peer review - How can I Get a Job Reviewing Math or Comp Sci Articles and Books in Advance of Publication?

I spend a great deal more time than other graduate school students identifying and figuring out how to fix mistakes in published papers and specialized books. Time and time again an author's careless error has sent me down a rabbit hole. In fact, finding the mistake and fixing it is often more interesting to me than the research itself. It dawned on me that I might be able to make a career out of editing working papers and books in advance of publication. However, I am not quite sure how to find such a job.

I am not seeking to publish my own research; I prefer revise and improve others' work. It seems like a useful thing to do: Author's mistakes becomes my personal headache, so that a dozen or more readers down the line do not have to independently run into the same issues (after publication). It is better to fix this sort of problem at compile time rather than run-time.

However, Most peer-reviews are unpaid and done by collegiate professors. I am not seeking a professorship; I don't even have a Ph.D. The highest degree under my belt is a baccalaureate (It is in mathematics at the very least).

When I took the GRE, I was in the 98th percentile for verbal reasoning. This and other indicators seem to show that I might be a good copy editor. However, I really would like to review papers in mathematics and/or computer science. Although editing at The New York Times, or at Tor Books™ might be someone else's dream job, I very much love math. I would like to focus at least as much time on the rigor and correctness of the mathematics done, as time spent on English grammar.

I am very good with logic (the formal kind), comfortable writing proofs, and unperturbed by mathematical symbols equations which make the general populace groan. I am better with graph theory and theory of computation than writing code; my math skills are strong. I have no previous job experience as an editor (other than a pitiful stint at my high school newspaper) and I am not sure where to start looking. I spend a great deal more time than my peers (in graduate school) identifying and figuring out how to fix mistakes in published papers and specialized books. Time and time again an author's careless error has sent me down a rabbit hole. In fact, finding the mistake and fixing it is often more interesting to me, than the research itself. It dawned on me that I might be able to make a career out of editing working papers and books in advance of publication. However, I am not quite sure how to find such a job. A penny for your thoughts?

citations - Using leaked proprietary information in scientific paper

I am working on a project in the area of IT security where we are analyzing a proprietary embedded system. While researching the system, we came across a confidential data sheet that was made publically available by a third party without the consent of the manufacturer of the system. The datasheet is marked confidential and usually only given out after an NDA is signed. It describes an outdated version of the system we are analyzing, but is partially relevant, as some parts of the system have not changed since then.

Is it ethical / acceptable to use and reference this resource in a paper?

"Related Work": this and this question ask about citing documents that aren't widely available (while my document can be found by anyone using Google, and none of the involved researchers have signed any NDAs).

Edit: To add some additional information that I added spread over a few comments:

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  The datasheet in question describes the security protocols used by an older version of a popular embedded security chip, current versions of which are being used in payment and access control systems

  
  


• 
  

  The manufacturer is aware that the data sheet has been leaked and is not happy about it, but has not gotten the datasheet removed from the third-party servers where it is located for the past two years. The reasons for this are unclear

  
  


• 
  

  The data is confidential (as in private-sector NDA-confidential), but not classified in a government sense.

  
  


• 
  
  

  The company has already stated that they would prefer if we did not publish based on this document, but that they would not be taking any legal action if we did, as long as all information was factually correct.

  
  

Answer

Sounds like you have found an interesting source and are considering the moral implications of using it. What I will say is based purely on personal opinion and probably what I would do unless instructed otherwise.

Leaks are a fact of life. With the proliferation of digital material they are commonplace. Look at Wikileaks, the Snowden revelations etc. Once material has become public there is - fortunately or unfortunately - no going back, regardless of how that information became public. It is the responsibility of the owner/creator of the material to ensure it says secure.

Dissemination of such material could be highly fruitful - but think of it this way - will your publishing research based on the material be ultimately constructive or destructive? Will it benefit just you or the wider world? Who is it really advantageous for? If the answer is just you, I would probably withhold your research based on it. If it has wider ramifications of great import, go with it. Also consider the reasons why it is confidential. Who does it serve - who does it protect? Was the confidentially because of financial reasons, incomplete research, company policy, or 'national security'?

There is a heavy moral tinge to this question, and you may have to do some soul-searching. But ultimately, if it serves the wider discipline in a positive way, and such servitude grossly outweighs the few individuals who it would ire, I would use it, as long as there are no legal implications for yourself [unlikely since a third party leaked it, but you can never be too careful].

peer review - How many papers should I be reviewing as a referee?

Like many academics with an active research program, I am asked to review many papers. Borrowing an idea from peer-to-peer file sharing companies, I try to keep a rough sense of my recent "ratio" of reviews I have done on other's papers over reviews my papers have received. I try to make sure I have a ratio that is consistently above 1:1. Since many of my papers (and presumably the papers I review) are co-authored, this seems very generous to me.

How many reviews should I be doing? How many is normal? Is a ratio an effective way to keep track of one's reviews? Is a minimum 1:1 ratio appropriate and defensible?

evolution - Hamilton's derivation of direct fitness from his 1970 paper

In his 1970 paper "Selfish and Spiteful Behaviour in an Evolutionary Model", Hamilton uses Price's equation to derive his well-known rule $rb -c >0$. My question is about one of the steps in his derivation.

Hamilton considers a population of $n$ individuals. Let $s_{ij}$ be the effect of individual $i$ on the fitness of $j$. The fitness of an individual $j$ is defined as $w_j = 1 + \sum_i s_{ij}$, $w=1/n \sum_j w_j$ is the mean fitness in the population, and $q=1/n \sum_j q_j$ is the average frequency of a certain allele. Using Price's equation, we get

$w \Delta q = Cov (q_j, \sum_i s_{ij})$.

So far so good. But Hamilton then says that this equation can be rewritten as

$w\Delta q = \sum_i 1/n \sum_j (q_j - q)s_{ij}$

Based on the definition of covariance (i.e., $Cov (X,Y) = E((X-E(X))(Y-E(Y)))$, this seems to only be the case if $E(\sum_i s_{ij}) = 1/n \sum_j \sum_i s_{ij} = 0$. But this would imply that the average fitness wouldn't change over time, which sounds odd for me. In sum, I don't understand this step in Hamilton's paper. What am I missing?

Answer

Actually the derivation is pretty straightforward. It's easier to use the fact that $Cov(X,Y) = E(XY) - E(X)E(Y)$ to derive this result. Suppose $x_{j} = \sum_{i} s_{ij}$.

\begin{align*} Cov (x_j, q_{j}) &= E (x_{j}q_{j}) - E (x_{j}) E (q_{j}) \\ &= \frac{1}{n}\sum x_{j} q_{j} - \frac{1}{n}\sum x_{j} q \\ &= \frac{1}{n} \sum x_{j} (q_{j} - q) \end{align*}

Choosing a book to gain general knowledge about biology

I will be first year undergraduate at Physics department next year and last year I was at the Medicine faculty. I want do double major in the second year of faculty with Molecular Biology and Genetics. The intersection of biology and physics is my interest. I have two books about biology, first one is What is Life?-Mind and Matter by Erwin Schrödinger and the second one is This is Biology by Ernst Mayr. Which one should I read to acquire general knowledge about Biology?

Answer

The books you have

The books you cited won't help you to get a solid and general basic knowledge in biology. I haven't read those books but I think that This is Biology is a book of philosophy of biology written by a biologist and philosopher. What is life is a very influential book written by a physicist who more or less predicted the structure of DNA that was later discovered by Watson and Crick. You won't learn much of biology through these books.

Book Suggestions

This post offers book suggestions for general introductory biology. Here is another post that may also interest you

If you are interested in a specific field of biology, then you may want to ask for book suggestions for this particular field. I think that most biologists that come from a background in physics are in the fields of theoretical evolutionary biology, bioinformatics and biophysics (incl. molecular biophysics).

Here are a bunch of other posts asking for book recommendations that I imagine you may like reading about.

And eventually you may want to read Value of mathematical models in biology although the post has been closed.

Of course, you might want to read a bunch of wikipedia pages such as Biophysics, Molecular Biophysics, Mathematical and Theoretical Biology, Biostatistics, Computational Biology, Bioinformatics.

publications - Updating a preprint when it is under review

I know that preprints deposited into a preprint server should be in a polished state. However, what should happen once it starts the review process? Should those copy-edits be updated on the preprint? What about updates when replying to reviewer's comments? What if the manuscript is rejected and I am rewriting the manuscript to be resubmitted to another journal in another format?

Answer

In principle, anything that happens to the content of a paper before printing (ie, formal publication) should be reflected in the pre-print. So yes, if you correct a bug while the paper is in review, or revise the paper for a new submission, then you should update the preprint.

However, some journals object to authors' posting post-copy-edited (or even post-refereed) revisions. And posting a revision while a paper is under review could interfere with the reviewing process. When in doubt, ask your editor.

Frequent updates may earn you a reputation for being sloppy, especially on a system like the ArXiv that publishes the preprint's revision history. (Why didn't you fix those bugs before you uploaded the first time?) But that's still better than leaving a buggy preprint out in the wild, thereby earning you a reputation for not even knowing (or caring) that you're sloppy. The right answer, of course, is to debug your papers before you post them!

human biology - What is the armpit hair for?

Modern human beings, especially women, cut their armpit hair. It seems to me the armpit hair is trivial/useless. Shortly speaking, what is the armpit hair for?

Answer

I have been trying to read up a bit on this. I started out looking on wikipedia and it seems there are three hypotheses which are not necessarily mutually exclusive.

1.Aid the wicking of sweat away from the skin

2.Reduce friction between the thorax and upper arm

3.Facilitate the release of sex pheromones

The first would seem possible because it would help to prevent over-heating of the lymph nodes under the armpits and that also fits with the fact there are a lot of sweat glands there.

The second, I can't find any citations which support this but I understand that people who shave their armpits tend to suffer from dry underarms. This could be a result of increased friction.

The third is apparently controversial although it seems perfectly reasonable and highly likely to me. There is a famous experiment by Claus Wedekind who got men to wear a t-shirt for a few days. He then got women to choose a most preferred male purely by the scent of the t-shirt and found interesting results relating to the MHC profiles. The armpit hair could help to trap the odour produced by the sweat and help with mate attraction, like some kind of scent sponge. I don't understand why this is so controversial, loads of animals influence mate choice with scent - perhaps people don't like to think we are genetically attracted to each other by sweat because it seems animalistic and less romantic.

In summary, there is no sure answer and it could well be all of the above, or something entirely different.

rna - What's the longest transcript known?

What's the longest functional transcript known? I'm wondering about RNA length post splicing, so not including introns.

molecular biology - Are eukaroytic promoters located in the 5' UTR region?

I was wondering if promoter sequences are located on 5'UTR region in eukaryotic organisms?

peer review - Is it normal for the manuscript submission date to change from the original submission date to the revisions submission date?

I submitted a paper to an ISI journal almost a year ago. The submission date of the manuscript was May 20, 2015. I received a referee report on January 15, 2016. The report was quite positive but asked for some major revision. I made all the required changes and submitted a revised version of the manuscript on March 10, 2016.

Ten days afterwards I received from the Editor a message that the manuscript would go into the refereeing process and Date received: March 10, 2016. Is it normal to change the initial submission date of the manuscript?

ethics - Independent Research and institutional review boards?

If I am conducting independent research (ie no university affiliation), do I need to worry about institutional review board (IRB) approval, if I am working in a field where it is normally required?

publications - Why publish in a journal instead of in arXiv or in my blog?

I don´t know what is exactly the value of publishing a high impact paper in a journal or magazine (electronic or not, open-access or not). I have several doubts about the benefits of publishing on a journal. Sorry for asking so many questions in the same post but separately it would result redundant.

Is it a question of money, pride, prestige?

Is not it better for humanity to be published in an open place accessible to all, in a simple language without such academic rigor?

If the reason is money, how much can I earn with a high impact paper?

If my publication shows new methods and algorithms that solve overwhelming problems that involve big costs for the pharmaceutical and aeronautical industry, can I claim copyright if they implement my methods and algorithms? Publishing in a journal is better in that case?

How could I prevent it from being used for destructive purposes?

Answer

I can answer a couple of your questions and may revise as I learn more.

If you publish something then in many places you have copyright already. Registration of the work may be required in some places and once was in the US, but no longer. Here, at least, if you publish something the copyright is yours and while your words can't be used without a license, your ideas can.

The way to protect "inventions" is through patent. This will almost always require registration (and cost), but is the only way to keep others from exploiting your ideas (as distinct from your words). But if I describe an idea that leads to a "process" or invention, but don't patent it, then others can exploit it freely. They might even try to patent it themselves, but you can (more money) probably prevent that.

One of the big problems for a researcher is gaining a reputation. This implies the need for your work to be seen by as many people as possible. Self publishing and writing a journal has the problem that it is difficult for people to find your work. Publishers, with all their problems, provide a partial cure for that, as do conference presentations.

Finally, for now, you are unlikely, in the absence of a patent and an implementation of the patent, to make very much money from publishing. The exceptions are textbooks for elementary economics or calculus courses, but only a few others. If you want to make money from publishing, write popular novels. (But "popular" is the hard part.)

One possible exception to the above, is that you can self publish successfully provided that nearly all of the people who would be your audience already know how to find you. If you have an already popular blog, for example, read by nearly everyone who cares, then you might be fine. But building audience is a hard task.

Disclaimer: I'm not a lawyer and the law varies widely around the world.

brain - Is mammalian vision processed as a sequence of frames?

I often read that people believe that human vision has an inherent frames-per-second rate (FPS) that causes stroboscopic effects - such as seeing the spokes of a rotating wheel apparently rotating at a different speed or appearing stationary when moving.

For example: in a Physics.SE answer to Can a “superhuman” move so fast that an average person cannot see them?

The human eye-brain visual refresh rate has an "effective frame rate" of around 30fps.

Have you never watched the rims of the wheel in a car next to yours? I can clearly recall many times watching as the wheels sped up how it appears to stand still then move backwards.

This surprises me as I would expect there is no synchronisation of neuron firing in the retina, that neuron firing rates would vary widely depending on light levels and that the brain has no need to process the continuous signals in fixed cycles or in cycles whose length is invariant.

I believe this question, or a good answer to it, would differ from What is the equivalent of shutter-speed in Human eye?

Is human vision in any way subject to a fixed frame rate of 30 FPS?

Answer

Short answer: no, there is no fixed frame rate or frame-based processing in mammalian vision.

Photons arriving at the photoreceptors at the back of the human retina interact with photo-sensitive pigments called opsins, and modulate their release of the neurotransmitter glutamate . The level of glutamate released from a photoreceptor then changes the membrane potential of the other neurons in the retina connected to the photoreceptor (bipolar cells, for instance). Signals are processed within the retina, then passed through retinal ganglion cells (RGCs), along the optic nerve, through sub-cortical structures and in to visual cortex.

This process occurs continuously, but all of the elements along the way have intrinsic time constants and other temporal constraints (number of photons required for opsin activation; recovery rate of the opsins in the photoreceptors; membrane time constants and refractory periods of neurons; synaptic delays; etc.). Persistence of vision (the effect underlying the perception of a movie as a continuous stream rather than a series of distinct frames) probably relies on the conjunction of many of these time constants.

Concretely, a flashed visual stimulus produces a response in (primate) visual cortex after around 30–50 ms (Maunsell and Gibson 1992). You can recognise and subsequently recall a lot of detail from a sequence of images flashed at around 100–150 ms per image [citation needed]. These are still not hard and fast definitions of the "speed" of vision.

Since we only learnt to produce movies as sequences of distinct frames, it's tempting to guesstimate the speed of human vision in those terms. Biology, as always, is more complicated.

As far as the "spinning rims" issue goes, there are many aspects of cortical and subcortical activity that tend towards oscillatory activity. In a system with an intrinsic frequency (for example, the neurons in the thalamocortical loop between LGN and primary visual cortex), providing an oscillatory stimulus can synchronise the system to the stimulus.

Many of the intrinsic time-constants I described above could result in a tendency to oscillate at some intrinsic frequency, and then be subject to phase locking due to a periodic stimulus close to that frequency.

email - As a graduate student, is it better to use a Gmail address or name@mywebsite.com?

As a grad student (Note: I am in the humanities, so nobody is really technically inclined), I have an address from my institution (.edu) but I rarely use it. I suppose I do "use" it, but it forwards to my gmail and usually I reply with my gmail address. Almost all of the other grad students, as well as many professors, in my program -- and elsewhere in my field -- do something similar; they don't use their edu addresses, but instead exclusively use gmail. I have been increasingly wary of Google's oversight and have been thinking about switching. But: Considering Gmail's monoculture among academics, is it more "professional" to use a Gmail account, or one that you personally own such as myname@myname.com? Or just weird?

To be clear: This is not about which email address to attach to a publication. That would clearly be my edu address, as it forwards to gmail. This is about what it 'says' about me.

neuroscience - How does a change in the potential across a neuron's membrane get turned into a signal that is sent down the axon?

I understand

1. 
   

   How a signal is propagated down the axon.

   
   
   


2. 
   

   How the membrane potential of a neuron changes during the course of it's "firing".

   
   

But I don't understand how physically the change in the membrane potential actual starts the signal down the axon.

A stimulus causes the voltage gated sodium channels to open and sodium ions rush in. This creates a positive charge density inside the cell and negative charge density outside. This difference is by definition a potential difference. Potassium gates sensitive to this difference then open, the potassium ions to rush out, which again flips the polarity of the inside and outside such that positive charge density outside the cell and negative charge density inside.

But how does that actually lead to the signal that is propagated down the axon? Can someone explain?

Answer

As you pointed out sodium as sodium enters the cell depolarizes (becomes more positive). Recall the sodium gates open the more positive the voltage is, which in turn opens more sodium gates. If a patch of neural membrane is depolarized, the charge diffuses into the nearby patches of neural membrane. This will open the sodium channels of the nearby membrane patch. Now once enough sodium channels open, the neuron will fire a action potential, at this point potassium channels open and potassium rushes out of the cell repolarizing it(making it more negative). Furthermore the sodium gates close at positive voltages which further repolarizes the neuron and prevents back propagation.

So the key is the influx of the sodium ions diffusing down the axon and causing a downstream depolarization of the axon.

I find this website instructive, as well as this picture:

Update: As the voltage builds up in the soma the charge spills over into the Axon Hillock (an area of high concentration of sodium and potassium gates) If enough sodium ions diffuse into the axon hillock and passes a (somewhat ill defined) voltage threshold then the sodium gates will open and start the action potential. Then the action potential proceeds down the axon as described above

A useful metaphor is the soma, and by extension the Axon Hillock, sums up the synaptic input from the dendrites, and again, if its over the threshold then the sodium gates open, if not, they slowly return to rest.

The synaptic input can be excitatory (cause depolarization) or inhibitory(hyper polarization) depending on the type of receptors and channels in the dendrites, but in general these voltage changes in the dendrite diffuse down into the soma and are eventually reach the axon hillock.

plagiarism - How to deal with a student found seeking an answer to a coursework question online?

I have just found that a student has posted one of their assignment questions on a forum and is seeking help in getting a solution.

I have a good idea who the student is, but no definitive proof. How would you handle this situation?

Answer

Identify the offline equivalent of the observed behavior, and then act as you would normally. Remember, that the burden of proof for academic dishonesty likely resides with you. This includes verifying that the poster is indeed the student you accuse.

I find this situation to be pretty common: https://chemistry.stackexchange.com/questions/2753/how-to-derive-partial-gas-equation. Most stackexchanges have a homework policy. I would consider homework questions posted to stackexchanges to be no worse than asking students who have taken the course before you or asking another professor. How you deal with it is up to you.

What would your response be if you saw a student collaborating on the problem in a study group? How do you respond if you find out that your student asked another instructor or a grad student in your department for help? If you learn the student worked on that problem with his/her tutor? If the student looked up the answer in the textbook or the solutions manual? All of these are common and to varying degrees accepted (if not liked).

I would guess your irritation over this is somewhere more than the student asking one of your colleagues (who being nice will actually do the problem) and somewhat less than the student stealing another student's answer. Identify the offline equivalent, and then behave as you would normally.

EDIT - I missed the last part of the question.

I have a good idea who the student is, but no definitive proof. How would you handle this situation?

If you do not have proof, then suck it up and let it go - this time. Next time put something in your syllabus. Either write a pretty severe sounding policy that exists to deter the behavior (because your policy will be basically unenforceable), or write harder questions and encourage them to use online forums with the caveat that they document all of their interaction. The second option shifts the burden of good behavior to your students.

Is an undergraduate physics degree the same everywhere in terms of coursework?

Is a degree in physics the same everywhere in terms of what is being taught or are there differences from one institution to the other ?

Answer

There are not only differences between institutions, but also within institutions. For example, at MIT "The Physics Department offers two different programs leading to a Bachelor of Science in Physics, giving students the opportunity to tailor their study of physics to their individual career goals. The focused option is an ideal preparation for those students who plan to go on to graduate school in physics or a related field, while the flexible option provides a strong background in physics for those whose career paths may not include graduate work in the discipline." while at UPenn there are 6 tracks.

citations - How can I assess the quality of a paper outside my field?

As per the title, I would like to determine whether a paper cited by a student comes from a reputable source or not, given that the paper's content lies outside my field. My first thought was to check the journal's website, as well as doing a Google Scholar search to see whether papers in other reputable journals cite papers from this one.

The particular case I am concerned with is a Psychology paper, appearing in AllPsych Journal [sic]. All the journal's webpage says is that:

The educational articles and papers published in AllPsych Journal are written by mental health professionals, psychology students, psychology instructors, and other authors outside the field of psychology. * They represent problems, solutions, and suggestions about everyday life and its relation to psychology. For submission consideration, please contact us via our feedback form.

This seems dubious to me, but nonetheless, a Google Scholar search suggests that some reputable looking publications have cited works appearing in this journal.

I suppose I have two questions then:

1. Are there any other techniques I can use to assess the quality of journals outside my field for this purpose. Ideally these should take relatively little time.


2. Is this specific journal considered reputable in psychology?

Answer

This question concerns assessing the quality of papers outside one's field.

The question seems to be more leaning towards the quality of journals outside of one's field. Here's a brief list of pointers (some of which also appear in this question):

The last point is particularly important. Though it is easy to discover if a journal is excellent or terrible, in between those extremes, there's a lot of grey. For example, new journals may be much-needed and drawing quality work from quality people, but they won't have a high h-index or an impact factor, etc.

For those grey areas, talking to an expert who knows the field is important.

AllPsych Journal

This doesn't seem to be a formal journal, but rather an informal way for authors to publish educational articles online. All papers are published on the web-site, there's no mention of an editorial board, a publisher, a means of submission, etc.

Of course, this says nothing of the quality/utility of the papers published there: just that it would probably not count in academic circles as a "traditional journal".

For the quality of a paper itself independent of the venue, check how many citations it has in Scholar versus it's age, check the nature of those citations, check the h-index and background of the authors, etc. (Of course these methods are only an approximation for reading it and making up your own mind as to its quality, but since it is outside your area ...)

teaching assistant - How to toughen up against hostile students as a TA?

I did not have a good experience when I TA'ed the first time. I faced a hostile student who refused to accept that he was wrong and didn't give me a good reason why he should deserve more marks. He showed a propensity for violence, shouted at me loudly, punched the table and gave me an extremely evil look. I was very afraid and shocked then.

I know I should have stopped the meeting and called the security. But I was at a loss then. I don't like that I was so easily frightened by a bad student. Though I haven't met such a student later, one never knows when the next time will be. Can anyone advise how to become tougher when facing such "evil" badly behaving students?

graphics - Should Figures and Tables follow a certain order or be at a specific location in a document?

This is a topic I constantly think about when writing a document.

Often after I complete a document in LaTex I would go through the document to make sure that the figures are where I want them to be (I want you here, not there!) and this is a very frustrating procedure.

My question is: How important are figure locations in a document, e.g. if the figure you refer to is not on the page where you are referring to it, perhaps even two pages after.

I have noticed that textbook publishers rarely give any thought to it and I cannot decide whether it bothers me or not. It would certainly make my life easier if I don't have to worry about floats jumping around in a LaTex document.

Any thoughts?

Answer

There are many policies that publishers imply considering figures. The most common ones are:

1. All figures or tables (so-called floats) have to be numbered and get a caption.


2. All floats have to be placed at the top of the page, or at a page solely made of figures and tables.


3. All floats have to be referred in the text by their number.


4. Every float has to appear no sooner than on the page where it is first mentioned (i.e. if it's first mentioned on page 5, it shouldn't be placed on page 4, but it can be placed on page 6).


5. Numbering should be consecutive (i.e., no 1 then 3 then 2).


6. The first reference to the floats should be consecutive (with the exception where you basically only "confer it" (with "cf." or alike).

Some journals want you to provide figures and tables separately, some don't care, some have typesetters that do it themselves, some don't force captions, some allow in-text placement, etc. Just check what you have to do. If nothing is said, I recommend complying with the rules above.

metabolism - When you lose weight, how does the mass exit your body?

As a thought experiment, consider the case of Angus Barbiery, who allegedly lost almost 200kg in about a year by not eating at all, save for necessary nutrients provided as supplements.

My question is, where did those 200 kilograms go.

And please, don't suggest that it was "converted to energy". 200 kilograms of mass would be approximately equivalent to 1.8*10¹⁶ joules. For comparison, Czech nuclear power-plant Temelín generates approximately 4.3*10¹⁶ joules of energy.

So how does the mass exit the body after the glucose is metabolized?

Answer

as CO2 and water

in respiration sugar (or fat) is combined with oxygen to produce energy(ATP and heat), water, and CO2.

fats are converted to Acetyl Co-A just like glucose is, the rest of the metabolic pathway is exactly the same.

What are mathematics graduate schools looking for?

I'm just curious. I have a strong GPA, but I heard that's not enough. I was told that among a GRE score, schools actually place stronger emphasis on performance in 4 classes: a proofs/logic course, analysis, discrete math, and a linear algebra course (this was apparently has less emphasis than the first 3). I was told that these classes are the bread and butter of most graduate math classes and are indicative of how well you can learn the more rigorous content. Is this true?

I have some research experience under the NSF in mathematical epidemiology with a few poster presentations and abstracts at conferences.

Do these schools care about extracurricular such as volunteering experience? I know these aren't going to get you into Harvard per se, but do they slightly augment your profile? I know academia is primarily concerned with research so this may not be too relevan.

graduate school - Are three year degrees from India equivalent to Four years degree in the US?

Is a three years bachelors degree in Commerce and three years bachelors degree in Law from India termed to be equivalent to have a four years graduate degree from the US?

neuroscience - Why do larger diameter myelinated axons have greater conduction velocities than small diameter myelinated axons?

A canonical statement I have frequently read is that "large diameter axons conduct action potentials at faster velocities than small diameter axons". After recently learning the effect of increased capacitance on the cell membrane (namely, that more charge is required for depolarization to occur...Are large cell bodies of neurons harder to depolarize than small cell bodies of neurons?), I find this canon to be rather confusing.

I have attached a picture to make my question clearer:

In the above picture, both neurons have the same myelin spacing. So, my question is why should the action potential in Axon B traverse the distance X1 to X2 more quickly than in Axon A. Shouldn't the increased capacitance of Axon B (due to its increased diameter) increase the time it takes for the action potential to travel between the two points?

hearing - How can we tell which direction sound is coming from?

Pretty self descriptive, without being able to view the source of the noise how can we tell the difference between a sound in front of us and a sound behind us if pitch, volume and distance are all the same.

Also assume that it is not biased to one side more than the other, e.g its not to your left or right but directly in front or behind.

I'm interested in knowing if it is a part of the ear that makes this distinction, or a function of the brain.

job search - What should I state for "expected salary" in a tenure-track job application?

I am applying to a tenure-track assistant professor job in an applied math department, for which the job posting states

Applicants should state their current and expected salary in the application.

Questions:

• Why does the department ask for "expected salary"? Is it because they are trying to exploit my naiveté?


• What number should I state in my application? If I state a number that is on the low side, will they use that to offer me a lower salary?

At the moment, I am thinking of just stating my estimate of the mean salary for new assistant professors at math departments, which according to a Tenured/Tenure-Track Faculty Salaries Survey is $71,412.

Answer

I feel it's kind of obnoxious to ask for an expected salary, and it does raise issues of whether the answer could be used to lower the initial offer (or decrease the applicant's negotiating power). I don't see anything wrong with giving a vague answer or just saying you are flexible. If you specify a number, you should try to choose one that's representative of the type of school you are applying to, as Danny W. suggests.

As for why they do it, one reason is that salaries vary enormously. A regional liberal arts college may pay less than half as much as a leading research university. Some U.S. states scandalously underfund their state universities, so there can be dramatic salary differences between what you'd think are comparable institutions. The net effect is that schools that aren't able to pay a lot worry about attracting candidates who have no idea how little they pay. They don't want to waste time trying to hire someone who will never accept any amount they could plausibly offer. One way to get around that is to announce a salary range. However, some departments are hesitant to do that, perhaps because they don't want to publicly emphasize how little money they get (and thereby humiliate themselves or discourage applicants). Instead, they ask for an expected salary and filter out anyone who names a figure far out of their range. I don't like it, but it seems to work well enough that departments keep doing it.

How can I create a DOI for a paper that was uploaded to arXiv but not published somewhere else?

I wonder whether there is any way to create a DOI for a paper that was uploaded to arXiv but not published somewhere else, and have the DOI points to the arXiv URL (e.g., not pointing to some researchgate page). While there are reasons that arXiv does not provide DOIs (Why does arxiv.org not assign DOIs?), I prefer to use the same identifiers for all my research papers.

Answer

Ultimately, no, you can't. There's no infrastructure to say "I want to get a single DOI for XYZ arbitrary url".

DOIs for most scholarly publications are issued through CrossRef. CrossRef do not assign DOIs directly, but delegate this to members or their agents. Members, who are usually publishers, pay a fee to the central consortium, and agree to issue DOIs based on a fixed set of rules.

As you can see from these rules, the general sense of membership is "organisations issuing DOIs for stuff they control". While there isn't an explicit prohibition against assigning DOIs to third-party material (which surprised me!), point 4 comes pretty close:

4. Members have an obligation to maintain the metadata and URLs associated with all registered DOIs.

There is also a general prohibition of 'duplicative' works including preprints:

12. Crossref only registers DOIs for Definitive Works (or Versions of Record, if not formally published) but not for Duplicative Works, as defined in the Crossref Glossary. This means that only original scholarly material, for which there is no actual DOI at the time of submission, and no expected duplication in future, is admissible for Crossref DOI registration. Crossref does not permit multiple DOIs to be assigned to certain closely related versions of a work, and hence does not support assignment of DOIs to Pre-prints or Post-prints of Definitive Works or to the Personal Version or a Self-archived Copy of a Definitive Work. For the same reasons, materials for which DOI duplication can be reasonably anticipated, such as an Authors Original Draft of a work being prepared for publication, are not admissible for Crossref DOI registration.

Putting those together, it seems likely that CrossRef's terms would prevent a member agreeing to issue a DOI for a (potentially duplicative) work hosted somewhere out of their control.

So, could you get a DOI from someone else, outside of CrossRef? Probably not. DOIs are only issued through a number of central registration authorities (eg CrossRef, DataCite). These have fairly well-defined areas of activity (eg DataCite won't issue DOIs for publications) and, to the best of my knowledge, none offer a "DOI for an arbitrary URL" service.

united states - Can a professor ask for money directly from students to print out handouts for class?

I'm currently taking a class that doesn't have a required textbook, which is why I took it. My professor is now saying that due to her scanning and printing out handouts for use we are each required to give her $15. I'm confused by this because isn't the money supposed to go through my university, as a fee for the class, rather than through her? I just want to know if she's allowed to do this

citations - How do I correctly cite the C++ standard or its drafts?

For my bachelor thesis, I have to reference a lot to the various C++ standard documents, be it the original standard or some of the working drafts.

How do I cite such documents? Many of the working drafts don't even contain a title page to extract information from.

Working drafts are available at https://isocpp.org/std/the-standard

Answer

I would cite the current version of C++ standard, based on the APA Style (6th edition), in particular, based on the APA guidelines for citing electronic sources (Web publications), as follows:

ISO/IEC. (2014). ISO International Standard ISO/IEC 14882:2014(E) – Programming Language C++. [Working draft]. Geneva, Switzerland: International Organization for Standardization (ISO). Retrieved from https://isocpp.org/std/the-standard

NOTE: When the current standard will be finalized and published, the citation will have to be updated accordingly by removing "[Working draft.]" phrase and updating the year (i.e., 2015).

collaboration - How to effectively e-mail a professor I met briefly about collaborative work?

Recently in a conference, I met a professor from an esteemed university and head of a research group I have been following. I told him about my research and he gave me his email address (though I could easily find it over the web, he personally wrote it down for me). He told me to write to him and he will direct me to his post-doc and see how we can collaborate. His research group has some testing facilities I would love to work with.

The following is the email I am aiming to write to him. Any corrections and/or suggestions will be highly appreciated.

Dear Professor XYZ,

Hope you are doing fine. We met at ABC conference, in TTT a couple of days ago. I introduced myself as the PHD student at 123 University and expressed my willingness to work on a collaborative project with your research group (utilizing your practical testbed for DDD project).

First of all, I appreciate the time you spent with me, and the opportunity to introduce myself, my research, and my interest in utilizing your testing facilities. Second, I would like your advice on how I can further proceed to initiate a collaboration between your research facilities and our RRR research group.

I will wait for your reply.

Thanks again,

Kashan

Answer

I always suggest being a bit more succinct, and mentioning (but not delving into!) the technical aspects of your work. How about this:

Dear Professor XYZ,

This is [name]; we met at AAA conference in TTT a couple of days ago. As you may recall, I am working on [xxx] and you suggested that your post-doc could get me started in your testbed for my [yyy] project.

I'm very eager to pursue this. Could you please introduce me to your post-doc? I'd be happy to set up a call or provide any information you might need.

Thanks in advance; I really appreciate the opportunity,

Kashan

botany - Why does freshly cut grass smell like a watermelon?

I found that, when I smell watermelon aroma outdoors, someone nearby has mowed the grass. Is there an underlying basis?

Answer

cis-3-hexenal is probably the main reason. It is one of the main chemicals in fresh-cut grass smell (lots of references besides wiki if you google it). This fairly comprehensive paper on watermelon odorants also says that they find a lot of cis-3-hexenal in fresh cut watermelon. See tables 3.1, 3.2 and 3.3.

funding - How much damage would I be incurring if I turn down an informal postdoc offer?

So I have been in touch with a prof for a few months about being a postdoc in his group. He promised (verbally) one year of funding saying he was not sure if his grant proposal for my second year of funding would be successful. After being in touch with him over six months, he let me know that he the proposal has been successful and he now has funding for my second year. In the mean time, my opinion about being a postdoc and going the academic route have changed quite a bit due to family and other personal circumstances and I want to move into the industry [I have an offer in hand too]. My question is, how bad would it be, in terms of loss of face, if I said no to being a postdoc with the prof? I haven't signed a contract with him or anything and all communication between us has been informal. How do I even begin to explain things to him? I haven't even given a hint to him so far.

phd - Admission in research based Master's/Doctoral programme with a bachelor's from a low-ranked University in India

I applied in Master's programmes in Europe / Asia (mostly Germany) this year and most of them were rejected or are still pending. My GPA in the Bachelor's is 7.19 / 10 while my TOELF iBT score is 100 / 120. Most of the Universities stated on their websites that the GRE (General or Subject) is optional, so I did not take the GRE.

After getting so many rejections and still being unable to figure out why, I am now thinking of strengthening my application to apply again in fall 2014. I have mailed universities / professors inquiring about reasons for rejection / shortcomings of my application, but none have replied. The only reply I get is that there were a lot of applications and mine just failed to compete with them.

I wish to know more about why my applications failed and how to improve? Also, as I don't know anyone around, I prepared my Statement of Purpose, Letter of Recommendations, Research Proposal, etc by going through the internet and information on website of universities (I did not copy-paste, but used the tips on how to write and stuff). I have no idea if the reason for my failed applications were because of low GPA / no GRE score or ill-prepared statement / research plan. Also, where can I get these checked and get suggestions on improving them?

I am very passionate about Artificial Intelligence, Machine Learning and Ubiquitous Computing. I am planning on quitting my job at Oracle Financial Services (where I'm working as as Associate Consultant, writing code since SEP 2011 after my Bachelor's) to prepare for my application and dedicate full time and energy. I am aiming for admission in top 20 universities for Computer Science of the world and also aiming for a good scholarship. I want to appear for GRE later this year and get very good scores to try to compensate for my low GPA. But, when I checked few top universities (like MIT), it was mentioned they don't accept GRE scores. How can I try and get into such universities?

My goal is to complete my Master's, PhD and then continue researching on my areas of interest. Furthermore, the Subject GRE for Computer Science has been discontinued as per the ETS website!

Is there any hope of getting in top universities with a Bachelor's degree from an unknown university which is practically nowhere in the rankings? What to do now and how to do it, I am pretty confused and hope that someone here can help me.

Thanks for your time.

Rahul

Answer

Focusing on test scores will not get you into MIT.

You need research experience — real, world-class, publication-quality, independent research experience. A paper at a recognizable (from MIT) conference or workshop would be a big plus. The top students from the various IITs have such experience.

You need a statement that clearly and compellingly describes your research interests, experience, and vision, with enough specific technical detail to be credible. As an example: Describe a recent result (not just a paper title!) of your potential advisor, and suggest a credible strategy for applying or improving it. Also, your statement should frame your ambition in terms of "doing great research", not in terms of "getting into MIT". The top students from the various IITs write such statements.

You need recommendation letters from well-known (at MIT) academics that praise your research potential in personal, specific, and credible detail, with positive comparisons against other students from your home institution who have gone on to a top-10 PhD program. Your recommenders must write the letters themselves; you should never even see them. In particular, you should explicitly waive your right to see the letters later, if such a waiver is possible; most US schools offer such a waiver in their recommendation forms. The top students from the various IITs have letters like this.

You need contacts. Or more accurately, your recommenders need contacts. Coming from "an unknown university" with a "low GPA", there is a serious risk that nobody will even open your application. If one of your recommenders knows someone at MIT, either personally or professionally, ask them to send a quick email (or have a hallway conversation at a conference) saying "Hey, we have this great student Rahul Thakur who's applying to your department; you should take a look!" Sending such an email yourself is unlikely to help. CS professors get tons of emails from random students at unknown universities; we call it "spam". The top students from the various IITs have these contacts.

You need some strategy. All else being equal, it is harder to gain admission to top CS PhD programs to study AI than to study other areas. AI seems to be the default areas for really smart, talented, qualified students who really have no idea what they want to do. Machine learning is either a subset or a superset of AI, depending on your religion. (Theory suffers from the same effect, to a smaller extent.) In your case, you're probably better off emphasizing your interest in ubiquitous computing in your statement. But remember, you need specific and credible technical detail.

Finally, you need luck. Graduate admissions is an inherently random process; no one should apply to MIT expecting to be admitted. Coming from an unknown university, your chances of admission are smaller than someone with exactly the same application coming from a highly-ranked school. Aiming only for MIT is foolish; limiting yourself to top-20 departments may be foolish as well. Don't rob yourself of opportunities!

After all, your real goal is to do great research, not to get into a top-20 program. Right?

lecture teaching method - How to adopt flipped classroom strategies without student complaints?

I have been adopting flipped classroom strategies (in upper-level chemistry classes ~20-30 students), but I often get feedback from students that they want me to "just go back to regular lectures" and that they perceive the flipped classes as more work.

I think the results are positive for student learning in my classes, although I haven't done formal assessments. I also personally appreciate the change of pace and style. Previously students might have felt that I wasn't giving enough concrete examples and this definitely solves the issue, as well as making me more responsive to a particular class's needs.

I am wondering about strategies to overcome student apprehension about active learning styles.

Answer

Here are some ideas from Linda Kober, author of a publication by the National Research Council's Board on Science Education, Reaching Students: What Research Says About Effective Instruction in Undergraduate Science and Engineering. This comes from Chapter 6, "Overcoming Challenges", in the section "Helping Students Embrace New Ways of Learning and Teaching":

• Make clear from the first day why these teaching strategies are effective, and be explicit about how they benefit students, and what is expected of students.


• Show students evidence of how research-based strategies will help them learn and prepare for their future life.


• Use a variety of interesting learning activities.


• Encourage word-of-mouth among upper-level students who have already taken the course.


• Listen to students’ concerns and make changes to address legitimate ones.



• Make sure that grading and other policies are fair [e.g., group work].

For details you can get a free PDF download here (note blue button in top right).

graduate admissions - Waiting until MS thesis is Published before applying to PhD?

I was wondering if it would be a good Idea for me to wait until after my MS program is completed and my thesis is published before applying to a PhD program. There is no chance of me publishing my thesis before the December/January deadline of the fall 2013-14 admissions cycle as I am only 2 semesters into my program and the project I am doing doesn't necessarily move as fast as other projects.

Its important to note that I have NO publications at this point, but I do have two presentations at international conferences. Also, my ugrad Gpa was slightly higher than a 3.0... and my Masters GPA is a 3.7. I'm also in the Geosciences, if that matters

So with all that in mind, would it be a good Idea to wait until that publication comes in before applying to PhD ?

Answer

No.

Why rob yourself of potential opportunities? Your chances of admission might be less than if you had a publication, but they're certainly bigger than if you don't apply at all. If you aren't admitted anywhere, you can always apply again next year, after your thesis is done.

biochemistry - What does the human body use oxygen for besides the final electron acceptor in the electron transport chain?

My biology teachers never explained why animals need to breathe oxygen, just that we organisms die if we don't get oxygen for too long. Maybe one of them happened to mention that its used to make ATP. Now in my AP Biology class we finally learned the specifics of how oxygen is used in the electron transport chain due to its high electronegativity. But I assume this probably isn't the only reason we need oxygen.

What other purposes does the oxygen we take in through respiration serve? Does oxygen deprivation result in death just due to the halting of ATP production, or is there some other reason as well? What percentage of the oxygen we take in through respiration is expelled later through the breath as carbon dioxide?

Answer

Oxygen is actually highly toxic to cells and organisms – reactive oxygen species cause oxidative stress, essentially cell damage and contributing to cell ageing. A lot of anaerobic organisms have never learned to cope with this and die almost immediately when exposed to oxygen. One classical example of this is C. botulinum.

Oxygen is incorporated in several molecules in the cell (for instance riboses and certain amino acids) but as far as I know, all of this comes into the cell as metabolic products, not in the form of pure oxygen.

The oxygen ($\ce{O2}$) we breathe is completely used up during aerobic respiration. The stoichiometry of this is given by the following simplified equation:

$$\ce{C_6H12O6 + 6 O2 -> 6 CO2 + 6 H2O + heat}$$

WYSIWYG’s answer goes into more detail.

graduate admissions - PhD in pure mathematics for a student in computer science

I'm a student currently pursuing my masters in computer science. My present area of research is computational algrebraic geometry (theory of grobner bases and tropical geometry).

Afterwards, I'm interested in pursuing my PhD in pure mathematics.

I would like know if I'll be elligible for applying to pure math PhD programs? And if yes, do I have any realistic chance of getting into one?

What else can I do to improve my chances of being accepted?

genetics - How do parents give their offspring a chromosome?

Whenever an organism sexually reproduces, it gives its offspring one chromosome from each of its pairs of chromosomes. My questions are

• Is this done randomly?


• Is it uniformly random?


• If so, what mechanism allows it to be random, considering that the laws of physics are deterministic?

(Note: I'm a little rusty on this subject, so if there are any errors in the question, feel free to correct them.)

Answer

Are the laws of physics deterministic? I think no one knows, currently.

In any event, yes, the segregation of homologous chromosomes during meiosis I is random: there is an equal probability for each chromosome of a homologous pair to segregate into a given gamete, and this is independent of other homologous pairs. This idea dates back to Mendel, who observed that the heritable “factors” (what we now know as genes) responsible for macroscopic phenotypes are inherited independently of one another (this is his Law of Independent Assortment). This isn’t actually true when considering linked genes, but is certainly true of chromosomes, as was described by Sutton in 1903:

...many points were discovered which strongly indicate that the position of the bivalent chromosomes in the equatorial plate of the reducing division is purely a matter of chance - that is, that any chromosome pair may lie with maternal or paternal chromatid indifferently toward either pole irrespective of the positions of other pairs...

evolution - Effect on fitness of mutations

What is the distribution/probability density function (PDF) of impacts on fitness of new mutations?

---

I very welcome any partial answer that does not give the whole PDF but just some information about the expected value or the variance of this distribution. Information of the kind: "If we consider only beneficial mutations, then the PDF is $P(X=x) = f(x)$" are also welcome.

When I say mutations, one might have want to reduce the concept of mutations only to indels and point mutations.

Of course the answer will depend on the species under consideration and from population to population but I welcome any answer that could give some insights. Eventually, some information according to what is generally assumed to be the PDF of effects on fitness of new mutations might be useful.

Here is a related question

Here is an article that assumes an exponential distribution of effects on fitness of beneficial mutations.

Answer

To a good first approximation $\overline{\Delta f} = 0$. Where $\overline{\Delta f}$ is the mean change in fitness down to any point or indel mutation. The reasons for this are as follows:

1. In the genome of higher organisms, most of the genome is non-functional ("junk") so most mutations will not have any effect regardless of the change made.


2. A substantial proportion of in-frame point mutations will be synonymous mutations that result in the same amino acid being coded for (actually this can have an effect on protein expression but I don't believe anyone has - yet - shown a fitness difference?)


3. Even where a mutation does alter an amino acid many amino acid changes have no measurable effect on the protein produced. Especially where the new amino acid has similar properties to the one it has replaced.


4. Even when a mutation does alter the protein function, or render the product non-functional, in many cases this will not impact fitness since fitness is conditional on the environment in which it is measured and not all genes impact all environments.

So the distribution, whatever it is, will have a large spike at 0. Probably this spike is several orders of magnitude higher than the next highest value. Further, we can be reasonably certain that $\overline{\Delta f} < 0$ since there are more possible ways to break a Gene through a point or indel mutation than there are to improve it. If this is the case, so that there is a large excess of mutations with a negative effect on fitness, we can conclude that the distribution of mutational changes in fitness will be non-normal (negative skew and spike at zero), and that the normal distribution will be a poor approximation.

research process - How difficult Is a PhD Program?

I am a Master's student in math who is doing pretty well so far. I aced my first two classes (real analysis) and my summer session in probability theory is going well, too. Even before my Master's study, I already thought of a PhD. Nonetheless, there are concerns:

1. 
   

   My good grades were the result of grit, not brain, meaning that I had to spend time to understand what the book is telling me. Furthermore, a lot of times during exam and homework, I had to try and fail a few times before arriving at the solution.

   
   


2. 
   
   

   I did not study math during undergrad. Before my Master's study, I gulped down three semesters of calculus, plus LA and DE in one year. So compared to other students, I am already behind. In the next two months, I will learn complex numbers on my own and review my linear algebra.

   
   


3. 
   

   I am a professional in a field that has nothing to do with math or research. After the holiday, I will speak to my advisor about taking a thesis class. It's not an insurmountable obstacle, but, in an unrelated field, I do have less time to concentrate on math.

   
   

At the end, how big is the jump from Master's to Phd? Especially after what I said in (1), I do worry that it is beyond my ability. I do not hold anyone responsible for my decision. So, please kindly offer your best assessment of my situation.

nomenclature - On the definition of gDCW (gram dry cell weight)

I need some clarification on the concept of gram dry cell weight.

The unit acronym gDCW stands for gram dry cell weight. My interpretation is that 1 gDCW is equivalent to 1 gram of dry cells, but I am not sure. Is this accurate?

For example, the dry cell weight of mouse cells is roughly 300 pico grams. Therefore, in this case, one gram of dry mouse cells contains $10^{12}/300$ mouse cells (1 picogram $=10^{-12}$ grams). And if one says that there are 0.6 mmol of alanine per gDCW of mouse cells, this means that the total alanine content of $10^{12}/300$ mouse cells is 0.6 mmol. Is this accurate?

publications - On the use of grant funds for extracurricular research

While reading the PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH section of some completed NSF award abstracts, I expected to find papers only within the limited scope of the goals of the proposal. To my surprise, I have found some papers in completely unrelated topics credited to the research grant that funded it. It doesn't even seem like a serendipitous finding or semi-related tangent either, but rather a complete deviation from the grant's intended purpose.

I'm sure that there are other justifications for attributing research grants for publications as stated in this post, but it made me wonder...

How can one justify using grant money to fund research outside of your intended purpose of the grant? Is this a common practice? Are there any negative consequences to using your grant to fund extracurricular research activities? Under what circumstances is it valid to do so and when is it inappropriate to do so?

cardiology - To get Standard ECG from PhysioNet?

I am trying to get standard ECG by using PhysioNet's ATM with parameters

but I get

It should be something like

How can you get complete standard 12-lead ECG out of Physionet database?

Answer

PTB Diagnostic ECG database here. Review here.

united states - What to do with students coming to office hours asking to check their homework?

As a teaching assistant (TA), how to handle the situation where a student comes to office hours asking to check their homework? I.e. the student hands in their solution to the homework and ask the TA to check for any mistake. Assume homeworks are worth somewhere between 20% and 50% of the grade.

If country-specific, I am interested in the United States. If field specific, I am interested in computer science, linguistics, neuroscience and maths.

genetics - Do human cells contain only one copy of the genome?

Does each cell contain only a single copy of its genome? Or are there ever 'extra' copies present.

Reason behind question: Wondering whether gene mutations could be corrected by referencing a 'backup copy'.. If such a thing exists..

Answer

As a quick answer, yes, most human cells carry 2 copies of the genome and are known as diploid cells. One copy comes from each of your parents, so they aren't identical, but usually pretty close. Sperm and egg cells only carry one copy of the genome and are known as haploid. During fertilization the 2 cells merge their copies and make a diploid zygote. At the chromosomal level, humans have 23 chromosomes, so a diploid cell has 2 copies of each so a total of 46.

As far as repairing damaged DNA, using one chromosome to repair its damaged counterpart is known as Homologous Recombination.

conference - "Will be recommended for publication in IEEE Xplore." What does it mean?

"All accepted papers will be published in the conference proceedings and will be recommended for publication in IEEE Xplore." The quote was taken from a conference site. Does this mean that accepted paper will definitely be published in IEEE Xplore once accepted, or does that mean that there is a chance only?

Answer

If it is an established IEEE-sponsored conference, then I would expect that it means they will definitely be published in IEEE Xplore. Typically, the IEEE simply transforms the conference proceedings directly into an IEEE Xplore collection, and that is the official archival proceedings of the conference.

The only publications that typically do not make this transition are those which are not presented at the conference (e.g., the authors don't show up), which the IEEE does not generally allow to be published as part of the final proceedings.

graduate school - 1 or 2 Year Master's Program

I originally posted this on math.stackexchange but was recommended to post here.

I have been admitted to two Master's Programs in math (both with funding). One is 1 year long and the other is 2 years long. I plan on obtaining a PhD directly afterwards.

The 1 year option lets me save one year. But I would have to apply to PhD programs within the first semester and it seems I would not have time to get good recommendation letters or make a strong impression from my Master's Program. The 2 years option would give me more chance to demonstrate what I've done.

If they are comparable programs, which would be the better choice?

research process - Is it advisable to hand in a thesis by visiting my supervisor's house?

I have to hand in the thesis to my supervisor, but I could neither find him in the faculty nor contact him, but I know his house.

Is it advisable to hand in a thesis by visiting my supervisor's house?

Answer

I wouldn't find it okay if someone would come to my house because of that. Work and personal life should be separate and it would be inappropriate to visit the supervisor there.

Does he not have an office? If nobody can tell you where to find him, then you should call him or write an email and ask for an appointment.

human biology - What are tendons made of specifically

From what I read on wikipedia they are made of collagen. Collagen is just a protein. Right? How is this collagen structured (I imagine like fibers). Aren't there cells in this fibers as well?

From this picture:

Is the pink stuff the collagen? and the purple stuff the tenocytes?

If someone can expand on this with a picture preferably, it would be great.

Answer

As you correctly say, tendons are made up of collagen fibers. Collagen is one of the most important proteins (or, to be more specific, family of proteins, as there are many types of collagen) forming connective tissue in the body.

Collagen molecules have a particular structure that allows them to form long fibers, composed by three different strands that form a triple helix. This is a schema of a collagen helix (each ball represents one aminoacid):

(source: Wikipedia)

These helices can then be bound together to form a collagen fiber, through the action of an enzyme called lysyl oxidase which binds two lysine residues from two different helices together (lysine is one of the aminoacids that makes up collagen).

Here is a scanning electron microscope of a collagen fiber:

(source: Science photo library)

Collagen is secreted out of the cells that produce it so, although there may be cells around the collagen molecules, it is important to understand that it is part of what is called the extracellular matrix, the extracellular structure that supports the cells in our body.

As for the photo you linked, it is an hematoxylin and eosin (H&E) stain of a tendon. Hematoxylin colours cell nuclei in dark blue, so the dark spots are definitely cells. The pink "waves" are indeed collagen fibers, the cells are probably the tenocytes, the specialized fibroblasts of the tendon, which produce the collagen.

gender - How to deal with an advisor who wants a "friendlier" relationship with me than I do?

I work as an assistant at a university in Australia. I joined the team consisting of my current advisor and his two PhD students. The other group members are men and they have a co-worker-like relationship with him. At first it was good, my advisor was very helpful (I have worked there about ten months and I published two papers with him, both in journals with a high impact factor). But when we started to get to know each other better, it unfortunately changed. I am a young woman and am afraid that he wants me to become romantically involved with him.

I try to keep this relationship work-only, as it’s the most healthy way, in my opinion, but sometimes my advisor seems to think differently. Here are some of the things that have made me think my advisor wants a romantic relationship with me:

• He comes to my room very often with no research-related reason and wants to talk, talk, talk about everything but work.


• Once, when I was busy working, he came to my room and asked if he could take a photo of me. I felt ashamed and did know what to say and then finally, he took the photo.


• Sometimes I think he is mad at me that I want to keep this relationship work-only, and then does not answer my emails about our research.


• He is very careful with all this, says those things only when we're together. A while ago I heard that his PhD student suggested to him that he spends too much time with me. He laughed and said it's not his business, and that we are working hard on some novel research method.

My advisor has powerful connections here at the university and I'm afraid no one is able to do anything about it. I’m only interested in having a professional relationship with him. However, I’m afraid that if I don’t agree to be his “very close friend,” he will try to kick me out of the university.

I can not move to a different city because of some family issues and can not change my advisor since he is the only person at the university who works on the research I’m interested in. What can I do?

university - What academic discipline does "Productivity Science" come under?

I wish to categorise my large collection of electronic documents. I need a foolproof set of categories to put each document in. I want to use a classification system similar to how university schools are organized:

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

Some of my documents are productivity tips (similar to Dave Allen's "Getting Things Done" book). I can't find an academic category under which productivity comes. The term "productivity science" doesn't seem to be a widely accepted term.

What is the most natural category to put the study of "Productivity" in? Psychological Sciences (or other Social Sciences)? Applied Sciences/Professions? I'm tempted to put it in Psychology because I have other documents based on Learning, Memory and Performance. The four of those seem best suited to Psychological Sciences.

Answer

My guess would be Business -> Industrial and labor relations -> Organizational

teaching - How to explain a bad grade to a delusional student?

I guess this comes up quite often in educational context. There is a student who attended a seminar where they were supposed to study an assigned research paper and deliver a presentation to the class. The presentation delivered by the student was very low quality as was also reflected by the low grade given by a group/committee of seminar tutors (from post-doc to associate professor level). The evaluation turned out to be a big blow to the student's ego and even after several weeks, the person can't digest the failure, despite very careful explanation on the spot, as well as several interactions and (failed) attempts to "better the grade by performing some extra work". The student is all the time coming back with requests for additional explanation of particularities of the failure.

What is/are the right pedagogical technique(s) to handle such a situation?

• clearly, the student has a high self-esteem and opinion about him/herself


• probably did not face a situation of a miserable failure before in the past


• the student does not seem to see/accept the relative difference in his/her performance and the rest of the peer group


• the committee of tutors was very careful in assigning the grade and went through a thorough discussion. This is not a question of the grade fairness, but a question of student's self-perceived feeling of receiving an unfair treatment

Answer

My first question to you would be

Did you lay out the assignment expectations and how the grade would be determined when you gave the assignment?

If the answer is "yes" (and I expect that it is), I would use that as a starting point for explaining to the student why he/she did poorly.

That aside, it seems that either (1) the student didn't understand what was expected (regardless of the question above), and/or (2) the student isn't prepared for the type of work required, and/or (3) the student had a bad day.

It sounds to me like the answer is firmly #2, as repeated attempts to improve the grade hasn't worked. Given that you've already spent a good deal of time with the student, it might be time to have a heart-to-heart discussion and say that it is time to stop thinking about that grade and to move on. Obviously, you need to do this diplomatically, but (as they say), to make an omelet you need to break some eggs, and sometimes a firm and diplomatic "get over it" is appropriate. I would pose the following questions to the student:

1. Do you have a clear set of goals that you are working on for the class?


2. Do you know what other grades are going to be part of the final grade for the class, and do you have a plan for making sure you are ready for each assignment / talk?


3. Do you conduct practice talks with other students in order to get constructive feedback? (if not, you should!)


4. (If the problem is English language skills) Have you sought out on-campus help with your writing or speaking skills? (this is available at many larger universities in the States)

Depending on how much time you are willing to devote to helping the student improve, you could also offer to sit in on any future practice talks to give pointers and feedback. Likewise for written work -- you could offer to pre-read assignments. This is a slippery slope, so tread carefully. You want to avoid having the student see you as an always-available tutor, but there are times when providing such support is just part of the job.

Finally, I would stress to the student that one bad grade does not make or break a student, and it is better to make mistakes while in school than later when they might mean more in the bigger picture. School is about learning, and you learn from mistakes.

job - Is doing a PhD just for the university requirement is a good idea?

I have an MSc degree and I work at university as a lecturer. However, the university has a policy where you should do your PhD within a given time frame. The problem is that I'm not interested in any area yet, nor am I interested in doing the work associated with a PhD.

Should I just go with it because the university forces me to do it, or should I just quit from the university and look for another job?

What do you think? Can I succeed if I start doing my PhD while i feel that I'm forced to do it?

Answer

In my university back in Mexico, they had something similar, if professors want to get ahead (income, professional, etc) they had to an additional degree (Masters, PhD)

I think that if you do not have the motivation, you'll have a lot of problems, doing a PhD is already a taxing endeavor, in the sense that many times you'll start wondering wether this was a good idea or not.

As in many things in life, if you do this because you are made to (like students that go to college because their parents want to) you'll have lots of resentment.

However, not all is lost, you can try looking for something you are really passionate about, and then try to do a PhD on that.

What should you do if you don't hear anything back from editor after a whole year from first submission?

I have submitted a paper more than a year ago, but still I haven't heard anything back from the editor. As of today I have no idea whether my paper has been accepted/rejected or is in a review stage. Only thing I know is that it has been received, for a got a confirmation of this soon after the submission. Needless to say that I've tried several times to get in contact with the editor to find out about my paper's fate, but I got not a single reply to my status update requests. What should you do in a case like this? I was thinking of writing to the editor again to let him know that I'm withdrawing the paper from him and submitting to someone else? Is this a good idea? Are there other paths one might walk down to?

Answer

If the editor isn't responding, it's time to escalate. The journal's web page should give contact info for an editor-in-chief and/or a managing editor. Contact one or both of them and let them know that you would like an update on the status of your paper, but cannot get a response from the handling editor (include dates of submission, dates you sent emails, etc). They should take care of the situation.

molecular biology - How can E. coli proliferate so rapidly?

The E. coli has a genome with approximately 5×10⁶ bp. The main DNA polymerase involved in its chromosome duplication (DNA pol III , the one with highest processivity) can polymerize ~10³ nucleotides per second. By a simple calculation, we would conclude that the whole chromosome duplication would take ~ 5000 seconds ( about 80 minutes, so more than an hour). The whole cell duplication would probably take much more than that, considering not only DNA Pol III is involved. However, in optimal conditions, E. coli can actually duplicate in ~30 minutes. How could that be possible?

OBS.: all the numbers used here are aproximate, but sufficient to account for the correct orders of magnitude.

Answer

Though Escherichia coli has only one origin of replication (oriC), replication proceeds in both directions from it. Thus, based on your calculations, DNA replication takes 40 minutes (which is still too long if the doubling time is 30 minutes). The solution is to start replication again before the previous round has completed, and here's some research which shows just that:

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Yoshikawa H, O'Sulliven A, Sueoka N. 1964. Sequential replication of the Bacillus subtilis chromosome. Prod Nat Acad Sci 52:973-980

Obviously, dichotomous replication is advantageous for bacterial growth because the bacteria can replicate chromosomes faster than by having one replication point. With one replication point, the replication time, and consequently the cell generation time, would be limited by the maximal rate of DNA polymerase.

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Cooper S, Helmstetter CE. 1968. Chromosome replication and the division cycle of Escherichia coli B/r. J Mol Bio 31(3):519-540

…cells growing faster than 40 minutes per doubling must initiate new replication points prior to the completion of DNA synthesis at the previous points; in other words, there should be multiple forks.

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Skarstad K, Boye E, Steen HB. 1986. Timing of initiation of chromosome replication in individual Escherichia coli cells. EMBO J 5(7):1711-1717

In rapidly growing cultures, with parallel replication of several chromosomes, cells will end up with 2n (n = 1, 2, 3) chromosomes if initiation occurs simultaneously at all origins. A culture with asynchronous initiation may in addition contain cells with irregular numbers (not equal to 2n) of chromosomes. The frequency of cells with irregular numbers of chromosomes is a measure of the degree of asynchrony of initiation.

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Fossum S, Crooke E, Skarstad K. 2007. Organization of sister origins and replisomes during multifork DNA replication in Escherichia coli. EMBO J 26(21):4514-4522

…initiation occurs at two origins in the ‘mother' cell. It can even occur in the ‘grandmother' cell at four origins if the time it takes to replicate and segregate the chromosome exceeds two generations.

This last image is interesting because you actually see the multiple replication origins in single cells by fluorescence microscopy.

zoology - Cockroach-like insect identification (India)

I just saw an insect in my room, and I have never seen anything like it ever before. I captured a photo, please see if you can identify it. It has got quite unique colours on its exodermis and it has 2 pairs of wings ( I was not able to get a picture of them) which are very similar in structure and position to those of a cockroach. In addition to that, it is able to fly, albeit for short distances.

I live in Kolkata, India and the length of the insect is approx. 6-8 cm.

Answer

It's a longhorn beetle (Cerambycidae).

Most likely, it's a Red-spotted longhorn beetle (Batocera rufomaculata), also known as a mango tree borer, mango stem-borer and tropical fig borer.

See this SE question pertaining to the same insect.

From Biolib:

Country check-list: China, India, Israel, Jordan, Laos, Lebanon, Madagascar, Malaysia, Mauritius, Myanmar, Pakistan, Puerto Rico, Sri Lanka, Syria, Thailand, Virgin Islands [Might Not be complete]

Food: Ficus carica L. (Fig), Carica papaya L. (Papaya), Mangifera indica L. (Mango), Shorea robusta Gaertner f. (Sal Tree)

It might also be B. parryi, which, similar to B. rufomaculata, is common in SE Asia (but which is absent from Western Asia or Africa where B. rufomaculata is also found). Since you live in India, both are possible. I will look for a key to determine how to differentiate the 2 species.

Meanwhile, here is a list of related species in the Lamiinae subfamily for further reference.

Also, a great resource (including keys) for wood boring beetles of the world!