What kind of citation is needed for a whole paragraph?

I'm writing a paper on The Beatles and in this paragraph I'm talking about the formation of the group. I got the info from their biographical book. So it's just a summarized version of a chapter. I have no idea how to state that this info is from a book?

Answer

Summarizing a chapter in a paragraph and citing it at the end, I think, is not a good idea.

It is better to write

Simpson mentions the formation of the group in Chapter 5 of History of The Beatles [12].

And then write your paragraph in italic.

Actually, if you can, put citations at the end of each 2-3 sentences. The following example is more proper when writing an academic manuscript.

The Famous English Rock Band Beatles was formed in 1957 [34]. First, John Lennon, the founder of the band, named the band as The Blackjacks. Then, with Paul McCartney joining the band, the name was changed to The Quarrymen [21].

How to convince suspension cells to adhere more tightly?

I'm developing a cell-based assay in 96-well plates that requires adherent cells, as they need to be washed at least twice during the protocol. I'm using in-house strains of HT1080 cells (some overexpressing a certain protein of interest) that unfortunately have been selected for suspension growth in chemically-defined media (50/50 CD-CHO/CD-293). I can convince them to adhere by culturing in DMEM with 10% FBS and growing them in CELLBind flasks, but they still tend to pull away if there is very much shearing force, such as during the wash steps, or when they're in PBS during the assay wash and incubation steps (maybe 2 hours total for now, I'm still optimizing that).

Unfortunately, the parameters of my experiments don't allow me to keep the cells in serum-containing media during the assay, as it would interfere with the uptake of my drug. Like I've said, when in PBS they start detaching, and I would assume the same in HBSS, which I don't really want to use anyway due to its low buffering capacity in CO₂ incubators.

Might DMEM alone (without FBS) provide a little more impetus to stay attached during the assay? What would the effect be of increasing the amount of FBS to say 15 or 20% during culturing - would that promote stronger attachment? I'm a little hesitant to coat the wells with poly-D-lysine, as my readout is on a fluorescent imager, and I'm worried it would substantially increase background. I don't really have enough time to re-select the cells for adherent growth (although if I'd known about these issues from my predecessor 3 or 4 months ago I would have started right away...), so are there any other tricks I can try in the meantime? Are there any media supplements I could use to promote adherin expression or something like that? Any tips or advice at all would be appreciated.

evolution - Is it possible there were multiple origins of life? And, if so, why did the one which became the common ancestor between all organisms prevail?

I have learned that all currently-living organisms come from a common ancestor, which I theoretically understand. However, my professor in a class mentioned that there is a chance that there were multiple origins of life, but that all the creatures living today all came from the same one and the others died. How can we be sure that before the other origins of life died, they didn't somewhat evolve, and the species from that origin didn't just evolve in convergence with those of this one since through natural selection both would need similar characteristics to survive on Earth?

Is it appropiate to put a funny funny slide in a Bachelor thesis presentation?

I always like to stray in a context related funny slide either at the beginning or at the end of a presentation because I do not like the overall stern atmosphere at presentations.

I also planned a funny slide that is related to the topic of thesis at the end of my Bachelor thesis presentation but I am not sure If I bring myself in jeopardy through this because I assume they have to be strictly just presenting the mere content of my work and nothing else. I am even afraid that my open question to the audience (which includes Professors and Students too) at the beginning of my presentation is regarded as a violation of this strict code.

Answer

I'd consider this a classic example of ‘if you have to ask, the answer's no’.

To expand a little on this: I don't think that humour is always forbidden in academic contexts. I've seen it used in both publications and presentations -- only very rarely, but usually successfully. The problem is that ‘appropriateness’ is massively context-dependent. It depends on exactly what kind of humorous content you have planned, exactly how you present it, the culture at your institution and department, who's in the room, what mood they're in, how your audience regard you, what preceded your presentation, what you have to lose if your attempted humour fails, and a hundred other factors. You are far better placed to assess all these factors than anyone else in the world -- especially strangers on the Internet who know absolutely nothing about the details of your situation. So, if you yourself are unsure whether it's appropriate, there's probably nobody here who can give you a more reliable answer -- which means that you should play it safe and leave the humour out.

One thing you might consider is addressing your question to colleagues in your own department, who will be far more familiar with the particular context of your presentation.

funding - Is it possible to get a professor position without having had any fellowships in grad school?

As a deferred action for early childhood arrival (DACA) student, I found out that I am not eligible for federal fellowships from the government or through the university.

Some universities allow for fellowships to DACA students if they meet in-state requirements but being a student who attended undergrad at another state, I do not qualify. (I applied to all out-of-state graduate programs)

With the DACA status, I can still apply and work as teaching assistant or research assistant to fund my Ph.D. program.

So my question would be, if I do not have any fellowships on my CV and only RA & TA positions, how much would this negatively impact me when applying for assistant professor positions, if at all?

Do hiring committees ever place emphasis on whether the student had had fellowships or not? And would it be more worth it to go into a Ph.D. program in-state where I may qualify for some federal fellowships made through the school (from a funding perspective)?

Answer

There's no way that you are going to be disqualified from faculty positions by not having a graduate student fellowship. There's no "has a fellowship" checkbox on rubric that search committees use. What will matter is a holistic evaluation of the quality of your research, your publications, your teaching experience, and your letters of recommendation.

Of course, evaluating junior faculty candidates is difficult and lots other things matter as well and can help reinforce (or cast doubt) on a committee's evaluation of a candidates quality. In that sense, a prestigious fellowship can be an additional positive signal in an otherwise strong packet. In that context, you should think of a fellowship as a "nice to have" — it does nothing to replace great research, great publications, and great letters.

In some ways, not having a fellowship might even help, if it translates into more work as a TA and RA. This might lead to teaching experience and publications, which will be viewed as more valuable than all but the most prestigious fellowships. For example, I've seen faculty candidates who had made it entirely through graduate school on fellowships dinged for a lack of teaching experience.

degree - Make my Professor a gift

I just received my diploma from my university. I'm very happy and my results aren't that bad either. Now, as the result is already known, I would like to thank my professor and my supervisor for their support.

Would it be acceptable, if I make them a gift to express my thankfulness?
I was thinking of a bottle of a good liquor for both of them.

teaching - What do instructors need to know to accommodate Muslim students?

Increasingly, my school has been recruiting students from Central Asia, so I see 1-3 Muslim students in each section.

Near the end of the last term, one student asked for leave for some religious activity. He was surprised when I said he could go, then he told me he had missed many Friday afternoon religious activities, but his advisor (or perhaps some other school administrators) said he couldn't leave. I heard a similar story from another student.

I realized that many of the other Muslim students may have similar problems, but they are too nervous to speak out and let me know. Since they remain quiet, I'm not sure how to accommodate them.

What are some typical things a teacher can do to accommodate Muslim students?

How do people changing fields after PhD overcome competition with "locals"?

There are a number of questions here about changing-fields. Those are mostly about how common it is, how it affects future career, or whether a move from X to Y is feasible (example 1, 2, 3). At any rate, it does happen — I have come across people with background in particle physics, astrophysics, or space science, who were all in postdocs in atmospheric science. A frequent motivation may be to resolve the two body problem. And some fields have a higher ratio of jobs to PhD graduates than others.

But if someone with a PhD in particle physics, astrophysics, or space science, applies for a post-doc in atmospheric science, how do they overcome the competition with candidates who do have PhDs specialising in (the right subfield of) atmospheric science? Wouldn't a potential host quickly dismiss candidates who show neither experience nor interest in the relevant field, even if they have spoken the person, when other applicants are pre-trained "locals"?

publications - Making additional changes to manuscript after the refereeing process is completed

After doing some revision to my paper to include changes suggested by the referee (who will not see the paper again, having recommended the paper for publication), is it OK for me to make a minor change of my own, in the manuscript (before I send it to the editor)? Should I declare this in the list of changes or should I wait till the paper is officially accepted for publication by the journal? Would it then be up to the editor to check the validity of the slightly changed statement?

(I've noticed something minor in the manuscript, which needs to be fixed - and amounts to changing a couple of words in the comments section).

quitting - Should I quit my PhD?

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

By its very nature, a PhD is stressful. If you're coping with other issues at the same time, the stress can become unbearable. Suppose a student is experiencing some of the following while pursuing a PhD, and wondering if they should quit. What tools could help them make the best decision?

• worried they're not smart enough


• stressed and unhappy



• homesick


• haven't made any friends, feeling lonely


• suffering from a mental health issue such as depression, panic attacks, or bipolar


• worried about a family situation (e.g., a sick relative)


• worried about money


• disagreements with advisor

ethics - Can authors from certain origins really not know about the gravity of plagiarism?

With respect to some cultures, in particular Asian ones, one often hears statements such as the following:

In this country, copying is regarded as flattery and thus people do not know the evils of plagiarism.

or (taken from here):

In some traditional cultures in Asia and the Middle East, for example, college students are expected to quote or paraphrase the best known political or religious authorities without attribution because readers, especially professors, are expected to know what texts are being circulated. Indeed, it might be a serious insult to the teacher if the student writer formally cites the text being borrowed.

Such statements may nourish prejudices or lead to it being considered an extenuating circumstance that a plagiarist comes from a such a country (see, e.g., this answer or this case). I wonder whether this phenomenon really has the extents that would justify the latter, more specifically: Is it conceivable that somebody makes it to the point where they author a paper or a PhD thesis without knowing that they must not plagiarise? Or: Can authors really commit plagiarism out of inexperience on this level?

Note:

• I am primarily interested in anything going beyond personal experience (there are individual statements in this article). A scientific study would be ideal, but is probably not the only possible way to fulfill this criterion.


• This is not directly about how the respective academic cultures nourish plagiarism and what aspect of the culture is behind this.

As all the answers so far have ignored this: I am not asking whether cultures differ in their attitude towards plagiarism – they clearly do. I am asking whether these differences reach a certain level.

research undergraduate - What are my chances of getting into an REU program?

I am currently trying to apply to 7 different environmental REU programs and was wondering what my chances of getting into one would be.

I am a current senior pursuing a B.S. in Environmental Science with minors in French and Environmental Toxicology and will be continuing my 5th year next year (I switched majors in Sophomore year). I go to North Carolina State University, a R1 university, my GPA is 3.92, and I am a female, Asian-American first-generation college student who comes from a low-income middle class family (close to my state's qualifications for the "poverty" line). I have experience as a research assistant who assisted with research on aquatic stressors on aquatic macroinvertebrates, and I won a research grant from my university to conduct environmental engineering research last year.

I am seeking to participate in an REU because I would like to pursue a PhD and would like to learn as much as I can through research experiences in preparation for grad school. Right now, I would like to experience research outside of my home institution since I would like to explore graduate school options and other kinds of environmental/aquatic research, and the living expenses being covered would be incredibly helpful for me since I nor my family would have no way of paying for my living expenses.

Unfortunately (or fortunately?), being at a R1 university and having had other previous research experiences, I am unsure as to how likely it would be for me to get accepted into an REU program. I understand that most of these programs seek underrepresented minorities from liberal arts or community colleges with little research experience, therefore I am seeking a realistic analysis on whether or not I can get accepted into an REU program. I was told by others that I should exclude the fact that I got a research grant, but I am unsure as to how to feel about fabricating the truth to make it seem as if I have had little research experience. I am at a loss for what to do, but I have to complete my personal statements by next Friday, and I am rather stressed about my odds of acceptance.

Any advice would be greatly greatly appreciated. Just as a heads up: there are unfortunately not many other REUs with research/themes specific to the field I am going into (Non-marine Aquatic chemistry/ecology), so that is why I am only applying to 7 programs. Most other environmental REU programs are focused on forestry, climate change, or marine & coastal sciences as far as I can tell.

titles - Why is it customary to call people with doctoral degrees doctors but not people with masters degrees masters?

Why is it customary to call people with doctoral degrees doctors but not people with masters degrees masters? They are both graduate degrees that supersede the undergraduate degree.

graduate admissions - current PhD applicant applying to another university

if a current PhD student applying to another university within the same country, is it required to expose the fact that he/she is currently enrolled in another university?
is it a right for the grad studies office to know my current status? if yes; why? what is the difference?

Specially in case if the student does not want to transfer the credits he/she has taken in the previous university.

Answer

Yes. If you are a student, you should say so in your application. Otherwise, your CV will have an unexplained gap for the time you've been at your current department. Unexplained gaps raise red flags with admissions committees.

In your statement, you also need to explain why you are applying to the new department instead of completing your PhD at your current department. Moreover, you must do so without disparaging your current department, even if you have legitimate cause to do so; nobody likes a whiner. Good reasons to move include a change in your own research interests, your advisor moving or retiring, following a spouse.

Above all, do everything above board. If possible, you should also request at a recommendation letter from your current advisor; if not your advisor, some other faculty member in your department. If you apply secretly, you risk burning all bridges with faculty in your current department.

Credit transfer is a completely orthogonal issue.

human biology - How does skin healing work?

I stacked my bike and split my head right open. About three weeks later the scab falls off and the skin is sealed over, like magic! How does it all work? How does the brain know that part of the body is injured and needs repair, or does the brain know at all? What kind of signals between brain/cells/body are involved.

Sorry it's probably a basic question for a biologist, but I come from a different field and have always wondered about this amazing process. It's also a very hard topic to google about, because most results are about spiritual healing, crystals, prayer and a lot of pseudoscience rubbish.

Answer

Healing in the body is normally independent of the brain. Following an injury, a process of inflammation attracts lots of cells to the site of the injury (including platelets, white blood cells, clotting factors). There's also vasoconstriction (tightening of your blood vessels) to reduce blood loss from the injury site. Your skin cells continue to divide rapidly until new skin replaces the damaged one which later falls off. This is a highly simplified version of the process but hope it makes sense. So in summary, healing takes place by cell division (also known as mitosis).

publications - How to make my papers accessible to other researchers?

I have published some papers in some conferences, but the problem is that the people in charge put them in bibliographic repositories, such as DBLP, and they take too much time to do that.

I would like to know how I can allow more people access to my publications, so they would be able to review them, use them if they want, maybe bring more ideas or even suggest that I correct something.

Initially, I was putting them in a personal webpage that I have created, but I took them off because I also got some papers accepted by ACM and IEEE and they require a payment to see them. In this last case, if I upload them for free (on my personal webpage) could I be charged with something by these institutions?

Answer

From the context of your question, I assume you are a computer scientist graduate student. (Computer scientist because you mention DBLP, and graduate student because you're worried about people finding your research quickly.) My answer is specific to computer science, especially the first two points.

• 
  

  Just post your papers on your web page already. Among other things, posting your own papers will allow Google Scholar to find and index them after only a few days. Despite scary legal language to the contrary, neither ACM nor IEEE (or SIAM, or AMS, or Springer, or Elsevier, or...) has any interest in suing individual researchers for providing copies of their own papers.

  
  
  


• 
  

  Post preprints of your work to the ArXiv and/or your institutional preprint server. Again, despite scary language to the contrary, granting a license to the ArXiv to publish your papers does not deprive ACM or IEEE (or SIAM, or AMS, or Springer, or Elsevier, or even ACS) the right to later publish peer-reviewed version of your papers later. Many publishers explicitly allow you to publish post-reviewed but pre-copy-edited preprints on the ArXiv and similar servers. Posting camera-ready versions is technically illegal, but neither ACM nor IEEE has any interest in suing individual users for such violations.

  
  


• 
  

  Post publication announcements on Facebook/Google+/Twitter/your blog. Yes, this works. Really.

  
  


• 
  

  Give lots of talks. At a minimum, you should give talks about your results in an appropriate local seminar. But especially for really strong results, you (or your advisor) should also arrange to have yourself invited to a few other institutions to give a talk.

  
  



• 
  

  Send copies of your work directly to a few colleagues. Just send them email with a link to your web page. (Don't blindly send papers as attachments; remember that some people read email over the phone and pay by the byte.) But don't just spam the whole world. Limit your email to the small handful of influential people that you are sure will be interested — other researchers working on the same problem, people whose results you directly improve or extend, your advisor, and—if you're nearing a point like graduation or tenure where you need letters—a few potential letter-writers.

  
  


• 
  

  Take the long view. It really is not important that see your results RIGHT NOW THIS MINUTE ZOMG NOW NOW NOW !!!!111¡¡¡CXI. Relax. Yes, DBLP and other indexing services operate with a delay of several months. (Although my impression is DBLP has gotten faster, thanks to some outside funding that allowed them to hire more than one human being.) And yeah, that's frustrating. But in the long run, those few months of publication delay are not going to make a bit of difference.

  
  

teaching - What is the point of a lecture when you have a textbook?

I never really understood the point of having a course with lectures when the course has a textbook. Sometimes the subject is so high-level or specialized or so modern that the contents are changing rapidly that there is no textbook (for example at the graduate level). But more often the textbook includes everything that will be said in the lecture, and much more: extra content, exercises, answers to exercises, appendices, etc.

I assume a STEM context, that is we can assume the textbook is available in the sense that there is one comprehensive source that contains undisputed facts, as opposed to a broad literature with lots of interpretations and opinions (as may be the case in non-STEM contexts).

So what is the point of a lecture?

evolution - Why are some fungi poisonous?

There are many poisonous fungi in nature. For example Amanita Phalloides. What reasons could a fungus need poison for? Some species, like venomous snakes, use poison to kill other species as prey. But what about fungi? I can't think of any purpose for poison in fungi. If poison has no real function in fungi shouldn't evolution get rid of it?

Answer

The same reason some plants are poisonous: to stop animals from eating them.

The visible part of the fungus is called, rather misleadingly, the fruiting body. It exists to produce and spread spores and thus produce the next fungal generation. Getting eaten, rather obviously, inhibits its ability to do this. Being poisonous discourages animals from eating the fruiting body and thus permits it to complete its life cycle.

How is evolution possible in contemporary humans?

I would like to know if evolution is continuing to happen in modern humans, assuming things like existence of the nuclear family structure, fidelity to one partner, etc. It seems to me the answer would be NO because evolution depends on differential reproductive rates, but in the modern world, all male humans have roughly 2.5 (or whatever the number) kids. Add in the process of culturally modified selection pressure, and it seems to me that even an "unfit" male would end up having a couple of offspring. The fittest male (or female) is no better off than his or her contemporaries because of this "leveling" effect.

However, the impression I get from the popular science media is that scientists think evolution is continuing to happen. I would like to know what the actual scientific consensus is, and why. Thanks.

Answer

It is certainly not true that "all male humans have roughly 2.5 (or whatever the number) kids". First of all, male and female humans have exactly the same reproductive rate. For obvious reasons, every time a male has offspring, a female must have had also. Last I checked neither male nor female humans are capable of parthenogenesis (certain popular religious beliefs notwithstanding).

Second, let's assume that the 2.5 number is correct. That would be the average number of children per couple. That does not mean that all couples will have 2.5, or even that most couples will have 2.5. It just means that the average will be 2.5. If, for example you have one couple with 6 children, one with 2 and two with 1, the average will be (6+2+1+1)/(1+1+2)= 2.5.

On to the main point. What does selection mean? In its simplest form, that the individual most likely to survive (the famous "fittest") is also most likely to reproduce. This is a very simple concept, the longer you live the higher your chances of managing to have offspring. If you die two weeks after birth it is going to be hard to manage to reproduce yourself. This has not changed.

So, what does "fitness" mean? It can mean many things. If you are a warm blooded creature at the beginning of an ice age for example, it could mean being better at regulating your temperature than your peers. If you are a 21st century human, it could mean being funnier on twitter than your peers. The two are not fundamentally different. They can both be selected for or against. As long as one mate is chosen over another, selection is happening and the "fittest" (in each particular context) is most often selected.

Add in the process of culturally modified selection pressure, and it seems to me that even an "unfit" male would end up having a couple of offspring. The fittest male (or female) is no better off than his or her contemporaries because of this "leveling" effect.

"Culturally modified selection pressure", as you call it, is still selection pressure. Cultural factors can change what it means to be "the fittest" but there is no objective gold standard of "fitness". While it may be true that in modern human society, different characteristics are selected for than was the case with early Homo sapiens, this does not mean that "evolution is not occurring". On the contrary, it is occurring but perhaps it is moving in a new direction. In fact, this is essentially a circular argument. By definition, "fittest" means most likely to survive and reproduce. It does not mean strongest or fastest or prettiest. It just means whoever is better at reproducing. If that happens to be those individuals who are best at square dancing, then it is they who are the fittest.

Take the example of a modern human with diabetes. Medicine allows diabetics to lead fully productive and largely normal lives. So, perhaps diabetes is no longer a selective criterion. This does not mean that the diabetic cannot be selected for or against based on their fitness on other scales.

Whatever the selective pressure, whatever it may be that defines a "good mate", if selection is present then so is evolution. The only way to remove a species from the process of selection would be to have all (or none) individuals of each and every generation reproducing at the same rate. This is clearly not the case with humans. Surely not everyone around you has, or will have, children? There you go, selection!

---

UPDATE:

In answer to your comment, yes indeed, in order for a selective pressure to make itself felt and affect phenotype (at the species level), it needs to be constant across several generations. However, even the absence of selective pressure affects evolution. As others have mentioned below, active selection is not the only mechanism of evolution.

Your main question however seems to be the following: If modern society (medicine etc) allows individuals that would not survive in the wild to reproduce, how does that affect evolution? The main points in my answer, and all others here, are:

1. 
   

   Even if we accept that modern humans have removed themselves from the purely "biological fitness"-based selection pressure (an assumption I am not at all sure is true), and assuming that this removal is constant enough over many generations (again unclear), even if all this is true, evolution is most certainly still occurring. It may even be faster since genotypes that would not survive in the wild persist in the gene pool, thereby increasing its diversity.

   
   


2. 
   

   As you point out in your comment below, for such social pressure to make itself felt, it needs to be constant across many generations. We are probably not there yet.

   
   


3. 
   

   Most importantly, as I said above, there is no such thing as an absolute biological fitness. When the ecosystem changes, so does the definition of fitness. Modern humanity's ecosystem, our habitat, is intimately connected with our culture and society. If an individual is better at reproducing in that context, then that individual is more fit.

   
   

website - Free web hosting for academics

I would like to have a professional academic webpage, and for different reasons, I don't want to use the website of my current workplace (mostly because due to some external factors, it's not currently possible where I work, but also because I consider changing affiliation in the future, and I'd like to avoid moving my webpage).

A possible solution I'm considering would be to rent a server somewhere, and to manage it myself, but I was wondering if it existed some dedicated solutions for academics, ideally coming for free (after all, I can archive my papers on arXiv for free, I have a free academic licence for Bitbucket, I use Dropbox with the free version, I can also use Mendeley and academia.edu for free, I currently have a free wordpress.com blog), with the constraint that I'd like to be able to write my own scripts (for instance to publish my personal list of publications Tool to manage and/or make available a list of my publications on the web? , or to manage a list of conferences I'm interested in).

Answer

I personally use altervista.org and I am satisfied with it. They give me 500MB space and 10Gb bandwidth for free, an address of the form yourname.altervista.org, run php 4 and 5 and a database service (with low performance in the free version), and allow a custom .htaccess. They offer paid upgrades and the option of putting banners for a revenue, but you can say no without any disadvantage.

They allow file upload only via (unencrypted) ftp, but you can automate that part easily.

It's not academics-specific, but as far as I can see neither is any other answer given up to now.

Should one list incomplete degrees on a CV?

When applying for jobs after my PhD, should my CV include an incomplete degree I read towards years ago? It's a field completely unrelated to what I'm doing now. However, before my final year when I started getting sups and failures by the dozen (my reason for quitting) things actually went swimmingly. I worked with a renowned professor as an undergrad research assistant for a spell and even published a paper (on my own) during that phase of my academic journey. I didn't get a certificate out of it, but I nevertheless feel I honed some valuabe skills then (and of course I have a transcript listing the passes and failures).

I have since moved onto a completely unrelated humanities field. Should I mention the incomplete degree on my CV? If I ignore it, prospective employers might wonder what I did for three years of my life, surely? Should I list my science publication on my CV when it is irrelevant to what I'm doing now? Does quitting and switching tracks make me look flighty?

Answer

Don't omit it. Changing your mind at some point during your education or your career is nothing to be ashamed of. Just make sure to put it in a way that does not imply that you actually got the degree.

Not listing it would be an error in three ways at least:

• experience even in unrelated fields is always valuable;


• if you omit that stint, there will be a hole on your CV, and you will have to explain it (so you'd better mention it upfront);



• you got a publication from it, so it was actually a successful experience, even if you didn't complete your degree

---

In fact, my advice would be to always list what you've done on your CV, even if it is not an academic activity. Even if you spent two years traveling and selling onion rings on Australian beach grill house, put it in your CV. The pros outweigh the cons (and if that experience leads a potential recruiter to turn you away, ask yourself: would you have wanted to work with someöne who has such as narrow view of life?)

graduate admissions - Leaving undergraduate schools attended off grad applications

Grad applications usually list all undergraduate coursework. Is it necessary to list all schools attended, even ones I did not graduate from?

teaching - Is it recommended for a professor to not entertain advanced questions for a basic course?

Recently I worked as a teaching assistant for a digital logic course. The topic for the day was full-adder. Professor explained the full concept of the full adder, along with question and answer session and then it is now the turn of TAs to clarify doubts of the students. One student asked me the question: what is the architecture of full adder circuit using currently in the most advanced CPU of laptops. I really had no clue about it.

But a new doubt raised in my mind that how should a professor react to such questions?

The professor may not know every aspect and every trend in the subject (s)he is teaching. If (s)he says that I don't know, then, the respect for the professor may go down. Else if (s)he says that it is beyond the scope of the course then the research aspirancy of the students may go down. Other methods are providing references later by saying I will send it to you/class later etc., but still, it is like saying I don't know, but indirectly. Because if one the student asks a question, then many people want to know the answer immediately from the professor. I feel that the professor should at least answer the question in a very short form.

So, the final question can be divided into two parts:

1) How should a professor react to the most advanced questions from their students of a basic course, if (s)he knows the answer?

2) How a professor has to react in the classroom for the advanced questions that (s)he doesn't know the answer?

biophysics - How to measure Na/K channel activation at the membrane level?

Assume that there are two different signals occurring on the ECG - during depolarization and repolarization in the standard ECG. I was advised not to use the standard ECG in measuring the exact electrical events during:

• stages 0-2


• 3-4

We can get data about the electric activity of neurons in vivo in Fig. 1 where some data about the electric activity of neurons is present. So my thought is that a similar technique could probably work with cardiomyocytes.

Fig. 1 Example of measurement for electric activity of neurons in vivo

I estimate that there is about 18% uncertainty when using the standard ECG because of the peak in the stage 1 (Gibbs phenomenon) and those two complete different phases.

When should you publish code on GitHub? Work-in-progress or after publication?

What is policy are you following about publishing data analysis code on GitHub? Do you do it after publishing or as a work-in-progress?

I developed a number of Python algorithms to analyse a large dataset, and I would like to make my work visible.

Answer

There is a movement gathering strength lately to encourage publishing the code:

Nature-Publish your computer code: it is good enough

Or, more vehement: If there is no code, there is no paper

The reasons outlied on the article are very reasonable. If you are expected to publish detailed derivations, experimental methods, and proofs of theorems, why would you be allowed to keep the code? No one will accept a theorem if you claim: "the proof is too messy to show, but hey, here are three cases where it works".

I think the best way is to publish the code used as supplementary material, and include a link to the repository, so people can get the improved versions. If you are concerned about people using too bleeding edge versions, make releases, but leave the development public. This will also help you get bugfixes and contributions.

Thank you for wanting to release your code. I really believe this attitude will help make research better.

Edit:

After some time, I have something to add. Most of the code in an application is there for "administrative purposes": load and write data, massage, check conditions... For publishing, that part can be as hackish as one needs it to be. The real "research" is usually in a small part. That is where one should dedicate one or two hours of adding a few comments and clearing the code.

For the rest, a docstring in the functions or a paragraph explaining the aim, should be fine.

Paper contributions and first authorship

Twelve months ago I started working on a project (which began at that time) with my advisor. Six months ago another student (refered to as A in the following) joined the project.

We are now publishing a paper on our results. My advisor asked me if I would find it reasonable that A’s name was put before mine in the article. Our advisor’s reason is that she believes A has contributed a lot more to the publishable results and making figures for the article.

I agree with this latter part: student A has definitely been the working horse behind these results and made the graphics for the article. However, my contributions were in the first 6 months of the project, laying the foundations for the setup, etc.

I’m not sure how to feel about my advisor’s question. Is my contribution worth less because they are further back in time? And does making article-figures count as “ammunition” to be put first in an article?

industry - What are the potential pitfalls of having a PhD?

This question follow's JeffE's comment here:

In most industries, a PhD has negative value.

I am curious about what potential negatives there may be with having a PhD, particularly in industries. For example, my PhD has applications for image sensors, and the potential of working in that field is appealing—would having a PhD be a potential barrier? Would it be a case of how explicit the practicalities of the PhD can be made? Would this make any difference?

Answer

Though a Ph.D is not necessarily a disadvantage, depending on the field and the nature of the Ph.D, it may also not be as competitive as the equivalent number of years in industry.

Think from a perspective of a hiring dev team leader who needs a good systems engineer yesterday to help integrate some obscure API from a vendor into their product. You're choosing between a pile of resumes.

On one, you have a candidate who has 3 years as a junior engineer in a company that worked on image sensors, 2 years of work as a systems developer II, and one year as a lead developer on a computer vision project. He's delivered seven projects in total and has worked in a highly cross-functional team of hardware and software engineers, salespeople, and on-site support staff. The products he worked on brought the company revenue of $86.3 million dollars over seven years.

On another, you have a candidate who has done 6 years in a Ph.D and 1 year worth of internships in total. He's worked on a computer vision project and has contributed a novel algorithm to solving "Line tracing under low UV light conditions" (I made that up, I have no idea if that's a real problem in computer vision), and has written six publications. He also has taught a course on 3rd year systems programming and has TAed robotics three times.

While they are both good candidates, chances are that unless you need someone who does "line tracing under UV light", the first candidate might be more attractive. Less training, less having to work with that person to integrate them into a product-based flow, proven record of delivering product and making sales, etc...

I personally feel that the "disadvantage" of a Ph.D is more about lost opportunity cost than an actual disadvantage. In many cases, the culture of academia vs. industry are different enough that it's like switching fields even if the technologies are similar. Basically, someone with 7 years actual work experience has enough to basically go from a new grad hire to a project team lead, whereas someone with 7 years of Ph.D is proven to deliver in an academic setting but not in a for-profit product-based one. However, at the same time, there are many industries that want to have Ph.Ds on their staff as well because they are long-term, deep thinkers who are rigorous and detailed.

Is evolution a fact?

Richard Dawkins in one of his videos says that Evolution is a fact and not just a theory.

He goes on to say that man and chimpanzees both evolve from apes. Is this correct (Is evolution a fact and did humans & chimps evolve from apes)?

publications - Is copying an image from a previous paper of mine and citing its source considered self-plagiarism or unprofessional?

Last year, I wrote a paper and it got accepted and was presented at a conference.

This year, I am writing a more in-depth paper about a similar subject; but since one of the figures in my first paper is adequate for my purpose, I want to reuse that one (of course citing it adequately).

Am I OK in doing that, or is that seen as self-plagiarism or unprofessional?

Answer

There is such a thing as self-plagiarism, but I would say that your case (reusing a figure that you created and providing a citation to it) is not an instance of it. I also don't think it is unethical or unprofessional. As Ran G. says in his answer, just make sure you ask permission from the copyright holder (if it isn't you).

university - How to remove gender bias from an academic job search?

I overheard some professors discussing the next round of hiring at my university and several were concerned about gender bias possibly playing an issue in the hiring process. An initial thought is to just go through CV's and black out an applicant's name. However, an academic job search makes it much more difficult to do this. Not only do applicants have CV's, but there are also typically 3 letters of recommendations as well as publication lists (which might reveal the identity of an individual if the paper is known by some of the hiring panel).

Some suggestions that were thrown out involve trying to find a way to scan through 2-300 applicant materials and black out/replace gender pronouns and names. From browsing StackOverflow, there is apparently quite a bit of difficulty with this from a programming perspective. Still, it seems the most efficient way to remove as much gender bias as possible in the process but doesn't seem to be widely used.

What are some of the best ways a hiring panel can remove gender bias from the application process?

This question could also potentially extend to ways to generally remove other forms of bias, such as ethnic bias.

Answer

Bias exists at many points of the hiring process. You suggested blinding the search committee to applicant gender but, as you point out, this is extremely difficult to do perfectly and completely broken by even small failures. For obvious reasons, blinding will also not be particularly relevant after you start interviewing candidates. I like the other suggestions to provide training to sensitize the committee to issues of gender bias.

Beyond that — and if your university policies allow it — you might also decide now (i.e., before the search) to interview at least one male and at least one female candidate. This way, you will give the best male and female candidates a full chance to convince you that they are right for your department. This ensures that at the top person of each gender makes it through the earlier stages of the process where gender bias may very well play its biggest role. At the interview stage, blinding would not have worked anyway.

This kind of policy is unusual but not unheard of. The most famous example I know if is the Rooney Rule in the US National Football League which requires that all teams interview minority candidates for head coaching and senior football operation jobs. Although this is sometimes cited as an example of affirmative action, it does not mandate any preference or quota to candidates within the pool of those being interviewed. If you're doing it right, it does mean that the very best candidates from under-represented groups will always have an opportunity to show their stuff at the final round.

If you found out that best person from the under-represented groups is really not as good as the best person from the over-represented group, at least you'll know that you gave the best member from each group a full hearing.

Update: I will point out that this answer basically assumes that all of your candidates will present as either male or female. As a result, is it very limited in the case of non-gender conforming candidates. These candidates may also be subject to even greater discrimination and this approach will not solve (and could even aggravate) those problems.

cell biology - What is the difference between the cellular affix -cyte and -blast?

The affix -blast means an immature cell, and -cyte indicates any cell. So how do we define if a cell is mature (-cyte) or immature (-blast)? How does this apply to odontoblasts and ameloblasts? Why are they not simply called odontocytes and amelocytes, respectively?

What are the criteria for using the affix -cyte versus -blast?

Answer

Short answer

- The affix -cyte means cell;
- The affix -blast means a germ (bud) cell or a cell that produces (building) materials.

Background
Cells are denoted as -cytes. There are many of them, e.g. melanocytes in the skin and chondrocytes in the cartillage.

Germ cells are denoted as -blasts. These cells typically are precursor cells such as the lymphoblasts that are undifferentiated precursor (stem) cells situated in the bone marrow that produce leukocytes.

Blast cells may also be cells that produce materials. Your examples are of that category; odontoblasts generate dentine, the main hard tissue of the tooth; ameloblasts deposit tooth enamel, which is the hard outermost layer of the tooth forming the surface of the crown. in that sense, also progenitor cells produce something, namely new cells. Hence, blast cells are cells with a chief building function, either materials or new cells.

There are also -clast cells - cells that destroy something. Fig. 1 below gives an overview of these cells as present in the bone, namely osteoblasts (bone builders that secrete the matrix), osteocytes (osteocytes are osteoblasts that are embedded in bone; they stop secreting matrix and only maintain it) and osteoclasts (different class of cells that mediate bone resorption).

^{Different cells in the bone. source: University of British Columbia}

Why then do not call odontoblasts odontocytes? - Because it would mean loss of information. It would be the same as calling a car and a bike both transport vehicles. Moreover, the example in Fig.1 is quite convincing, as osteocytes and osteoblasts are considered to be different cells altogether (although the former is derived from the latter).

human anatomy - Will I grow taller? How can i tell?

I'm 17 and I'm about 160 cm and my weight is 47 kg . I just want to know if I will still grow taller ?

professors - Can one excel in graduate school with a demanding family life?

The essential gist of my question relates to what the real, unvarnished realities are of graduate, post-graduate, research, fellowship, and professorship attainment - when you aren't a single person with no pressing demands other than feeding yourself.

[EDIT: I am humbled by the incredibly helpful and thoughtful responses so far, all of which are +1 from me. I'll leave the question open a few more days before clicking 'accept' on any one, but you all have my gratitude and I hope others will benefit anywhere near as much as I have. ]

What I don't know is what succeeding in this path truly requires in time committment and family support.

Right now I can handle a 12-14 credit course schedule with 3.7-4.0 GPA (in the top 5-10% for college and program, dean's list, etc), work part-time, and still have time to be home and not have a burn-out/breakdown - and the academics are the easy part by far! I could do more, but I need to work more too.

What I really need to know is how sharply different is the time/dedication curve of graduate work and above. I realize each step is a filter that removes most of the entrants (most people don't get a degree, most who do don't attend/finish graduate school, most who do don't seek a PhD, most who do don't seek/gain professorship...and on and on). But I don't know how severe the stepping is - I'm not talking "tenured professor at MIT or bust" - I realize that bar is many orders of magnitude higher.

Background Details: As an "adult, returning" undergraduate student with a (disabled) wife and kids, I'm halfway through a bachelor degree now. I've located a field of study (in a focus of Industrial Engineering) that has made me very interested in altering my life path to include seeking a Masters and maybe even a PhD/professorship (my father was a professor, so its not a purely novel concept to me). I've met and spoken with my advisor and 2 other professors with experience in related fields, and all is encouraging; I have a graduate school in mind, I've received lots of great advice on preparing for school (on this forum and in person), I test well (no GRE fears remain), good grades/class rank, good prospects for future strong referal letters, etc - a comparitively charmed existence for which I am very grateful! I just have to investigate whether I can make it through with an intact, cared for family!

Any guidance you could provide me, and other aspiring "non-traditional" students alike, would be appreciated immensely - thank you!

Answer

I feel for once I am somewhat qualified to give an answer here.

A bit of background to know where I am coming from and hopefully give some insight to my situation. I am currently finishing my second year in a MA Mathematics program and beginning my first year of my Ph.D. in Mathematics in the fall. I am married with two children(a 3 year old and an 8 month old). I had my first child during undergrad and my second child came two weeks before the current school year started. I attend a smaller department that is most certainly less intensive in regards to the expectations that another school would have(such as a top tier research university). I've been a Research Assistant for the past two years doing active and successful research with an amazing supervisor. This past year has been the most stressful since I decided to take three core year long sequences, which is a great deal of work to keep up with.

Above all, put your family first.

I would hope this goes without saying, but it can be easy to lose sight of this when you're up to your neck in homework/deadlines. When something comes up with my family, I drop my schoolwork to deal with it. I make it a point to always put my family before school. I'm sure there are professors out there who would argue otherwise, but I'm grateful that my professors seem to (hopefully) understand the situation and that I just can't put in the hours that other students can. I generally score lower on average than other students but I think I do fairly well. Could I do better? Absolutely...if I were to put in the hours and sacrifice time with my family I could score better on my tests and homework, but that isn't what really matters in the long term to me. Of course I want to do well in school(and I generally do!), but sometimes I have to make a choice and school gets the axe.

In the end, you choose your own priorities, and I would suggest opting for spending time with your family over finishing that HW. You just can't get those moments back.

Having a Strong Support System

I would absolutely not be able to do this without the support of my wife, family, and friends. Without my wife to help out with the kids and pick up some extra housework when studying for tests/finals/my oral MA exam, I would certainly have dropped out or (worse) ruined my marriage or become a terrible father. I make sure to try and do extra work whenever the stressful times pass and try to make it up to her as I can.

We are lucky to have family close that can help out with childcare and babysitting when I need to go in on an off day or want to stay late for a seminar. Without the support system we have in place, I'm not sure I could physically do it. If you have a similar support system, then it will be a huge relief to your stressed.

I should also mention that without some amazing people at my department, I wouldn't be able to succeed. Professors have been amazing with deadlines if the time just wasn't there for me some week. My RA supervisor has been absolutely amazing as well. She's extremely understanding with the kids and even being cool with me bringing the little one to meetings if everything just fell apart for that day. If I had a less understanding supervisor, I probably wouldn't have made it.

Time Management

This is probably the trickiest part. Time management is always important, but it's extremely important to successful manage school and family. You just don't have all the time that other students do so when it's time to work you need to remove all distractions and get as much done as possible. I arrive at school between 8-9am and in between classes I work nonstop on homework or studying until I leave at 3-4pm. I have a computer in my office, but I purposely keep it off unless I absolutely need it on. I disable the wifi on my smartphone and removed nearly all the time wasting apps(facebook, games, etc..). I check my e-mail probably twice, once near the beginning of the day and once around the time I'm getting ready to leave for the day.

I do take small breaks from work to socialize with other students or check in with professors as needed, but I strive to make sure that I don't waste an hour doing absolutely nothing in someone else's office. Socializing is an important part of graduate school, so don't neglect it but don't let it consume all your precious time.

When I come home after school I shut off school mode. I spend the rest of the night with my family, eat dinner, and help get the kids into bed. Once the kids are in bed then I'm free to do homework. I don't always go straight into homework though because it's important to me to spend time with my wife relaxing and watching an episode or two of TV shows to wind down. It doesn't happen every night, but I usually make an effort to take it easy on weeknights when I don't have school the next day. The "school nights" I usually retire upstairs to work on homework. I'll work until midnight or later depending on how early I have to get up and I'll average around 6 hours of sleep. It's not great, but sacrifices have to be made somewhere.

Finally, in my opinion, give yourself the weekend. Once I leave school on Friday, I'm done with math until at least Sunday night. The weekends are prime family time and we spend every weekend visiting the zoo, science center, art museum, the park, or virtually anything else the kids would enjoy. I initially thought it would be impossible to take the entire weekend off schoolwork and still succeed, but I've been doing it for 2 years. This past year was the worst, but I stuck to it and I can safely say I managed to survive it and do just fine in my courses.

Dealing with Stress

Let's face it, you'll be stressed. Grad school is stressful as all hell to begin with, but then you go and toss kids into the mix? It's insanity, and you have to handle it somehow. I'm a fan of exercise, which takes up that precious time but is totally worth it. You have to feel as good as you can and any sort of activity is a great way to relieve stress. You could also do another hobby, or something that you do to relax. I'm also an avid reader, so losing myself into a book every now and then is great. The time I have to read varies, but it's one of my top hobbies. Find something you enjoy and do it frequently to relax.

Sometimes it just can't be helped. If you find yourself really freaking out, you really should seek out the school's counseling center. They are no doubt used to overworked students and having a place to lay all your problems on the table and have a trained therapist help you sort it out is probably exactly what you need.

---

To sum it up, I put my family before everything else. School takes a high priority but there are far more important things in my life than getting an A in every course. Schedule your time wisely, remove distractions, and work when it's time to work. Do something relaxing for yourself on a regular basis. Give your family the attention and time they deserve. You can't get those moments back and no letter grade in the world is worth that sacrifice.

Above all, make sure you are happy. It's such a small thing but I've seen students absolutely miserable hating what they are doing. Don't be that person! Life is too short to waste it being miserable. I suggest every 6 months or so, take a step back and evaluate how you feel about your situation(this should apply to anyone, not just graduate students). For instance, I vow to myself that if there ever comes a time when I begin to genuinely dislike what I'm doing, I will quit and find something else.

Good luck and don't forget what's really important. Grad school has a way of giving you tunnel vision and destroying you emotionally...just don't let it do it too often. :)

phd - How to deal with supervisor who required me to share all my work with him?

I am graduating with my Ph.D. very soon. In addition to my thesis and published journal papers, my supervisor required me to copy all my work—code, figure files, data, etc.—to him before my leaving. However, all the works during my PhD have been done by myself from scratch, including the ideas and research gap searching, although he was the co-author of the papers. And my scholarship has been provided by the university. So I feel this requirement is not reasonable.

In fact, my supervisor didn't like my research topic and we had very little communication during my Ph.D. study. He gave me very little help on my work and was also never interested in my work and research field. In this case, could you suggest me on the following two specific questions:

1. 
   

   Should I share all my works with him? If yes, why and if no, how to negotiate with him?

   
   


2. 
   

   If I can only share partial works with him. What is a good strategy?

   
   

Answer

It is highly likely that you have a clause on "inventions" and/or "invention disclosure" which you may have signed during your admission process. If you still have it, refer to it to see what it says. In most cases, the ownership of the IP and any related materials belong to the University and so your supervisor is supposed to have a copy of your work for archival purposes.

If you do not have it, the admissions office of your department/university may have a copy of the official policy which you can refer.

united states - If most universities in the U.S are non-profit, why are they so expensive?

Tuition can easily get in the tens (if not hundreds) of thousands of dollars for a 4-year degree. This is unarguably many times over what the university needs to cover the costs of offering their services. Why is this the case if they are usually run under a non-profit architecture?

Where is all this money going?

etiquette - Should I include funny pictures in my slides?

I am preparing slides for a short (10min) talk at the group meeting. The talk is about a fairly serious piece of (pure) mathematics, and it so happens that there is a very relevant one-panel webcomic. A thought appeared to me, and got some support from my fellow PhD students, that it would be cool to include this comic, perhaps at the final thank-you-for-your-attention slide.

I am probably not going to do it, so I'm asking mostly out of curiousity: Would this be a bad idea to go ahead and include a comic on the final slide?

Note: The comic is genuinely funny (based on a sample of 6 non-randomly selected students). It is not - as far as I can tell - offensive in any way. It could come across as somewhat silly.

Answer

Human cognition is a strange thing, and I won't pretend I know it well enough to give you a guide, but I will suggest that you simply consider your audience and how you want them to move through the information.

A dense, heavy talk with few breaks will tire most audiences.

A light talk that doesn't require much thought will result in many people letting their mind wander.

A talk which carefully weaves the "story" with a variety of dense to light moments, may actually improve retention.

Adding levity in the form of a joke or humor, if the joke is very relevant to the talk, can actually increase retention, as long as it isn't too much of a distraction. Placing it appropriately is key, though, and I wouldn't do it at the end, because that's what people will remember. The last few sentences should be a quick summary of the talk and should be memorable.

Placing it in the middle, during a transition - for instance between the problem statement and the methodology - could be good, and allow a release of tension if the problem statement was pretty densely packed.

Starting off with it, as an into to the topic and a method to get attention is also a pretty good choice.

In all things, though, consider your audience first. What is the journey you are taking them on, and when would be an appropriate point for a rest break, a transition, a wake-up, etc.

graduate school - What are the roles and responsibilities of an adjunct faculty?

Is adjunct faculty's duty limited to teaching? Do they have any role in course design, grading, etc.?

What are the other responsibilities, as an adjunct faculty?

Answer

There's a wide range of people called adjunct faculty. For example, it may include working professionals in the field who serve as part-time faculty (this is common in law and architecture, and I've seen it with industrial researchers in computer science). Depending on the circumstances, this sort of adjunct may be treated much like the other faculty in the department, except for being part time. However, I assume you are talking about the most common use of the term "adjunct", at least in the US, namely low-paid, low-status faculty typically teaching part time on temporary contracts. (They may be working full time overall, but only part time at any given institution, so the universities can avoid paying benefits.)

For this sort of adjunct, it really depends on the details of the contract, and it may vary between universities, as well as depending on issues such as whether any of the courses are online. A typical arrangement will include some amount of course design (at least at the level of creating a syllabus), lecturing, grading, and office hours. Typically there is no committee work or other service and no research duties.

computer science - Am I naive to think I can focus on professional programming and still be active in the field of CS as a whole?

I am working full time currently as a programmer in a summer internship. In the fall I will be continuing school and working part-time as a programmer.

I believe that I want to be a professional programmer and someday a software engineer.

However, I am very interested in all the areas of computer science that I have been studying. I hear occasionally about how some computer science majors end up being "just programmers" and not "computer scientists." There seems to be a common thought that becoming a programmer means that you give up the field as a whole and the possibility of contributing to the field.

I would like to be a professional programmer, but also a lifelong learner in the field of computer science. Am I naive to think this is possible?

Answer

I am a professional programmer with a PhD.

I have had a colleague, who was working as a programmer and continued even publishing in his unrelated field (chemical engineering/textiles), so if you are dedicated, it is even easier for you to do, since your area might be related, but still it is not a light undertaking. But if you can find a more research heavy R&D position in the industry, of course that would make it easier.

I am personally planning to teach adjunct classes, to keep me fresh about theoretical basis.

Hope my two cents helps.

evolution - Why don't mammals have more than 4 limbs?

Arthropods have 6 or more limbs and arthropods with 6 limbs appear to move faster than arthropods with 8 limbs so I wonder whether this might have something to do with fast and efficient locomotion. But, this is just a guess. I wonder what the official explanation is, if it exists.

Answer

Number of legs in terrestrial vertebrates

Not only do mammals have four legs but actually all terrestrial vertebrates (which include mammals) have four legs. There are slight exceptions though as some lineages have lost their legs. Typically snakes have no legs anymore. Apesteguia and Zaher (2006) discuss the evolution of snakes legs reduction and report a fossil of snakes with a robust sacrum. Cetaecea (whales and friends) have lost their hind legs but we can still spot them on the skeleton. See for example the orca (killer whale, easily recognizable to its teeth) on the picture below. Pay attention to the small bones below its vertebral column at the level on the left side of the picture.

I also want to draw attention to the importance of the definition of legs. I guess that we would call something a pair of legs if it is constructed using a similar developmental pathway than current existing legs. If we are using some broader definition, then a prehensile tail as found in some new world monkeys, for example, could be considered as a leg (but only a single leg, not a pair of legs obviously). A list of animals having a prehensile tail can be found here (Wikipedia).

Did you say Natural Selection?

I think (might be wrong) that you have too selectionist a view of evolution. What I mean is that you are wondering why mammals have four legs and you're looking for an explanation of the kind "because mammal have this kind of need of locomotion and for this purpose four is the most optimal number of legs". Consider the following sentence: "If there is a need, natural selection will find a way!". This sentence is wrong! Evolution is not that easy. This false view of evolution is sometimes referred to as panselectionist.

The reality is that it is not easy to evolve such a developmental pathway as drastic as having an extra pair of legs that are well integrated into the body of the carrier of this new trait. Such an individual would need a brain, a nerve code, a heart and some other features that are adapted to have extra legs. Also, assuming such a thing came to existence it is rather complicated to imagine how it could be selected for. To go slightly further, you have to realize that there are many stochastic processes in evolution (including mutation and random variation in reproductive success) and an organism is a piece of complex machinery and is not necessarily easily transformable to some other form that would be more efficient (have higher reproductive success). Often going from one form to another may involve a "valley crossing" meaning that if several mutations are needed, intermediate forms may have low reproductive success and therefore a high amount of genetic drift (stochasticity in reproductive success) to cross such valley of low reproductive success. See shifting balance theory. Finally, even if there is selection for another trait, it may take time for the mean trait in the population to shift especially if there is only little genetic variance. A complete discussion on why the sentence "If there is a need, natural selection will find a way!" is wrong would fill up a whole book.

Gould (1979) is a classic article on the subject and is very easy to read even for a layperson.

Why 4 legs?

Terrestrial vertebrates have four legs because they evolved from a fish ancestor that had four members that were not too far from actual legs (members that could "easily" evolve into legs). This is what we call a phylogenetic signal. The explanation is as simple and basic as that. You can have a look at the diversity of terrestrial vertebrates here (click on the branches).

Number of legs in invertebrates

Arthropoda (Spiders (and other chelicerata), insects (and other hexapods), crustaceans (crabs, shrimps…) and Myriapoda (millipedes) and Trilobite as well)) evolved from a common ancestor who had a highly segmented body. From this ancestor, many groups have fused some segments. In these taxa, each pair of legs is attached to a particular segment (I don't think the segments are still visible in spiders today). In insects, for example, all 6 legs are attached to the thorax but to 3 different segments of the thorax, the pro- meso and meta-thorax (see below).

As a side note, it is interesting to know that the wings in insects did not evolve from the legs (as it is the case in birds and bats). There are two competing hypotheses for the origin of insect wings. Wings either developed from gills or from sclerite (chitine plate, the hard part of the insect). When insect first wings, they actually evolved three pairs of wings (one on each segment of the thorax). At least one pair has then been lost in all modern species. In the diptera, a second pair of wings have been lost and are replaced by halteres, particularly easy to spot in craneflies (see below picture). In millipedes, the link between segmentation and legs is even more obvious (see picture below). You can have a look at the diversity of Arthropoda here (click on the branches).

Pictures

Update 1

Asking how likely it is for a given population to evolve a given trait is extremely hard to answer. There are two main issues: 1) a definition of the question issue and 2) a knowledge issue. When asking for a probability one always needs to state the a priori knowledge. If everything is known a priori, then there is nothing stochastic (outside quantum physics). So to answer the question one has to decide what we take for granted and what we don't. The second issue is a knowledge issue. We are far from having enough knowledge in protein biophysics (and many other fields) to answer that question. There are so many parameters to take into account. I would expect that creating a third pair of legs would need major changes and therefore one mutation will never be enough in order to develop a third pair of legs. But, no I cannot cite you any reference for this, I am just guessing!

Following the wings example in insects. Insects have had three pairs of wings. While some mutation(s) prevented the expression of the third (the first actually) pair many of the genetic information for this third pair remain in the genotype of insects as they still use it for the two other pairs. Taking advantage of that, Membracidae (treehoppers) developed some features using a similar biochemical pathway than the one used to develop wings. Those structures are used as protection or batesian mimicry.

Update 2

Let's imagine that an extremely unlikely series of mutations occur that create some rodent with 6-legs. Let's imagine this rodent with six legs has a larger heart in order to pump blood to these extra legs and it has a brain that is adapted to using six legs and some changes in its nerve cord so that it can control its 3rd pair of legs. Will this rodent have higher reproductive success than other individuals in the population? Well… let's imagine that with its six legs, it can run faster or whatever and has a very high fitness. How would the offspring of a six-leg mother (or father) and a four-leg father (or mother) look like? Will it be able to reproduce? See the issue is that it is hard for such trait to come to existence because 1) it needs many steps (mutations) and 2) it is hard to imagine how it could be selected for. For those reasons, there exist no vertebrates with 6 fully functional legs.

Well, let's assume it does and in consequence, after 200 generations or so, the whole population is only made of 6-legged individuals. Maybe the species got extinct then and no fossil record has ever been found. This is possible. It is not because something has existed that we necessarily find something in the fossil record.

biochemistry - Why don't antiseptic agents kill 100% germs?

I've seen innumerable antiseptic, mouthwash, handwash advertisements that claim to be able to eliminate as much as 99.9% of all germs over a surface...but why not the remaining 0.1% (i.e- why can't they eliminate all germs)?

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Clarifications:

What they mean by "germs":

Being a student of Biology, I can tell that the term "germs" is crudely defined. I would prefer to use "pathogens" (less ambiguous), and I suppose the guys that market these products have (roughly) the same idea in mind. Pathogens normally include bacteria (monerans), protozoans, fungi and viruses... so I guess these are the "germs" they're talking about.

What I'm looking for in an answer:

Why is it that these (commercial) products can't eliminate 100% of all pathogens? Is this due to the inability of antiseptics to act on a particular (class of) organisms? If so, what's the problem there? Or is it because, the guys who market stuff like this assume an arbitrary amount (0.1%) of the pathogens present on a surface (say, the human hand) is located in microscopic niches that are inaccessible to the antiseptic solution? (If it isn't possible to provide a blanket statement in this regard, use of Listerine as an example will suffice)

In other words:

Is an antiseptic's inability to eliminate 100% of all germs due to its "chemistry", or is it due to physical factors?

Also,

Do antiseptics/mouthwashes/handwashes even kill 99.9% of all germs in the first place? Or is it (as I strongly suspect) an example of marketing fraud?

Answer

This is actually an interesting question! Let me answer both the parts separately, taking the example of Listerine^® mouthwash.

Is an antiseptic's inability to eliminate 100% of all germs due to its "chemistry", or is it due to physical factors?

In most of the cases, this is due to the physical factors. Clearly, your mouth is not a flat surface. It has many depressions and elevations. And these irregularities are the perfect hotels for all kinds of pathogens. Also, it is difficult for most chemicals to reach those spots and stay there for long enough so that they can act on the pathogens. Thus, most of these chemicals would be unable to kill 100% pathogens because of their inability to reach all of them. Also, in rare cases, it might also be due to chemical factors(!) Yes, I'm talking about antibiotic resistance. And in that case, it would be practically impossible to kill 100% pathogens, no matter whether they're hidden or exposed.

Do antiseptics/mouthwashes/handwashes even kill 99.9% of all germs in the first place? Or is it (as I strongly suspect) an example of marketing fraud?

For that, lets first see what Listerine^® contains. As given on its website, its main ingredients are (I'm simply copying what they write on their page, followed by checking whether its true):

• 
  

  Eucalyptol – with antibacterial properties, this eucalyptus-derived essential oil works as an anti-fungal agent within the mouth.

  
  


• 
  

  Methol – this natural oil as germ-killing abilities to help halt the growth of bacteria.

  
  


• 
  

  Thymol – this powerful oil is derived from the ajowan herb, and helps decrease the risk of gum disease.

  
  
  


• 
  

  Methyl Salicylate – for minty freshness from morning til night, the flavouring agent in this essential oil is, well… essential!

  
  

We just need to know whether these ingredients really work or not (why? We'll talk about this later on) and I'll skip methyl salicylate for this (they don't even claim that it is antimicrobial). Beginning with eucalyptol, it has been shown that oil of Eucalyptus globulus (of which eucalyptol is a component) has antimicrobial properties against Escherichia coli and Staphylococcus aureus (see Bachir et al, 2012). It has also been shown to possess antifungal properties (Safaei-Ghomi et al, 2010). Coming to methol, it has also been shown to have antibacterial properties against various Staphylococcus and Lactobacillus species (Freires et al, 2015). Finally, there have been lots of studies about the antimicrobial properties of thymol. You can check out the Wikipedia page for information.

So, where is the percentage? The point is, the exact percentage depends on a lot of factors. When an enterprise, such as Listerine^®, claims that their product has been shown to be 99.9% (or any number) efficient against bacteria, they need to cite the particular study through which they claim this number. But they can not, in any case, be definite that their product will be 99.9% effective everytime. How effective a product is also depends on the conditions under which it is tested. Mostly, these tests are performed on a petri dish in a laboratory, something very different from your mouth. Thus, although they can claim that their product is scientifically proven to be 99.9% effective, they cannot claim it to be 99.9% effective when you use it. Again, they cannot claim 100% effectiveness because this makes them liable (saying our product has been shown to be 100% effective requires them to show that even a single microbe did not survive on the petri dish they used for experiment). Also, this gives them a way to escape in case anybody complaints about their product not being effective (since they caught infection even after using their product). In such situation, they can easily say that their product is not 100% efficient!

biochemistry - Can the human body create glucose out of fat?

I read conflicting views about whether or not the human body can create glucose out of fat. Can it?

Answer

Only about 5–6% of triglyceride (fat) can be converted to glucose in humans.

This is because triglyceride is made up of one 3-carbon glycerol molecule and three 16- or 18-carbon fatty acids. The glycerol (3/51-to-57 = 5.2–5.9%) can be converted to glucose in the liver by gluconeogenesis (after conversion to dihydroxyacetone phosphate).

The fatty acid chains, however, are oxidized to acetyl-CoA, which cannot be converted to glucose in humans. Acetyl-CoA is a source of ATP when oxidized in the tricarboxylic acid cycle, but the carbon goes to carbon dioxide. (The molecule of oxaloacetate produced in the cycle only balances the one acetyl-CoA condenses with to enter the cycle, and so cannot be tapped off to gluconeogenesis.)

So triglyceride is a poor source of glucose in starvation, and that is not its primary function. Some Acetyl-CoA is converted to ketone bodies (acetoacetate and β-hydroxybutyrate) in starvation, which can replace part — but not all — of the brain’s requirement for glucose.

Plants and some bacteria can convert fatty acids to glucose because they possess the glyoxylate shunt enzymes that allow two molecules of Acetyl-CoA to be converted into malate and then oxaloacetate. This is generally lacking in mammals, although it has been reported in hibernating animals (thanks to @Roland for the last piece of info).

publications - How to shorten an article before submitting to a journal

Does anyone know a good online source for guidelines for shortening journal articles? I've just finished a paper that I'm going to submit soon, but I think it is far too long. Its current length is 30 journal pages. (I know that because I've obsessively figured out what formatting would get me to have 1 word processed page for each journal page of a specific journal.) This is in the humanities.

So I just want some good guidelines for things like "get rid of 'the fact that'." The only such things that I found online were directed at people writing their college-admissions essay, which has to be very short, like 500 words.

Answer

Just to add to the many answers already here, I'll put what I usually do. I'm often quite verborragic while writing, so this is a common problem for me, as we can all see :)

1) Revise every single sentence, not only to remove stuff that is not needed, ("To this end", "such as", ..., I usually use that stuff to "link" ideas while writing, but they are not needed and usually can be cut out without significant change), but also, as said previously here, to better express your points. Be concise.

2) Remove trailing sentences in the end of paragraphs that do not use the full width of the column. Some times you have one or two words dangling on the end of a paragraph that waste a whole line. At one time, I managed to get a little less than half a page of space on a eight page article just by doing that.

3) Check the references. If the journal is not against journal names abbreviations, do it. The same trailing thing applies here as well...

However, those tips only work if you are close to the mark... For instance, one of my articles was reduced from 10 to 8 pages after the first review... We had no choice but to cut content and move it to supplementary material.

Always keep in mind what information you want to convey...

databases - Is there a master list of journals?

I'm looking for a repository of journal data. More specifically, a listing of every known journal name and various attributes such as ISSN, rankings, peer review, etc. I know Cabell's offers this information, but expressly forbids mass-downloading. Is there a better source for Journal data?

Which texts are good for beginners to understand evolution on the genetic scope?

Are there good texts to study the evolution, how it works, and how mutations and changes lead to evolution of the organism ?

And how does the information increase through the long time using mutations and other mechanisms?

Can you recommend specific texts?

species identification - Can anyone help confirm this tiny insect larvae?

Can anyone help identify this insect larvae?

Found: UK, autumn, in a bed.

Size: less than 2mm

The bed was searched thoroughly and no others were found, but is there likely to be more of them?

Thanks!

authorship - Author without institutional or professional affiliation

Here is the case: An author has made substantial contribution while not been related to any institutional or professional affiliation.

The question I sent to Nature:

An author has made substantial contribution while not been related
to any institutional or professional  affiliation.


Is it okay for this author to include his personal email and postal
address as his affiliation in the manuscript?

Nature answer:

Thank you for your email. At this stage, please just include the author and mention this in your cover letter so that the editor is aware of the situation.

The question I sent to PLOS ONE:

According to your submission guidelines "Each author on the list 

must have an affiliation". However an author has made substantial     
contribution while not been related to any institutional or
professional affiliation.

Is it okay to include "Independent Researcher" as an afilliation
in this case?

If not, what is the recommended Affiliation for this Author?

PLOS ONE answer:

Thank you for getting in touch and for your interest in submitting your work to PLOS ONE.

Your suggestion of recording the author as an "Independent Researcher" for their affiliation is acceptable. May I ask you to clarify in the cover letter if this co-author is self employed (i.e. charges for their advise/service) when submitting your work.

If you have any further questions, please do not hesitate to contact us again.

Any thoughts and previous experience with something like this is greatly appreciated.

Thank you!