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"...