Will auditing impact graduate school admissions?

I am in my last semester as an undergraduate and in a class in a field that I do not consider myself knowledgeable (but interested). I fear that I will be stressing rather than learning. The audited class will be a part of my final transcript, it will not appear until I am done with the class. I am also applying to graduate schools this semester, will this impact me? (It is not a part of my major, it relates to my minor, but I have fufilled the requirements for my minor so it is still an extra class, and as an auditor I do all the work (tests and assignments) and come to every class because I want to learn)

ethics - Asked again to review a paper, when the authors don't wish to modify it

I have received a manuscript to review for a journal. The interesting thing is, I had already reviewed this article (exact same title, abstract and author list, almost exact same content) for another journal a few weeks ago where I recommended that it be published, but only after major revisions of both form and content. When I first reviewed it, I wrote a two-page review, listing some questions and several “actionable” comments, ranging from some concerns about exactness of the text (some conclusions didn't seem fully backed by the results) all the way down to trivial stuff (grammar, a few typos, graphic issues with the figures, etc.).

Now, the manuscript has come to me for review again, but it is almost unchanged from the first version. None of the serious stuff has been addressed, and even most of the trivial stuff was not fixed (there's at least one remaining typo, and the figures still aren't fully legible). However, I think this behavior from the authors is clearly a bad signal, which should be somehow conveyed to the editor: they're not willing to amend their work, and would rather do some journal-shopping.

What would you suggest me to do? Should I just re-send my earlier review? Add a note to the editor about my knowledge of the “history” of the paper? Or maybe even include it in my review, so the authors are aware that people know of their behavior, and maybe feel bad enough to change their ways?

---

PS: I wrote it in the present tense, but it's actually a story from my past. I'm not sure I did the right thing at the time, and I think it's better to actually formulate it as an open question…

Answer

Personally, I would inform the editors of both journals. For the new editor, I would attach your earlier review, and recommend rejection.

Then it's up to the new editor to decide what to do in this situation. This falls in the category of ethical problems, and I think most journals recommend that reviewers contact the editor immediately in such a situation. Perhaps the journal has a policy for this, or the editor may discuss the matter with other editors or the chief editor.

Let me add why I find it unethical. Peer review relies upon the volunteer labour of anonymous reviewers. Reviewers may invest significant time, and do not really get anything in return. If authors of a manuscript completely ignore reviews, and instead submit an unchanged manuscript somewhere else, I would, as a reviewer, be quite annoyed. At the very least they could reply to the reviews, state point-by-point that they disagree, refuse to change anything and then submit it somewhere else; but completely ignoring is wasting peoples time.

phd - How to respond to the teacher who puts the feet up while talking to student?

A friend of mine who is from Japan told me that his professor in USA puts the feet up while talking to him. He was saying that he felt very bad with that. Is this acceptable culture in USA academia?

Answer

I've done my PhD in Japan, and have had much contact with professors in America and Japan.

The academic relationship and work culture in both countries are very different. In America it is generally not regarded as bad when someone puts their feet on the table while talking to you.

I had bosses and advisors in the US who did this. However, in Japan, the advisor-student relationship is more respectful and professional.

I would like to tell you that you should ask the professor to refrain from putting their feet on the table, but if they do it in their office, it is pretty much up to them. Since the office is the professor's space, I do not think it is your friend's business to ask them not to do it.

biochemistry - How is ATP involved in muscle contraction?

The sliding filament mechanism as explained by my text does not elaborate on how ATP is involved in the cross bridge binding and contraction process. How does muscle contraction utilize ATP?

In my text explains this is the procedure for a contraction:

1. Ach released by motor neuron cross cleft and binds to motor end plate


2. AP generated in response to binding of Ach gated channels and propagates down T tuble


3. T tuble triggers Ca2+ from sarcoplasmic reticulum


4. Ca2+ binds onto tropinin on actin filament and removes tropomyosin


5. This opens up sites for myosin to attach to actin using protein heads


6. Actin filament is pulled toward the center of sarcomere, causing contraction

I see that the action potential definitely needs ATP in order to be generated, aside from that I am surprised that the actual contraction via cross bridge binding does not seem to need ATP.

Answer

ATP prepares myosin for binding with actin by moving it to a higher-energy state and a "cocked" position.

Once the myosin forms a cross-bridge with actin, the Pi disassociates and the myosin undergoes the power stroke, reaching a lower energy state when the sarcomere shortens.

ATP must bind to myosin to break the cross-bridge and enable the myosin to rebind to actin at the next muscle contraction.

The muscle contraction cycle is triggered by calcium ions binding to the protein complex troponin, exposing the active-binding sites on the actin. As soon as the actin-binding sites are uncovered, the high-energy myosin head bridges the gap, forming a cross-bridge. Once myosin binds to the actin, the Pi is released, and the myosin undergoes a conformational change to a lower energy state. As myosin expends the energy, it moves through the "power stroke," pulling the actin filament toward the M-line. When the actin is pulled approximately 10 nm toward the M-line, the sarcomere shortens and the muscle contracts. At the end of the power stroke, the myosin is in a low-energy position.

After the power stroke, ADP is released, but the cross-bridge formed is still in place. ATP then binds to myosin, moving the myosin to its high-energy state, releasing the myosin head from the actin active site. ATP can then attach to myosin, which allows the cross-bridge cycle to start again; further muscle contraction can occur. Therefore, without ATP, muscles would remain in their contracted state, rather than their relaxed state.

Summary from: https://www.boundless.com/biology/textbooks/boundless-biology-textbook/the-musculoskeletal-system-38/muscle-contraction-and-locomotion-218/atp-and-muscle-contraction-826-12069/

Also this:

Essentially look up the cross bridge cycle (http://muscle.ucsd.edu/musintro/bridge.shtml)

I would also suggest reading it from the master himself here: Huxley, A. F. "Muscular contraction." The Journal of physiology 243.1 (1974): 1-43.

Suitable introductory book on Bioinformatics for a computer scientist?

Do you have any suggestions on a suitable introductory text on bioinformatics for a computer scientist? Any recommendations with pros and cons of different books would be appreciated. I'm mainly looking for a brief introduction since I'm a novice to this field.

I found some books like

1. Systems Biology by Edda Klipp,


2. Introduction to Bioinformatics by Arthur Lesk



3. Bioinformatics For Dummies


4. Bioinformatics and Functional Genomics by Jonathan Pevsner


5. An Introduction to Bioinformatics Algorithms by Neil C. Jones and Pavel A. Pevzner

I would like to develop software related to sequencing applications, so any suggestions should ideally aid in this goal.

human biology - How many, and how severe, are known single gene polymorphisms for obesity?

A fairly recent meta-analysis of studies examining the association between adult obesity and polymorphisms of the FTO gene (Peng et al., 2011). The paper looked at 59 studies and concluded that, "FTO may represent a low-penetrance susceptible gene for obesity risk", although the association was weaker (or non-existent) for some ethnic groups.

Are other polymorphic genes which are currently known to be more strongly associated with obesity risk than the FTO gene?

Answer

MC4R, TMEM18, GNPDA2, KCTD15, NEGR1, BDNF, ETV5, MTCH2, and SH2B1 have also been identified as being associated with adult onset obesity risk, however FTO currently appears to be the one with the strongest evidence. For example see Thorleifsson et al. (2009), Elks et al. (2010) and Willer (2009)

independent researcher - How to choose a good research problem?

I am working to get a PhD, maybe next year this time around. Currently, this is my second year. I have published 3 papers. All of them are not about one problem but consider different problems. My strategy to find a research idea/problem is given below.

1 - Read papers whose titles are either interesting or I have some apriori understanding of those titles.

2 - Understand those papers as best as I can. That is, I try to understand each detail presented in the paper except the simulation results (this is because I think simulation results are hard to reproduce).

3 - I analyze the paper and try to find a very small problem which can be addressed (i.e. I can solve it) by the methodology of the paper.

4 - If I am successful at step 3 I start working on that problem otherwise I repeat the process from step 1.

By applying this strategy I have been able to write 3 papers and I have submitted a fourth (I am not satisfied with those papers because at very best they can be considered average papers). But my concern is that the problems addressed in those papers do not belong to one area. As far as I have seen, for the profiles of some of the renowned researchers in my field their PhD work is focused on one area. One main thing I console myself with is that almost all of those researchers had good supervisors. My supervisor does not even read the draft/reviews of my papers and the suggestions that he provides during the meetings are so broad that the problem becomes intractable. Under these circumstances what are your opinions: Is there any better strategy to do research?

I will be very thankful to you for providing me suggestions or commenting on my dilemma.

ecology - Are there any animals that gradually approaches the predator to search for food?

I was wondering if there is an animal (or insect, bird, etc.) that eventually comes close to its predator to search for food, but only does so if it couldn't find food in the environment it is in. So it first searches part of the environment farthest away from the predator, but gradually comes closer and closer to the predator as it searches for new food. That is, over time it dares more to come closer to a, lets say ambushing predator, since it has ran out of food (or perhaps for other reasons). Similar behavior is ok, but note that the key behavior that I want in the animal is that it "gradually" comes closer and closer to the predator.

Thank you.

Answer

The behaviour that you describe is common in most animal species, as part of the natural trade-off between access to food, minimizing risk, habituation and hunger. Animals usually choose to forage in high-quality habitats that has a low risk of predation, but if food sources are depleted (or competition and/or territoriality is high) they will move to other areas with lower food quality or higher risk (since they are desperate for food).

In general, the effect of predators are both direct (killing of prey) and indirect (changes in prey behavior to avoid predation). The indirect effects means that prey will often choose to feed in habitats that are suboptimal from the perspective of forage quality, which will have negative effects on their foraging efficiency. These types of indirect effects of predators are often labelled as 'The landscape of fear' or the 'ecology of fear' (see e.g. Brown et al, 1999). However, as food resources run out this will trade-off against the fear of predators (along with possible habituation effects), which will lead to the behaviour you are asking for. You might also be interested in Gamelius et al (2014), as an example of how prey behaviour can be influenced by the presence of predators (here, roe deer and lynx), but there is a large number of studies looking into these issues. The review "Fear in animals: a meta-analysis and review of risk assessment" by Stankowich & Blumstein (2005) will also give you a good background and many examples.

The use of scarecrows is a simple way to understand the 'landscape of fear'. By placing a scarecrow in a field you strengthen the "landscape of fear" (by adding an artificial 'predator'), which will modify the behaviour of perceived pest species (prey), so that they avoid the areas around the scarecrow. However, if the animals you want to scare away ("pests") run out of food they will take larger risks and venture closer to the scarecrow to forage. Over time, they will also become habituated to the scarecrow, and will discover that it doesn't seem to pose a big threat, which will decrease the effectiveness of the scarecrow.

References

publications - Is it appropriate to ask an author for an English translation of a paper?

I have found an interesting paper which is very relevant to my research. After reading the abstract in English, I would like to continue to read through the methodology and its discussions. However, only the abstract is available in English, and the content is in another language which I don't know.

I really want to read through the content as some of the figures are very interesting to me. I have tried to translate it using Google Translate, but it is very difficult to understand.

Is it appropriate to send a polite email to the author, asking for a translation of your paper in English? Does the author have the obligation to do so?

Answer

As far as I'm aware there is no obligation to provide a translation of a published paper from one language to another.

I think it would be rude to ask for a translation of a paper. However, it would generally be fine to enquire as to whether such a translation exists, or whether similar work has been published in English.

More broadly, it may be in the author's interests to provide an English translation in order to increase the impact of his or her work. If the work is really important to you, you could always pay for a translation. At the extreme end, perhaps where there are a large number of important works in a particular language, you may even want to learn the language.

How to write a CV for a PhD application

I am currently looking to apply for a PhD program in physics. I was wondering what sort of information I should include on my CV/how it should be formatted?

Given that the PhD is a research degree, I thought I should highlight research experience? I am currently working on a paper from a summer internship that will shortly be submitted for peer review. How do I draw attention to this? My Master's research project is still ongoing - how do I mention this at such at early stage in the project?

Any tips at all will be very helpful.

Thanks

Answer

Academic CVs vary quite a bit from a traditional CV in ways that will help you illuminate your research experience. While there are plenty of (conflicting) guidelines about how to structure or format an academic CV, the following sections are generally included (if you are at the stage of your career that they are relevant), not necessarily in the order below:

• Basic demographic information (name, contact address, possibly birthdate and marital status and photograph, depending on the country)


• Brief statement of your research area/interests/objectives


• Degrees obtained/in-progress (institution, supervisor, thesis title, GPA)



• Academia-relevant jobs (e.g., research assistantships, teaching assistantships, tenure-track appointments)


• Publications (especially in the case of junior researchers, also papers that are under review/in submission)


• Awards or honors or grants


• Teaching experience (including in labs, if you are a junior researcher)


• Supervisory experience (if you have helped co-supervise other students)


• Service (reviewing duties, committees on which you've served, organization of workshops/conferences, editorial work)


• Research project experience (where you can outline work that you have done in a research lab)


• Presentations and seminars (especially if you have been to any conferences or workshops)


• International network (if it is important to show that you have international collaborators)


• References (presumably your previous supervisors)

In your case, specifically, the fact that you will have submitted the paper is quite important, because at that stage you can list it as a paper (under review) on your CV.

Regarding your masters thesis, you can indicate a working title for your thesis when you list your Masters under your education. This implies research experience and the area in which the experience has been acquired. You can furthermore describe under your research project experience what skills/roles you have had in the lab in which you have conducted your Masters research. (You can also indicate here your summer internship, since it sounds like it was research-focused.)

Furthermore, you can highlight the especially salient points again in your cover letter, especially if there are elements of your Masters experience that relate to the specific PhD programme to which you are applying.

job search - Can non-teaching staff write teaching recommendation letters for academic jobs?

When applying for academic jobs in the US, one is often asked for a recommendation letter from someone who can attest to your teaching abilities. Suppose someone has been involved in various workshops, programs, discussion groups, etc. about pedagogy through a Center for Teaching Excellence (or a comparable office) as a graduate student or postdoc; is it acceptable for a non-teaching staff member from this center, who has facilitated such activities, to write a teaching recommendation letter for academic jobs? In particular, how are such letters perceived by hiring committees?

Edited to clarify: I was envisioning that such a letter would be in addition to a teaching letter written by a faculty member in one's department.

Answer

I would view the letter favorably if the letter writer made it clear that they had observed the candidate's teaching.

I've seen some TA training programs where the TA's are observed in the classroom and get formal evaluations by someone involved in the training program. A letter of recommendation from such a person would be quite valuable from my point of view (and assuming that the letter was positive this would be helpful to the candidate.)

On the other hand, if the person that you're considering is just a faculty development specialist who runs workshops that you've attended and hasn't directly observed your teaching, then such a letter would be much less useful (read useless) to me.

botany - Why are some plants frost tender?

Why do some plants have the ability to stand frost, while others can't? Does it have to do with the size of the water vacuoles in the plant cells?

Answer

All cells are susceptible to cold, but freezing is particularly difficult. If the water in the cells freeze, it would usually burst the cells (water expands when it turns to ice) and tearing the cell membrane (totally killing it).

Some plants and animals have adapted to colder temperatures by putting antifreeze proteins in their cells. A lot like adding antifreeze to the radiator of a car, this lowers the freezing temperature of the water in the cell.

So the answer is that some plants have adapted to colder climates with the help of additional genes. There are other things that have to change too - the chemical reactions in the cell will go haywire when temperature changes too, so lots of genes must make adjustment for a fully cold adapted plant.

research process - What are some of the issues one should keep in mind while choosing between a fully funded offer and another with no funding?

I have been offered a place for a masters program in 2 places. One which is fully funded and another one where there is no aid that has been offered at the time of admission.

I guess if the everything else was the same between the two then the answer is obvious, which is to go for the funded one. But the problem in my case is this: In the fully funded case I have been offered a place in a research group I have no primary interest in (and no previous knowledge of) and something which I would not have definitely chosen if I was given a choice. So in sum, although it comes with a lot of money, the work is something I'm unsure if I will enjoy.

In the second case, there is no aid. The tuition fee + living is something which is not completely unaffordable for, I hope to manage those with loans and some family money. Aside that, I feel there is a lot of flexibility (or at least some flexibility), as I can choose my domain of work and my advisor once I have enrolled, and maybe been through a semester. Also the coursework here is a lot more closer to my preferred area of research.

Additional info: Comparing the two universities as such, the second one (the one without aid) is higher ranked than the other one (with full funding).

So given all this, how do you think I should make a decision and what is your opinion on the same?

Edit: Both programs are research-based and require a thesis.

teaching - How can teachers reduce student suspicions in discrepancies and irregularities of grading?

From experience, many teachers dislike it when students compare grades, but that often shows the discrepancies and irregularities in the grading system. What other methods should teachers implement in order to keep grading transparent and fair?

Consider the following situations in your answer:

1. 
   

   Curved Grades

   
   


2. 
   

   The possibility of an error in grading, which leads to an imbalance in the grade distribution.

   
   
   

Some teachers immediately assume that just because a student wants to compare papers that he/she is just interested in increasing their grade. This is not the case! Some teachers make mistakes so instead of brushing it off, by assuming that students want to "grade-lawyer" or the like, they should consider the possibility that an error has been made. The goal of this question is to reduce such responses.

Answer

Something I used to do (I no longer teach) was to grade in such a way that there should not be an issue if any student compared his/her graded test with any other student in the class. And this certainly happened in my classes (indeed, I sometimes did this myself when I was a student), from the first classes I taught in 1983 to the last classes I taught in 2005. By the way, I taught math. I suspect the methods I describe are much easier to carry out in math than in some other fields, such as literary criticism or philosophy.

Something I started doing after a few years of teaching was to photocopy my solutions/rubric sheet and handing a copy of it back with each student's test. Before this, I often handed out solutions to save class time (and office hour time), and at some point I realized I could save even more of my personal time by simply handing back what I had already hand-written for grading purposes, without bothering to rewrite (or type) it again in a neater form. The solutions I used for grading purposes were often brief, but for rubric purposes I would always include steps that I expected some students to miss, so it actually worked fine with most students when they consulted it to see what they did wrong or how to correctly work the problem. And for those places where I was too brief for a particular student, they tended to consult with their neighbors sitting next to them and together they almost always managed to figure things out, so I tended to only get the less trivial types of questions. As for the rubric, what worked best for me was to treat the rubric as a "work in progress" in the sense that I made grading decisions whenever a certain type of error showed up, rather than trying to anticipate them in advance.

One policy I had and which I often reminded students about was that they should never be afraid of asking me about a question for fear that their grade could decrease. If they saw anything that seemed to be an inconsistency in grading (and this only happened on very rare occasions because I tended to document for myself almost every kind of mistake made as I graded tests), then I wanted them to let me know. If in fact I did make a mistake, then my mistake would never lower their grade, but it could increase other students' grades if my mistake was an inconsistency in how many points were counted off for a certain type of mistake on their part. Also, if I saw on a student's paper brought to me where I made an oversight by not counting off for something incorrect, then I would mark in ink a correction (so the student wouldn't at some later time think what was incorrect was actually correct) and include a comment that this was found after the tests were graded.

One issue I used to often see students and teachers arguing about was points taken off for correct answers that were obtained by not entirely complete work. I learned early on that this can cause trouble when trying to justify your grading to students. The most straightforward way I found to handle this was to simply design problems whose solution requires all the things you feel are important, and of course often reminding students when working problems in class prior to a test what type of work is acceptable and what type of work is not acceptable. For example, the standard elementary calculus method for determining the global maximum and global minimum of a continuous function on a closed and bounded interval involves finding the values of the function at the critical points (where the derivative is zero or undefined) in the interior of the interval and the values of the function at the endpoints of the interval. So if you give a problem where both extrema occur at the endpoints, or both extrema occur in the interior of the interval, then the student could get the correct answer using correct (but not entirely complete) mathematical reasoning by only considering the critical points or by only considering the endpoints. The way to fix this is to design the problem so that one of the extrema is in the interior and the other extrema is at an endpoint. Better still is to arrange it so that there are at least two critical points, with at least one critical point lying outside the interval and at which the function's value is greater than the global maximum on the interval or less than the global minimum on the interval.

mathematics - Do graduate schools care more about my grades in math courses or my general GPA?

I'm currently a junior in mathematics at UIUC. I have been doing pretty well in my math courses (mostly A and A+). I will be completing a graduate course in topology, a second course in abstract algebra, and a complex analysis course before I graduate. I feel that I can work hard to maintain good grades in my math courses, but my non-math courses are not that good (some B and C's).

• Do graduate schools care more about my math courses grades more or my general GPA more?


• Will poorer marks in non-math courses hurt my chances of getting into good grad schools?

titles - What is the meaning of “Samuel C. Collins Professor”?

I would like to know the specific meaning of Samuel C. Collins Professor in the above screenshot. It is a title for MIT faculties or the award with the same name (Samuel C. Collins)? Or something else?

Answer

It's a named professorship, which means a couple things. Generally, endowed chairs are better paid and have some extra funds associated with them. These are typically funded by a gift to the Institute. In this case, somebody presumably gave a gift in honor of Prof. Collins, who was a pioneer in low-temperature work.

Dr. Samuel C. Collins, Professor Emeritus of the Massachusetts Institute of Technology, internationally known as the father of practical helium liquefiers and founder of the MIT Cryogenic Engineering Laboratory, died on June 19, 1984 in George Washington University Hospital, Washington, DC.

In 1946, Dr. Collins and his colleagues at MIT built what became know as the Collins Helium Cryostat. The device provided for the first time reliable, relatively in expensive and adequate supplies of liquid helium. His invention was of great interest to physicists because it opened the door to extensive experimental low-temperature physics

The existence of the endowed professorship is a honor to the memory of the eponymous Samuel Collins, and it is an honor for the current faculty member who holds it.

phd - Can I publish parts of the Ph.D thesis as a paper in a journal?

I recently finished my PhD thesis which will be published as a book soon. Now I'm wondering if it's possible or allowed to submit parts to a journal?

Normally the process would be the other way round I think: Submitting papers and "gluing" them together for the thesis. I've read the guidelines of some journals which state "that the work described has not been published before" or that "Papers must present scientific results that are essentially new".

Answer

As a general rule, you cannot publish anything as original research that has already been published. (You may be able to reprint it in other venues, but most research journals do not do this.)

Of course, the trick is what counts as "already published". Nowadays, many publishers (including all mathematics publishers, for example) do not count informal distribution on the internet as prior publication. It's common not to count extended abstracts from conference proceedings, although the journal may require some revisions or extensions. Nobody counts submitting a dissertation as prior publication, even if the university makes it available for download or purchase, and technical reports are generally in the same category.

On the other hand, publication as a "real book" definitely counts as prior publication and would rule out journals. Of course, this just brings up the question of what a "real book" is. Basically, if it's published by a serious academic publisher, with some nontrivial selection and editorial advice, then that counts as publication. On the other hand, if it's some random publisher printing copies of Ph.D. theses and selling them online, then you could make a strong case that it's not really published (and that this is not so different from ordering a dissertation copy).

However, I think you need to discuss this explicitly when submitting your paper. For example, you could add a sentence to your submission letter along the lines of "This work is based on my thesis from University X, which is available for sale by Y but has not been traditionally published". It's much better to deal with this upfront than to have someone later ask "Wait, why is someone selling copies of this work online?"

photosynthesis - Where does all the carbon go?

I found it hard to get numbers on global primary production, but apparently it's somewhere around 50-60 $Gt / year$ for carbon content in the terrestrial production, and a similar figure for the oceans. Global oil and coal extraction together are around 10 $Gt/year$, only a part of which is pure carbon (iirc, around 80%). Since carbon in the air actually increases, does that mean that most or all of the carbon fixed in Net Primary Productivity go back into the atmosphere through consumption and destruction of the biomass?

I was assuming that the biosphere in total was fixing more carbon that it emitted, and that the surplus was what turned into oil and coal. But with these figures it looks a lot more like a full circle that nets to zero input / output. Which is true, or is that unknown?

Answer

Good question! The way that the carbon budget stays balanced was a bit of a mystery until recently. The amount of carbon in the atmosphere (and the rate at which it was increasing) was lower than models suggested that it should be, given rates of photosynthesis, respiration, and other carbon releasing processes. Somewhere, there was a "missing carbon sink" that wasn't being accounted for. After many years of debating whether the sink was terrestrial or aquatic, it turned out to be a little of both (which is the conclusion to just about every debate in ecology), although somewhat skewed towards the terrestrial (I think). Forests were sequestering more carbon than had been thought, and so were oceans to some extent (although ocean sequestration relied on a chemical reaction that is in danger of reversing if the water warms up too much). For a thorough account, see this article.

But it sounded like you weren't wondering what the missing sink was so much as how there continues to be enough carbon in the air for plants to photosynthesize (if I'm interpreting your question correctly). Carbon gets back into the air for the most part because of cellular respiration, which all organisms, including plants, do. Net primary productivity takes plant cellular respiration into account, but there are still tons of living things on earth eating plants (and thus taking in their carbon) and then breathing it back out after they break down the carbon-containing molecules for energy. There is also natural combustion and volcanoes and such putting carbon back into the air.

EDIT (to address the new part of your question): Oil and coal were produced when large quantities of carbon were buried deep under ground (and thus subjected to lots of pressure) for thousands of years. This is suspected to have happened during the aptly name Carboniferous era, which featured giant plants and, scientists hypothesize, no decomposers to break them down. Since we have much decomposers now, and much smaller plants, oil and carbon are not currently being produced. This is why we call them non-renewable resources. By extracting them from the ground and burning them, we are taken carbon that had effectively been removed from the pool of actively cycling carbon and adding it back in.

The carbon cycle doesn't really have input or output (except the occasional carbon exchange with outer space), because it is defined as already including standing sinks like oil and coal. When we take carbon out of a sink, like oil or coal, it needs to go somewhere else. Terrestrial and aquatic sinks can store some of the additional carbon that we're adding to the not-underground part of the cycle. However, they can't store all of it, so some is staying in the atmosphere instead.

Business School professors - how different are they?

I recently saw a listing of professor salaries at various departments in Stanford. I found that the folks at GSB earn significantly more than what other Dept. people do. This is the motivation for my question:

1. 
   

   How different are B-school professors? Many of them work on areas that lie on the intersection of Operations/CS/Economics/Applied Math. But why do they enjoy a greater pay (if at all they do)?

   
   
   


2. 
   

   Are industry contacts available easier for B-school faculty when compared with engineering or science department professors? What sort of projects do B-school professors work on in collaboration with the industry? How is the pay-sharing deal between the industry, the prof and the university worked out?

   
   


3. 
   

   How different is teaching MBA students from engg. or science undergrad students? Does teaching MBA eat up more time or is more demanding than usual?

   
   

Answer

I can address questions 1 and 2 (although for 3, all I know is that my friends say it is very different).

1. 
   

   When you are negotiating over salary, your leverage is determined by the best alternative you have. To keep from losing you to another employer, your job must offer a better combination of pay and benefits than anyone else (including benefits like job security, having interesting colleagues and students, having flexible hours and the ability to choose your own projects, etc.).

   
   

   People in the humanities have very little leverage except from other academic jobs. Mathematicans have more, because there are applications in industry or government, so they get paid somewhat more, but this leverage is limited by the fact that many mathematicians don't want non-academic jobs. Computer scientists have a lot of leverage, and business school faculty have even more.

   
   

   So basically it comes down to this. Business school faculty often have expertise that is in high demand outside academia and could earn them a lot of money, and there's at least a stereotype that they care more about monetary compensation than some professors do (which makes sense, given their interest in business). This means that to attract excellent faculty, business schools have to pay enough that job applicants would rather work there than in the business world.

   
   

   In principle, this is no different from other departments: literature faculty also have to be paid enough that they don't leave for the business world. It's just a question of how much that is.

   
   


2. 
   

   This really depends on the subfield. Business school faculty are certainly more likely to do outside consulting than scientists are, but there are no universal rules (some business school professors do none at all, and some scientists run their own companies). Occasionally, a company will sponsor a university program according to some negotiated agreement, but consulting generally does not involve a pay-sharing deal. Instead, the faculty member simply consults part-time for the company, without using university resources, and is paid directly by the company. In the US, universities typically allow a certain amount of time to be spent on outside consulting, for example one day per week, with no special approval needed.

   
   

brain - Why is the prefrontal cortex called such?

Pre means before. Frontal means front.

What does cortex means? Brain?

Is it the front most part of the brain? Is it located at the most frontal part of the brain and that's why it's called prefrontal cortex?

Is morality processed at ventro medial pre frontal cortex or at anterior singular cortex?

My background: I am a programmer. I just want to understand humans brain the way a programmer understand computer. It seems that we don't have CPU. We have huge analog based memory. And we got registers instead of tons of abstract variables. Understanding why certain part of the brain is named under certain things will help me a lot in remembering where exactly that thing is and why. It's something very useful in my ways of learning math and programming.

Basically there are 2 theories.

1. Prefrontal cortex is named as such because it's before (or in front of) prefrontal lobe.


2. It's because it's behind prefrontal bone (the way other brain lobes are named)

Some people told me to just look that up on wikipedia. If you can show me something in wikipedia explaining the exact answer I am looking for I will be very happy.

Answer

The prefrontal cortex (PFC) is a part of the frontal lobe (Fig. 1).

Lobe means

[A part] demarcated from the rest of the organ by a fissure (crack), sulcus (groove), connective tissue or simply by its shape. For example, there are the frontal, parietal, temporal, and occipital lobes of the brain.

Cortex means

The outer or superficial part of an organ or bodily structure (such as the kidney, adrenal gland, or cerebellum or a bone); especially: cerebral cortex

The frontal lobe is called as such, because... it's in the front of the brain.

The prefrontal cortex is called that way because it forms the frontmost part of the frontal cortex. Prefrontal means

anterior to or involving the anterior part of a frontal structure

Anterior meaning

situated before or toward the front

Indeed Siddiqui et al (2008) mention:

The anterior part of the frontal lobe referred in the literature as ‘pre’-frontal lobe has been simultaneously referred to as ‘frontal granular cortex’ and ‘frontal association cortex.’ The anterior most portion of the frontal lobe is occupied by the PFC...

<sub>Reference
- Siddiqui et al., Indian J Psychiatry (2008); 50(3): 202–8</sub>

^{Fig. 1. The frontal lobe includes the prefrontal cortex (PFC). source: Socratic}

advisor - What to do when you hear many bad stories about your supervisor on the first day of your PhD?

Today was the first day of my PhD. It's a very prestigious institution and I was extremely excited to start. However, it seems there is a general feeling of discontentment with people in the group and I was told some stories that, quite frankly, shocked me to the point where I was legitimately considering packing up then and there.

I was told that the supervisor of this group has extremely suspicious working practises, blocks papers from students to give the credit to 'preferred' students, has insanely unrealistic expectations (I was told that some students were expected to work through the night regularly), blocking people from graduating to get more cheap labor out of them, and many more things. The term "psychopath" was thrown about a lot.

I have recently completed my master's in a group where there was an extremely poor PI with an incredibly abusive and parasitic attitude towards the group. I don't really wish to go into it because I want to maintain anonymity, but suffice to say that I do not want the same experience in my PhD.

As you may realise, I'm extremely concerned that I've made a truly terrible decision and I would like some advice going forward. I realise that this is only my first day, and I am not going to make any rash decisions without more context and experience, but what should I be looking out for? How do I protect myself from abusive behaviour? And, most importantly, how do I decide when enough is enough and I should cut and run?

I would really like to get the PhD as I'm extremely passionate about the subject, so in order keep a science career possible I think if the option to quit is on the table, it would have to be in the first year. I don't however think that a career in science is worth the exchange of the toll on my mental health that an abusive boss will cause.

Answer

I believe you should step back and reconsider your options. If you gather any solid evidence supporting what you have been told, start focusing on your next step full time.

Strategically, you must realise you probably find yourself in an advantageous position. I believe you're being paid or at least supported as a PhD student. From what you said, this is exactly where you wanted to be. You have plenty of institutional resources and time in your hands. Make use of these, to your favour. You have received privileged information about serious issues in your group, right at the beginning. Not many are that lucky.

I once found myself in a similar situation. I joined a group far from home, as a PhD student. You know the scene: moving elsewhere, arranging rental, basic furniture, saying goodbye to the world, and there you arrive fresh in the cool morning to start a new life. Within 4 days of work my closest colleague closed our office door during lunchtime, and told me the workplace was absolute crap. That "the boss" clearly only liked having pretty girls as students, and on top of that we were both outsiders from other institutions. So that we would have to live off scraps of whatever is rejected by locals -- funding, data, attention. And I had no salary yet. I seriously considered packing up and leaving. But I didn't. I decided to stay stay and measure myself to "the boss".

Long story short: it worked. For four bloody years. It all proved true. Examples: The "boss" didn't make any effort towards securing my salary, but after I cornered and yelled at him at least he signed the necessary papers: I got the funds. He hinted reallocating my funds to lab equipment "for the girls", but I vehemently denied and summarised by an email statement with copy to others. He asked me to keep raw data file records, I gave him incomplete sets. Etc, etc, etc. Towards the end of my PhD I hired a lawyer regarding a conflict with the department (I had exposed plagiarism by a local big-shot) and clearly seeing a lawyer around reaffirmed a safe distance to my "boss". I was usually left alone.

Main advice here: being ready to quit makes you ruthless. I wasn't too afraid of dropping my PhD from start so I played all cards. My focus is in getting things done, not degrees. This "ex-boss" is an insecure professional who apparently never had anyone stand up against him before. Also I had full support from a co-advisor who was highly interested in our project, and that guy does have a strong, political personality. I went through my PhD between this delicate balance of power. My "boss" was eerily uncomfortable (I believe scared) in my presence and my co-advisor mediated any significant conflict towards the completion of the collaboration. I finished my PhD fairly easily (from a technical point of view) and today I remain active in the same topic of research.

I am not saying you should do the same. I am not saying it was easy or usually comfortable. Perhaps I should have left and gone elsewhere. But it worked nonetheless. Because I was warned and thus made up my mind, and a strategy. This is what I recommend you to do.

Good luck.

research process - What are the time demands on a PhD student who is helping set up a lab?

I am mulling over pros and cons of different advisers and a quirk I have found with some of the newer professors is the issue of lab start up activities. I have seen some anecdotes online about it being a bad deal overall, but I wanted to pose a few questions to the community on academia...

A few questions

1. What constitutes as normal and what is a red flag for PIs requiring start up assistance?


2. Are there benefits to being involved heavily with lab setup if you are not really committed to the academia route?


3. What generates the time sink that seems to overburden most students?


4. How can you mitigate this impact to time to degree?


5. Where does one draw the line between beneficial experience vs being taken advantage of?

Any anecdotes, tips or advice on evaluating would be much appreciated

Answer

From what I have seen in general for molecular biology labs, there is generally a risk. Some of this risk is connected to the PI and some of it is connected to factors outside their control. I am in my 7th year right now and finishing up but my lab just moved across the country to set up a new lab. While this does not affect me, we have rotation students and I can see the impact it is having on them.

1. What constitutes as normal and what is a red flag for PIs requiring start up assistance?

This will vary based on the lab's research needs. You can expect to be involved in a lot of organization/inventory, equipment setup, purchasing, account setup, and above all, a lot of waiting around. If the PI has a lot of specific needs within the building, then there may be specialized construction that has to take place. This could take week to months - both for the actual construction as well as general red tape and unforeseen delays.

In general, you should know that your research will almost certainly be delayed. However, there are other ways to use your time that I elaborate below.

For red flags, I would say that you should try to determine the funding situation of the lab and what grants are active. There is no point waiting around if you have to wait even longer afterwards to get started on funding to come through. If you notice that the PI has had the lab space for 3-6 months and still has no progress, that could be a major red flag. On the other hand, the PI could be using that time very effectively to write grants and make connections. This is very situational.

2. Are there benefits to being involved heavily with lab setup if you are not really committed to the academia route?

This depends on what you chose to do instead if you are not following the academia route. If you work in industry - say R&D or testing for a major company or a career technician, many of these skills may be of use to you. Other potential benefits could relate more to your PI and future research. For example, a startup lab may have a new, enthusiastic professor exploring new areas of research. This can be an exciting environment to be in. There may be new students to change up the dynamic. It might be a great environment to bond with colleagues and so forth. This depends highly on the PI in question.

As NMJD pointed out in the comments, many of the tasks you will be involved in during lab set up could be very useful if you ever decide to stay in academia. You will be ordering equipment, setting up new technology, and budgeting for most of your academic career. This experience could also serve to prepare you if you ever start a lab of your own.

3. What generates the time sink that seems to overburden most students?

A lot of the burden comes from waiting time (which isn't exactly a time sink). Setting up labs take a while but it isn't physical labor or time involved that takes the longest. Much of it comes from processing, financial constraint, and red tape.

I would be far more worried about these kinds of issues that may happen after setup:

• Delays in setting up animal facilities/breeding pairs or animal lines.


• Cell culture contamination problems in a new building/room.


• Weird technical variability in experiments.


• Getting used to new department/building procedures


• Filling the responsibilities of departed graduate students that took care of the day-to-day in the lab



• Lack of mentorship or guidance

4. How can you mitigate this impact to time to degree?

Depending on the nature of the setup and how far along the lab is, you may be able to use this time to become deeply familiar with the literature in this field or participate in grant writing. This would be excellent for your training and is very important. Take some statistics classes - it is far more important than most molecular biologists will have you believe!

Get to know people. Get to know the field and co-workers. Go have drinks with other labs and learn about their research. Find collaboration opportunities. If your program requires you to be a TA, get that out of the way early on. Focus on your classes.

You can use this time to either prepare for the lab post-setup or get things out of the way that would interfere with your research later.

5. Where does one draw the line between beneficial experience vs being taken advantage of?

Ultimately, I think you really need to talk to students in the lab or those nearby to get a better sense of what it's like "from the inside". You can only glean so much from the outsider perspective. Just know that in most cases you are taking a risk. But you can offset this by using your time wisely. If it's research you really want to do, it may be worth the risk.

If the trade-off between the time spent waiting and working through the bumpy starts are not outweighed by the research opportunity that could be provided then it is not worth it. If you find yourself wasting time, doing menial labor, and see no end in sight for the start up it's not worth it.

You have to decide if it's worth it and it can be difficult without already being there.

Good luck!

abiogenesis - Synthetic life creation - status of attempts

First I apologize for my incorrect English and for lack of modern knowledge regarding the subject (I studied biology a long time ago).

I'm interested to find out:

• 
  

  if there were successful attempts of life creation from conditions that we suppose were dominant on early Earth

  
  


• 
  

  if there were not, are such attempts still being conducted?

  
  

To clarify, by "life creation" I mean the accidental creation of entire organism in conditions of organic compounds, water, electricity, radiation etc. being present (Abiogenesis).

If this is already answered here, I'm sorry for asking, I have researched this, this, this and this question with no luck.

Answer

There have been lot's of attempts, no success so far, a few groups are still working on. However, many steps forward have been done in the last decades.

Starting from the Miller experiment which demonstrated that the building blocks of life chemistry can be obtained starting from fairly simple chemical compounds. Following, Luisi and Szostak showed that 1) nucleic acids can polymerize without the help of enzymes and 2) autocatalytic micelles form spontaneously in many different conditions. It is also important to remember the work of Otto that showed how different molecules can self-replicates.

There are many more examples reported in the literature, still, the complete "creation" of life from matter has not been yet accomplished. However, the results from the experimental work done so far suggest that it is only matter of time and lots of combinatorial work. Unfortunately, there are little to no investments in this field. It's very hard to get the funds needed to start an international cooperation (like the one made to sequence the human genome or to build the CERN's Large Hadron Collider) with the goal of actually making life in the lab. I think that the work of a few (uncoordinated) groups will not get to the goal in the next few years.

publications - What do you call an academic who puts their name on an article they didn't write?

In the medical domain, it frequently happens that papers are written by a pharma company or it's contractors and then given to an academic to publish.

The word "ghostwriter" seems to be appropriate for the person who actually wrote the paper. What's the best word to describe the person who is officially the first author of such a paper but who had little input in it's writing? I'm searching for a specific word to categories the behavior.

Answer

Phrases like "guest author", "honorary author", or "courtesy author" have been used to describe this practice.

References:

copyright - Public dataset without license: what is allowed?

Many public scientific datasets are accompanied by a license, for example variations of Creative Commons are used quite often. However, in many cases public academic datasets lack any licensing information. Here are two examples:

At PhosphoSite we find it is "created by Cell Signaling Technology is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License", so permissions of usage are clear from the license.

Here is an other dataset where we don't see anything about licensing, not even a statement that the data is free to use for academic purposes. It only states that "can be downloaded", but what can I do after downloading? Can I redistribute it, modify it, sell it? From the context I suppose they intended their data for public use, they are happy if more people use it so they get more credits and citations. But this is just an assumption.

The copyright holder is clear in both cases, the permissions are missing in the second case.

I am wondering, if I write a software using this data, or I construct a more complex dataset including this data, what solutions are legally correct:

1: The software downloads the dataset at each user's own machine from the original source and processes it. However this is not always possible or not easy to implement.

2: Distribute a copy of the original dataset, or a modified version, with attribution to the original source. This is more problematic, I think, but I am not expert in law.

Asking for permission is an obvious solution, but in case of dozens of datasets, it is a tedious and long process to contact all the copyright holders, and wait for their responses. Also, some datasets are supplements of published papers. In this case, if the journal has a license, e.g. Nucleic Acids Research is published under Creative Commons, is this valid for these datasets?

Answer

This may vary by country, but in the US at least, the default terms (if no alternative is specified) are "all rights reserved", which means that you are not allowed to reproduce the work (the dataset), prepare derivative works from it, sell/rent/lease it, or publicly perform or display it. In particular, redistributing it to others is not allowed. In practice, the authors may be fine with it, but legally speaking, you're not allowed to redistribute the dataset in the form it was published in, without having explicit permission (which could be provided by a Creative Commons license, for example).

If you wanted to reproduce the dataset in a different form that conveys the same information, that may or may not be allowed. It would be up to a court to decide whether that counts as a derivative work or just a use of the underlying ideas, and a copyright lawyer could advise you better on whether your desired use is legally acceptable.

You are allowed to read the published dataset and use the ideas contained within it (i.e. the data) to draw conclusions. Copyright law does not allow for the restriction of those rights. I think doing an analysis on the data and publishing the results of that analysis (but not the data itself), as you would do in the process of writing a paper, is generally considered to be fine.

Do professors in Germany have other payment than their standard salary?

I checked the salary scale for a W3 professorship position in Germany. The annual income is about 75K Euro which seems pretty low for someone managing about 20 people. Is there any other payment beside the base salary? For example, some additional payment from DFG/EU projects or for supervising students?

Answer

As Dirk writes, W3 only gives the Grundgehalt (base salary), which varies by state. As a public servant, you will automatically get a few hundred EUR on top if you are married and/or have children (Familienzuschlag). Note also that in some states (Bayern, Hessen, Sachsen), your W2 or W3 Grundgehalt will currently increase in two steps after 5/12 or after 7/14 years.

You can supplement the Grundgehalt with various Zulagen. These are pay increases, not one-time bonuses. You can get Zulagen either for a set period (befristete Zulage, i.e., a temporary one), or for the rest of your working life (unbefristete Zulage).

• 
  

  You can negotiate so-called Leistungszulagen (a performance bonus), for instance if you manage to get lots of third-party money, publish a lot, or supervise a lot of dissertations, or similar things. You typically discuss multi-year targets with your dean and/or university president or chancellor.

  
  


• 
  
  

  Some German states (Brandenburg, Bremen, Hamburg) currently give you a non-trivial Grundleistungszulage without any preconditions.

  
  


• 
  

  You may get Funktionszulagen if you hold particular offices, like being the dean or managing a larger group, or managing a specific institution or institute.

  
  


• 
  

  If you get an offer from a different university, you will start haggling with both the new university and the one you are at. Both usually want you, so both will offer you a Berufungszulage (a "job offer pay increase", at the university that extended the offer), or a Bleibezulage (a "staying pay increase", at the university that tries to keep you). In contrast to industry, this kind of haggling is normal. (In industry, if you get an outside offer but stay in exchange for a higher salary, your manager will usually assume that you won't stay much longer.)

  
  

As a brand-new professor, you may be able to get a small initial Berufungszulage, but most other Zulagen will only be negotiatable after a few years.

The Deutscher Hochschulverband is a good place to look for additional information. This is basically a union for professors and almost-professors in Germany, and they offer coaching to their members. Very much recommended in your first (and subsequent) salary negotiations - they know what you can reasonably demand and what not. A membership is definitely worth the dues. They also publish the pay scales currently here, in German, although this link will likely rot over time.

In addition, you can get additional money from outside sources:

• 
  

  You can have consulting contracts in industry. You will usually need to clear this with your university, and your outside commitments will likely be capped at 8 hours per week or similar, but this can of course still mean serious money.

  
  


• 
  

  If you are a professor at a medical school or a Universitätsklinik, you will be able to see private patients and take home some of their payments, although this has been getting less lucrative in recent years, with the clinic keeping a larger cut from younger professors. You could set up your own practice on the side, but this would again be subject to limitations set by your employer.

  
  


• 
  
  

  As Wrzlprmft notes, you can get a little money out of the Verwertungsgesellschaft Wort, or VG Wort - see some information in English here. It essentially disburses monies as payments for people using your copyrighted works (they get their money from various sources). It's a very German institution. This will usually not be a lot of money, especially if you publish with a lot of coauthors. Here is what Academia.SE knows of VG Wort.

  
  


• 
  

  However, if you do publish a book, you will be able to keep any payments from the publisher. This will again usually not be a lot, and it's not specific to Germany.

  
  

---

Finally, note that a professor in Germany is a Beamter (public servant). This means that you pay far less in social security contributions, since you by definition can't lose your job (so no joblessness insurance contributions), and the state will pay your pension (so you don't need to contribute - although saving for your old age is still a good idea). The state also pays for part of your medical bills and those of your dependents (Beihilfe), and since you are a good risk (see above on not losing your job), you will get good deals on remaining health and other insurance policies. Bottom line: out of 75k EUR, you will take home a larger fraction than if you earned the same amount in industry.

etiquette - Lecturer ridiculing me in front of class for making a mistake

The situation is, that I have a B.S. from computer science and I was awarded for my final thesis. Because of this I was offered a position in research, where I'm working for the 3rd month now.

My colleagues told me, that the best way is to study another subject, more concentrated on theoretical mathematics. So I changed my field and this year I'm beginning my major degree in mathematics. I must say, I'm not happy with this choice at all, because courses which I wanted are not opened this year, so I'm stuck with bunch of courses I didn't want to study at all.

But, the real problem came today. We had a class of Complex number computing and the lecturer knew about me being new in the class. He called me to the front of the class and I was supposed to solve some task. I'm not very experienced in this field and I was very nervous, so I made a mistake (even if I knew the correct solution, I guess a panic overtook me).

And then he started to humiliate me in front of all my colleagues. He told me that this field is "not for everybody" and that in math classes there are "only very clever people" apparently targeting the fact I came from other field where the math was only in applied form and the main subject was programming and algorithms. I was feeling like an idiot standing there and listening to his abusive speech. The other classmates were laughing at me and I was just standing there and waiting for it to stop.

Then he told me to complete the solution. I wanted to solve the task step-by-step to prevent doing any more silly mistakes, but he didn't let me. After I wrote one step (completely correct), the lecturer told me he wants me to do it faster, not in so many steps and he added some more "funny" notes. Finally, I solved the task and made a little mistake in notation of result. He pointed it out very loudly, so everybody could hear it.

This experience destroyed the lesson for me completely. I couldn't pay attention for the rest of the class and I was ashamed to talk with anybody.

Now I'm terribly afraid of this lecturer, but it's not possible "to change" him, he's the only one for this subject, which is compulsory.

So, what would you advise me to do to prevent this situation next time?

I'm trying my best to adapt in the new field, but there are a lot of things I'm missing, so it takes a lot of time to learn it and with the research duties it's not really easy, so "just get better" advise would be great, but not achievable in short amount of time.

---

Edit:

I thank you all for your support and recommendations!

I'll just add some details:

• The problem of my courses is, that the branch of study I wanted to attend is not opened this year because of some changes in subjects etc. So I had to choose between two similar fields and this is one of them.


• So, if I wanted to change the branch, I would lose the whole year.


• I'm studying in the Czech Republic - universities are free for Czech citizens and I was accepted without admission exams, because of my previous results.


• I haven't offended the lecturer in any way, I literally had no chance to do it, because I've never saw him before the lesson.



• I noticed, that my classmates are pretty hostile even toward each other sometimes. I'm quite disappointed by this, because my previous classmates were usually friendly, but, I must simply deal with it.


• I understand, that I must improve in this field (and not only this one). As I wrote in the last paragraph of my question, I'm really trying my best, so I can only hope that it'll be enough. The problem is, that I have pretty much duties in research too, but I really don't want to abandon it, to be honest, it's the only thing which cheers me up this year in the university :-)

---

Edit 2 - Advice & Encouragement

I've worked as much as possible during the term. Still, I was just surviving the course. Finally I made a choice and arranged several consultations (with other professors than the one mentioned in the question).

I strongly suggest this for everybody in the similar situation! Professors really didn't think I'm stupid or, at least, didn't tell it :-) After that I understood most of the topic pretty well and it cheered me up, so I was much more self-confident (still very nervous, but not desperate like before) and I had the best score from the final test.

I got even my satisfaction in the end - after the exam I met with the rude professor. To my surprise he told me, that I've surprised him very much with my score from final test and that I was "fighting bravely".

So, he probably really wanted to see if a "non-math" person will be able to withstand the pressure and pass his course.

My only and best advice is consult with professors as much as possible! It can help you tremendously and you'll get a lot more self-confident in the topic if you can see, that you aren't too stupid to get it.

Answer

There is nothing you can really do to prevent this behaviour. You can just report it to the university.

There should be a committee dealing with teacher behaviour; things may vary depending on your country and university, so I cannot be more specific. If you have student representatives, contact them.

Describe the abusive behaviour with as many details as you can, refrain from putting your own personal judgement and emotions into the facts, and have a colleague student support you as a witness.

environment - Why is Homo sapiens not categorized as an invasive species?

According to Invasive Species Advisory Committee (ISAC), the definition of the invasive species is “a species that is non-native to the ecosystem under consideration and whose introduction causes or is likely to cause economic or environmental harm or harm to human health.”

But considering the following facts, why is this species not categorized as an invasive species? Homo sapiens:

• 
  

  is non-native to the most of the ecosystem which it is inhabiting, since it originated from a certain area of Africa and spread quite recently.

  
  


• 
  

  has often caused environmental problems by decreasing the local species after its introduction, as it is known that the number of species in the planet is drastically decreasing ever since the advent of Homo sapiens.

  
  


• 
  

  is likely to cause the same problem after introduced to new environment where homo sapiens hasn't inhabited yet.

  
  

http://www.invasivespeciesinfo.gov/docs/council/isacdef.pdf

Answer

Ignoring for the moment the question of politics, let's consider the various definitions of the term "invasive species" that are in use. Colautti and MacIsaac write in their discussion of invasive species terminology (1):

The greatest confusion [among the discussed ecological terms] surrounds the common term ‘invasive’ and its various derivatives (Richardson et al., 2000a). Explicit or implicit definitions for ‘invasive’ include: (1) a synonym for ‘nonindigenous’ (e.g. Goodwin et al., 1999; Radford &Cousens, 2000); (2) an adjective for native or nonindigenous species (NIS) that have colonized natural areas (e.g. Burke & Grime, 1996); (3) discrimination of NIS established in cultivated habitats (as ‘noninvasive’) from those established in natural habitats (e.g. Reichard & Hamilton, 1997); (4) NIS that are widespread (e.g. van Clef & Stiles, 2001); or (5) widespread NIS that have adverse effects on the invaded habitat (e.g. Davis & Thompson, 2000; Mack et al., 2000).

Note that except for #2, all the definitions require that the species is a nonindigenous (non-native) species in the area under consideration. Therefore, while humans may be considered to have been an invasive species for much of our species history, under most definitions of the term we no longer qualify because except in a few places (mainly the arctic, antarctic and marine environments, where human presence is minimal) we are now a native species.

See also http://www.smithsonianmag.com/science-nature/are-humans-an-invasive-species-42999965/?no-ist

Should I accept review requests from dubious journals?

I'm a graduate student with, so far, one published article in a peer-reviewed journal. Since the article came out, I've been receiving increasing amounts of "academic e-mail spam" from people wanting me to attend their conferences, publish in their (usually pay-to-publish) journals or order research supplies from them. _{^{(The latter kind tend to be the easiest to filter out — even though my field is biomathematics, it doesn't mean I have any use for frozen mouse embryos whatsoever.)}}

Some time ago, an e-mail turned up asking me to review a manuscript, conveniently attached to the message, for a pay-to-publish open access journal in a somewhat related field. Googling for the name of the publisher, I found them described as e.g. "a borderline vanity press".

At the time, I wasn't really sure how to react. On one hand, I could think of several reasons to just go ahead and review the manuscript:

• 
  

  The main complaint about the publisher seems to be that their peer review is insufficient — a claim supported by the fact that they seem to be picking random grad students as reviewers. Still, given that they're at least making some effort at peer review, surely I should encourage them in that? After all, if nobody agreed to review manuscripts for them, how could they ever improve their review process?

  
  


• 
  
  

  Declining to review the manuscript might deprive the authors — who, if the journal is indeed a "scam", are presumably the victims here — of useful feedback. Surely they at least deserve that much return for their time, efforts and money?

  
  


• 
  

  Also, if the manuscript did get published in a scientific journal, no matter how dubious or marginal, it would enter the body of scientific knowledge, and might be used as a reference by others. Given that, surely it is my duty as a scientist to try, given the opportunity, to do what I can to ensure that it is at least correct?

  
  

Still, despite these arguments, I initially found the idea of willingly responding to spam to be deeply unsettling at a fundamental, almost visceral level. Also, I felt concerned that, by doing volunteer work for a possibly unethical publisher, I'd be supporting their business model and perhaps lending them an undeserved appearance of legitimacy. In particular, given that the subject of the manuscript wasn't that close to my own field, I worried that it might have errors that I would not be capable of spotting, and that, even if I made this clear in my review, the publisher might still use the review to support the publication of a possibly flawed article.

(Edit: Just to be clear, I wasn't worried that they'd reveal the names of reviewers, just that, even if I was the only one who sent back a review, they might still use it to claim that "yes, the paper was peer reviewed.")

In the end, the decision was actually rather easy: after a cursory glance at the manuscript, it became clear that there was no way I could support its publication as written, especially given that large fragments of it were clearly plagiarized, and I wrote back to the journal stating as much.

However, if I ever receive a similar request again (and I assume I probably will, sooner or later), what do you think I should do with it?

Answer

You have no obligation to accept reviews from any journals.

In the long term, you should of course accept review tasks, since the review system is built on everyone doing their part in return for the reviews you get on your own papers. But if you think the journal is not serious, there is no need to waste your time on a review.

The problem will lie in identifying what is real and what is not. Apart from researching the journal yourself, as you have done, you should also ask more senior scientists of their opinion.

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Edit: Following up on the request for additional input on whether reviewing for dubious journals could be harmful in some way:

I think the greatest risk is that you may provide legitimacy to a journal that is not legitimate. It may be harmful to you if the journal in some way represents, let's say, creationism, in that you may become associated with something you really do not support.

I do not see any clear problem for the authors whose paper you review. Their greatest problem, assuming they are common scientists, should be that they submitted it there in the first place.

Personally, I delete all e-mails with requests from journals I do not know of. I know the journals in my field, and the new serious journals that have sprung up have a firm basis in the community, so they are also "known". I do check on some of these unknown journals occasionally, out of curiosity, and I particularly check the sort of papers they publish and the editors of the journal. That usually tells me if the journal is of interest.

Some of these journals may be legitimate, but they end up being extremely narrow regionally in terms of the origin of their authors and editors, and thus probably also their readership. A new journal is a difficult thing to get accepted unless you start with a wide base in the community, so some of these journals may be very legitimate but still have to prove themselves somehow. The problem is how to distinguish good from bad, and that is truly not easy in many cases.

thesis - How to get specific guidance from busy advisor?

I need to graduate this semester, my master's project is far behind schedule, and I'm not getting the guidance I want from my advisor. How can I work with him to handle this productively?

I have to defend my thesis in two months because my funding will be gone after this semester. I have zero data because my project is computer-based and involves an initial stage of bringing a simulation into equilibrium, after which we can get usable results. I've been working on this preliminary phase since June and it's still far from our "usable" threshold. In the meantime, I've been working on everything I can do without final data (practicing trial analyses, writing a literature review and methods section).

I'm getting only vague guidance from my advisor, who is admittedly very busy. He has a large research group, administrative responsibilities and outside collaborations, so I certainly understand that my project can't be his first priority. He told me that I have to graduate this semester. I've kept him updated about the project status and my current steps, and he says that is all "fine" and I'm doing the right things, but that it's impossible to predict when the simulation might work, and "that's just how research is." I've expressed my concerns more than once, and he's typically responded by telling me not to "over-think things" and not to "freak out." At our most recent meeting, I said that I doubt the simulation will be working in the next few weeks and asked what I should do in that case--he said "you still have two months, we'll just have to see what happens."

My advisor is well-established and respected in his field. He has a strong track record of graduating students, and he's certainly more experienced and knows much more about research than I do. I should trust him when he says everything is fine, but it doesn't seem fine to me. I can't realistically expect everything to start working in the next few weeks when I've made insufficient progress for eight months so far. I have no backup plan for what to do without the data.

How can I express my concerns so that my advisor will listen? How can I do better at getting specific guidance?

Edit to update: I did reach out to other students and postdocs for help on the technical issues, and I've been doing that since June as well.

Edit for how it all turned out: I talked again with some other students, and came up with a new strategy. My advisor was a little skeptical but agreed we could try it. Luckily the new approach turned out much better. He is still too busy to give the project much attention, but as long as I can finish the entire project and write up everything in a month (no stress, right??) I should be fine!

evolution - Are all mammals capable of sneezing?

I only know dogs and humans sneeze... so do other mammals sneeze as well? Is it possibly an evolutionarily-determined immunological trigger?

Answer

This national geographic post discusses many mammals that sneeze. It doesn't come right out and say all, but suggests most mammals have a cough and sneeze reflex:

Mammal coughs and sneezes come from throat and nasal passages, respectively, says Bill Milsom, a comparative physiologist at the University of British Columbia.

Mammals, he says, are the only animals that process food in the mouth by chewing. In other types of animals, like reptiles, "food is swallowed whole or by chewing, and breathing is suspended during the event."

The same expert discusses non-mammals that sneeze, marine iguanas and fish.

You don't even need nerves or muscles to sneeze, per this Cell Press article

Sponges 'sneeze' without the benefit of nerves or muscles

collaboration - How to handle team member who is unable/unwilling to collaborate

Okay, this is a problem I am really scared of lately. I am always willing to learn something exciting whenever I do any coursework. However, this adventurous mind of mine is risky and can often put my grades in jeopardy. Now, the problem is, there are "unfortunate" times where I have to collaborate with other students. It then becomes a serious issue of ego clash, when my classmate wants an easy way out, while I want to be all out conqueror (which I think should be the goal, since I am spending my time at college to learn something new, not to respect and elongate my comfort zone). So, it often happens that this internal squabble is very detrimental to the overall group performance and at the end of the semester the overall outcome results in a hodgepodge. Moreover, I end up having a bitter relationship with my classmates.

So, my question is how can I motivate my project partners to do something interesting and challenging, without distracting them to think that the project is hard(which it ultimately can be).

P.S: Thanks for pointing out my mistakes, I will be more careful with my attitude.

Answer

I am always willing to learn something exciting whenever I do any coursework

Great.

However, this adventurous mind of mine is risky and can often put my grades in jeopardy.

Less great. I am concerned that you are setting up a false dichotomy. Being ambitious in coursework does not have to involve risk of poor grades. It is part of being a mature student and researcher to learn how to reach for the stars in such a way that not attaining your full expectations does not result in complete failure but in work which is itself still valuable. (This is admittedly an "advanced lesson": I have known people who have made it to the tenure-track without learning it...sometimes with grave consequences.)

It sounds like you are getting an assignment -- let's say a coding assignment since I see you are a computer science student -- and planning something much more ambitious than is actually asked of you, even to the degree that the chance that you will not be able to pull it off gives you a bit of a thrill. But you don't need to work in this way. With planning -- and applying some insight early on; it's not all grunt work -- you can design a project in which you first complete what is asked of you and then move on to the more ambitious aspects that you are (happily) more interested in. Coding work in particular is best done incrementally. If you work on code over a long period of time, it is much more useful for everyone if some of the code that you write can be used (and tested, responded to...) right away than if you write things in a way so that you have nothing that works until the very end.

So far this advice is just for your own work. In collaborative work I think you should be clear about (i) what you are definitely going to do -- i.e., what your collaborators can count on you doing -- and (ii) what you would like to aim for in your remaining time (which if you are talented and hardworking, you will almost certainly have). Also, if you are actually more talented/quicker/have more time to put in, then it is reasonable to use at least some of your leftover time to try to help your collaborators with their projects. That will certainly go a long way to getting your collaborators on your side and avoiding bitterness.

In general, when you are working with other people you should stop every so often and really try to view things from their perspective. This sounds almost condescending, but it is not meant to be and it is really a skill: some people are good at putting themselves in others' shoes and others just can't let go of their own perspective; the former are much more valuable team players. One tip here: would your classmates describe themselves as wanting "an easy way out"? Or do they have goals which are just different from yours in some way? Moreover, do they see your flirtation with failure that, in your own words, can often put your grades in jeopardy and think, "Gosh, I wonder whether whoknows is going to come through with what we agreed he would do or come back proud of the fact that he bit off more than he could chew?"

evolution - Genetic Diversity and Adaptation

I am somewhat new to evolutionary biology, having studied it on my free time as a computer science student. There is one particular thing that has always bothered me for which I have not seen a good treatment, relating to adaptations to the environment with respect to genetic diversity. If it is possible for a population to adapt to rapid environmental changes, and they don't have an adaptation for dealing with change directly (such as a complex brain), it seems to me that every generation must have present within them almost every possible environmental adaptation that the population is capable of expressing (including many irrelevant ones and a few relevant to the particular environmental challenge). Otherwise, it may take too many generations to deal with a change, which may be disastrous for the population.

So my question would be: how does an evolutionary biologist explain the mechanics behind the ability for a population to adapt quickly? Are most environmental changes slow or gradual enough that the population has a few generations to happen upon the mutations that will allow it to survive, and have generally been successful in this regard for 3.5 billion years? Or, are a large majority of possible adaptations present in almost every generation, and just serve no purpose or advantage for most of the population if the provided "benefit" is unneeded (i.e., are effectively neutral)? Or something in between?

Answer

It is a good question. The question is hard to answer though because

• The answer is not completely resolved


• There are many influential parameters hidden behind this question.

Your question, as I understand it, can be formulated as

Do natural populations have enough genetic variance to directly respond to an environmental change or do they have to wait for this variance to be created through mutations?

To address this question, I will have to assume you have some intermediate level of knowledge in evolutionary biology.

How do we call these two alternatives?

Adaptation can occur through selection on:

• Standing genetic variance


• De novo mutations

How can we tell them apart?

This section is mainly inspired from Barrett and Schluter (2008).

Adaptation from standing genetic variance and from de novo mutations tend to yield different genetic signature.

In comparison to de novo mutations, adaptation from standing genetic variation is likely to lead to

• Faster evolution
  
  
  
  • Because there the respond to the new environmental is immediate, there is no need to wait for more mutations.
  
  
  • Because the fitness variance associated with the trait under selection is very low even when the first mutation occurs.
  
  
  
  
  


• Fixation of more alleles of small effects.
  
  
  
  • Because phenotypic variance is alleles of large effects are likely to be deleterious in the previous environment and would therefore be purged out of the population quite quickly
  
  
  • Because, if adaptation occurs from de novo mutation, it is likely that only few mutation would have occurred that would allow adaptation
  
  
  
  


• Spread of more recessive alleles
  
  
  
  
  • Because recessive alleles can reach a relatively high frequency in the previous environment even if deleterious in the homozygote mutant.
  
  
  • Because recessive alleles represent little to no fitness variance at low frequency and are therefore likely and it would therefore take much time for adaptation to occur from recessive alleles if they just appeared through de novo mutations.
  
  
  
  

You will note that my explanations are non-exclusive and are overlapping. They all boil down to

• Loci causing high fitness variance in the previous environment are unlikely to be source of adaptation from standing genetic variance


• Loci causing high fitness variance in the new environment are likely to cause adaptation.

If you have a hard time to understand these concepts, then you might want to have a look at Fisher's fundamental theorem, Mutation-selection balance and eventually follow some intermediate level course on the mechanism of natural selection.

Which mechanism is more common?

Do most adaptation occurs through selection on de novo mutations or through selection on standing genetic variance? This question is very hard to answer. It depends on

1. Type of adaptation


2. Population of interest

1. The type of adaptation

The answer is likely to differ depending on whether we are talking about

• adaptation to a changing environment over the whole species range
  
  
  
  • How fast is this environment changing is important too as you noted in your post.
  
  
  
  


• A single population that detach from the rest of the metapopulation to slowly colonize a new environment


• Adaptation to a universally (independent of the environment) beneficial trait


• Coevolutionary process


• etc...

2. The population of interest

Different populations retain different level of genetic diversity. This level of genetic diversity depends on

• Demographic parameters
  
  
  
  • such as the population size and its variation through time
  
  
  
  


• Evolutionary history
  
  
  
  
  • Such as the number of recent selective sweep
  
  
  
  


• Environment
  
  
  
  • Such as the diversity of environments present over the range of the species
  
  
  • Such as temporal variations
  
  
  
  


• Genomic architecture
  
  
  
  
  • Such as the presence of strong epistasis that could cause large amount of hidden genetic variation (see for example Hermisson and Wagner, 2004) and the eventual "revelation" of this previously hidden genetic variation through new mutation or a new environment (see for example La Rouzic 2008).
  
  
  
  

Example

Three-spined sticklebacks are present in salt water and fresh water. They occupy several geographically isolated bodies of fresh water (connected by salt water). All populations present in fresh water environments show similar phenotypic traits. We have first thought that sticklebacks have adapted repeatedly to this freshwater habitats (repeated evolution) through de novo mutations. However, some papers suggest that, as the marine population of sticklebacks is so big, that it is possible that there is standing genetic variation for these traits that are selected for in freshwater habitats. Below are some papers of interest