evolution - Are there any multicellular forms of life which exist without consuming other forms of life in some manner?

The title is the question. If additional specificity is needed I will add clarification here.

Are there any multicellular forms of life which exist without requiring the consumption (destruction) of other forms of life in some manner? Thus purely on inorganic material.

I do understand that the definition of life is a semantic distinction, so for this discussion I will assume the one Wikipedia provides:

"Life is a characteristic distinguishing physical entities having signaling and self-sustaining processes from those that do not, either because such functions have ceased (death), or because they lack such functions and are classified as inanimate. Biology is a science concerned with the study of life."

I am open to considering alternative suggestions.

Thank you.

teaching - In-class, allowing students to address professor informally ('tutoyer' / 'tutear')

Supposing that Dr. A is teaching an undergraduate-level course, what would be the pros and cons for Dr. A to allow students to address himself in an "informal" manner?

By "informal" here I mean using what is employed in a number of languages for informal conversation. For example, this would be tutoyer in French or tutear in Spanish. (Hence, the question does not apply for an English-speaking classroom, but does apply for a French or Spanish-speaking one).

EDIT (clarification, thanks j91): In Spanish, French, German and other languages, the second person singular has two versions: "Tú", "Tu" and "Du" are the informal versions in Spanish, French and German, respectively, and "Usted", "vous" and "Sie" are the formal ones in the same order. "Tutear" is the act of using systematicaly the informal version and, in theory, should be avoided when speaking to a person in a position of authority.

Answer

The effects of the decision to invite your students to address you informally, and whether this is considered appropriate at all, are very culture-dependent. In general there are several trade-offs. How you balance them depends on your personal judgement. My experience is that of a German who has worked both in Germany and Austria.

Possible upsides of having the students address you in an informal manner (tutoyer/tutear/duzen) include:

• Students may be less concerned about perhaps embarrassing themselves in front of the "authority figure"; they may be more inclined to participate in class discussions and ask ("stupid") questions.



• Less perceived role conflict on your side, if you are a very junior lecturer and empathize more strongly with the student side than more senior staff.


• A more relaxed and friendly atmosphere in general

Possible downsides:

• Students may be more willing to negotiate about grades etc.; and less distance between you and the students can make it hard to say "no"


• Politely ignoring each other can be harder if you encounter students in a different social setting


• Explaining or even just giving a disappointing grade feels more personal and unpleasant when you have crossed the line between you (tu, Du) and "You" (vous, Sie).

career path - Postdoc opportunities in mathematics

I am expected to finish my Ph.D in mathematics (if relevant, more specifically - in commutative/homological algebra) by the end of this academic year. I am studying in a somewhat minor university, although my supervisor is a well know figure in his field.

Following my supervisor's advice, I submitted applications for postdoctoral positions in about 20 top level universities in the US. As most of these universities already finished hiring for this year, I suspect I made the mistake aiming too high, and would probably get negative answers from all the different employers.

Assuming this is the case, I am now wondering what should be the next step in my academic career. One option is to stay at my current university for another year (but with a much lower salary, as my scholarship will come to an end). I should mention that my supervisor highly discourages this option, as he thinks that I should get more involved in the research community of my field, and my current university is a poor place to do so.

Alternatively, I am wondering if there are any other opportunities for postdocs in Europe or the US for the 2013 academic year, in my relevant field, of which the deadline still did not pass.

Any advice or idea for my situation would be helpful.

Thank you

Can I force evolution in a group of cells by removing all the smaller cells?

I actually have algae growing in water in a container. I was thinking if it was possible to filter the water so that all the small cells will be filtered out and only the bigger ones will remain to reproduce cells that tend to be bigger. Is that possible? What type of filter should I use?

plagiarism - Professor does not care about cheating, what should TA do?

I am a PhD student, working as a Homework marking TA in a school where cheating is extremely blatant. The university has an extremely strict policy against cheating. Hundreds of students in math courses alone are reported each year, and suspensions are given to severe/repeat offenders. I have personally reported cheating many times.

Based on this environment, most courses have shifted away from Homework grades, and more toward Quiz/Test grades.

My course is a low-bar mid-level math course, very likely to be the last math course ever taken by the students who enrolled in the course.

The marking distribution of my course is done in a way where the homework mark weight is so absurdly high that cheating on homework would almost guarantee a pass.

I had realized this at the beginning of September, and discussed with (confronted) the instructor. The short summary of the response is that the instructor doesn't care about cheating.

The professor doesn't want to put in the effort to deal with cheaters. The professor thinks the students cheating would not be overly unfair to other students who don't cheat. The professor also does not want me to try to catch cheaters.

I have made clear that cheating on homework almost guarantees a pass, and he/she agrees, and is ok with this.

The homework are all questions from the textbook, and a solution manual is readily available on google.

In this week's homework, I have found more than 100 students who have copied from the solution manual, where at least 50 students copied word for word (if reported, the cheating done can be easily proved by the school.)

I suspect I only caught a portion of all cheaters, as buying solutions at this university is too blatant.

I would like to ask the community of my next steps.

If I were to report the cheating to him/her: Would I anger the professor, since this is against his/her wishes? Would I build a tense relationship with him following this? (There is still a whole semester ahead, and possibly years in the same university.) What would be done in the end? What if he ignores the report, what should my next steps be?

If I were to report to the undergrad chair: Would it be inappropriate to skip reporting to instructor first? Would I also build a tense relationship with the instructor by this move? I am almost positive that there would be action by the undergrad chair on the cheating behavior.

I could also report to both simultaneously. I could also do nothing at all, in which case the cheating would without a doubt continue for the whole term, with the vast majority of students taking part.

I personally disagree with the professor, as I believe that it is unfair for the minority of students who don't cheat. Due to the high homework marks, a mark curve is highly unlikely, so the students who don't cheat are truly getting lower marks because of the cheaters.

The instructor is in the beginning of his/her career, and not retiring. The university is in North America, very large (more than 50,000 undergrad)

Edit3: As I continue to grade, I have found more and more cheaters, in the hundreds, approaching 50% of the class.

Thanks for all the suggestions asking me to "let it go". After much consideration, I can not take such advice.

Thanks for all the suggestions of asking me to "not skip the chain of command". I have since realized this may have severe consequences, and have decided against it.

I have contacted only the instructor with minimal details of the situation. Thanks for all the support and best wishes from the community, I sincerely appreciate it.

Recommendation Letter Request: No response

I am applying to graduate school, and I am having a problem with recommendation letters. I need three recommendation letters with two of them being academic reference letters. Honestly, last year, I had requested two recommendation letters from two of my former professors for my law school applications. However, in the end, I decided not to pursue law school for a number of reasons, despite being accepted to one. Currently, I am applying to a number of different schools' masters' programs in the field I plan to study.

As I mentioned earlier, I am having difficulty with the recommendation letter process. I wrote emails to those two professors about my situation, and one professor was willing to revise her former recommendation letter for my new masters' programs applications. However, I have yet to hear back from the other professor. I had written a senior thesis under that professor, and I was hoping to receive a letter from him. After I sent an email to that professor a few weeks ago, and received no response, I sent him a follow-up email yesterday. I received no response to that follow-up email either. If there is no response, does that mean a discreet "no"? Should I send another follow-up email a few days later? Or, should I find another academic recommender at this point? My first application deadline is in the middle of December.

behaviour - Why do humans suffer anxiety when they view "Trypophobia trigger images"?

When you type Trypophobia Trigger Images in google, you see a variety of images with irregular lumps and bumps among some more gory images.

Many people report that these images induce phobia like symptoms of anxiety.

Why do we get anxious when exposed to these images? What advantage is there to be had from this response?

I find the reasons like this ABC news report on ants and spiders. But still didn't get it any info from it.

Answer

Trypophobia is not a recognised specific anxiety disorder (Washington Post). It is worth mentioning that anyone can have a phobia to anything, this is merely a question of whether many people associate these spatial patterns with anxiety. Nevertheless, the response of individuals to these images can be quantified (Le et al., 2015). Ultimately the findings show that a response of trypophobia is not correlative with anxiety. Note that here we are discussing anxiety in a phobia response test. Typically anxiety manifests as sweating, dizziness, headaches, racing heartbeats, nausea, fidgeting, uncontrollable crying or laughing and drumming on a desk. This is not merely feeling uncomfortable.

One hypothesis was that these images had irregular spatial patterns that cause revulsion. A study found that in nature some animals and plants may use this patterning as a warning mechanism and that it is associated with poisonous animals (spatial pattern quantification of 10 poisonous animals versus 10 control animals p=0.03), and indeed spiders were among those that use irregular patterns (Cole & Wilkins, 2013). Note that this hypothesis was presented in a psychology journal so the evolutionary mechanisms remain, in my opinion, not fully explored and scrutinised.

Hover over the below yellow box to view a lotus seed head, which has typical irregular spatial patterning presented in the 2013 study.

This image is often reported as inducing trypophobia.

Answer: In summary, humans do not reliably feel anxious when viewing these images. It also remains unclear why some people do get anxious or uncomfortable when viewing these images. It is perhaps to do with an aversion to some potentially harmful animals, but evidence remains scarce.

Non academic career for PhD in Biology

This question has asked previously for PhD in mathematics and computer science in this StackExchange forum. However, the situation will be completely different for Biology graduate because of the skills we learn during our PhD. Math and CS graduates have lot of open options (?) looking at their quantitative reasoning skills, which are not enough for biology. We learn lot of logic, reasoning and statistics, but is that enough to survive in a highly competitive world?. So I was wondering: is there any alternative career option for PhDs in biology?

P.S: There are few options I am already aware of, like teaching in school/university, quality control posts at various firms, R&D in pharmaceutical companies. I was wondering if there are any other options which are not very obvious from our skills.

Update (18 Sep 2015)

After reading comments and answers, Following more options have raised

• Science communication


• Librarian


• NGO and firms for data analysis

Answer

There have actually been some studies (if I recall Mike The Mad Biologist's blog covered them awhile back) suggesting that biology graduate students are somewhat less happy than their peers because many of the specialized skills they pick up aren't immediately transferrable. For some aspects of "biology" this isn't true - for example, a mathematical biologist is likely just as qualified to exit into a quantitative field as an applied mathematics student, some fields of biology involve code, etc.

Failing that, some other options colleagues who are biologists have pursued:

• Government positions. Some of these are "academia-lite", some of them are markedly different, but there are several branches of government that hire biologists in some form.



• Teaching at the high school level. You're likely overqualified, but that's not a bad thing, and there are private high schools that very much value "X% of our faculty have PhDs..." as something to tell parents.


• As you mention knowing exist already, there are biotech companies that exist, and employ biologists in many capacities.


• Conservation organizations, private foundations, etc. may be of interest, especially if you're more ecology oriented.


• Depending on your research area, what you did, etc. you may be able to brand yourself as a "data scientist" - at the moment it's pretty vague as to what exactly that means.


• Science communication - university offices that do outreach, news organizations, etc.


• With the addition of an MLS, a career as a research librarian is also potentially an option.

genetics - What DNA does a self-fertile plant's seedling have?

Some plants are said to be self-fertile. An example is Prunus tomentosa.

Assuming that no cross-pollination happened with other plants, if a self-fertile plant such as prunus tomentosa produces a seedling, what DNA will the seedling have? Is the seedling's DNA an exact copy of the parent plant's DNA, or do the genes get rearranged?

Answer

Selfing (aka self-fertilizing) differs from cloning. When selfing occurs, the offspring is not an exact copy of the parent. When cloning occurs, the offspring is an exact copy (except for a few mutations) of the parent.

Selfing implies that an individual will produce two gametes (typically a spermatozoid and an ovule but that might be a bit more complicated) and these two gametes are fusing to give the zygote (egg or offspring if you prefer).

As a consequence, when selfing, meiosis is occurring (and therefore segregation and recombination) so that the offspring is not an exact clone of the parent but rather some kind of a rearrangement of the parent genome (with a few mutations of course).

neuroscience - Does antidromic conduction occur in the brain under normal conditions?

So I am reading a book on neuroscience and they mentioned in passing that the action potential is capable of travelling in either direction along the axon (orthodromic vs antidromic), The wikipedia antidromic article states that the effect is often used to confirm connections in laboratory experiments.

What I'm now wondering is if the phenomenon has been observed with normally behaving neurons in situ (as normal as a neuron under experimental observation can be anyway) and therefore possibly needs to be factored in when modelling neurons in software or is it safe/justified to treat the information as only flowing in one direction (orthodromic)?

Answer

Under physiological conditions, action potentials are generally assumed to travel one-way. Action potentials are generated in the dendritic region, and travel from the soma to the axon terminal. Because voltage-gated sodium channels are inactivated after having been active during action potential generation, the action potential cannot travel backwards because the tail-end of the action potential is basically temporarily shut down (Fig. 1). The duration of inactivation of sodium channels determines how fast a neuron can fire, i.e., it determines the refractory period of neurons (Purves et al., 2001).

^{Fig. 1. Action potential conduction and refractoriness. Source: Zoology.}

When neural tissue is artificially electrically stimulated, however, action potentials can be generated anywhere along the neuron. When an axon is activated somehwere in the middle with an electrical stimulus, an action potential will travel both ways, i.e. normally to the axon terminal, but also antiodromically to the cell body.

However, it has been noted in vivo that some neurons do show antidromic action potentials under physiological conditions (Jansen et al., 1996). For modeling purposes I would not bother too much about this, though, because antidromic action potentials are generally only observed under artificial conditions.

<sub>References
- Jansen et al., J Neurophysiol; 76(6): 4206-9
- Purves et al., ed. Neuroscience. 2^nd ed. Sunderland (MA): Sinauer Associates; 2001</sub>

graduate admissions - Should I explain a single bad grade in my personal statement?

Overall, I have always maintained a good standing in all of my undergrad classes. Most of my grades are either As or Bs. With only one Junior level course with a D. Is it worthwhile to explain this one bad grade? I am afraid that since all my other grades are good, I will only be highlighting that one bad grade by talking about it.

publications - Rules for affiliation for student doing unpaid research in his/her free time?

Lets say an undergraduate student does some research in his/her free time and wants to write a paper about the findings. What are the rules regarding affiliation when the student tries to publish?

• The student is required to include the university as affiliation, because he/she is enrolled in a program at the university


• The student is not allowed to include the university as affiliation, because he/she is not officially hired/approved to do research under the name of the university


• There are no rules, the student can choose


• ...?

I guess for graduate students / postdocs / professors it is mandatory to include the university as affiliation, as they get paid by the university to do the research they are doing!?

Answer

I don't think there are any "official rules". (I can't even find a clause in my employment contract that officially requires me to list my university on my papers.)

But as long as you are a student, it's a good idea to list your university as an affiliation. Even if the university isn't paying you, you do benefit indirectly from the intellectual environment and resources that the university provides: professors, fellow students, library, internet, health insurance, nearby coffee shops, and so on. It costs you nothing to be generous. Also, for better or worse, readers will take your paper more seriously.

publications - Affiliation on a paper written mostly in previous position

If research was done and paper was mostly written at institute A, but then it finally got accepted while the author moved to institute B, say, 3 years later. Should the affiliation of the author be

1. Only Institute A: because 95% of the support was from here, and work was done here


2. Both Institute A and B: in some sense, both institutes supported the work



3. Only Institute B: this is where the author is affiliated at the moment

related: Changing affiliation on publication

Answer

There are no fixed rules but I would opt for your option (2). The affiliation is intended to aid in facilitating contact with the author but is of course useful to a department to show count the paper as a product from that institute. By listing your former address first indicating that that is where you did most of the work and then adding the second as present address provides the best and useful information for all parts. Option (1) means your present location is not disclosed which is a missed opportunity to locate you. Option (3) has the disadvantage that your former department are not associated with the work you performed there. So although all are acceptable, (2) would be the best (most polite and useful) way in your situation.

yeast - Sources for common laboratory Saccharomyces strains?

I'm used to working with bacteria - some of the more common laboratory strains sometimes come with an order from some vendors. What's the most convenient source to order common straings of Saccharomyces for lab work?

Answer

The Saccharomyces Genome Database has a list of sources here. One of them is the Japanese Yeast Genetic Stock Center: I checked their site out and found that they charge ¥390 per strain which is around USD4. There is also a USD5 fee on all orders. I searched for a couple of standard strains, and these were in the catalogue, so it looks like a good possibility.

(Incidentally I have used USD here rather than $ because there seems to be a bug when typing that symbol twice in a post - try it and you'll see what I mean.)

teaching - Undergraduate not doing homework (case method)

I've recently started teaching undergraduate students using the case method (management subjects). However, I'm finding that most of the students simply don't do the reading at home. Even though I (so far) have used only short cases (just a few pages), they still just don't do the work.

For those unfamiliar with the case method, if the students do not do the reading before coming to class, there is little to discuss in class. In the end, I feel like the class time is wasted.

Because of the design of the course, I actually don't have the flexibility to have this affect their grade other than to simply fail them. I cannot, for example, reduce their grade by 10%.

If anyone uses the case method with undergraduate students, I'd love to know how you get students to actually do the reading / thinking work required before they get to class.

Answer

I have some experience with lab practice in physics and chemistry, where we routinely ask students to read up on the work planned and do some preliminary calculations before they can come to the lab, in order to maximize their use of actual lab equipment. It's sometimes hard to motivate students for things that should be done in advance, but there are ways you can improve their involvement:

1. 
   

   Make sure that the amount of material is compatible with the time they have to study it, and the demands on their time by other courses. If you're going to require something of them, it should be within reasonable limits. Also, make sure you convey that point to them: I have, on a few occasions, had to reschedule things to give them more time, because the material was very heavy and taking more of their time than I had assumed, or because they just had many other things to do (e.g., a full week of exams).

   
   


2. 
   

   Be crystal clear that reading the material before classroom is actually one of the requirements of the class, and that it is entirely necessary to actually pass the class.

   
   


3. 
   

   If you want further motivation, introduce some sort of evaluation of their reading at the beginning of the lecture: get two or three students to come up, and argue the case (or whatever it is you do in those lectures) before the others. Then, give them a frank assessment of how they fared, including “you failed miserably because you didn't do your homework”. Even if that evaluation doesn't count for the final passing/failing grade, it will motivate them and might introduce some friendly competition.

   
   



4. 
   

   If some of them still don't do a thing, fail them. After all, you had told them (and more than once) that reading the material is a requirement for passing.

   
   

authorship - How to offer a reviewer to be co-author?

I currently have a paper submitted to PNAS. We had two rounds of revisions, and following detailed suggestions from one reviewer, we have improved our proposed algorithm a lot: its complexity is now significantly lower, and the idea he suggested makes the overall method more robust in handling noisy signal.

I feel that this reviewer's contribution extend far beyond his original role, so much that I feel it would be ethically honest to have him as a co-author. To be crystal-clear: if he was not a reviewer, but a colleague with whom I had discussed this before submitting the paper, he would clearly be entitled to authorship, no question.

But… he is a reviewer, so I am wondering how (if at all) we should ask him to join as co-author. Right now, I am ready to submit the twice-revised manuscript, and I have no doubt that it will be accepted (second review was “minor revisions”). The options I can see are:

• In my cover letter for the revised manuscript, explain the situation to the editor and ask him if he could (with the reviewer's agreement) lift anonymity and allow the authors' list change.


• Wait for the manuscript to be formally approved, and only then write to the editor asking for the same thing.


• Do nothing, for example because it is frowned upon. This would pain me greatly, because the reviewer really contributed very significantly to the algorithm, and I believe he should be able to claim authorship for this contribution (if he sees it fit).

So, what are accepted practices? How should I handle this matter?

Answer

Seconding other comments and answers: surely no one would be offended if you tried to make such an offer...

However, as already noted, if your offer is made prior to final acceptance, it might be misinterpreted, as your trying to clinch acceptance.

And that possibility surely has to be systematically excluded, so a foresightful editor and/or journal would surely not want to set such a precedent. A journal would not want authors to (be able to) solicit reviewers as co-authors, since this would create a conflict-of-interest situation, and cast doubt on the general validity and impartiality of their refereeing process!

That is, while it would be weird and awkward to publicly state such a policy, I would anticipate that the journal/editor would object as a matter of principle, to putting the reviewer on as a co-author.

Sensible reviewers would also understand this situation, for similar reasons, and in advance would expect no reward beyond "job well done". Even the anonymity of the referee should be maintained, as a matter of principle. Thus, we do often find effusive thanks to "the anonymous referee"...

united states - How to convert Italian grades to American and U.K system?

I just graduated in aeronautical engineering (master of science) at the Polytechnic of Milan. In the Italian university system, students who finish their major get a final grade that that goes from 66 to 110 (plus honors). In my particular case, I got a 103/110.

Since I am writing my resume/CV in English, I would like to convert my Italian final grade to the American (GPA?) and U.K system.

Can anyone suggest me what conversion I should follow?

publications - Is it necessary to ask permission before including someone in the acknowledgements of a research paper?

I had the impression that obtaining written permission before including someone in acknowledgements was required. Therefore, I just wrote to someone asking for written permission to include him in the acknowledgements of a paper, and he said he didn't think it was necessary. I don't recall where I got this notion from - perhaps the rules of a specific journal? So, I was wondering if there are any general rules about this or not, or are they perhaps journal specific?

molecular biology - Growing E. coli at room temperature?

If I were to do a blue/white selection of transformed E. coli on LB agar ampicillin plates at room temperature (23⁰C) for about 2 days and 18 hours, will I run into the issue of satellite colonies or any other issues?

Open-source the project code before or after publication?

I recently completed a part of my project and communicated a paper to a conference. Let's call the paper's title as "project x: for this and that". Now, I wish to open-source project x to facilitate reproducible research and to have more (at least some) people use it (and cite it!).

Are there any specific drawbacks or risks involved in open-sourcing project x on, say, Github or Sourceforge? Do note here that I would still be improving on project x, and possibly sending the extended version to a journal (my area of work being Computer Science).

I understand that if a conference/journal requires double-blind review and my project is searchable on the Internet, I am revealing my identity to the reviewers. This is bad, right?

Are there any other cons I should be considering? And are there any pros of open-sourcing before a making it into a publication?

Answer

Double-blind reviews are usually more common in conferences. For example, I don't know of any journals using double-blind review in my field (machine learning). I'm going to assume revealing your identity is not an issue (if it is, circumstances differ).

Whenever relevant I provide an implementation along with a paper. This also helps reviewers, in case they want to fiddle with an algorithm under slightly different circumstances than those reported in the paper (which is a good thing!). When an implementation is provided, the option is there.

The pros are increased visibility, reproducibility and (in my opinion) credibility since you allow everyone to try for themselves instead of taking your word for it in the paper. On rare occasions, your software may become quite popular during the review period, which may positively impact the paper under review.

A potential con is that someone may discover a critical bug in your implementation. From the perspective of software engineering this is always helpful since you can then improve the software. For the associated paper this may be a good, bad or irrelevant thing, depending on the type of bug:

1. One that does not influence the results reported in your paper: no big deal. Simply fix and move on. Best case this improves the user experience of your software, worst case you lost a bit of time fixing something unimportant.


2. One that does influence the results: big deal. This will at least delay a potential publication. Ofcourse it is better to find such errors and fix them instead of publishing erroneous conclusions, but this may have an impact on credibility.

human biology - Why can't we grow more teeth?

A similar question but about teeth healing themselves is Do teeth have the capacity to heal?.

---

So I understand that teeth have the capacity to heal themselves to a certain degree. It appears to be that part of the reason they can't heal all of themselves is that they are not surrounded by cells. In that case why can't we grow teeth back?

If a tooth is grown in the gum, or somewhere else, it would be surrounded by cells and so should be able to grow back right?

It appears that sharks can grow their teeth back:

New teeth are continually grown in a groove in the shark’s mouth and the skin acts as a “conveyor belt” to move the teeth forward into new positions.

Why can't we do this?

Answer

Unfortunately, the answer to your question isn't as well researched as other areas, I believe...let's add some complexity into this.

You're correct, teeth does "grow" in the gums. And it does start off surrounded by cells (look up: tooth bud, cap, bell stage)!

The tooth originates from an interaction between the ectomesenchyme (likely originating from the neural crest cells) and the epithelium of the mouth when it is forming while you're still an embryo in your momma's tummy.

Unlike sharks, which are homodonts (meaning, their tooth are all of one morphology), we are heterodonts (e.g. we have different shaped teeth - e.g. molars, canines, incisors, premolars). There are a couple of theories to why this occurs (look up: clone model, field model, odontogenic homeobox code - a combination of all these theories). Basically, a bunch of genes transcribe for proteins and signalling factors that create the complexity of your tooth shape and position in the mouth.

Basically, this means, our teeth are going to take longer and require more energy and effort to carve into (yes carve! lot's of the tooth shape is create by apoptosis of the regions around the "cusp" area when it is developing).

When your primary/baby teeth pop out, they serve functions such as developing speech, allowing you to eat, strengthening your jaw muscles (which in turn helps to develop your mandible and shape of the face), all this so you can have a great bite when you get older!

Luckily, sharks don't speak much underwater, so they probably don't give a poop about having properly lined up teeth. Their teeth grows everywhere. Proper bite for eating various nuts, fruits, meats and vegetables? NAH. WE JUST CHEW OFF LEGS. WE CAN ONLY SHRED STUFF. Sharks need strong ankylosed teeth (ankylosed = like an anchor? teeth are anchored into the mandible of the shark).

In contrast, humans have teeth in gomphosis (sockets), which gives our teeth some cushioning and sense of proprioception (the sense knowing how hard you're biting) when we bite on something extremely hard, to prevent us breaking our teeth - thus helping us preserve our teeth. Sharks don't have that, they just break their teeth.

Humans do finally replace their teeth, after our jaw grows enough for us to accommodate them at a genetically planned stage. This happens by tooth germs (cells) being bud off (like a flower yes :D) from the baby teeth. Note though, your 1st adult/permanent molars are already beginning to form when you're still in your momma's tummy.

I believe that the continuous creation of teeth requires more energy, but takes less time (sharks). For humans, one time creation of teeth requires less energy, but takes wayyyyy more time (and also has to be timed correctly with all our other growing bits).

TL;DR Evolutionary reasons and different functional uses of teeth between sharks and humans probably determine why we only have two sets of teeth (diphyodonts). That being said, it would be cool if we were like rats (have molars/incisors) though, which replace their teeth anytime its lost. Maybe one day we can evolve into it? Yay!

---

Some interesting points: You mentioned teeth "healing".

Your teeth is made up of enamel on the outside, which is NEVER replaced. It "heals" by remineralisation which is not exactly the same as growing new crystals on top of it. Kinda complex, won't go into it.

However, your teeth is always forming new dentine, which is below the enamel. In a way, your tooth really is growing back all the time. Because a new layer of dentine is deposited everyday (like...4 micrometers). This is because the dentine producing cells, called odontoblasts, are still around. In contrast, the enamel producing cells, called ameloblasts, are removed when your tooth has developed. I THINK, the reason is to make space in your enamel so it can be fully mineralised and completely filled up by hydroxyapatite. (Too much fluoride when young can block this removal of ameloblasts and its proteins like amelogenin and enamelin = forming holes, which cavitate resulting in fluorosis).

Hopefully all that answered your question. But, it was fun for me to rant anyway. Cheers.

death - An academic who died over 50 years ago still has Google Scholar profile with verified email. How can this be?

I'm surprised to see that an academic who died over 50 years ago has a Google Scholar profile with a verified email (https://scholar.google.com/citations?hl=en&user=5qvdHjQAAAAJ):

How is that possible? I see the email domain, melipona.org, is some online shop.

Answer

Verified email just mean that the user has done the confirmation in his/her inbox. It means in that case that the person that created this profile has an email with the domain "@melipona.org".

Usually, people will do this verification with their institutional email, adding credence that this is the right person, but technically, anyone within an institution can do it for anyone else inside that particular institution.

advisor - How to conduct an effective regular group meeting?

My research group has regular group meeting but I usually think it is not effective. In particular the research area of the group is very diverse, every time I just listen on something I cannot understand and have totally no interest on it, and I believe other members think the same way as I do when I am presenting. While it is a good way to expose to something new, and know other group members what they are doing, this is not effective for my own research. I know group meeting has its point (What is the purpose of the weekly research meetings that advisers often have with their research group?), but how can it be conducted in a more effective way?

As a supervisor:

1. How frequent should a regular group meeting be? It depends on the field, and I hear something like daily to three months.


2. When should a regular group meeting be? I know some groups insist on Monday morning, some groups choose Friday evening which is terrible.


3. How long should a group meeting be?


4. What level of detail should a supervisor comment to one's work? From every experimental concepts, to a vague conceptual suggestion?

As a student:

1. What should a student prepare before a group meeting to have an effective meeting? To present every problem he/she faces, or just some significant results (if there is)?


2. Should a student question other's member work? Sometimes it may be constructive, but it can also be an interruption.

If you are a faculty, how do you conduct your group meeting? As a research student, what can you suggest for an effective group meeting? An effective group meeting can greatly help on one's research work, otherwise it is just a drain of energy, time and motivation.

Answer

You have a lot of questions interspersed within your question, but it sounds like the main issue is

the research area of the group is very diverse, every time I just listen on something I cannot understand and have totally no interest on it, and I believe other members think the same way as I do when I am presenting.

I have had the same problem in the past. I'm a professor who works in a variety of related subfields, some very theoretical and some fairly applied. Most of my students and postdocs have been focused exclusively on either something theoretical or something applied, and their backgrounds range from computer science to mathematics to electrical engineering, so there is often a disconnect when they try to communicate what they are doing. Here is my advice.

For students:

1. Try to broaden your focus and interests. It is natural that you have a very narrow research focus as a grad student, but if you want to get and keep a job afterward you'll almost certainly need to broaden your focus. I find that in general the best researchers almost always have broad interests (though they are able to focus their energy narrowly when needed). Group meetings are an opportunity to become acquainted with topics that are on the horizon of your current knowledge.


2. Use group meetings as an opportunity to improve your communication skills. Teaching non-experts about your work is a critical skill in any research career. Other students in the group do not know nearly as much as you about your research topic, but that doesn't mean that you cannot make it interesting and accessible to them. Often this means leaving out the "details" and explaining just the essence of a problem. Trust me, some day soon you will need to make your work interesting and intelligible to people who are much further removed from your specialty.

For advisors:

1. Help students to present their work in a way that the others can understand. Often this means prompting the student, especially at the beginning of a presentation, to add important assumptions, motivation, or background. The student has started to take these things for granted, but without them any non-expert is quickly lost.


2. Don't let the conversation drift too far into a very specialized discussion. If you and the student are the only ones who have any idea of what is being discussed, it's probably time to say "let's discuss this further after the meeting".


3. 
   

   Use meetings for skills development. This was already mentioned in this related answer. Instead of focusing exclusively on research, group meetings can also include discussions of things like:

   
   
   
   
   • How to write papers
   
   
   • How to read papers
   
   
   • How to search the literature
   
   
   • How to manage a bibliography
   
   
   • How to give good presentations
   
   
   
   • How to write a proposal
   
   
   • How to keep a lab notebook
   
   
   • How to keep up with newly published research
   
   
   • How to stay organized and be productive
   
   
   • How to referee a paper
   
   
   • Software tools for all of the above, and for research
   
   
   
   

These topics are useful and interesting to anyone involved in research.

Answers to other parts of the question

• I hold group meetings once a week, and they last 1-2 hours


• Students are strongly encouraged to question and comment on each other's work


• We meet at lunch time, and there is food. That doesn't sound important, but I think it is.


• I try to save very detailed comments for my one-on-one meetings with students. Otherwise, the group meeting can devolve into a conversation between the advisor and just one student.

evolution - Why Did 6 Great Ape Species Survive But Only 1 Hominid Species?

My dad asked this question when I explained some circumstances surrounding Homo sapiens survival against all odds.

We know there is only one hominid species left in the world, Homo sapiens. We also know that there are only 6 other species of great apes left: 2 species of chimpanzees, 2 species of gorillas, and 2 species of orangutans. These 7 species are the last remaining in the family Hominidae.

All the other hominids besides Homo sapiens died out tens of thousands of years ago, and we believe the reason our ancestors survived is because we were more "adaptable", meaning we were not restricted to a single environment but could survive in many others. This is the reason we later spread out all over the world, and probably why we gained "sapience" and are able to contemplate these grim circumstances.

At one point, following the eruption of the Toba volcano 70,000 years ago, there were between 1,000 and 10,000 mating pairs of Homo sapiens left, though there may have been other hominid species alive at the time. My dad asked, if the hominids faced such grueling environments and all but a few died, why did the great apes fare any better? Why are there 6 extant non-human Hominidae species left, but only 1 hominid species?

Answer

Determining why one species (or group of species survived) while others did not can be difficult to answer, but I can offer one possible explanation for the genus Homo: competition. Competition between similar species is one possibility. Consider for example gorillas or chimps. The two species of gorillas occupy different habitats so they rarely compete with each other for resources (food, water, shelter, etc.). The two species of chimpanzees have non-overlapping ranges (or minimally so) so again they do not compete for resources.

Chimps and gorillas do overlap with each other for parts of their range and even potentially use the same resources, although no competition for resources has been observed (see this primate factsheet and McNeilage 2001). The same applies for the orangutans, which lives on two different southeast Asian islands.

The genus Homo is an entirely different story. As you may know, Homo first evolved in east central Africa. The first species to leave Africa and disperse across Europe and Asia was Homo erectus. This migration out of Africa happened as early as aout 1.8 million years ago. Homo sapiens had not yet evolved. However, while H. erectus was establishing itself across Europe and Asia, populations still in Africa continued to evolve.

Modern Homo sapiens evolved in central Africa perhaps about 250-200,000 years ago and dispersed out of Africa about 100,000 years ago. Homo sapiens also dispersed across Europe and Asia. Both H. erectus and H. sapiens co-occurred across parts of their range. Some have argued (Stringer and Andrews, among others, I believe but I'll have to be at work before I can verify ths reference) that H. sapiens outcompeted H. erectus, leading to its eventual extinction by competition. They occurred together and used the same resources, so H. sapiens could have caused the extinction of H. erectus. This has been called the replacement hypothesis. The later evolving species (H. sapiens) replaced the earlier evolving H. erectus.

However, Templeton (2002) has argued that the two species interbred so the species became integrated rather replaced (if I am interpreting him correctly).  While I don't dispute the possibility of interbreeding, I am skeptical of Templeton's complete dismissal of replacement.

Complicating the picture is H. neanderthalensis. Genetic evidence published by Green et al. (2010) suggests that Neanderthals diverged from H. sapiens (in central Africa) between 800,000-500,000 years ago and also dispersed out of Africa.  They also provided evidence of interbreeding between H. sapiens and H. neanderthalensis in Europe.  Modern H. sapiens may also have outcompeted H. neanderthals. 

All of this was occurring during the Pleistocene ice age. Europe was experiencing repeated bouts of extensive glaciation. Thus, it is also possible that climate change caused or contributed to the extinction of H. erectus, H. neanderthalensis, or both.

In summary, the processes that led to the extinction of other species of Homo are complex and likey interactive. Competetion among species is, in my view, well within the realm of possibility but would be extremely difficult (if not impossible) to test. Climate change is also a very likely contributing factor. There are several other hypotheses but I have tried to hit the major highlights.  The debate is certainly not settled.

McNeilage A. 2001. Diet and habitat use of two mountain gorilla groups in contrasting habitats in the Virungas. In: Robbins MM, Sicotte P, Stewart KJ, editors. Mountain gorillas: three decades of research at Karisoke. Cambridge (England): Cambridge University Press. p 265

molecular biology - How are there alternative initiation codons?

According to wikipedia and the original complete sequence of the K-12 genome, there are multiple non-AUG start codons such as GUG and UUG. How is this possible? I'm particularly curious about the mechanism of translation initiation in the absence of the canonical tRNA^fMet.

Answer

Actually, the start codon, no matter whether it is AUG or GUG/UGG, always encodes for Met. So the translation is initiated by tRNA^fMet (prokaryotic translation). The 30s ribosome subunit binds to the Shine-Dalgarno sequence and then it scans the dowstream mRNA sequence for AUG and the tRNA loaded with Met, which has the CAU anticodon form the most stable interaction. But apparently, only two-bases-interaction between the start codon (GUG, UUG) and the fMet-tRNA anticodon are sufficient for the initiation of translation (1). I will look more into the literature.

1. Initiation of translation in prokaryotes and eukaryotes

muscles - How do crocodiles stay fit?

My 8 year old son asked me a question I could not answer (and Google, at least in so far as we tried, was no help either).

We were watching a documentary about Salt Water Crocodiles in Northern Australia.

The crocodiles seem very energy efficient: they barely move if they don't absolutely need to (and when they do, it is mostly to eat). Particularly, they hardly ever run, but when they do they are very fast and powerful.

So the question he asked me was: how can crocodiles remain so fit if they don't do any exercise?

If humans just sat around and moved only to eat, ran only when they absolutely had to, our muscles would atrophy. Other mammals seem to be in a similar boat to us humans.

Why not crocs? What distinguishes animals that need to exercise to be strong from animals that don't?

This is the closest question I could find here, but I don't think it assists in answering this question: Do insects' muscles become stronger with exercise?

Answer

Let us start with difference between humans and crocodiles. There are lot of differences but the one which matters in current discussion is thermophysiology.

Unlike humans, crocodiles are cold blooded animals (more specifically ectotherms). These animals needs to get heat from environmental sources to maintain their body temperature. As contrast to humans who can get heat from internal metabolism. That is the precise reason crocodiles are seen always not moving and basking in sun light when it is cold (while go to shade or water if it is hot). Read this for more elaborate strategies they use. If you want scientific reference, you can check this, this or this.

On your exercise point, there are few reports which suggest exercise can enhances aerobic capacity in young crocodiles. In this study they actually put crocodiles on treadmill and checked affect on their respiration. This report suggest crocodile uses 3 different kinds of muscle mechanisms for lung ventilation. These three act differently in different conditions (means one acts during rest while other during high metabolism). However I couldn't find any information regarding atrophy.

how can crocodiles remain so fit if they don't do any exercise? What distinguishes animals that need to exercise to be strong from animals that don't?

Short answer: Their body metabolism.

Their body metabolism is different from human's. Although doing exercise might help in their aerobic capacity as mentioned in reference above.

conference - What are some general good principles for creating a poster for a poster session?

Should one create slides similar to those that one uses in a good powerpoint presentation? Or are there things that a poster should include that a powerpoint should not include? (and vice versa)

Answer

1. 
   

   The title is your bait, the first paragraph is your hook. Make the bait big and tasty, make the first paragraph catchy.

   
   


2. 
   

   A poster is primarily an advert for you. Secondarily, it's an advert for your research. Thirdly, it's an advert for your department. And it will succeed at those things best, if it gives the casual reader an easily accessible introduction into what's novel about your research.

   
   



3. 
   

   Know the flow: it should be clear to anyone reading, what they should read first, then second, and so on.

   
   


4. 
   

   Make it clear that it's your work. Get your name and affiliation in big letters, with a photo of you. Include your contact details, and make sure you can be reached on them during the conference.

   
   


5. 
   

   Don't use powerpoint. A poster is graphic design, so use a graphic design package such as InDesign. If you don't have an eye for graphic design, design the poster with someone who does. Most departments have at least one natural talent. It's often the person who keeps winning the "best poster at conference" prize. It's orthogonal to (i.e. independent of) quality of research.

   
   


6. 
   
   

   Use a big, clear typeface. Not everyone you need to reach has the healthy, clear vision that most students have.

   
   


7. 
   

   Briefly state the problem, the method, the results, and the implications.

   
   


8. 
   

   Pretty pictures are crucial. The words are there just to supplement the explanation of your work given in the pictures.

   
   


9. 
   

   Test, test, test. Print it out life-size (tiled sheets & sticky tape are your friend), show it to a couple of colleagues (one hot on your area of research, and one hot on design), watch the order in which they read things, ask for feedback. Implement any advice on content that comes from the one who is hot in your area of work. Implement any advice on design that comes from the one hot on design.

   
   
   

ethics - Potential issues with uploading copyrighted material to TurnItIn?

My university uses TurnItIn to check student's work for plagiarism and collusion. I think the underlying TurnItIn database includes both submitted work and material it has found by crawling the web, but not material behind pay walls. One major issue with TurnItIn, and presumably all plagiarism detection software, is that it can only compare submitted work to material which is in the database. This means that TurnItIn either misses when students copy from textbooks which are behind a pay wall or matches other sources which have plagiarised the textbook.

My department's academic misconduct committee is thinking about seeding the TurnItIn database with the textbook chapters that are most often used by the students by submitting a number of "assignments" that are copies of the textbook chapters. This would require an individual member(s) of staff to submit assignments that contained copied copyright material. Is it possible that this could get the staff member in trouble in the future? We were thinking about adding something like:

The following submission is intended to seed the TurnItIn database and is an exact copy of FULL REFERENCE.

Would this work, or would TurnItIn realize that it is being given copyrighted material and purge it from its database?

Answer

This is a bit long for a comment, but I also acknowledge that only someone from TurnItIn could categorically answer this.

Since TurnItIn does not provide access to source material (other than small sections which actually match the submitted paper), I do not see how it could be a copyright issue. I get matches all the time from papers submitted to other schools, yet, TurnItIn does not allow me to see that paper.

Additionally, much of the content within TurnItIn is under copyright (blogs and others) and they do not purge it, further implying that they would not have a problem with your plan.

All that said, unless the content is quite new, or changed regularly, as soon as one student includes content, any other student including that same content will trigger a flag for you.

So, I do not believe your plan will have any problem but I am also not sure you need to worry about it unless you have a special set of texts you believe other students around the world will not have access to.

teaching - How should I feel about a professor using an entire online course for his own course?

I'm taking a machine learning class at a school in South Korea. I've heard some good and bad things about this professor in particular, but I didn't really know until I actually took his course.

I've noticed that my instructor is literally following the exact course of the well-known online machine learning course taught by Coursera co-founder Andrew Ng. The print-outs he uses in class are also taken from the online course, and the examples and jokes he uses are also the same to the T. There are other print-outs he takes from Youtube which I happened to find which he seems reluctant to address when I asked him about it.

Perhaps I am thinking/acting out of my place, but I just don't think that it's appropriate, and maybe I feel a bit cheated because many students (including myself) have to work several jobs to come up with tuition money, and it doesn't feel good that I'm paying a large amount of money for a potentially free online course.

How should I feel about this? Is this more commonplace than I feel?

EDIT

I haven't mentioned the quality of education I'm getting through the course.

The quality is low, which is what led to my initial frustration. I honestly couldn't care less what material instructors are using as long as they cite the source and are able to use it to everyone's benefit. This instructor is not only not citing the sources, but is reluctant to tell me where he got them when asked about it.

Regarding the class itself, I've found myself in situations where asking the instructor of this particular class a question is often either not answered in a clear manner or is answered with "Just email the TA's," which has led me to seek answers either online or elsewhere.

Perhaps this is my prejudice, but when I ask a professor from an internationally accredited institute of higher education a question on machine learning, I am hoping to get a detailed explanation on the mathematical or conceptual reasons to how certain algorithms were formed or how we can prove they are sound. Not just an answer that goes along the lines of "Hmm well when I was working on this project this algorithm worked best, and you can find the proof online."

Answer

Copying an entire course from Coursera is definitely not commonplace. Some parts of ML courses are fairly 'standard' (there are only so many ways one could define linear regression), but lifting material without proper credit can range from annoying, unethical to outright plagiarism. It's fine to take some examples and use them (with proper credit), but it's generally expected that an instructor adds some value of their own.

I don't know how you should feel about this. Sounds like you already are feeling pretty annoyed (I would!). I can answer what you can do about this.

The minimum I would do is report this in the student course evaluations. Write a detailed report of everything that went wrong. If you school's administration cares in the least about their teaching, this will get someone's attention.

The best thing you can do is rally the entire class. If it's just you - well, you're just an angry student who's not getting the material and is trying to squeeze a good grade. If a significant number of complaints come in (even 10 students is a good amount), that's going to get people's attention. Does your university have a student union? An ombudsman? If you go through them this will also get people's attention.

You can also try to (discreetly) reach out to the person in charge (professor in charge of curriculum, the department head etc.). I would not confront the lecturer directly if I were you, unless you don't mind getting a bad grade. It is very unlikely that this instructor will be removed from the class, and if they find out you reported them they may be very biased against you: reporting paints a target on your back (this is another reason to have more people complain, the instructor can't fail all of them and get away with it!).

The likeliest outcomes here are that the professor will not be teaching this class in the future, and that's about it. Alternatively, they'll be required to stop this bad practice in future iterations of the class (say, if your department is understaffed). I don't foresee them facing disciplinary action, unless this is not the first time that this has happened.

Good luck!

Drawbacks of making public which journal a manuscript is submitted to, while it is under review?

Many researchers list out their submitted manuscripts on their website. Some specify the journal name, like

Smith J, Oliver J (under review) My awesome paper. Nature.

while others don't, like

Smith J, Oliver J (under review) My awesome paper.

One reason I can think of as to why some don't mention the journal name is that they may get embarrassed in the case where the current journal rejects the paper. Then, the "circle" will know this paper gets rejected from Nature first and then ends up in an inferior journal.

Besides this, are there any other considerations preventing people from mentioning to which journal they submit a paper to?

P.S.: I am asking because my advisor is a researcher who only mentions accepted papers on his webpage. As a student hunting jobs, I feel it is advantageous for me to mention my submitted papers on my webpage. I hesitate to do so, as I worry I may make my advisor unhappy by announcing in which journal our papers are currently under review.

publications - What should/can I do on finding an error in a published article?

Recently I found a paper that has a number of typographical errors, esp in equations. Should one notify the authors or the publishers on such issues? How do the approach change if the article is somewhat aged?

When should/can one write a 'Comments on ...' article? How different is an Errata and a 'Comments on ...' article?

Answer

Here's what I would suggest:

• First, alert the authors to the issues. Wait to see how they respond, or do not respond. But in all cases, they should be the first you write to.



• If the issues do not severely impact the correctness of the work or its utility, stop there. It's probably not worth making a fuss about something most readers will either not use, or can easily correct themselves.


• If you publish something on the topic yourself, especially if you build on the authors' equations or otherwise use them, you should make a note of the issue in your article.


• Finally, if you believe the issue is important and/or the equations are widely used, you should contact the journal's editor and ask for guidance.

Errata are “authored” by the original authors. Publisher's corrections also exist, when the responsibility for the issue (typo in equation, misprint in figures, etc.) is that of the publisher.

graduate admissions - How much score in GRE computer science subject test is considered 'good'?

I'm applying to MS / MS-PhD programs in CS this fall.

I don't have a good GPA (2.86 on a scale of 4). I have experience as a research assistant under a professor and also a couple of good projects.

Right now I'm working as a developer, so I have around 5 months of experience. I have a GRE score of 314 on 340. I'm giving subject test to improve my chances of getting into a grad school. What score can be considered 'good'? I don't have much time to prepare and I am a little rusty on some of the topics, what is the good advice for a crash course for subject test in, say a week or so?

phd - Gap year before post-doc?

I have been in a rush to accomplish academic goals since I remember myself. Started my PhD right after undergrad and did my Masters on the same time. Now I am about to submit my thesis and feel kind of burned out, having spend so many years in a far from perfect working environment.

Academia has always been my goal (I like both teaching and research and I am not interested in industry), which is why I started a PhD on the first place, but I really feel I need a big break to think clearly of what I really want before applying for a post-doc. I also read this somewhere: "The rest of your life you are going to be a scientist. This could be your last chance to be something else. Take it."

So I thought a "late gap year" would be ideal for me. I would get to travel, which I love, volunteer in wildlife conservation and in schools of developing countries and take some time to clear my mind, so that when I am back, I can take the right decision for a post-doc and be totally dedicated in it.

Up to now I have a decent resume with a 5th paper in preparation (including first-authored) and several international conferences, fellowships and awards. However, I am very concerned on the impact such a gap would have on my CV, since I want to apply in high reputation universities/institutes, where competition is fierce.

Should I tell a future PI I did a gap year and if not, what would be the appropriate excuse for a year off? Also would this gap have an impact in future job-seeking (mainly for positions in academia)? Finally, I am also worried about the reaction of my current PI (who has been asking me lately, which lab I am planning to apply for a PD) when I tell him my plans. The last thing I want is a reference letter from an angry PI.

*EDIT*My field is Molecular Biology. I performed my PhD research at several European countries and I am flexible with post-doc positions (Europe/Israel/US/...) depending on the projects available.

Answer

As usual, if you include information about geographic location (both the current one and the one(s) in which you intend for the future) and your field, you can get more specific advice. Advice which is generalized across all the world's academia is at times extremely superficial.

I will speak from the perspective of American academic mathematics. In this subculture, taking a full year off before starting a postdoc looks bad: the competition for postdocs is extremely fierce right now. For every postdoc position there are at least five other people who wanted that position but couldn't get it. So employers really want to give jobs to people who are sure that they want them, not those who are feeling "kind of burned out" or "need a big break to think clearly of what I really want".

If you take a full year off instead of applying for postdocs, then unless you have something amazing to show for yourself at the end of that time, the year off will definitely hurt your applications. Whether or not you can actually do work during a "year off" seems highly field dependent: in mathematics this is certainly possible; in laboratory science this seems much less feasible.

Here is some advice that I would offer you:

1) If you want to take some length of time off, try to secure a job upon return before you take the time off.

If this happens then in some sense you do not really have an employment gap, and that will look much better on your CV.

2) Consider taking a smaller amount of time off than a year.

A year is a really long time to put aside one's career. In fact many people would have trouble supporting themselves (especially if they have families or dependents, which I guess you do not) over such a long unpaid stretch. It is also more than enough time for your academic skills to atrophy. In some academic fields (pure mathematics not so much, although in some subfields this could still come into play) a year off is enough to make your entire research program less fresh and cutting edge. Anyway, imagine that you are competing with many talented young people who spent the first year after getting their PhD working their butts off. Do you really want to spot them an entire year headstart? As other people remarked in a closely related question: whether it is fair or not, you should imagine that a big clock in the sky starts ticking the second you receive your PhD. From that point on, people will be evaluating your work not just in an absolute sense but relative to the time elapsed from that point. Adding in an extra year makes almost anyone's profile look much less strong.

I think you should consider taking a shorter amount of time off: either a semester or a long summer. As the American academic calendar runs, you will have a built-in vacation of about three months just by virtue of being an unemployed PhD over the summer. I really enjoyed this time: I moved into an apartment downtown in the city where I grew up but hadn't spent more than a few weeks at a time for my entire adult life. It really was refreshing and recharged my batteries. However, it also depleted my savings: by the time the new semester rolled around, I really needed the paychecks.

If you need much more than three months' break from a career, you should ask yourself: are you sure that this career is really for you?

reference request - Where are predatory publishers based?

Is there any research/study/survey that looked at the location of predatory publishers? (e.g., x% are based in country A, y% are based in country B, etc.)

I am mostly interested in English-speaking venues and the field of computer science. Trends over time are welcome as well.

economics - How much of an onus is on the teacher in an undergraduate course?

I am an assistant professor at an undergraduate college in India. I teach a rigorous compulsory course in microeconomics, requiring some intermediate-advanced math knowledge. There is no add/drop option at my University/college, nor is there an option to take a course in a later semester. I don't decide the syllabus or the final exam--it is set centrally. We are a publicly funded University and have a diverse set of students.

General math preparation in my country is low, due to poor schooling standards and sometimes, students are not clear about basic concepts: for example, in a third semester intermediate microeconomics course, some of them don't know how to write the (linear) equation of a budget frontier (something taught to them in the first semester). Unless they understand such things, it is impossible for them to grasp the rest of the material, since all topics are related. Is it my responsibility to explain concepts taught in introductory-level courses? I welcome all questions and have a generally amicable attitude, so students don't feel intimidated in getting a clarification.

However, I do get frustrated sometimes when having to answer something very basic, that too repeatedly. I get glowing feedback for most of my courses, but despite being appreciated for my effort and the clarity of explanation, a group of students (around 20% of the class) repeatedly under-performs, which upsets me a lot. How much should I hold students responsible for their learning?

data - Bulk download Sci-Hub papers

I wonder whether it is possible to bulk download all papers stored in Sci-Hub.

---

I am aware of the questions:

but they focus on arXiv.

Cross-posted question on Open Data (not encouraged by Stack Exchange policy): Bulk download Sci-Hub papers

job search - What are the most important criteria to consider when hiring postdocs for a research group?

One of the most important challenges that academics will face is group management. Although this takes many forms for graduate students, undergraduate assistants, and so on, I believe postdocs are a fairly "universal"—a professor hires a postdoc specifically for his group.

However, it's not necessarily clear what qualities to look for in a postdoc.

• 
  

  Does it make a difference if it's your group's first or second postdoc, versus the n'th postdoc?

  
  



• 
  

  How much weight should one give to letters of recommendation?

  
  


• 
  

  How do you analyze a publication record, especially when towards the end of the PhD, many papers are often still unpublished and therefore "embargoed?"

  
  


• 
  

  Are there any criteria that applies specifically to postdocs that might not be considered in, say, hiring for industry or business?

  
  

Answer

My answer, item by item:

• I think that there is a difference if this is yet another postdoc or your only postdoc. But most important, we should pay attention to the ratio postdoc/permanent researchers. If the ratio is low (few postdoc, lot of permanent researchers), you can choose to work with "junior" postdoc (=someone not completely capable for working alone), while if the ratio is high, you need postdoc that are in fact already at the level of an assistant prof. But at some point I think we must ask ourselves if we always need one more postdoc. I guess this will depend on the field. In theoretical fields, when we hire a postdoc, this is to work with him. In some more practical fields, we tend to hire postdoc to make them working for us. The two cases are different : in the first case we need someone that will have ultimately an academic position, in the latter we need someone for coding, experimenting, etc.


• Personally, I am not interested in the letters. I ask for references and I take my phone to know more about the candidate. Letters are always telling that the candidate is great, even if this is not completely true.


• I ask the candidate his/her papers, even those unpublished, and I read them. Then I contact some of the other authors to know more about who done what.


• Clearly yes. A postdoc is a researcher, I think that the way of working is very different : you can spend a lot of time without being "productive" when you are a postdoc, which is not the case in industry. This can be depressing, so we have to make sure that a postdoc (which has less guidance than a PhD student) can handle that.

ethics - Non-profit organization, IRB Approval, and publishing?

I'm working with a non-profit organization at the moment and we're planning to conduct a survey on ~93,000 to find certain attitudes and the correlation associated with them. We're hoping on having our results being published in a reputable journal if possible, because we've done a lot of research and background reading to have a pretty solid study design written down. Is it necessary for us to have IRB approval to publish in a reputable Psychology/Educational academic journal? Additionally, even if it's not explicitly stated in the manuscript guidelines, are there "unspoken" rules about stating IRB approval before submission?

application - Applying to do a PhD after a(n unsuccessful) period of job hopping

Disclaimer: Since this question is explicitly about applying to do a PhD, I figured that the Academia SE was a better fit than Workplace, but do correct me if I'm wrong.

How can I explicitly, concisely and effectively explain a period of frequent job-hopping in my employment record in my application package (e.g. in the cover letter, statement of interests, research proposal and/or in my CV itself) which was due to a period of "soul-searching", after which I realized that I definitely do want to do research? I assume that my problem is two-fold:

• Being away from academia and the core material of the PhD for several years, meaning that my CV has very little in common with what I want to do despite having studied it years before (cf. "Getting into gradschool from a 'real job'")


• Having proven myself to be a job hopper

Answer

Job hopping is potentially a problem in getting into a PhD program. The fear of admissions, obviously, would be that your lack of commitment to one thing will show up again in your studies, and you will tire of this quickly, too.

However, it may be less of a problem here than in looking for new employment in industry. Some reasons:

• You are making a category shift, and as such all of your previous jobs may be seen as "one thing", and you are now switching to a completely different thing.


• There is quite a bit of anti-industry bias in some parts of academia. Therefore people considering your application might be more sympathetic to your work history. They might think "of course this person couldn't make it in the soulless, evil corporate world, but they will flourish in the academy." (Of course this is a bit of a caricature, but you get the idea).


• You are more likely to have a chance to tell your story. As discussed in the linked question, a "job hopper" may have their CV rejected well before they get to interview, having no chance to explain the circumstances. But when applying for a PhD, it is quite likely you will get far enough to have some personal interaction and explain your circumstances.


• They may be making less of a commitment to you than an employer would be. Particularly if you are looking at unfunded PhDs, they may be more willing to take you on, even if they think you are a risk, since you are paying them (not the other way around).

What should you do about it?

• Contact some professors at programs you are interested in. Share your story and interest in graduate study. This personal connection may help your chances as an applicant, and you can also get advice from them that will help determine whether (and where) you have a chance of success.


• Work hard on your personal statement. It should demonstrate clearly why you want to do a PhD, how you arrived at this conclusion, and show some commitment to this as your direction in life.



• If going directly into a PhD program doesn't seem feasible, consider alternative options. A master's program would be a lot easier to get into, and you can often then transfer into a PhD once there. Or, consider employment at an academic institution (such as work as a research assistant) where you can build up some recent academic experience while also making connections that will help you gain admission.

human biology - Why can't you just take a vitamin? Why you need a healthy diet on top of that?

From what I understand, your body needs certain amounts of vitamins and minerals to maintain health. Why can't we just take enough pills to obtain these vitamins and minerals?

Answer

This is more of a biochemistry question and to be honest its a little bit out of my league because I have not had the necessary grad classes to explain nutrition but indeed I will try.

Unknown metabolite cofactors and things like ionization, oxidation and state of matter are the reason that straight up vitamins are rejected by the body and cause really expensive urine and a difficult time otherwise excreting.

Metabolism involves a vast array of chemical reactions, but most fall under a few basic types of reactions that involve the transfer of functional groups. This common chemistry allows cells to use a small set of metabolic intermediates to carry chemical groups between different reactions. These group-transfer intermediates are the loosely bound organic cofactors, often called coenzymes.

Each class of group-transfer reaction is carried out by a particular cofactor, which is the substrate for a set of enzymes that produce it, and a set of enzymes that consume it. An example of this are the dehydrogenases that use nicotinamide adenine dinucleotide (NAD+) as a cofactor. Here, hundreds of separate types of enzymes remove electrons from their substrates and reduce NAD+ to NADH. This reduced cofactor is then a substrate for any of the reductases in the cell that require electrons to reduce their substrates.

Therefore, these cofactors are continuously recycled as part of metabolism. As an example, the total quantity of ATP in the human body is about 0.1 mole. This ATP is constantly being broken down into ADP, and then converted back into ATP. Thus, at any given time, the total amount of ATP + ADP remains fairly constant. The energy used by human cells requires the hydrolysis of 100 to 150 moles of ATP daily, which is around 50 to 75 kg. In typical situations, humans use up their body weight of ATP over the course of the day. This means that each ATP molecule is recycled 1000 to 1500 times daily.

-wikipedia

If you did not like that explanation of cofactors maybe you will this:

Whole foods offer three main benefits over dietary supplements:

Greater nutrition. Whole foods are complex, containing a variety of the micronutrients your body needs — not just one. An orange, for example, provides vitamin C plus some beta carotene, calcium and other nutrients. A vitamin C supplement lacks these other micronutrients.

Essential fiber. Whole foods, such as whole grains, fruits, vegetables and legumes, provide dietary fiber. Most high-fiber foods are also packed with other essential nutrients. Fiber, as part of a healthy diet, can help prevent certain diseases, such as type 2 diabetes and heart disease, and it can also help manage constipation.

Protective substances. Whole foods contain other substances important for good health. Fruits and vegetables, for example, contain naturally occurring substances called phytochemicals, which may help protect you against cancer, heart disease, diabetes and high blood pressure. Many are also good sources of antioxidants — substances that slow down oxidation, a natural process that leads to cell and tissue damage.

-The great Mayo Clinic

vision - Is it a limitation of the eyes, or the brain, that we can't see a moving bullet?

Are the photoreceptors in our eyes not fast enough to register the fast moving bullet, or is the brain not powerful enough to make sense of something happening that fast?

Answer

It's less a problem of speed and more of raw photon count. Assuming a brightly lit day, the bullet will move so fast that it doesn't reflect enough photons to register against the background. High speed images of bullets usually involve a very bright flash (and other controlled settings) for the camera to pick it up. (Also, a very short flash helps the bullet to appear stationary in the image.

On the other hand, seeing where your bullets are going is pretty useful. Therefore tracer bullets were created, which are essentially a pyrotechnic flare that you substitute in every 5th bullet, typically in machine gun ammunition. Proof that if you make a bullet bright enough, you can register it just fine.

http://en.wikipedia.org/wiki/Tracer_ammunition

microbiology - Why are there no known photosynthetic archaea?

I'm taking a microbial physiology course and we noted that, while some archaea are phototrophic, there are no known photosynethetic archaea. Are there any physiological characteristics that make archaea less suited for photosynthesis? Or is it simply a matter of there likely being photosynthetic archaea, but they have not yet been found (which seems like it could easily be the case, given that there are many extremophilic archaea)?

funding - Why are many funded PhD programmes in the UK not open for non-EU applicants?

I once wanted to do a PhD in the UK, but found out that the opportunities were limited for those coming from outside Europe (I did my PhD in Norway instead). I think it is still the case today. I am wondering why this is so.

EDIT:

Additional thought: I am wondering, for instance, if the vacancy were open to anyone in the world, would it not increase the chance of getting the best applicants? Also, what differences are there in the UK system compared to other countries (e.g. Norway) which open their PhD vacancies to anyone?

genetics - Probability of carrier for recessive trait given parents are carriers and sister affected

I'm trying to understand more about inheritance of an autosomal recessive trait that runs in my girlfriend's family. How could I start looking at this?

My girlfriend's sister, C, is affected with a recessive trait. Her parents, A and B, are confirmed unaffected carriers. Am I correct to assume my girlfriend, D, is a carrier with probability 50%? Or must I take into consideration that we know the state of C given she is affected.

Furthermore, if I (E) have a child with my girlfriend, what is the probability that our children are either carriers or affected? My carrier status is unknown.

species identification - What sort of seed pod is this?

My son found this floating in a stream in Massachusetts, in the northeastern US. It was intact when he found it, but he cracked it open to see what was inside. I did some Google image searching, but couldn't find anything. Any idea what it is, and where it came from?

Answer

It's actually not a seed pod, but rather a gall (see here or here for more info about galls). Specifically, it most likely is a gall belonging to the Oak Apple Gall Wasp (Amphibolips confluenta). You can read about this species and its gall here.

neuroscience - Can a single axon propagate multiple simultaneous action potentials?

I have not been able to locate any research that indicates whether a single axon of a neuron or nerve cell can conduct multiple simultaneous (i.e. spatially separate) action potentials. I am aware that in many neurons refractory periods would preclude this possibility, however in some cases delays along axons are large enough.

Is this the case? Can you point me to any citations supporting your answer?