Confusion about the duration of different phases of the cell cycle such as G1, G2 & S

We all know that normally most of our cells (which are alive and have nuclei - except for cells such as "stem cells", "red blood cells", etc) spend most of their lives in interphase.

But the Interphase itself is also composed of other parts, other stages, including G1, S, and G2.

Is the staying duration of the most human cells in each stage(G1,G2 & S) is comparable to the other stage?

For example, is it true to say that:

"Most human cells, which have the ability to divide(passing the cell cycle), spend most of their lives on stage G1 than S phase or vice versa."?

Usually, which stage is the longest or shortest?

It is quite clear that the G1 is normally longer that G2 and as far as I know the G2 is the shortest stage in interphase, but what about G1 and S?

Is stage S usually longer than G1?

Is there any information?

ethics - Supervisor asking me to list a co-author who has literally done nothing

I am in the final stages of writing a paper to submit at an IEEE conference. I am the primary author, in the sense that I did most of the work and most of the writing. I have three other co-authors who have contributed a significant amount of advice and proofreading (one of whom is my supervisor).

Last week, my supervisor told me I should add person X as a co-author (in addition to myself and my three existing co-authors). I have never met X and they have contributed absolutely nothing. It's not even clear if X has looked at the work we have done!

My response was as follows: "Fine, if X at least looks at section Y to make sure it has no errors, I'll put them as the last author." This has not yet happened, with less than a week to go before the deadline. My supervisor is still insisting that I add X as an author.

What should I do in this circumstance?

Answer

Based on what you have said, this seems to be a clear ethical violation.

I would send an email to your supervisor asking him/her if X has had a chance to look at section Y. This will force them to either state yes or no as to if X participated. Play dumb if you have to.

Hi [Supervisor]

Has X had a chance to look at section Y in the project? As I remember, we discussed adding X as an author as long as X verified the results of section Y. I just want to be sure that I get the right authorship on this paper.

Thanks, Mahkoe

Getting written directions from your supervisor on this will document any unethical behavior that he/she is suggesting you participate in. Your supervisor will have to either directly tell you to add X even though they have not contributed to the paper, or they will be leveraged into conceding that X does not deserve authorship and should not be added.

If your supervisor still insists that X be given credit in spite of doing nothing, you have a few options:

1. You can seek out the advice of your department chair or graduate coordinator.


2. You can refuse to put X in as an author and make your supervisor mad with you.


3. You can comply with your supervisor and chalk it up to yet another predatory, manipulative adviser taking advantage of students.

You decision here depends significantly on how receptive your department is to students and how much you are willing to risk losing if your supervisor tries to retaliate. I am understanding of the fact that you may or may not really have the leverage to directly turn your supervisor down on his/her demands. Such is the life of a student in academia. A small number of professors know you have no clout and routinely take advantage of students in these situations. And sometimes, it is better for your own sanity and career to let X and your supervisor commit ethical violations and publish your paper without further grief.

genetics - Two mice heterozygote and black are reproduced. Find the probability of getting the filium dark and heterozygote

Well, here's what I did: P: Aa*Aa

F1: 1/4 AA, 1/2 Aa, 1/4 aa, SO the answer is 1/2, but out teacher did this: AA(1) Aa(2) aa(1) and she said we divide the number of filium for the phenotypes number and get 2/3. This is the probability. I don't get it.

Answer

Okay so in your teachers answer there are four offsprings. . You used all offsprings when you made the division so 2/4 = 1/2.Your teachers 2/3 comes from the fact that 3 out of four is black, but only 2 out of that 3 black is heterozygote so 2/3 is good by this logic. I think that your teacher's logic faulty because you have to take into consideration all the offsprings. Basic genetics and Mendel's law tells us that crossing two heterozygotes with independent alleles result in a 3:1 ratio in phenotype separation in the next generation with 1:2:1 genotype separation -- that is what basically both of you have wrote. The fault is in the getting the probability - basic maths tells us that in an independent experiment, the probability variables have to sum up to one. In your teacher's logic this basic rule is not kept, because finding homozygous non-dark offspring would be one (there is only one non-dark filium and that one is homozygous). So by this logic all filium are non dark-homozygous, but then what about the others. I hope you see the problem with that logic.

emotional responses - Postdoc overwhelmed by incomplete work

I take on more than I can handle and everything is left incomplete. Constant reminders from my previous supervisor, my current advisor, and colleagues, increases my anxiety level and sometimes I end up entirely avoiding work. I haven’t completed a paper as first author in the last two years, although I have two papers ready for submission for the last two months and two more I could complete with a week of uninterrupted work on each paper. These papers have been dragged so much that now I am losing interest in making any more changes. I will appreciate any suggestion for dealing with anxiety regarding works that I should have completed more than a year ago.

funding - When does the co-authorship line end for a PI's data

As I understand it, in the engineering field, the person who has research money and/or a project that leads to the collection of data, is put on research papers that directly use that data. I guess the most common of this is for PHD students whose advisors funding or project is the reason they have data.

I am curious about when this ends in regards to collaboration. If one person gets a project and funding and collaborates with a different lab/department/professor/researcher and through this, gives a portion of the funding to that person or place, what is the convention for authorship? Does the PI of the project go on all papers that use the data, or only papers they directly do with their own staff/students?

ethics - Ramifications of withdrawing publication offer (question from student editor)?

I am the editor of a student-edited journal at a graduate school. We extended a publication offer to an author that has published with the journal in the past, and with whom I do not wish to burn any bridges. The normal process of an offer goes like this: (1) extend the offer, (2) author either accepts or rejects, (3) send copyright agreement, (4) author signs and returns copyright agreement, (5) we edit and publish the article.

The author accepted the offer within the time frame (step 2), but we have not progressed beyond that. I have to withdraw/rescind the offer because we have maxed out our page numbers for this year. I tried telling the author that I would be happy to work with the incoming editor in chief to see if they want to make him an offer to publish next year, but he insists that because he accepted the offer we are now obligated to publish it next year. I reminded him that we have not sent him a copyright agreement or entered into a publication contract, and even if we did so the journal reserves the right to terminate the agreement at its sole discretion. He essentially said that his acceptance of the publication offer formed the publication contract and now we have to publish him or else (said he turned down other offers, etc.).

I feel terrible about the situation (we've tried our best to never put authors in this position, and have never had to rescind/withdraw an offer before). Since I've only experienced this from the editor's point of view, I'm wondering what published authors have to say about the situation? Is it your understanding that once you accept an offer you've formed a contract with the publication, and they are obliged to print it? Have you ever had an offer withdrawn, and did it burn all bridges with that institution/publication?

etiquette - Is a business card necessary for a graduate student?

I know some PhD students have their own business cards, but I don't know if it is a standard practice for PhD students to have their own business cards. I think a business card can be useful for networking in conference or collaborating with some industrial partners. So, is are business cards necessary for a PhD student or other graduate students attending conferences?

PS: in case it is field-specific, I would like to know the different practices in different fields

Answer

It's probably discipline-specific, but I hand mine out all the time. That being said, I talk to lots of vendors of computer hardware that I want to get back in touch with, so exchanging cards is helpful. As a grad student, it might be worth having some small cards from someone like Moo that have your name, email, affiliation, and a link to your website. It might be easier to hand those out than to carry 20 preprints of your article when you're giving a talk.

All that being said, it'd be pretty unusual to push your cards on people you meet at conferences. If someone asks for your information, or a copy of your publication, you might offer the card, but I wouldn't volunteer it unless you've been asked for something. It's just not part of the culture in most of the fields I have experience with for students to do so.

mrna - Is exon order always preserved in splicing?

Are there any cases in which the splicing machinery constructs an mRNA in which the exons are not in the 5' -> 3' genomic order? I'm interested any such cases, whether they involve constitutive or alternative splicing.

Answer

I don't have any literature to back this up but I doubt that it occurs (at least frequently).

For example, imagine a simple three exon gene. Upon splicing exon 1 to exon 3, exon 2 would be excised as part of the intron lariat and subsequently degraded. So in order for exon 2 to be spliced to exon three you would need to either have splicing between exon 3 and exon 2 in the lariat or another copy of the pre-mRNA. This is typically called trans-splicing but it only occurs in specialized systems such as spliced-leader sequences in C. elegans.

publications - I have an article in the field I am just interest and has no overlap with my major. Should I mention it my SOP?

Related questions:

Besides physics as my major, my other interest is linguistics, and as you can see, there is no overlap. When I was in high school, I wrote my first article in linguistics. It hasn't been read by any professor or published in any specialize journal, not because it was rejected, but because I haven't tried to do so. I had a graduate student in linguistics review it for me, and it seems that she finds it interesting. As far as I know, there is currently no material on the topic I researched available on the internet, which indicates that the topic is new.

Because (1) it is the first article I have ever wrote, (2) I did it when I was 16 or 17 (although I have updated so much it lately) and (3) the topic is new so far, I consider it my proudest scientific activity. I think putting it in the SOP will make a steady point that "I was born for scientific research." Will it be useful if I do that, or just mention the latest article in physics I wrote?

nutrition - How is a substance classified as a vitamin?

From wikipedia

A vitamin is an organic compound and an essential nutrient that an organism requires in limited amounts.

There are many essential nutrients to an organism. Glucose for example. However, not all of them are classified as vitamins. Is there a clear, non-arbitrary definition of vitamin? If not, who decide what ought to be called a vitamin?

Answer

1) Vitamin D is a bit of an umbrella term that actually refers to a whole group of related molecules. One of these, vitamin D$_3$ (cholecalciferol) is formed spontaneously from ergosterol in the presence of UV radiation, which happens in the skin when exposed to sunlight. Cholecalciferol is then converted to calcitriol, the active form, in the liver. Here is some information on the metabolic pathway.

2) Actually, if you consider the definition carefully, only a few molecules are essential for human growth and nutrition, in the sense that they cannot be replaced with something else, and are required in small amounts. For example, the majority of amino acids can be synthesized by the body from other amino acids, and are therefore nonessential. The remaining amino acids are essential nutrients because there is no synthesis pathway -- but they are required in large amounts and not considered vitamins. This distinction between "large" and "small" might sound strange, but it is important since it tells you if the nutrient is consumed for energy/growth (like amino acids) or has some "supporting" role, such as antioxidants, cofactors for enzymes, or hormones (like the vitamins).

That said, it is sometimes a bit fuzzy if a nutrient is essential or not. Vitamin D is a borderline case: it should perhaps not be called a vitamin, since it can in fact be synthesized by most adults in adequate amounts. However, vitamin D deficiency can occur if one does not get enough exposure to sunlight, and this can cause the disease rickets. Some researchers have suggested that this is one factor behind evolution of lighter skin in northern human populations, since dark skin pigment reduces UV radiation needed for vitamin D synthesis.

phd - What should I ask my potential Ph.D advisor in advance, before actually signing a contract?

I'm currently applying for a Ph.D in Germany. Next week I'm sitting down with my potential Ph.D advisor to have a talk about the program.

Currently I'm collecting questions about things like

• teaching duties included?


• working hours


• what's the salary?


• vacation?


• budget for conferences?

I think I'm missing some important stuff.

My real question is: What should I ask my potential Ph.D advisor in advance, before actually signing a contract / starting?

(The question What questions should one ask to the former/current students of a professor before deciding whether to do PhD under him/her? is related, but I feel it doesn't fit my situation)

PhD admissions - Contacting multiple profs from the same university

Presently, I am writing to potential PhD guides in US universities. There are two professors from the same department who work on topics that cannot be considered closely related, but I would be happy to work under either of them.

I have already written to one of them, who has asked me to go ahead with the application process. I am now wondering whether I should mention in my mail that this (contact with first prof) has already been established, while still conveying that I am adequately interested.

Upon a positive reply from the second prof, what would be the best way to talk about both profs in my Statement of Purpose? I want to keep both options open, while not being rejected because the admissions office/the professors thought I wasn't specific enough with my application.

meiosis - Why do some organelle (like ER and Golgi complex) cannot be seen under microscope during cell division?

I have recently read in a book that organelles like ER (endoplasmic reticulum) and Golgi Complex cannot be seen under a compound microscope during cell division. Why does this happen, and where do the organelles go during that time?

Human Evolution in Modern Times

I understand that evolution occurred to form the current hominids from a common ancestor millions of years ago. As evolutionary processes take a long time, is there proof of evolution occurring with humans today?

Answer

Yes, there are examples. First: If you want to say, that humans and monkeys evolved, than it is better to say that they evolved from a common ancestor. This makes quite a difference.

If you are looking for examples of human evolution then one of the most obvious traits under evolutionary selection is pigmentation. There is a clear correlation with lattitude (and this UV-index):

The changes in pigmentation occured - seen from a evolutionary perspective - pretty recent when humans moved out of africa and to other regions (see here). See these papers for more details:

Other examples would be the tolerance for lactose (the sugar contained in the milk) in adults which arose during the last 5-10.000 years. Normally only babies can process these sugar which is contained in large amounts in the mothers milk. When they are weaned, usually the enzyme is not expressed anymore. However with the settling of the humans and the domestication of cattle this changed, so we can still drink milk and eat milk products without producing intestinal problems. See here for more details:

A third example would be the sickle-cell anemia, which happens due to a point mutation in the human hemoglobin protein. This causes an aggregation of the hemoglobin molecules in the red blood cells which then leads to a reduced elasticity (see here for more details). It also leads to a protection against malaria (most likely by the reduction of the life span of the erythrocytes). The areas with high prevalence of the sickel cell anemia in africa correlate pretty nicely with the distribution of malaria.

If you look further, you will find a number of different examples, where evolution is present after humans went through a genetic bottleneck (meaning the number of humans was drastically reduced).

publications - Is it acceptable to list unpublished papers in a PhD application for computer science?

I have a couple of papers that are works in progress or in the submission process. Can I list under my publications list (and clarify they are not yet published but on the road to it)?

Answer

There are 4 different stages of a paper:

1. 
   

   In preparation. In maths, this means: we know it's true and we're writing it down. In engineering it can be: measurements done. Etc.

   
   



2. 
   

   Submitted. That's clear what it means. I'd just add: In general, you don't say to which you have submitted it, just in case it got rejected and you re-submit it elsewhere. However, for an application, I would include this information to show the level of journals or venues you aim at.

   
   


3. 
   

   Accepted or To appear or In print. You've got a final "ACCEPTED NOTIFICATION" from the journal. Maybe the proofreading wasn't done or whatever, but now it's clear that the paper will be published (well, it need not, but that's a borderline thing). I personally prefer to write "accepted" since that's clear. Both "to appear" and "in print" may indicate that the volume and pages have been assigned, which need not be true.

   
   


4. 
   

   Published. It's published.

   
   

You can include papers in all 4 categories in your application. I would actually say that for 2,3,4 you ought to include them. For the ones in preparation, consider the significance of the paper, it can look like: The applicant hasn't done anything yet on it and is just blowing up his publication list. Of course, you have to say in which stage the paper is (well, not for stage 4 papers).

human biology - Will the heart keep beating if it's separated from the body?

The heart is a vital organ in our body, as it drives blood circulation. I was wondering if a heart keeps beating if it is separated from the body? If yes, then why?

Answer

Short version The heart has the ability to beat independently of the brain as long as it has oxygen. The heart will eventually stop beating as all bodily systems begin to stop working shortly after brain death. Remember the heart can beat, but your diaphragm and lungs wont. hence the cardiac muscles undergo asphyxiation and die off. However, immediately after death, there is enough oxygenated blood in the body to keep thing moving for a while

Long version There is a simple explanation why.

As you know every muscle in the body has to receive stimuli from the neuromuscular junctions (and subsequently the nervous system) in order to contract.

The heart is a bit different in that it is not regulated by the brain, but the regulatory mechanisms lie within the heart itself. The heart conductive system contains a special group of cells called the pace maker cells (SA node) that fire at regular intervals and cause the heart to beat.

Each heart beat is triggered by an electrical pacemaker - a group of cells in the heart that have the ability to generate electrical activity. They cause electrical impulses to spread over the heart and make it contract. The largest natural pacemaker of the heart is called the sinoatrial or SA node and is found in the right atrium. From it, specialised groups of cells that carry the electrical charge lead off to the rest of the heart.

(Taken from here)

The brain regulates the rate of the heart beat sure, but it does not send the signals that cause the heart to beat in itself.

In short, even after disconnection, the SA node still sends the impulse down the AV node and purkinje fibres that spread out across the cardiac musculature and cause them to contract, causing the heart to beat. This will continue for a while till they run out of energy and stop.

You can read more about it here:Wiki

pharmacology - What is the benefit of fever during infections?

When people get sick, they often develop a fever. What is the effect of an increased body temperature on viruses and bacteria in the body? Is it beneficial to the infected body? Importantly, often fever-reducing agents like aspirin are prescribed when people are sick. Doesn't this counteract any benefits of fever?

publications - How to get priority acknowledged, when a paper in mathematics is a special case of your own paper, but it does not cite your work?

I am a researcher in Mathematics and I have recently found that it has been published a paper X whose main result is a (very) special case of a result of mine, which has been published more than an year ago. From the journal log, I can also see that paper X has been submitted after my paper has been published.

However, the author of the paper X was not aware of my previous result, indeed she did not cite my paper.

I am wondering if it would be possible to make the journal of paper X acknowledging my priority on the result, and in such a case how to do so.

I have often seen journals publishing short notes with the title "Acknowledgement of priority", in which it is explained that a published result was already proved by someone else, but I have no idea of how it works.

Thanks for help.

UPDATE: I wrote to the author of the paper and I have got no response.

publications - What does the typical workflow of a journal look like?

What steps does a manuscript typically go through from submission to publication (or rejection) in a typical journal? How are these steps referred to, in particular by editorial systems, and how long do they each typically take?

Note that this question is about the typical situation and hence not about:

• Journals with an atypical workflow, e.g. those that allow for an instantaneous reviewer–author interaction.


• Exceptional steps or rare occurrences such as withdrawal or clerical errors.

This is a canonical question on this topic as per this Meta post. Due to its nature, it is rather broad and not exemplary for a regular question on this site. Please feel free to improve this question.

Answer

Feel free to edit this answer to improve it, in particular to add other names you know to be used for the individual steps or to extend the maximum typical durations from your experience. The source for the diagram can be found here.

This step is usually performed by the non-scientific staff of the journal. It may include for example:

• Checking for missing or broken files.


• Checking compliance with length requirements, if any.



• Checking central formatting requirements, e.g., line numbers, if required by the journal.


• A plagiarism check.


• Excluding manuscripts of very low quality, such as automatic translations or manuscripts with very poor language.

Also known as: technical check, initial QC (AIP), admin checklist (IEEE), Awaiting Editorial Office Processing (ScholarOne), quality check (NPG)

Typical duration: A few workdays.

Based on the topic of the manuscript and suggestions by the authors, an editor is assigned to handle the manuscript. Depending on the journal, the assignment may be done by technical staff, the journal's chief editor, or automatic by submission category or author suggestion. With some journals, editors are invited and not assigned.

Also known as: with editors (APS), editor assigned (Editorial Manager, AIP), AE assignment (IEEE), assigned to the editor (NPG)

Typical duration: A few workdays to several weeks.

The editors decide whether the paper should enter the review process or should be rejected directly, e.g., because it does not fit the journal’s scope or requirements on importance or quality. A rejection at this (or the previous) stage is called desk reject. The paper may also be returned to the authors for reasons other than rejection, such as to request more data or clearer figures prior to formal review.

With revised manuscripts, the editors assess whether the existing reviews have been addressed adequately. If yes, they either proceed with another round of reviews or jump to editorial decision immediately – this mostly depends on the magnitude and nature of the revision.

Also known as: with editors (APS), waiting for potential reviewer assignment (AIP), under review (ScholarOne), assigned to the editor (NPG)

Typical duration: This strongly depends on the journal: With some journals, it is less than a week; with others it may take a month, in particular if several people are involved in the decision or the initial quality hurdle is high.

The editor selects a number of potential referees to review the manuscript. Should a referee decline to review or not perform the review in a certain time (as given by the editor or journal), the editor usually has to select a new referee. The main exception to this is if the other referees already provided sufficient reviews at this point.

With revised manuscripts, usually the reviewers from the previous round are selected. The editor may also decide that certain or all reviewers need not see the manuscript again, as their comments have been adequately addressed.

Also known as: with reviewers, with referees, under review, awaiting referee assignment, awaiting referee reports, awaiting reviewer scores (ScholarOne), reviewers assigned, manuscript assigned to peer-reviewer/s (NPG)

The initial selection of referees is usually comprised in the previous step. Some editorial systems give the status as with editors (or similar) if a new referee needs to be assigned and no other referee is currently assigned. Others will show under review regardless.

Typical duration: This strongly depends on the field and journal. It typically ranges from a few weeks to several months, but in some cases (particularly for highly theoretical work where intense proof-checking is expected), it may be as long as one to two years. Moreover, the key factors for the duration of an individual peer-review process are how soon the reviewers perform the review and how many reviewers decline or fail to review the manuscript. Thus, even for a given journal, there is a strong variation of review durations. Some journals give their statistics on this time (or a related one) on their webpage.

Based on the reviews, the editors decide whether:

• The manuscript shall be rejected.


• The manuscript needs to be revised by the authors before it can possibly be accepted. If the authors submit a revised manuscript, the workflow is mostly the same as for the initial submission.


• The manuscript shall be accepted as it is.


• A decision requires further reviews.

Also known as with editors (APS), review completed, required reviews completed (Elsevier Editorial System (EES)), awaiting AE recommendation, awaiting decision (ScholarOne), awaiting EiC decision (IEEE), Editor Decision Started (AIP), Decision Started (NPG). This may be followed by a short stage denoted decision letter being prepared (or similar).

Typical duration: A few workdays to a week. This may take longer with some journals, in particular if several people are involved in the decision.

The article is copy-edited and typeset by the publisher. Occasionally, requests to the authors may occur at this stage, e.g., due to low-quality figures.

For some journals, a pre-copy-editing version of the manuscript will be put online at this point under a category like Just Accepted, with a warning that the current version has not yet been copy-edited and may change further before publication.

Also known as: in production, in press

Typical duration: This mostly depends on the publisher’s backlog – between a few workdays to over a year, roughly correlated with the length of the publication delay (see below).

The authors are sent the paper’s proofs, i.e., the paper as it is about to be published. If corrections are necessary, it goes back to copy editing and typesetting.

Also known as: proofs with authors, Galley proof

Typical duration: Most journals request proofs to be returned within a certain time, usually between 48 hours and a week (reasons).

For some journals, particularly newer ones with an online-centric publication model, an article will be published immediately after the previous step has been completed.

Other journals with a more traditional process will queue up the publication for collation into a journal issue with other articles. The time before this issue is published depends on the size of the journal’s publication backlog and can range anywhere from a few weeks to several years.

Many journals with an issue-based delay provide “online early” access to articles so that they are available to the community before the final issue date. Articles thus often acquire two publication dates: one for online and one for print publication.

1. IOP Publishing: An introductory guide for authors


2. IEEE: Peer Review and Decision Process for Authors

molecular biology - Was there originally a non-ribosomal way of synthesizing proteins?

Proteins are synthesized on ribosomes from mRNA copies of regions of the DNA. But ribosomes themselves are made up of proteins (and RNA). So how could the first ribosomes have arisen? Was there previously some other way of making proteins other than by ribosomes and mRNA?

email - Logistics of asking for letter of recommendation after graduation

I graduated from by undergrad two years ago (this May) and now I am applying to law school and require letters of recommendation from my undergrad.

Although I did well in their classes and spoke with them to some extent outside the classroom, I haven't stayed in touch with my professors, so I am not sure how well they would remember me, due to the length of time.

My question is how I would logistically go about asking for LOR's. I live relatively near the University, so I could conceivably ask them in person, but it would seem odd to just drop in on them randomly (at office hours?). Would this be the best approach?

Or should I email them ahead to ask to meet? If so, should I allude to the fact that I want to discuss a letter of recommendation in these emails or should I just ask to meet without giving specifics.

Final point: I am planning on applying September, so does it seem to early to ask in this March, or is that not an issue?

Thanks for any answers/suggestions!

quitting - Just started a postdoc, but it went REALLY bad, REALLY fast. Stay or go?

I just started my 2-yr postdoc, but things have gone sour really fast. So, I really need some career advice as to what to do. Over several months, I did the interviews with the supervisor and the lab and things seems to be really great (although I got a strange feeling that the lab members were trying to deter me from joining, see below).

I joined the lab last week, and the condition of the lab and the equipment was really poor (but the supervisor said it was great...), but I got along with the supervisor and the lab great. However, this week took a turn for the worse. My supervisor has been vicious with me for several days and we have had a major conflict almost everyday this week, which I believe is a bad sign when something like this happens when starting a position. The other members of the lab said that the supervisor is frequently is overbearing, micromanages, and has "lost it" on them for reasons as asking for vacation. As I said, I met with these lab members via Skype over the summer and I felt that there were trying to warn me not to join the lab, and today they confessed that this was true. One of the lab members did file a complaint against the supervisor. The situation was that the supervisor typically makes numerous phone calls during weekends and the one time the lab member did not answer, the supervisor was furious with her. She then made a complaint to the appropriate person in the department.

I am concerned about the supervisor and more concerned that this is not going to help my career at all since the mentoring by this supervisor is poor quality (this is how the other lab members feel after being there for almost 2 years. They are leaving immediately after that). She has promised a good work environment, additional pay to the NIH base pay, flexible time off and great equipment, but all of this is not true. The other lab members confirmed that this happened to them too. Basically, this supervisor promises a lot of things and does not deliver.

So with all of that being said, is it wise for me to leave ASAP and look for a better opportunity OR is it best to stay put and complete the 2-year postdoc (or most of it). I don't favor leaving a job this soon and would rather give things a chance, but this place has been extremely BAD. Furthermore, the lab members feel that this is not a good workplace and confirm that the behavior of the supervisor will continue (they have their reasons for staying, but really regret joining). For these reasons, I don't feel staying is beneficial to be perfectly honest.

I would rather not have to ask for advice about this, but I am in an uncomfortable situation and any advice is extremely appreciated. Hopefully I expressed this clearly... I'm kind of a mess right now.

EDIT: I have resigned from the position. But, I have obtained a new position with someone I know well and has helped the careers of people I know. Aside from the conflict with the supervisor and the experiences of other people in the lab, the position I'm resigning from just does not offer any development for my career as per my impression prior to arriving in the lab. Unfortunately, what attracted me to this position was not the reality. Even giving this position more time would not change the condition of the equipment I have to work with (and the lack of equipment), the lack of safety practices in the lab, nor would it change the supervisor's lack of organization, leadership and the control of her emotions. Also, I discovered that all of the current lab members plan on leaving within the next few months. Past/current postdocs typically do not last more than 2 years.

immunology - Why are Natural Killer cells considered cells of Innate immunity?

Kuby Immunology says

They (NK cells) do not express antigen specific receptors and are considered part of the innate immune system.

Though they also have receptors for antibodies that bind to NK cells and help detect antigens or pathogenic cells that are killed by the secretions of their cytotoxic granules.

Couldn't we then call them cells of Adaptive immunity?

graduate admissions - Is top 20% GRE scores enough be a strong applicant for an EECS/ECE PhD program?

I am going to take the GRE soon. My practice tests end up being at V: 158 (80%) and Q: 162 (80%). I didn't care too much about the quantitative section in the practice test so my real score should be higher. However, my Verbal seems accurate. I don't know about the writing, but I'd guess to around a 5 if things go well.

Question: Are these scores good enough for a PhD in electrical/computer engineering or computer science (not decided yet, something in EECS) at schools like MIT/Stanford/Berkeley? Should I be wasting my time preparing for the GRE? I had thought that GRE was completely useless, but after some searching online it seems it actually carries weight.

What is the purpose of peer evaluation of teaching?

At my UK university all new teaching staff, as part of the requirements to fulfil the requirements for a Post Graduate Certificate in Higher Education (PGCHE), have their teaching observed by a member of their department, a member of another department, and a member of the Education Department (who run the PGCHE course). I don't understand the advantages of being observed by the three different people. What should I strive to get out of each observation?

Answer

I'm attending a similar program at my university (also UK based), and I was observed by a senior member of my faculty, and by another attendee of the same program.

The main point was to initiate a reflective process of our teaching. Hence, the observation was not an evaluation, but simply the collection of some pieces of evidence, that described our lecture. Our actual assignment was not the observation in itself, but how we reflect upon the evidence, by describing how we feel about it, how we analyse it, what conclusions do we make about it, and what are the next steps we decide to engage on.

Interestingly, I've collected different types of evidence from my two observers: the senior member of my faculty made some observations in particular related to the content of my lecture, while the observer who was on the same program made some observations related to some of the techniques taught in the program that I used during the lecture. In both cases, all observations were really useful to start the reflective process. I can only assume this is the rationale for you to have three different observers.

career path - Are there any professors with PhDs in Humanities from Asian Universities working outside of Asia?

tl;dr: "Are there any professors in Humanities working in North America or Europe who have recieved their PhDs from a University in Asia (Japan in particular)?" (I'm specifically interested in Asian Studies, but any Humanities would be of interest. Also, any permanent or semi-permanent teaching position would be of interest)

I'm currently a second year masters student from the U.S. in an Asian-studies related field at a University in Japan, and am considering whether I should continue on for a PhD there. Graduate students and professors from the U.S. have more or less told me that getting a degree from Japan would be more or less "career suicide" (my words not theirs) because degrees from even well known universities in Japan are not considered on the level of well known schools in North America or Europe.

Obviously there's a lot to consider when thinking about going for a PhD, but I am specifically looking to contact people in the humanities, particularly Asian Studies, working in North America or Europe who got their PhD from a University in Asia. I'm specifically interested in Japan, but degrees from S. Korea, Taiwan, Hong Kong, Singapore, China or even India or other parts of South or Southeast Asia would be welcome. Thank You.

journals - Should I agree to review papers as a postdoc?

I am a post doc in mathematics, and was just sent a request to review a paper. This is the first time it happened to me. I never heard of this journal before, but it is a Springer journal, and upon checking the editorial board it looks like a respectable journal. Also, the paper looks quite interesting, so it appears that I shouldn't worry about it being dubious.

I wonder however, if this is a good time in my career to do such a job. Given that I am a postdoc, constantly in the run for the next job, and probably this will take some of my valuable research time. Is it normal for postdocs to review research papers? Should I accept it? If so, should I mention the fact I review for this journal in my C.V?

Answer

Yes, reviewing papers is an integral part of your job now, and a very beneficial one at that!

It's true that the first papers you will review will take you quite a bit of time, but it's a sound investment (unless you consider dropping out of academia next month). You'll improve your reading and ability to read between the lines. It will help you gain a wider view of what others are doing in your field, because it will force you to really go through the paper in depth, not just skim over it as we are so often forced to do when a paper is not at the core of our own research.

Moreover, it will give you invaluable experience when you write your next papers, because you will be able to put yourself in the reviewer's shoes! You will see better what could be problematic for a referee in the presentation of your work.

As for whether you should list it on your CV: yes!

phd - Can I legally omit the fact I hold a Ph.D. degree?

I am about to complete a Ph.D. in Hong Kong and would like to study in the United States. I hold a first class B.Eng. degree in Electrical Engineering. I have a CGPA of 3.67 out of 4 in my current PhD studies, two journal publications (IEEE Transactions) with two more to be submitted soon. I would consider this a fairly good academic record.

For career purposes, I would like to obtain a Ph.D. degree (in a different but related field) from a top American university. There aren't post-doc openings in my current research area, which is why I am considering another PhD in a related area.

Question: Is it considered illegal to not mention that I hold a Ph.D. (hopefully) during application? I noticed some schools frown at what some would call a "professional" or "serial" student.

NB: I have read responses on this question and I am satisfied with them. But I feel there's need to make my question clearer for those who did not understand. Some universities clearly state on their websites that they will not consider applicants who already hold a Ph.D. while some others do not specify this. My question was more for the latter. But now I know that other than dealing with the university, it will require lying on visa application, as some people wrote below.

Thank you all for your contributions.

Should a student use the email account provided by the university to communicate with professors?

I am an undergraduate and I do not know much about the rules of writing an email. The email system used by our university is not convenient at all: it responds slowly, often crashes, and its common to miss important emails.

I need to email profs in our school and other universities. Is it necessary for me to use the email account of the school? Can I use my personal gmail account? Is it informal or impolite?

Answer

In the cases I'm familiar with (U.S. universities), using your own e-mail account should be completely fine, subject to some obvious caveats. One is that it's best to have an e-mail address that doesn't look foolish or offensive. People sometimes choose very strange usernames, and you don't want that to reflect poorly on you; furthermore, you should make sure your e-mails include the name your professor knows you under. Another issue is that if you are asking for sensitive information such as grades, your professor will likely be unwilling to send this information to an outside account without some verification that it belongs to you. Finally, you should make things simple for anyone you correspond with. For example, if you use several accounts, you should check them frequently or forward one to the other, so that there are no delays if someone sends something to an account you didn't expect.

One common solution is to set up your university account to forward to your private account, and to set up that account so you can send e-mail listing your university account as the sender/return address when necessary.

research undergraduate - How to approach principal investigators for internship/job positions

1. 
   

   What would you recommend as the best way of approach principal investigators for internship/job positions? I'm undergrad, with a planned graduation this winter and I want to get some experience before grad school.

   
   
   
   
   • Should I try 'cold' messaging? I want to go abroad and I'm not well networked there.
   
   
   • I've been on exchange and performed rather well. Can I use this experience to my benefit?
   
   
   
   


2. 
   
   

   (Somewhat less important) Ideally I'm looking for research experience in Computational Neuroscience. I already have some research experience, I've done graduate work and I majored in cognitive science and mathematics but I come from a Liberal Arts & Sciences college. Will my LAS background be seen as a disadvantage?

   
   

job - Does obtaining citizenship somewhere help in applying for a faculty position there?

Would obtain the citizenship of a country help to be a more successful applicant for an academic job?

More specifically, for example consider that an international scholar, who currently holds a postdoctoral position, obtains a permanent resident or the citizenship of a country. Would this help to be a more successful applicant for a tenure-track faculty job at universities, such as in US, Europe, China, Japan, Australia, etc? Comparing to those who don’t have the resident permit/citizenship, with a similar background and academic contributions.

genetics - How does the modern theory of evolution solve these apparent problems?

I hold to the truth of Evolution, but I've encountered several problems with it, that I can't answer, and I can't find an answer for, despite much research. If would be great if anyone can answer these supposedly fatal problems for Biological Evolution, since I find it troubling that there appears to be no answer for these.

Problem/Question #1:

The first one is called the mutation protection paradox. Simply put, Evolution has evolved mechanisms to protect itself from mutations, that if left unchecked, would build up and wreck the biological system, yet the mutation repair and protection mechanisms guard and stop the very changes that allow Evolution to occur, which is mutation.

Is there an answer to this paradox?

Problem/Question #2:

The problem of genetic entropy. John Sanford has supposedly shown in his book Genetic Entropy and the mystery of the genome, that the human genome is degrading so quickly, that we could not have evolved from ape like creatures over millions of years.

The problem is supposedly that we have 100-300 more mutations than either of our parents. This is supposed to mean that 100-300 new mutations accumulate in every person, in every single generation. Then it's said that these mutations are so small they cannot be gotten rid of by natural selection, and that the vast majority are harmful to the human genotype.

Because the mutations are unselectable, they are left to build up in all people until the entire human race becomes extinct, and it is estimated that this should have occurred in less than 80,000 years. So if Evolution were true, we wouldn't be here to talk about it.

The person presenting this problem gave answers to two responses. He gave a response to the Evolutionist retort that most mutations are not harmful but neutral by saying "most mutations are neutral from the perspective of the organism’s physical fitness (phenotype), but all mutations must have effect on the genetic content (genotype). In no way are mutations truly neutral – they all must have effect on the genotype, even if they only affect the efficiency of transferRNA production. And as pointed out above, most are harmful."

Then he gave a response to the Evolutionist retort that -almost all of the unselectable mutations will occur in non-coding regions of the DNA (the so-called, Junk DNA), and therefore have no effect. Thus, the individual will not die and the population will not become extinct- by saying quote:

"Non-coding DNA does not code for proteins and scientists have previously thought it is largely useless. But mutations in the non-coding DNA won’t make them without effect since non-coding DNA helps during embryonic development and can be a part of many diseases. The idea that non-coding DNA absorbs mutations, thereby making them neutral, is false and is merely an argument from ignorance."

Is there an answer to this?

Problem/Question #3:

This can be called the meta-informaton paradox. How it goes is that you have two types of dynamics. Primary DNA which tells what proteins to make, and meta-information which tells the cell how to maintain the primary DNA. So it is said that primary DNA and meta-information are completely dependent on one another. If they become unrelated to each other, both become unusable and the animal would die.

The problem is that mutations are random, and thus completely independent events, and this means primary DNA and meta-information would evolve by completely random and independent events and thus would not be able to stay relevant and related to one another, which then creates a barrier stopping microbes to man evolution from taking place.

Problem/Question #4:

The person claims his calculations show that there is 1 chance in 10 to the 150 billion, that all species have evolved, each from a previous species. Here's how his calculation works.

He says he is being as generous as possible with Evolution, and has five assumptions:

Assumption 1: Evolution must occur by a net gain in new information. However, this is completely disregarded. We will simply assume that all beneficial mutations produce evolutionary change (including so called 'neutral mutations' which become beneficial later on).

Assumption 2: The rate of beneficial mutations is widely thought to be 1 for every million mutations. Indeed, scientists have observed millions more harmful or 'neutral' mutations than beneficial mutations. But we will assume that the frequency of occurrence is 1 beneficial mutation per 1,000 mutations.

Assumption 3: It will be assumed that 5,000 mutations are needed to make a species 'evolve' into another species (where the two species cannot interbreed). Although the number needed for new single-celled species to arise is probably less, other higher animals require millions more beneficial mutations than accounted for here (40 million mutational differences exist between chimpanzees and humans[1], though different genus).

Assumption 4: We will assume that the total amount of species that have lived in the past is 10 million. In fact, this is the upper end of the estimate for species living today. If 99% of all species have become extinct as many Darwinists claim, then our assumption is extremely generous.

Assumption 5: It will be assumed that every single beneficial mutation is fixed in the population after occurrence. This is very unrealistic (in favour of evolution, of course). Beneficial mutations can be lost from a population in a variety of ways; sexual reproduction and death being just a few causes.

Calculating the chance that 50 million species have evolved from a common ancestor:

Chance of 1 beneficial occurring: 1 in 1,000.

Chance of 2 beneficials occurring: 1 in 1,000².

Chance of 5,000 beneficials occurring (needed to make one species evolve into another): 1 in 10^15,000 (i.e. 1 in 1,000^5,000).

Chance that 10 million species evolved: 1 in 10^{15,00010 million}.

Therefore: 1 in 10^{150 billion}.

Can someone with only a bachelor's degree teach at a community college?

Can someone with a bachelor's degree teach at a community college, or are they required to have something more?

citations - In Google Scholar, is it possible to view the list of papers cited by a specific paper?

For any paper on Google Scholar, you can click "Cited by ..." to see a list of subsequent papers that cite the original paper.

However, is it possible to see a list of papers that the original paper cites? I realize that one can simply view the paper itself for the list of references, but I would like a way to see it as a list of links in Google Scholar, similar to the "Cited by ..." list.

career path - Where do people leaving academia go?

Is there any extensive research/study/survey that looked at where people that leave academia go?

I mostly interested in the computer science field (machine learning) in the US, but curious about other fields and locations as well.

People leaving academia can be PhD students or after (tenure-track, tenured, soft-money research positions, national lab researchers, etc.).

evolution - How was the resemblance between apes and humans explained in pre-Darwinian biology?

Humans and apes have somewhat obvious similarities, these must have been apparent to natural philosophers before the possibility of a common ancestry was first proposed in the mid-1800's. These proposals were not formally made in Darwin's On the Origin of Species (1859), but his general ideas of common ancestry were built upon in Thomas Huxley's Evidence as to Man's Place in Nature (1863) and then Darwin's The Descent of Man (1871).

How was the resemblance between apes and humans explained prior to this shift in thinking?

Answer

The time before Darwinism, people believed life as an entity which is created rather evolved. But there were great biologists interested in the relationship between species, who deliberately thought of evolution ideas and some of them believed in ape-human similarities and placed humans and apes in same group.

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In 1699, Edward Tyson, an English anatomist, dissected an ape specimen(chimpanzee) and showed that its anatomy closely approaches ours.But he didn't established any relationships between humans and apes. It was first done in 1738 by Swedish scientist Linnaeus in his book Systema Naturae .After that in 1759, Lamarck, a French naturalist who was Darwin's predecessor in general theory of evolution, stated that humans were derived from up-right walking apes.

In 1759, just half a century before Darwin was born and precisely one hundred years before he published his famous book , "Origin of Species", Linnaeus, the great Swedish scientist, discovered that man was a mammal. He then placed man in the Order of primates, which means literary the first, or the highest,order of mammals.It comprises all the monkey like forms, including the man-like apes. Reference

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References

Primate Evolution and Human Origins - Russel L. Ciochon & John G.Fleagle

Human Evolution: A Guide to the Debates - Brian Regal

I am interested in graduate studies, but I was dismissed from my undergraduate program for poor grades. Where do I go from here?

I've had a tumultuous undergraduate experience, to say the least. After being suspended freshman year, being re-admitted in the Spring of 2014, and a rough 2014-2015 academic year, I've been dismissed from my university.

It's extremely upsetting and has left me a little bitter, especially since my trouble in school has been due to ADHD, depression and anxiety that went undiagnosed for an extremely long time as well as an unpleasant living situation to say the least. I have no record of misconduct and was active in student organizations excluding social fraternities. I tried to appeal the decision, but got was rejected. I'm planning on going to a local community college in the fall to at least get an associates degree and transfer to another university, but I'm not sure how well it will go.

I have always loved academia, and ideally want to go to graduate school. Ever since I was a kid, my whole goal was to go to graduate from college. Now it is seeming less and less likely. I feel like my academic record could hang over me for the rest of my life, keeping me not only from continuing the education I want, but also keeping me from a career or leaving home. I'm at an unfortunate crossroads and I don't know what the next step I should take is.

That said, do I still have a chance at completing an undergraduate program and - hopefully - completing a graduate program? While I ideally want to continue my liberal arts education and eventually go into a post-graduate program, should I make a more achievable goal? My cumulative GPA is around 1.5, and I feel as though that it will affect the admissions process almost everywhere I go. Essentially, can I still get my degree, or will most universities not accept me at all on grounds of my academic record?

---

Related question posted here

Answer

You could probably start at an open-admissions community college in September, if that's what you wanted to do. You would probably need to spend some time there and SUCCESSFULLY COMPLETE YOUR COURSES to build successful reapplication package to a better school.

Any reapplication process would very much involve you proving to an admissions department why and how you became a student who is likely to successfully complete their program and become a graduate that they will be proud of. You need to convince them that your past record is not indicative of what your future record will be. The bad news is that this will not be easy.

The good news is that should you manage to turn things around, graduate admissions committees would be likely to look at you as an interesting candidate who has taken an adverse academic situation and made it better.

Think long and hard about your situation. Even if you treat the anxiety, ADHD, and depression (and I wouldn't recommend trying to start again without dealing with these fundamental problems) there will always be that next problem to overcome. If that next problem will shut you down the same way, you're setting yourself up for the same outcome. Treatment should be a part of your plan to avoid this.

Think about your academic experience, and how that's likely to change. Will future-you be a "B" student, and have an enriching academic experience, or will future-you be constantly on academic probation, constantly on the edge of separation? The former is great, but the latter can be an anxiety-producing monster that will leave you miserable for 4 years, but can still be an important career developing step. Unless you plan on a degree from an open-admissions school (like Brooklyn College, which can give you a fine education that can lead to graduate programs!!), you need to be able to convince a school that you won't fall in to this class, or you just won't get accepted. More importantly, if you think you'll fall into that class anyway, are you up for it? Can you tolerate the long, unpleasant experience an make it through to the other side, and is this worth it to you?

If you plan to continue in school at this point, and you don't plan to enroll in a community college in September, you should be planning on how to keep moving forward and not stagnating. If you need to spend some time getting the ADHD and depression treated, do it. Keep doing things that will develop your maturity and keep moving you to the next step, as opposed to marching in place. If you look like you're not progressing, chances of admissions get even slimmer.

Keeping in mind that an academic experience is a means, and not an end, take a good introspective look at your life plan and career plan and how your education fits in. I highly recommend spending the $4 for http://www.amazon.com/Control-Your-Time-Life-Signet/dp/0451167724/ref=asap_bc?ie=UTF8. It looks like a time-management book, but its much more -- or rather its a time management book on many different time scales -- this moment, weeks, years, decades -- and how to use your time to achieve your goals.

postdocs - Requesting feedback from a postdoctoral application

I have recently applied to a postdoctoral position, I reached the interview stage (which took place by video conferencing with the group leader and a postdoc), and was ultimately rejected.

I would like to ask for some brief feedback so that I might be able to improve my future applications, but the only email exchanges I have had were with the HR/recruitment people during the application process (it is a nameless 'recruitment' office that got back to me with the outcome of the application).

Which route would be best for asking for feedback: -

(i) email the HR/recruitment people to ask if the group leader would be willing to provide some brief feedback

(ii) email the group leader directly (as I have no previous email contact with them, I would need to find the email address from their website)

Some pitfalls I can see to asking the HR people are: (a) that they may just not pass on the message if they are busy; (b) it could be more work for the group leader if not done directly with them; (c) they could ask the group leader in person who then forgets; (d) I am also a little worried that the HR office may pass on the message in a not very kind way (e.g. "X candidate wants to know if you can send feedback" - rather than the more polite email I could send directly thanking them for their time); (e) if there is any policy of not allowing panels to provide feedback.

Some pitfalls I can see to asking the group leader directly are: (a) it may not be taken very well since there is an online system in place and a recruitment person who manages the application process; (b) they may be even more busy than usual and dislike the direct interruption; (c) as I don't have their email address I would have to find this online, which doesn't look very casual - I would prefer not to come across as someone angrily looking for an explanation for why they have been rejected, I am genuinely just trying to improve my future chances of finding a position.

I am sure there are many other factors I haven't considered.

Finally, please can someone suggest any tips they may have for writing a request for feedback? What format of email would be least irritating for an interviewer aside from just being brief? Does anyone have direct experience of this (from either side)? Even anecdotes of things you may have received in the past that were particularly good/bad may be helpful.

Answer

Asking for feedback on your application from someone who has turned you down is generally unlikely to yield useful information, and it may annoy them by making them choose between saying something unsatisfying or not replying. Here are some of the issues that have run through my mind when I've been asked for feedback (which is not common but happens every once in a while):

1. 
   

   I wonder whether I'm dealing with someone argumentative or difficult, who will try to dispute my explanation or change my mind, use the feedback as evidence in an accusation of misbehavior or dishonesty, or misquote me to others. Even a perfectly reasonable applicant might feel upset if they re-apply next year and get rejected again after having felt they addressed all the issues I raised.

   
   


2. 
   
   

   In most cases there's nothing objectively wrong with an application. All I can say is "your application was good but we liked someone else's better", which is not informative.

   
   


3. 
   

   Comparisons with other applications are crucial, particularly with the successful application, but all the details of other applications are confidential. It's difficult to explain why we liked someone else's application better without revealing anything that isn't already public knowledge. There won't be a simple quantitative explanation ("you should have published two more papers in high-prestige journals"), but rather a subtle qualitative comparison that is difficult to summarize in the abstract.

   
   


4. 
   

   Furthermore, letters of recommendation are one of the most important parts of an application, and their contents should not be revealed to the applicant. It's tough to give useful feedback without touching on the letter contents, especially because most concerns I might mention would at least make it clear that the letters didn't resolve these concerns.

   
   


5. 
   

   In some cases, I can identify a problem with an application that is not based on letters of recommendation or direct comparisons with other applicants. However, these problems are often not easily fixable (e.g., "we just didn't find your paper topics interesting"). Pointing them out feels like adding insult to injury. It might be useful for the applicant to hear that they never had a chance at this job, but I don't want to be the one to say so. The best case scenario is that the applicant always remembers me as the person who delivered this insulting news, and the worst case scenario is that I make the committee look foolish if we misjudged the applicant.

   
   
   

It's only in rare cases that I have genuinely useful feedback, something fixable that I can ethically reveal to the applicant and that might make a real difference in the future. (This usually indicates that either the applicant's advisor is negligent or the applicant is not listening to advice.) I've never had someone ask for feedback in this situation, although it might happen someday. In a few cases I've tried to communicate this information through a backchannel, such as one of the applicant's letter writers.

In your case, there's almost certainly nothing seriously wrong with your application on paper, or you wouldn't have been interviewed. Assuming you didn't do anything dreadful during the interview, you presumably fall into the second case above (your application was good but another was even better), and I doubt anyone will be able to give you satisfying or useful feedback.

If you decide to ask for feedback, I'd recommend indicating that you are aware there might be little or nothing to say. For example, you could send a thank you e-mail and include something along the lines of "I realize that you may have no constructive feedback to offer beyond that another candidate was an even better fit for the position. However, should you happen to have any advice for how I can strengthen future applications, I would greatly appreciate it." This relieves the pressure by giving them an easy way to decline to say anything substantive, while bringing up the topic just in case. I don't think there's any need to do this, or that it is likely to result in useful feedback, but it can't hurt.

publications - Are there many journals that do not accept TeX?

I have been told by our head of department, a veteran academic with a lot of publications behind his name, that I am not allowed to write my masters dissertation with TeX, as many journals do not accept TeX documents, and now I have to use Word.

I can almost not believe that journals would prefer Word over TeX, or is this in actual fact true?

I would appreciate answers from people actually working in academic publishing.

Answer

The answer is that in some fields (La)TeX dominate whereas in other fields (La)TeX is largely unknown. Obviously any field where equations are required is more likely to be using (La)TeX for writing and publishing. However, it is not uncommon that journals, or rather, type-setters of journals, use LaTeX for final production regardless of submitted format. The same applies to book publishers. But, the fact is that the use varies and one needs to check with the journal to which you wish to submit.

The fact that you are not "allowed" to write your thesis with (la)TeX is perhaps because your advisor does not use it. I am an avid LaTeX user and am struggling to convince both colleagues and students in my department to at least try using it so I know how difficult it can be. In the end, I need to use both to be able to communicate with my colleagues and peers. So although I do not see why you should not set the thesis in (La)TeX in the end, you probably need to use word for the manuscript so that your advisor can provide input on files you supply. But, check how many journals actually use LaTeX in your field and strike up a discussion with your fellow students and your advisor. I think it is worthwhile to be fairly fluent in using many tools.

Edit: I will just add that I was convinced by a friend to use TeX (not LaTeX, it was a long time ago) when I wrote my thesis (a monograph at a US university) while almost no-one in the department used TeX; but then my advisor always provided feedback from double-spaced printouts which were platform independent. Those were the days.

graduate admissions - Should an applicant to an university mention that her spouse is currently a student in the same University, as part of her SOP?

While writing one's Statement of Purpose for applying to a grad program, should one mention that her spouse is also a grad student in the same university? What are the pro's and con's of that approach - while on one hand, it shows that the candidate is very likely to accept an offer made by the dept, it might also imply that the presence of her spouse is the main reason the applicant wants to get admitted, which might not sit well with the Admissions Committee?

Answer

This really can be a two-edged sword.

Pros: You are likely to really come and stay since your spouse is there. You can argue that you know much (positive) about the place through your spouse which has made you select the place.

Cons: You may be seen as applying because your spouse is there and not because you think the place is exactly where you want to go and be. In other words, you make a choice out of practical and not academic reasons. (largely what you already stated)

So, first of all, it is no-ones business why you apply to go to a certain place. Of course the people who read your application will evaluate your interest and so anything that strengthens the application is good anything that doesn't can be left out. Although the location of one's spouse should not be grounds for admitting (or not) a person, it is possible people read things into the fact that you did not originally anticipate. If you want to state that you already know the place is good, you may do so by demoting your spouse to a friend. I have to confess I am not at all happy about writing this which seems so negative towards mentioning your relationship but it stems from knowing that you cannot predict how people interpret things and it is therefore better to be neutral and focus on the academic rather than putting up personal reasons for a choice.

genetics - Are there more descriptive ways of naming genes and gene interactions?

I couldn't help but notice just how non-descriptive the gene names that modern genetics is using. Currently I'm reading "The new science of Evo Devo" by Sean B. Carroll and here are some examples of gene names used:

• Fzrb


• Krox 20


• Hoxa2, Hoxb4


• ZPA


• FGF8


• sonic hedgehog

While these names identify genes uniquely, they do very little to express what and where the gene does, or how it is related to other genes (While FGF8 may be related to FGF7, it's relationship to XYZ10 is not obvious).

I get the need to uniquely identify genes , and the book is an example of just how hard it is to presently write about a lot of genes at once. The author creates a picture of what's going on, but the gene names get in the way. Even in cases where a gene has a semi-descriptive name, like "eyeless", the reader has to remember that it's actually the gene responsible for eye formation.

Are there are any efforts underway to systematize or name genes for a given organism in an expressive manner?

As a programmer, I write code for a living, and having descriptive names makes it easier to look at someone else's code, read about code and even discuss it with novices. For example:

• initializeDataModel


• createViewHierarchy


• userDidSelectLayerAtIndex

Modern programming tools make using descriptive names easier, because of autocomplete - typing in the first few letters of a programming structure completes the rest. Even google has a list of autocomplete suggestions.

We are all familiar with the Internet, where biology.stackexchange.com/questionname resolves into a specific page. Stackexchange is the site we are visiting, and Biology is a subset of that site. There are other biology websites, but biology.stackexchange.com uniquely identifies this site. The use of "biology" in the address gives readers a general idea of what the site is about and relates it to other biology sites. Our web browsers resolve the address into a proper string of bytes and get the right page. What if we name genes like like

• com.drosophila.eyeformation


• com.chicken.limb.structure.ZPA


• com.human.development.geometry/XYZ10

,and whatever technology we use would actually resolve that descriptive name into a gene or a series of gene interactions?

Answer

Many gene names are descriptive, e.g. DRD1: dopamine receptor D1, TOP2A: DNA topoisomerase 2-alpha, or PTGS1: prostaglandin G/H synthase 1. These are examples of genes that have a clearly defined main function.

The genes you listed are involved in development, and there describing the function of a gene becomes much more difficult. E.g. sonic hedgehog is involved in patterning many organs, from brain structures to teeth. How would you assign a descriptive name?

The analogy to (programming language) functions does not work for many genes, because they were not designed to fulfill one function, but evolved to do many different functions. For genes that have many functions, we just need a unique name. The multitude of functions is catalogued elsewhere.

(Bonus descriptive gene family name: MAPKKK: MAP kinase kinase kinase)

Realised afterwards that I committed mild plagiarism in a paper I wrote as an undergraduate, what should I do?

A few years back, while still an undergraduate student, I wrote and submitted a paper to a (low-tier) journal. It was accepted and published. None of the professors in my college were familiar with the subfield in question, so I did it all on my own, without their supervision or assistance.

It was only later on that I realised that I was guilty of plagiarism. I did write the paper all on my own, and always provide appropriate citations, but sometimes I would quote single sentences or parts of them directly from my sources without indicating that they were direct quotes (even if these unmarked quotes were always followed by a citation to the original source).

It has now been several years but I keep feeling guilty about it, and worry that one day someone will notice it and call me out on it. Or at least notice it while reading the paper and think worse of me. But since it has been several years since the paper was published, I also don’t know what I could do about it. I have thought of putting something like a public admission and apology on my website (from which the paper can also be downloaded), but maybe I’m overthinking it and nobody would actually care. In that case it would feel like a bad idea to needlessly draw attention to something that nobody would have noticed otherwise. But the paper has been cited some times, and I have reason to expect that there will be people reading it in the future.

Should I do something about it or just let it be?

publications - Why are most scientific articles locked behind a paywall?

Can someone give me a legitimate, convincing argument as to why scientific papers should be locked behind subscriptions and paywalls? That unless you happen to be on a campus, you can't get view a manuscript without paying an often extortionate amount?

Answer

Once upon a time, before the internet existed, the only way to distribute scientific content to a worldwide audience was through print. There are obvious costs related to printed publications such as paper, ink, printing, distribution, etc. Commercial publishing houses were established, which took care of this task, as well as the editing, the type-setting, organizing the review process (mind that the reviewers are typically not paid, but they still have to be found, contacted, etc, and all of that also costs money in a pre-internet era).

Many of these commercial scientific journals gained a certain reputation over time, and it became attractive for scientists to try to publish in the highest valued journals. For the publishers it was (and is) attractive to maintain the journal's reputation (e.g. expressed in its impact factor, etc), in order to attract an abundance of high quality manuscripts, select the best ones, and keep a large audience.

This was (and to a large extent still is) the status quo when the internet arose. This is also basically the answer to your question.

Now with the internet, it is perfectly possible to reach a large worldwide audience without the costs of printed journals (e.g. ArXiv). Also, peer review could be organized in an alternative manner. However, the commercial publishers have a lot of interest in keeping the old business model alive, as it is the source of their revenue.

So why are things largely as they were 50 years ago? There are a couple of reasons for this. For one, there is the absence of a platform that fully replaces the ring of scientific journals, including a reliable peer review process (or accepted alternative). Furthermore, people tend to do what they are used to doing in the past, and senior researchers (the ones who take the decisions) are used to publish in the traditional venues, and teach the juniors to do the same. Lastly, many researchers are (at least partially) evaluated with respect to the reputation of the venues they publish in, which keeps the old and established journals alive.

How to come up with research ideas?

As a very new researcher who is exploring the best way to generate ideas, some guidance on this question would be very helpful. I have found that this is NOT easy. Ideas seem to pop out of my Professor every day and I wonder how he does it. This question is broad;

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  How do you tend to come up with initial/seed ideas? What is your search method (if you have one)?

  
  


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  What proportion of your ideas for past papers come from; (i) colleagues, (ii) intentionally browsing the literature for ideas, (iii) on the spot inspiration, (iv) conferences, (v) other?

  
  


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  How do you prioritize research ideas?

  
  
  


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  Is there any special, generalizable method that you've discovered to sift out those ideas that are likely to be unrealistic early on in the process of idea generation?

  
  

Based on small amounts of anecdotal evidence I have reason to believe that there is vast heterogeneity among professors regarding the above questions. For example, economist Steven Levitt says he works on 22 papers at once. A professor I know will have maybe 25% of this at any one time.

Related but not duplicate: Is there any software or tools for managing developing research ideas?

Answer

Okay, as you say, this is very broad, and possibly argumentative. So, I'll try to section off my answer for your various sub-questions, and talk not so much about how I do come up (and organize) research ideas, but how I see it done by everyone (including me).

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Coming up with ideas

The most exciting phrase to hear in science, the one that heralds new discoveries, is not “Eureka!” but rather, “hmm... that's funny...” — Isaac Asimov

It's probably very akin to asking a large number of artists “how do you come up with inspiration?”, i.e. you can probably get one thousand different answers, and yet not useful answer at the same time. However, there are some elements that I think are common to all. You can't “trigger” new ideas to come into your mind, but you can put your mind into the right disposition to host these new ideas: recognize them and welcome them. Below is a list, certainly partial and limited, trying to detail my perspective in this matter:

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  Be challenged! Nothing sparks ideas more than being confronted with contradiction, healthy criticism, a spirited debate, maybe a bit of competition. Some people manage to do that by themselves, arguing against their ideas and improving them. I myself (and most of the colleagues and students I have seen) need an echo chamber, someone to discuss things with. If they're not exactly from your field, all the better, as they may have unusual/naïve/silly questions or expectations.

  
  

  To give an example, some of the most “successful” ideas I have had came while answering questions, for example from a PhD student or colleague, and replying by “no, it doesn't work like that… in fact, it's probably always guaranteed to be false, because… see, it's linked to X… or maybe it's not? hum…”

  
  



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  Be curious! Ideas come from problems. Identifying worthy problems in your field of research, and dissecting larger issues into of specific problems of manageable scope, is at least as hard as coming up with new ideas. In the end my feeling is that, especially for a researcher, all ideas are the result of one’s curiosity.

  
  


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  Manage to get some free time for thinking (and not: teaching, supervising, tutoring, reviewing, writing, sleeping, …). Body and mind. Sure, an idea can pop into your head any time, but it's probably less likely to happen when you teach basic calculus all day that when you get some time to really think.

  
  


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  Know your field, know where a new development need to occur, what is currently missing. Read review papers, search for such ideas through people's articles or blog posts, discuss with senior colleagues who have a comprehensive view of the field, …

  
  

  One of the ways you can come with ideas is by analyzing how different groups work in your fields, seeing what has been addressed and avoided, what big questions are still open, and how you can link between different works to build a coherent global picture… This is not always successful, but it usually generates some good ideas along the way!

  
  



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  Explore more or less closely related fields, and see if there is something from your background that you could apply to their problems, or ways you could build something together. Such ideas tend to be very strong, because you can oftentimes apply an entire branch of knowledge (ideas, methods, algorithms, etc.) to a very different problem. In that case, the added value comes from your different perspective, as you might try things that others would not think of.

  
  


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  Ways have been devised to come up with new ideas on a given topic, either alone or in group sessions. Brainstorming is probably the best know such method (and might be the most popular, in one form or another), but a really large number of creativity techniques have been developed. They can be applied both to enhance creativity or to boost problem solving efficiency.

  
  

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Organizing ideas

A quote often attributed to Kant: “someone’s intelligence can be measured by the quantity of uncertainties that he can bear”. If that true, that has serious consequences for research. Accepting that your mind can only efficiently support a finite number of ongoing research ideas, you have to come up with ways to write them down, organize them, prioritize them, come back to them later, etc. Just as you cannot juggle with as many balls as you'd like, such “external” tools will help your brain focus on the ones that you assign high priority (or the ones to which it gives high priority; the brain works in funny ways).

Most people use very low-tech tools for that:

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  Notebooks, either sorted chronologically or thematically; in the later case, open a series of blanks pages for each new project/idea, and flip through the book whenever you want to check on them. I use a Moleskine (WP) for that purpose; having a nice, leather-bound notebook somehow helps me “value” it more and treat it with care (always have it with me, actually use it).

  
  


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  Post-it’s scattered through one’s (real or virtual) desktop. Downsides are obvious.

  
  


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  More people than I thought actually don't use any tools, and just keep all in their mind. Apparently it can be done, but I don't advise it.

  
  
  

But more complicated methodologies have been devised, that are supposed to help you with it:

• Mind mapping, either on paper or software-based.


• Using todo-list flat or two-dimensional todo-list software, or more complex task-tracking software (see, e.g. Trello).


• The software side of this question is already covered (though possibly not extensively) here on this very Q&A site.

Finally, don't underestimate the possibilities opened by delegating: people in charge of a specific project or sub-project (PhD students or post-docs) can be tasked with maintaining a list of ideas by all contributors of the project, to come to later on.

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Answers to your miscellaneous smaller questions:

What proportion of your ideas for past papers come from; (i) colleagues, (ii) intentionally browsing the literature for ideas, (iii) on the spot inspiration, (iv) conferences, (v) other?

Most ideas are hardly “traceable” to one source or another. A given idea might have formed in my head during a conference, seeing how people were failing to address a certain issue, then crystallized during a discussion with colleagues, but would never have occurred to me if not for a literature review I had performed a few months before.

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I'll come back a bit later and continue working on this answer :)

job search - Job applications reviewed "until the position is filled" (i.e. soft deadline): What does that really mean?

I noticed that many ads say "Review of applications will begin on Day X, and continue until the position is filled". I wonder how this kind of search works. Assume the search committee received a certain number of applications on Day X. Usually none of the applications is from a superstar that you definitively want to hire, but let's say between five and ten are good enough for you to hire one of them. What would the search committee do? Would they contact the candidates, arrange interviews and hire the best one there? Or would they still wait for a month or two just to see if a superstar would apply after all?

Answer

"Review of applications will begin on Day X, and continue until the position is filled" is also translated as:

We want you to get your application in on time, but if you're totes amazeballs and late we'll overlook it.

The motivation is the same as what was mentioned. If you say that there's a hard deadline for submissions, and then Dr. Awesome Sauce applies a day later and gets hired, you're opening yourself up to a lawsuit from all the Dr. Not-So-Awesomes.

Practically, academic hiring works on a calendar, and universities compete with each other. For example, in computer science it's rare to be making a first offer well into May unless you're at the University of I'm-So-Cool and know that you can afford to be last. And even then it doesn't always work. So practically speaking there's a deadline of sometime in March to make decisions on offers and start wooing your preferred candidates.

This means that you can't realistically process a new application any later than early-mid February (because it takes time to collect references and organize a trip)

research process - How should I deal with discouragement as a graduate student?

I am a third year (starting fourth year in the fall) PhD student in mathematics. I've passed all qualifying exams and am currently doing research. As far as I can tell, I am not doing poorly. I have the good fortune of having a great advisor, being in a very supportive department, and having friends and family who genuinely care about my success.

The fact is research is hard. It appears to consist primarily of staring at a problem for days and days and days without getting anywhere. Sometimes, rarely, I do figure something out and that feels wonderful, but the overwhelming majority of my time appears to be spent banging my head against a mostly figurative wall. I am not complaining about the material being hard, and I am not averse to putting in hard work, but I get frequently discouraged when I realize the vast volumes of mathematics that I yet know nothing about (and probably never will). It's very hard to quantify progress - in particular, there are too few tangible returns after too many hours worked. I find myself thinking along the lines of "Oh, if only someone actually smart were thinking about this problem they would have solved it in moments" and so on.

I've talked about this to some number of people; here is some advice I have received:

• Take a day off. Putting in hours upon hours of trying things doesn't magically lead to a solution, particularly if the brain is tired and just wants to sleep.


• Have a hobby. Since math research doesn't exactly provide instant gratification, a hobby might provide some instead.



• Talk to other graduate students. Realize that many graduate students go through this.

I'm interested to know how other folks have dealt with being discouraged as a graduate student. Does it get better with time and experience? Is this a sign that research is not for me and that I should seriously consider a life outside academia?

Answer

The fact is research is hard. It appears to consist primarily of staring at a problem for days and days and days without getting anywhere. Sometimes, rarely, I do figure something out and that feels wonderful, but the overwhelming majority of my time appears to be spent banging my head against a mostly figurative wall.

Yes. This. And it wouldn't be so damn tempting if those bricks didn't wiggle just a little bit every time I slammed my forehead into them. Sometimes I think my eyes must be playing tricks on me, what with the repeated cranial trauma and all. But then I remember how good it felt the last time my head actually went through the wall, and so I keep plugging away.

I've found it extremely useful to have two or three walls to bang my head against at any given time. Surprisingly, sometimes banging my head against one wall actually makes one of the other walls weaker. But most walls prove considerably stronger than my head; so it's helpful to have options, so I don't feel so bad about walking away with some scalp intact.

If you're very lucky, one good smack on the bricks will actually bring the ceiling crashing around your ears. That takes a long time to clean up, but sometimes the debris will knock down other walls for you. And then you have a whole new set of even bigger walls to bang your head against!

I find myself thinking along the lines of "Oh, if only someone actually smart were thinking about this problem they would have solved it in moments" and so on.

Do not listen to the Impostor Syndrome. Everyone "actually smart" is hearing exactly the same voice in their head saying "Oh, if only someone who actually knew how to hit walls with their forehead hit this wall, it would come down like a stack of cards." when in fact the wall really is made of brick.

Does it get better with time and experience?

Yes. Eventually, you'll move from hoping that you'll be able to knock down a wall with your head someday, to being surprised at how often the walls you hit with your head actually fall, to finally believing that you really can knock down walls with your head sometimes. (For me, the second transition happened some time after tenure.)

But your head will still hurt.