urine. See reference 2.

However, reference 3 found that this diuretic effect (which is only present at high concentrations of caffeine) diminishes due to tolerance when people regulary drink tea or coffee. They do not see any diuretic effect from normal tea, coffee or caffeinated beverages.

The explanation for this effect is most likely a misinterpretation of our observation. We seem to produce more urine when we drank tea or coffee, but we wrongly compare it to a time when we drunk nothing. If we would compare it with a time, when we drank the same amount of water, the effect (you have to pee more when you drank something) would be the same.

Drinking tea and coffee will therefore help to keep our waterbalance, as would water, juice or softdrinks.

References:

1. TOLERANCE AND CROSS-TOLERANCE IN THE HUMAN SUBJECT TO THE DIURETIC EFFECT OF CAFFEINE, THEOBROMINE AND THEOPHYLLINE


2. Caffeine and the Kidney: What Evidence Right Now?



3. Caffeine ingestion and fluid balance: a review.

evolution - Are humans the only species who drink milk as adults?

I was drinking a glass of milk the other day and that got me thinking that no other animal to my knowledge drinks milk past their infant stages. One could argue that cats might but it isn't good for them to do.

Are humans the only animal that are able to drink milk as adults and not have it cause issues?

Of course, I know some people do have lactose intolerance too.

Answer

Good observation!

Gene LCT

Mammals have a gene (called LCT C/T-13910) coding for the lactase enzyme, a protein able to digest lactose. Lactose is a disaccharide sugar found in milk.

Expression of LCT

In mammals, the gene LCT is normally expressed (see gene expression) only early in development, when the baby feeds on his/her mother's milk. Some human lineages have evolved the ability to express LCT all life long, allowing them to drink milk and digest lactose at any age.

Today, the inability to digest lactose at all ages in humans is called lactose intolerance.

Three independent mutations

Tishkoff et al. 2007 found that the ability to express LCT at an old age has evolved at least three times independently. Indeed, they found three different SNPs (stands for Single Nucleotide Polymorphism; it is a common type of mutation), two of them having high prevalence in Africa (and people of African descent) and one having high prevalence in Europe (and people of European descent). The three SNPs are G/C-14010, T/G-13915 and C/G-13907.

Pastoralist populations

Lactose tolerance is much more common in people descending from pastoralist populations than in people descending from non-pastoralist populations, suggesting a strong selection for lactose tolerance Durham 1991.

Selective sweep

On top of that, Tishkoff et al. 2007 focusing on the locus 14010 (one of the three SNP's mentioned above) showed that there is a clear selective sweep (which is a signature of past and present selection) around this locus.

They estimated the age of the allele allowing lactose tolerance at this locus (allele C is derived, the ancestral being G; see nucleotide) at around 3,000 to 7,000 years (with a 95% confidence interval ranging from 1,200 to 23,200 years) and a selection coefficient of 0.04 - 0.097 (with a 95% confidence interval ranging from 0.01 to 0.15).

I recommend reading Tishkoff et al. 2007. It is a classic, is short and is relatively easy to read, even for someone with only basic knowledge in evolutionary biology.

I don't really know... but I would think so, yes!

Drink vs digest thoroughly

As @anongoodnurse rightly said in his/her answer

"Drink" and "digest thoroughly" are two different things

Pets

According to many dog health websites (such this one for example) claim that there is also variance among dogs where some dogs are lactose tolerant and others are lactose intolerant. I could not find any paper on the underlying genetics of lactose intolerance in dogs or other pets. It is not impossible our pets have also been under selection to be able to digest lactose as we humans could have given milk to them. It is also possible that pets do not actually produce any lactase at adult age but rather that some pets are just able to deal with having indigestible lactose in their guts! But then again, "Drink" and "digest thoroughly" are two different things.

Tits and robins in 20th century England

A funny and famous case is the case of blue tits and robins in the 20th century, in England. At that time, in England, the milkman was bringing the milk at home in the morning and would leave glass bottles with a simple aluminum cap in front of people's home. At some point, blue tits and robins learnt that by pecking through the aluminum they can get access to the milk. See this (non-peer-reviewed) article that tells the story.

Somewhat related

There are already a number of good posts on milk digestion in humans on Biology.SE. Consider having a look at:

job search - When during the application process should a candidate mention that their spouse is also looking for a job

When during the application process should a candidate say that their spouse is also looking for a job?

The issue of academic spouses who want to find employment close enough to live together is colloquially called the "two body problem", and it is a perpetual challenge for job applicants.

The italicized question came up in a recent comment thread on this site, and I realized there is no post on Academia.SE about it. So I am making one.

I have seen many answers to the question, which usually fall between two extremes:

1. 
   

   Don't mention your spouse in any way until you have a job offer, then bring up the question of a job for your spouse. Sometimes the advice even recommends taking off wedding rings during interviews.

   
   


2. 
   
   

   Mention the spouse immediately in your application cover letter.

   
   

Each has its advantages and disadvantages, certainly, depending on the specific circumstances of the applicant and school being applied to.

Because many people, like me, have a perspective limited by their own life experience and the schools they have worked at, I expect that there should be many different answers to the question, expressing different perspectives. I think that collection of answers would provide an extremely useful resource for job applicants.

In the thread I linked, another user left a comment:

... I'd particularly be interested in seeing answers supported by data, as there seem to be a wide range of opinions, each supported by apparently convincing logical reasons and/or anecdotes.

I don't want to limit answers here to ones based on data, but answers that do include broad data would be particularly welcome.

This kind of question has also been asked on MathOverflow.

computer science - Best-practice models for "research" code?

I have been a professional software developer for a number of years, I'm also an academic researcher - and my research has involved lots of software development.

I sometimes feel as though my industrial experience has been a hindrance in my research, as the goals of writing software in a research context feel contradictory to the goals in industry.

In industry, code needs to be (ideally): maintainable, bug-free, refactored, well-documented, rigorously tested - good quality - best practice says that these things are worth the time (I agree).

In academia, the goal is to write as many quality research papers in the shortest possible time. In this context, code is written to run the experiment, and might never be looked at again (we are judged on our papers - not our code). There seems to be no motivation to write tested, maintainable, documented code - I just need to run it and get the result in my paper or whatever ASAP. Consequently, the "academic" code I've written is poor quality - from a software engineering perspective.

The problem is that I either spend too long making (unnecessarily) getting my "research" code to industry-quality, or I publish work based on "bad quality" code, and I feel like a fraud.

My career progression is dependent on me writing "bad" code!?

The "craft" of software development is a huge subject - but where is the best practice for academic research? Nobody writes unit tests for conference paper code!

Does anyone find them in a similar situation? Does anyone know of formal methodologies for "research" code?

publications - Pen name similar with real name: Zu Yangzu instead of Zu Yang for papers

East Asian countries have some very common last name. This is so common that there are 10s of millions people with the same last name. In the western tradition of citing papers by authors' last name, this makes East Asians very indistinguishable with each other.

I somehow feel this makes it hard for Asians to be remembered and known in western academia.

If someone's name is "Zu Yang" on the passport, what if he just puts his name as "Zu Yangzu" in his papers?

Will it cause some academic trouble?

Well, if some people are using pen names on their papers and they experience no trouble, then that's an enough evidence that I also can do this.. but I don't know any case. Does anyone know?

Answer

In CS, no publisher I am aware of strictly requires the name on the paper to be your unaltered true (in the sense of "as written on the passport/birth certificate/ID card/...") name. Customs in other fields might differ, although I see little reason to.

However, some issues might arise where the name from the paper has to match with some other information about you. These issues can sometimes be solved, but you should be aware of them:

Funding agencies may wish to see what you published. If you use a different name on the papers than what you are known as to the agency that funds your position, your participation in a paper you indicate to have contributed to may not be obvious.

Publishers sometimes ask for some meta-information such as your personal website on your institution's website. If you have no influence on how you appear on that personal website (again, because that information may be administered by your employer), the connection might again be non-obvious. The publisher might not care, but readers who see your paper and look at your website might assume an association mistake by the publisher unless the website explicitly states in a prominent place you are using a pen name.

Things might indeed get more complicated if you are in a field that puts emphasis on conferences:

• Your conference registration might be coupled to the publication of your paper, in a way that the former is a prerequisite for the latter to happen. Some conferences explicitly ask upon registration which paper (number) you will present, but others will try to do a simple name-match. If you decide to register with your pen-name, though, a chain of other problems might ensue:
  
  
  
  • Conference registration is sometimes coupled with hotel registration, and the hotel will need to know your real name.
  
  
  • Your funding agency probably needs some registration confirmation from the conference, which may have to show your real name to serve as valid proof that you really paid for and attended the conference.
  
  
  • Even before that happens, you may need a confirmation of acceptance of your paper as a valid proof that you are required to embark on the respective conference trip, which can be more difficult if the confirmation of acceptance is seemingly directed at a person of a different name.
  
  
  
  

While it is a minor issue (because the existence of workarounds is likely), sometimes employers provide business cards with the information they know about you, without a way to indicate something such as a custom name. Handing out such business cards on conferences (point from above), or also other kinds of meetings with collaborators from other organisations, might be confusing with respect to your publication history.

Note that the workplace-specific items are also relevant because they might apply to any future employer of yours, not just the current one.

writing - Which is the better scheme for a poster: “tell a story” or “important first”?

In an attempt to make a poster of my work, I search for tips on the internet and books and I meet two opinions that conflict with each other:

Tell a story:

1. Why do we choose this (Objective)


2. How do we do? (Experiment, simulation, etc)


3. What do we find? (Result/Conclusion)


4. What can we do more? (Future work)


5. Reference

Important first:

1. Result/Conclusion


2. Objective


3. Experiment, simulation, etc


4. Future work


5. Reference

In my opinion, I will choose tell a story if the audience is not in my field, and important first if the audience has a good knowledge on what I do. But I am still confused if this is right. And should I apply this to my paper work?

Answer

Posters are hard to get right. They require design skills and knowing what the core message of your paper is. Presenting them requires people skills. Aside from this, different areas seem to have different criteria and norms when it comes to this so if you want to fit in you should try to follow those.

---

But in general, most scientific posters I've seen are really terrible in terms of tools for communication: they have far too much text and get into far too much technical detail. For example, on this site posted in the comments on the question, there's some nice visuals but all of the posters have, in my opinion, far too much text.

One excuse for a lot of text on a poster I often hear is that people will can read them on their own between sessions or whatever. In my own area and experience, I don't buy this argument: that's what the paper is for and I rarely see anyone reading these literal walls of text in their spare time.

The advice you've gotten from the internet seems to follow that thinking: the thinking of printing a full paper on a poster in bullet form. An A0/A1 wall of text is not the best way to sell your work, nor is a boring traditional narrative of introduction, methodology, results, related work, conclusion or whatever.

I say this from the perspective of someone who's gone to too many poster sessions and gotten trapped at a poster where someone for some reason decided I would be interested in spending 20 minutes silently listening to them recite the slightly abridged version of the paper that they had for some reason decided to printed on their poster. One guy even seemed to expect me to leave after he was done. After he had finished reading the conclusions at me he had a look on his face that said "who's next?".

Okay so that's one extreme.

---

For me, the secret to a good poster presentation is two-fold: the poster and the person in front of it.

In terms of a poster session, people will probably have some food with them, people might even have some drinks, you should not assume to take more than 5 minutes of their time, they're probably not going to get all the technical details and they're definitely not going to read a wall of text. At least one would hope that they wouldn't read it because that would imply that you'd be talking to yourself since they cannot read text and listen to you at the same time (unless you're reading aloud the text that is).

When I was working with students on posters, I would always advise them to dispose of the idea that they can or should communicate the full technical depth of a work on a poster to a passer-by in five minutes.

Their goal should be to motivate and communicate enough of the core ideas of the work to convince people passing by their poster that the paper would be worth taking the time to read and to teach them something cool.

In terms of that goal, I would bring the student to a white-board and tell them to pretend I was a conference-goer who knew nothing of the work but we met at a coffee break and I asked them to tell me about the work. They can use the board or ... if really needed ... they can point to something in the paper. While presenting, they should appear enthusiastic (without overselling) and emphasise why the work is important ... why I should care, and what the main results were.

They should also listen to what I say ... it should be a conversation. They should make sure that the person they're talking to is following them ... that they don't just launch into a 10 minute soliloquy at the first person that looks in their direction but that there's an element of interaction.

After that exercise whatever they were trying to represent on the board or whatever they needed to point at in the paper: that and pretty much only that is what goes on the poster ... diagrams, examples, main results ... things they can point to help them explain verbally what the work is about.

Then we'd sketch out a poster and try make it visually appealing ... try to tell a visual story with it ... try to make it attractive for people to come over and ask what it's about.

Not that the end result is always perfect, but the approach does lead to a better result in terms of a communication tool than the wall-of-text approach that seems so bizarre to me in the world of scientific posters.