publications - Corrigendum to correct formatting/aesthetic errors previously brought up during proofing process

After a lengthy review process, I finally published my first paper. Unfortunately, upon seeing it in print, I was immediately dismayed.

During the proofing process, formatting errors appeared on the table, presumably as a result of the conversion to the journal's table template. The table in question was supposed to have three 'sub-headings' but was formatted such that two sub-headings appeared different from the other two (bold vs framed between two horizontal lines and capitalized). Amongst other corrections, I brought this up during the proofing process by highlighting that the three sub-headings were formatted differently and to correct it so they were all stylized in the same way. When I was notified of my article being published online, however, I found that the changes to the table were ignored. I sent an email asking what could be done and was informed that although they understood I had certain corrections, that no changes could be made now it was online and instead was offered to publish a corrigendum.

Since these changes are aesthetic and not related to the content, a corrigendum (at least to my understanding) would not change anything to the appearance of the figure as corrigenda are published as a separate note, making a corrigendum not really worth it. At the same time, I'm frustrated that after having put so much time into proofreading the article to ensure no mistakes appeared, that one appeared anyway that had nothing to do with me. I wish I could say it's a minor aesthetic point that only I would notice, but after sending out my article to colleagues and friends I received numerous comments about this particular formatting error.

I suppose I have two questions. First, how cut and dry is the rule of not being able to correct articles once they are published? Or is it simply indicative of a lack of willingness or goodwill on the publisher's part that could, perhaps with some more insistence on my part, give way? And if there really is nothing that can be done, is it worth publishing a corrigendum?

Thanks for any insight you can offer.

EDIT: Looking everything over for the n-th time, I now see a couple other errors (eg. inconsistent capitalization in the legends). The thing is these mistakes were not present in the proofing stage (I have the proof file as proof); they were tacked on after the fact, when it was too late to do anything about it. Is this something I should contact the editor-in-chief about?

EDIT 2: Thanks to all for the feedback and suggestions. I ended up contacting the journal manager, informing her that I would not be requesting a corrigendum but that I would be placing a complaint to the editor-in-chief. I was contacted the next day and informed they would fix all the errors in the article.

EDIT 3: So all the original errors were fixed, however I noticed yet another error was introduced that was absent in the previous version. I'm giving up my crusade for now, and will simply not publish in this journal in the future. Thanks again for all the advice.

Answer

The publisher is being dishonest when they tell you that nothing can be done now that the paper has appeared online.

The problem is that they failed to make the changes you asked for. This means that the fault is on their end, not yours. They should be responsible for correcting the paper according to your recommendations, and, if necessary, issue a publisher's note indicating that the changes were made as a result of failing to address your corrections.

publications - Having preferred and non-preferred reviewers in journal submissions

IEEE asks journal authors to submit the names of their (non-)preferred reviewers. Given it may not be appropriate to list an acquaintance as a reviewer, how does one judge if an anonymous person will be a good reviewer or not?

Is giving "non-preferred" reviewers akin to the author confiding about his academic relationships to the editor? Do people really need to fill this column up at all?

Answer

It is generally worthwhile to identify people who both should and should not be invited to review a paper. Obviously most journals now require you to suggest names for reviewers—however, the editor is generally under no compulsion to invite these people to review the manuscript, if they feel other people are more suitable (or are more likely to accept the invitation).

The list of "non-preferred" reviewers is meant for "conflicts" rather than "conflicts of interest." If you have a direct competitor, or someone in the past who has been inappropriately hostile to your work, then you should list them here. However, as the original poster suggests, this could also be used to list "obvious" referees who shouldn't be candidates for a given paper if they are also collaborators of the authors (but perhaps not in the present work).

zoology - Would a colony with only one male and female collapse?

This is a thought experiment:

If we form a population with only a single founder pair, can this population survive? What would happen? Would this inbreeding cause the population to go extinct? Could such a population continue to exist indefinitely?

gene expression - Can intron become exon in alternative splicing?

From this image

We can see several exons that are actually introns in other genes. It's not a really a different gene, it's an alternative splicing of a gene. My background is not biology so is it possible for alternative splicing to behave like this? I only know that alternative splicing is just exon skipping and introns will just stay introns and not become exons. Can someone explain this to me and give any suggestions on which part of biology (or genetics) I need to learn. Thank you.

career path - How can I get into computer science research as a high school student?

I am in High-School but want to pursue research in Computer Science, but as you know High-School usually does not offer any such options or tasks.

So I want to explore avenues where I can get these options and tasks as I am very very interested and really want to do it.

I would also like to say that I have good-strong knowledge of C++, C and assorted APIs from that (3 years programming for 5+ hours daily). So I wouldn't call my self too new to programming and think I can handle programming and so on.

Now, these are my questions:

1. 
   

   How can I get involved in research?

   
   


2. 
   

   How can I contact academics to ask them for research position or even an intern position in research for that matter without coming across as a "waste of time"?

   
   

Answer

Good on you!

I have a relatively simple suggestion: do a replication study. First, find a collaborator -- a fellow high school student or college student of similar skill and experience. You'll learn more in a team than doing it alone. Second, read a dozen or so research papers (probably conference papers) in the field or sub-field that interests you the most. Pick one, preferably the simplest one you can find. Your goal is to replicate the methods as described in the paper and compare your results to theirs. (Don't pick one where you have access to their code.) Once you have a paper picked out (or a few), recruit an adviser/mentor -- either a college professor or an experienced researcher. You'll want to meet with your adviser/mentor weekly to talk about progress and problems you encounter along the way. Mostly, this weekly meeting holds you and your partner accountable for progress.

In my field (Computational Social Science) there are many simulation models that are simple enough to be replicated from their specification. This varies widely in subfields of Computer Science, so your mileage may vary.

The point to all this is to get you an experience in the realm of research without requiring that you first go through all the preliminaries. By focusing on replicating one paper, you only need to understand the material and methods in this one paper. You aren't trying to break any new ground. Instead, you are following in the footsteps of other researchers. If they have done their job well, then you should be able to replicate their results. Replication is a valuable scientific endeavor in itself.

thesis - Supervisor keeps "showstopping" defense with nit-picky grammar errors

My supervisor keeps on delaying and postponing my defense date, taking long periods of time between revisions (1 month of "revision" where the document is in his hands). He has done this 2 times already, so I have been sitting here waiting for a total of 2 months now. This last "revision" he sent it back to me with six or seven nitpicky grammar errors, (ie places I had left out words such as "the" or "when"), and the content-related comments he had were extremely trivial.

I feel like he keeps on showstopping my defense date due to nitpicky grammar errors, and it is impacting my career (obviously, my Master's degree now has 3 years on it, instead of the expected 2). At this point I don't care about grammar errors (and I believe we must have found them all already) or clarity of expression or making perfectionist type improvements. I feel really angry and I feel like writing a letter of complaint to my graduate program director. Each term I have to stay bleeds more money out of my account, and the situation is making me really upset.

So far, I've been very polite and professional and have not "exploded". I've hidden my emotions and my anger and not complained about what I feel is getting quite ridiculous. Should I complain? Should I let him know how I feel? Or should I just keep on going with it and "grin and bear" until it's over?

teaching - How to make group work work?

Occasionally I have some material to cover that is best presented in the form of take-home group projects.

Some student groups manage to find a way to coordinate their work well and to complete the projects successfully, with every team member benefiting from the collaboration. Other groups do not do so well:

• Some groups evenly divide the work, but still work in isolation, losing the benefits of working with peers.


• Some groups push the work to one or two students, while the remaining students merely contribute their name.

I wonder if there are strategies or tools instructors use that can encourage more groups to operate successfully while they are working outside of class?

evolution - How can natural selection occur at species level whilst not occuring at the individual level?

The chapter by Douglas Futuyma in 'Evolution' (Losos et al 2013, Princeton) states that natural selection can occur at the species level. Futuyma states that if natural selection occurs at the species level it does not occur at the individual level:

Neither gene selection nor species selection has molded the advantageous characteristics of individual organisms; rather, they have affected properties at the gene level or at the species level.

But how does natural selection occuring at the species level not affect individuals? Surely any selective advantage of a particular species must occur among particular individuals of that species. For example, if Species A is selected because it is browner than Species B, this will be because individuals of Species A are browner than individuals of Species B.

Answer

I think you have misunderstood the passage. Here is a larger section (found at google books):

Natural selection can also occur at the level of species, for certain characteristics enhance the rate of origin of new species or diminish the likelihood of species extinction. For instance, the number of species in lineages of herbivorous insects has generally increased faster than in closely related lineages that have other feeding habits. Neither gene selection nor species selection has molded the advantageous characteristics of individual organisms; rather, they have affected properties at the gene level or at the species level. But individual selection, selection among individual organisms within populations, is at the center of evolutionary theory. It is at this level that selection explains most of the adaptive features of organisms.

Going through this part-by-part; the first two sentences state that lineage/species selection can occur, in the sense that species traits can enhance the speciation rate of a lineage or decrease their risk of extinction, relative to other lineages (e.g. in herbivorous insects).

He is then saying that the traits that are the target of this selection are not traits of individuals but traits/properties of the species/lineage.

An example might help to explain the point. For instance, it has been argued that pelagic larvae in sessile ocean species will lead to higher dispersal rates, which means that species can colonize new environments, and this can lead to speciation through adaptive radiation (Jablonski & Hunt, 2006). A larger range will also correspond to lower extinction rates (everything else equal). The trait might also be fixed within a lineage (so there is no variance at the individual level within-species), and if so, this lineage as a whole could have higher speciation rates and lower extinction rates compared to a sister lineage that lacks pelagic larvae.

The individuals within species will naturally have the underlying traits (pelagic larvae), but the traits that are selected at the lineage level (extinction risk & speciation rate) are not properties of individuals but are traits of the lineage/species.

He then ends by continuing with "normal" individual selection, and states that processes at this level is responsible for most adaptive features of organisms. It should also be noted that lineage selection is still considered controversial, and it has been shown that it is inherently much weaker than selection at the individual level. Personally, I think there are some very good examples of how species/lineage selection can function, but to what extent it is an important process for species and organisms is an open empirical question. If you are interested to look further, Jablonski (2008) and Okasha (2007) are two good starting points.

Research in "Research Engineering"

from Wikipedia:

Software engineering (SE) is the application of a systematic, disciplined, quantifiable approach to the development, operation, and maintenance of software, and the study of these approaches.

I was wondering if there is something similar for research, something that we could call Research engineering. I imagine it to be a research field on its own, with students "researching on how to do research". I believe software development has benefited a lot from research in SE. Maybe research could also benefit from Research engineering.

The questions are:

• is there some institute or some university department in the world where they work on Research Engineering?


• in which faculty you would position such department/institute?

Edited: After getting a couple of good answers, I am still not completely satisfied, so I would like to clarify my question. What I am really interested in is indeed a "software engineering" approach. I am not interested in philosophical or sociological research. In fact, the question I had originally in mind was whether it's possible or not to apply actual software development methodologies to research. In more concrete terms, I am wondering whether anyone has studied the application in research of models similar to the waterfall, or the spiral model, or things like extreme programming, Scrum, etc... (Note: these are just examples, please don't comment to each of them one by one).

human biology - How does anger relate to blood pressure?

Anger is an emotion generated by neural processes in the brain and is associated with elevated blood pressure. How can an emotion, which is totally related to brain, result in blood pressure changes?

Answer

Anger is a common emotion in most animals and it is highly related to stress. At time of anger body usually releases stress hormones and the body's way to respond to stress is by sympathetic nervous system activation which results in the fight-or-flight response.

Anger is an emotional response related to one's psychological interpretation of having been threatened. Often it indicates when one's basic boundaries are violated. Sheila Videbeck describes anger as a normal emotion that involves a strong uncomfortable and emotional response to a perceived provocation.

Anger may have physical correlates such as increased heart rate, blood pressure, and levels of adrenaline and noradrenaline. Some view anger as an emotion which triggers part of the fight or flight brain response. http://en.wikipedia.org/wiki/Anger

Stress and anger trigger the release of stress hormone Cortisol in the body. Mild releases of Cortisol can give the body a sudden burst of energy,it also may increase the heart rate to 180 times a minute and blood pressure from 120 over 80 to 220 over 130.

Anger is processed in hypothalamus and amygdala,the roles of two peptide hormones, corticotropin-releasing hormone (CRH) is responsible for the production of Cortisol (Primary stress hormone) and arginine-vassopressin (AVP) produces Vasopressin, which triggers blood pressure by increases reabsorption of water by the kidneys, this results in contraction of blood vessels which raises blood pressure.

The human stress response involves a complex signaling pathway among neurons and somatic cells. While our understanding of the chemical interactions underlying the stress response has increased vastly in recent years, much remains poorly understood. The roles of two peptide hormones, corticotropin-releasing hormone (CRH) and arginine-vassopressin (AVP), have been widely studied. Stimulated by an environmental stressor, neurons in the hypothalamus secrete CRH and AVP.

CRH, a short polypeptide, is transported to the anterior pituitary, where it stimulates the secretion of corticotropin (4). Consequently, corticotropin stimulates increased production of corticosteroids including cortisol, the primary actor directly impacting the stress response (5). Vasopressin, a small hormone molecule, increases reabsorption of water by the kidneys and induces vasoconstriction, the contraction of blood vessels, thereby raising blood pressure. http://dujs.dartmouth.edu/fall-2010/the-physiology-of-stress-cortisol-and-the-hypothalamic-pituitary-adrenal-axis#.VH7k8cnQoX0

graduate admissions - Why do many PhD programs expect a higher average physics GRE score for international students than US students?

Browsing various PhD admissions programs, I consistently find that there is a higher expectation of international students on the physics GRE for admission. For example, at UT Austin, the average score on the physics GRE for students accepted for Fall 2011 was 907 for international students and 777 for US students.

Why is there such a difference in expectations?

journals - What should an editor do if the authors have guessed who the reviewers are?

For whatever reason, authors are occasionally able to guess who the reviewers of their papers are. Sometimes these guesses have even gotten published:

"We appreciate the very candid critical insights of 2 anonymous reviewers, M. Gompper, and K. Beard." In Conservation Biology.

"We do not gratefully thank T. Appourchaux for his useless and very mean comments." In ESA.

What is the best way for an editor to handle these not-necessarily-correct guesses, if they are noticed:

• during peer review (e.g. in the cover letter or author response to reviewers)


• after acceptance?

Answer

I suspect this is rare enough that there is no "standard procedure".

If I were the editor, I'd ask for #1 to be deleted as the authors presumably cannot really be sure who the reviewers are (unless they are known to have voluntarily revealed their identities).

I'd ask for #2 to be deleted as it is simply in poor taste. If they want to complain publicly about the review, they can do so in the "letters to the editor" column (if they are more polite about it), but it doesn't belong in the paper itself.

If the authors make guesses about the reviewers in the cover letter (not in the manuscript itself), I'd just ignore them, or perhaps say something like "Obviously, I will neither confirm nor deny your guesses."

(Disclaimer: I'm not an editor.)

botany - Are two colors (red + blue) necessary for LED grow lights, or would either color be sufficient?

Below are some chlorophyll absorption spectra from other answers here. There is strong absorption at both the blue/violet end, and the red end of the spectrum, and presumably both of these contribute to steps in water splitting used in photosynthesis.

Do the two broad but widely-separated peaks correspond to different steps, so that both are required? Or is it sufficient to have light present in one band alone?

If both are required, how are they used differently?

If not, why do LED grow lamps have both? Would twice-as-bright light with either wavelength be just as effective and useful to plants?

---

That horribly un-natural purple light looks cool in high tech settings, but it's kind-of ugly in ones living room.

note: Originally I had though that Chlorophyl A and B corresponded to the two peaks, but clearly this is not at all the case. From here:

Both Chl-a and Chl-b primarily absorb red and blue light, the most effective colors in photosynthesis. They reflect or transmit green light, which is why leaves appear green. The ratio of Chl-a to Chl-b in the chloroplast is 3:1.

above: From this answer, also seen here.

above: x2 From this answer.

Answer

tl;dr: Sort of?

Logically, either red or blue light should be sufficient. Chlorophyll a and chlorophyll b preferentially activate different photosystems, and both photosystems are required in green plants.

Practically, we're in luck and someone has actually done the experiment.

As the original study reports, plants need a little blue light to grow into the right shape. Red-only plants produce oxygen and grow, but they take weird shapes. It seems like plants can grow on red light, but they use blue light to work out where light is. See here for a reasonably lengthy treatment on most of the obvious combinations.

funding - Is it legal to use tourist visa waiver for academic visits?

All countries have visa waiver for certain nationals, but it is only for touristic purpose. People use this scheme for attending scientific meetings (isn't it some kind of business trip?).

Anyway, academic visits, in which the guest is paid, is definitely a business trip. For example, when an academic organize a paid two-week course in the host university, or when visiting for a join project in which he is paid.

For example, a German academic traveling to the United States for two weeks for working on a NSF-funded project in which he is paid.

1. 
   

   Is it theoretically illegal to travel without Business Visa for such academic visits?

   
   


2. 
   

   If yes, how often it happens in practice?

   
   

graduate admissions - Am I too old for academia after a PhD?

Currently, I am applying for PhD positions at United States and Canadian Universities. I will be 35 when I start my PhD in Computer Science/Machine Learning, and probably I will finish it around the age of 40.

Will I be banished from academic positions considering a possible PostDoc time and what about industry positions ? Should I plan my study towards industry or academia from the research perspective ?

authorship - Should I try to avoid being the single author of my patent/paper?

I invented something as part of my job in R&D, and I plan to patent it and get clearance from my company for publication in an academic conference. All the key novel ideas are mine, and I implemented them all and ran all the experiments.

However, I just don't feel comfortable about putting down my name as the sole inventor and author. When I see single-author papers, they always make me wonder if the author is dishonest and/or bad at working with others.

But no matter how much I look at my paper, I just don't see any noteworthy contribution to it from any of my co-workers. We were working on the same problem, but each taking a different approach.

Hence, the solution I've come up with is to put a co-worker's name on my paper and ask (force?) him to make some contribution to it, like helping with the literature citations and/or experiments.

But even then, I'm pretty sure he won't contribute much and I'll still end up doing all the work.

Do I really need to go out of my way to avoid being a single author? :(

Answer

As the proud author of many papers with all sorts of numbers of authors, anywhere from just myself to dozens of co-authors, I see no reason to avoid being a single author.

In evaluating a researcher, I would only have concern with their ability to collaborate if they show a preponderance of single-author papers. If somebody has a mix of single-author and multi-author papers, then my reaction will instead be more positive, because it shows they are both capable of collaboration and also capable of initiating truly independent work.

So: go for it on your single authorship (and/or inventorship)! Just make certain that your co-workers agree with you that they should not be authors/inventors, or else you may have an entirely different type of problem on your hands.

graduate admissions - Choosing universities or programs

I am currently applying for two universities for graduate studies at the US, assuming both universities accept me (Hopefully) should I choose the university that fits me better or the university which is more selective (like ivy league universities).

My concern is that smarter students will overrun me in the top university, is this a valid concern or there is no academic competition between students since the admissions office and the designated department would not have accepted me in the first place if I had a non competitive enough profile?

Answer

My concern is that smarter students will overrun me in the top university

Well, the good news is that the smarter students will be concerned about you overrunning them. It's called impostor syndrome, and virtually everyone at a top institution has it. (And I don't just mean the students...)

Also: being around people who are (much) smarter than you is a good thing, because it means you will learn more. (That's why you're hanging around a university, right?) The other good news is that in grad school, you will no longer be competing against your peers. The bad news is that you will now be competing against the entire academic community in your chosen area of study. So, it's probably good to have some other smart students around to talk to. Right?

My experience as a student at a Extremely Well-Ranked School is that other students are very supportive, and empathetic to the experience of getting through a tough program. In short: don't worry. It will be ok.

should I choose the university that fits me better or the university which is more selective

Isn't this a tautology? The university that fits you better will fit you better.

A less sarcastic reply is: there is nothing that matters more in grad school (or in life in general...) than your relationships with the people immediately around you, namely, your advisor and the other members of your research group / lab. Even brilliant students who do not have a good working environment or a supportive advisor will flounder—I have seen it time and time and time again. In contrast, students who are not exceptionally brilliant but have a good relationship with their advisor / group tend to do well, at least well enough to move on to a satisfying career after grad school. Prestige, fame, money, and beauty are all higher-order terms. Pick the place where you will be happy.

human biology - How does a person get AIDS?

I am inquisitive to know about how a person contracts AIDS. Among the common masses it's still the belief that having sex with multiple partners causes the disease but that is not the case when read online that it can come only from persons carrying the virus.

So, if a person (male or female) is carrying the virus (HIV positive) does it mean that he/she is suffering from the disease or the person may be carrying the HIV disease and still be free from AIDS. If so how did this chain reaction of spreading the virus start?

Also is it true that immune systems of some rare people in this world can fight with this disease.

Answer

You read right: it can only come from people already infected through:

• sexual contact


• contact with an infected person's body fluids (blood transfusions), although not all fluids carry HIV (saliva, tears)


• from mother to child (pregnancy, breast feeding)

Having unprotected sex with multiple partners statistically increases the risk of stumbling upon someone infected.

A person carrying the HIV virus may not show symptoms of AIDS, because the HIV infection passes through a stage of clinical and symptomatic latency (the asymptomatic HIV or chronic HIV) which can last up 20 years (average of 8 years) when only uncommon symptoms like fever and weight loss show up.

Where it started? It is believed that HIV originated in non-human primates in West-central Africa and were transferred to humans in the early 20th century. The virus adapted and became strong, because the virus from primates is typically suppressed by the human immune system within weeks of infection.

HIV is a retrovirus that primarily infects components of the human immune system such as CD4+ T cells, macrophages and dendritic cells. It directly and indirectly destroys CD4+ T cells.

So it destroys the cells reponsible of its removal from the human body. Hard to believe that there are people whose immune can really destroy the virus. A virus lives inside the cell it parasite, so the immune cells must destroy one the other. Also the virus infects and kills them (the good ones). However, as MattDMo suggested an infected person may take antiretroviral drugs and the disease progression can be slowed down.

Source: Wikipedia - HIV, AIDS

citations - How to find DOI for article in JSTOR?

I have a link to an article on JSTOR. I can't see the DOI mentioned. Is there a standard way to find the DOI? Do all articles on JSTOR have an assigned DOI?

Answer

DOI's are managed by Crossref.org. For each DOI, Crossref's database has a redirect to the current location of that digital object, and the owners can move things around and update the Crossref database as needed. When you follow a link to https://doi.org/, the crossref servers redirect this request to the current location of that paper. As mentioned in another answer you can lookup an article in the crossref.org database to see whether or not it has a DOI.

Recent articles have typically been assigned a DOI by the publisher, and most publishers put the DOI on the title page of the paper so it's easy to find that way.

Older articles were originally published without a DOI, but the publisher may have assigned one after the fact. If the publisher has not already assigned a DOI, then JSTOR may have assigned a DOI to the article that will point to the copy of the article in the JSTOR database. This is a service offered to publishers by JSTOR, but not all publishers use it. Thus not all articles in JSTOR have DOI's.

It appears that the article you linked to has not been assigned a DOI by either its original publisher or JSTOR and thus has no DOI. I can't find the article in the crossref database. The "stable URL" that you linked to is probably the best way to link to the article.

publications - Requesting raw data from previously published research

I am working on a mathematical model to help explain some experimental results and generate new hypotheses. Unfortunately, I have neither the resources nor interest to gather experimental data, but in this particular sub-field publishing a model without showing its usefulness on some experimental data is not common.

There are several existing experimental findings that can be explained by my model. However, they are presented in other modeling papers and the raw data is not available with the paper or on the authors' websites. In the papers they only present partially-analyzed data (for instance, they show results averages over participants, but not individual participant's results; or sometimes they only give the results of statistical tests).

I want to contact the authors for their raw data and have 3 related questions:

1. What is the protocol for contacting by email to ask for authors' raw data? Is this common?



2. Will the researchers expect to be invited on-board as co-authors? Or is a citation to their papers, and an acknowledgement of the form "AK would like to thank X, Y, Z for providing their raw data" sufficient?


3. If my model (without fits to specific data) is in a pre-print state then should I send a pre-print to the authors I contact? What if the pre-print points out weaknesses in their approach to modeling similar problems?

Answer

This will, as it seems nearly all questions on this site, vary based on field. My answer applies to Epidemiology and medical research only. Your mileage may vary.

• 
  

  It is very common for this to happen in my field. There has been an increasing emphasis on using meta-analysis and systematic reviews to summarize bodies of work, and with those there is almost always a need for some more information, raw data, etc. to come from study authors. It's fairly routine now. They may not say "yes" for a number of reasons. One may be that they're working on their own projects in a similar direction. But there are others - that privacy laws prohibit releasing data to just anyone or their funding dictates similarly is a fairly common one. So be prepared for "no".

  
  


• 
  
  

  As for the authorship question, it likely depends on the extent of your data request. Generally, if you're just asking for a few numbers that go into a reported value, then in all likelihood, an acknowledgement is more than sufficient. If, on the other hand, you're asking for access to the raw data from their 5 year, many thousands of dollars cohort study? You're likely going to have a member of their study team be an author on your paper, and there will be far more extensive approval processes than just "Sure, .csv file is attached."

  
  


• 
  

  "If my model (without fits to specific data) is in a pre-print state then should I send a pre-print to the authors I contact? What if the pre-print points out weaknesses in their approach to modeling similar problems?" For the initial contact, I'd suggest it isn't necessary, because what you're really trying to find out is "Is the release possible". At later stages, I would expect to see what you were doing, either in a full explanation, or as a pre-print. As to your "What if?" question - so what if it does? Science is about improving the methods we use.

  
  

life - are sperms considered living

recently i got into a debate with this question on hinduism.se ,

as the link given above shows, are sperms considered as living or non-living

as far as my knowledge is concerned, sperms undergo locomotion, senescence, more over the best thing to say they are living is they contain genome, i.e. haploid sets of chromosomes

so in short are sperms living or non-living

Answer

The question of what is living is nothing but a matter of definition. We can only tell you what are the standard definitions of what is a living thing but no absolute truth exist behind these definitions. Therefore, I am afraid that all discussions here will bring anything new to your ethic or religion related discussion.

I want to argue that the @user137's answer is very misleading for two reasons. First, he based his discussion exclusively on the "reproduction ability" definition of life. Second because his definition of reproduction might be misleading as well.

Reproduction is not only cell division obviously. Following this same definition one would not consider a human to be a living things but only to be a collection of living (and non-living) things. It is important to understand that a spermatozoid is just one phase of a life-cycle. This phase yield to the next phase. That's it. It seems weird to say that a kid is not alive just because he cannot reproduce. It seems weird to say that a grandmother is not alive because it cannot reproduce. You can say however that a kid is a living thing that cannot reproduce and at another moment of its life cycle it will be able to reproduce (assuming it will survive to this age). One should not think of spermatozoids as something totally detached from the human phase as we know it. These things just form a cycle and it seems to me miseleading to say that a part of this cycle is not alive. Saying such thing would yield someone to think that two living things create non-living things that by fusion will become alive. That seems weird. But again, it is nothing but a matter of definition. I cannot say that user137 is wrong, I cannot only say that his definition seem neither useful, intuitive nor common among biologists.

You may want to have a look to life-cycle and to understand what are the haplontic and diplontic phases with a bunch of wikipedia readings.

Other concepts such as the ability to synthesize its own components, having a boundary between interior and exterior and ability to response to environmental stimulis are often used in order to define what is a living thing and what is not.

graduate admissions - Is Math GRE not worth it?

Finished bachelor's and master's in mathematical finance. Applying for PhD in math, which may or may not be in a university that requires General GRE or Math GRE

Based on my other questions (like this) and what I read online, the General GRE and the Math GRE are taken only as required for application or taken with the intention of possibly applying somewhere where it is needed. Like a high grade helps little in admission but a low grade helps a lot in non-admission.

So showing a high grade in Math GRE to a school that doesn't require it in general would be all the more not very helpful in applications?

Let's say I apply to a set of universities in different countries where none of them require any GRE.

It seems to me that the only reason for someone to take for example the Math GRE other than being required is to strengthen your application based on your bachelor's or master's not being math.

Answer

The vast majority of math Ph.D. programs in the US will require both the general and math subject GREs, so unless you specifically avoid those schools specifically, you probably will have to take them. How schools use the GRE varies a bit, but for someone whose record isn't as strong, it can play a valuable role in reassuring schools, since it's the only thing they have which is uniform across schools and recommenders.

For schools that don't require them, they will likely assume that you have taken the subject GRE, and will assume that not sending in your score means it is really bad. If your score is really bad (less than 30th percentile), then it's probably better to not send it in, but if it's not abysmal, then probably you should send in the scores.

Is it common for an undergraduate thesis in pure mathematics to prove something new?

What do undergraduate students in mathematics do for their thesis, if they have done one, besides expository or applied math?

I was thinking that the kind of research they do is something applied, say using math in social sciences or a problem in one of the less rigorous natural sciences, or discussing such a problem (that's what expository is, right?).

To me it seems something non-expository or non-applied is an original contribution to mathematics, something that PhD students do.

I attended some pure math undergraduate thesis presentations. I was quite surprised: Did they prove anything new? Never bothered to ask due to fear of looking stupid. Would it be out of the ordinary to expect an undergraduate proves something new? If they did not prove anything new, what the heck are they talking about?

It seems like if it's not new, they are giving a lecture. If it's new, that seems like a PhD-level accomplishment.

I mean, do math undergraduates frequently prove new things?

Answer

I'm going to disagree with Oswald. In my experience, undergraduate students do not often prove new things in pure math. I wouldn't even say master's theses often contain new results. There are a few main reasons for this.

Firstly, pure mathematics operates at a level that is not very accessible for most undergraduates, even those doing research. Undergraduates doing research are often well out of their depth and holding on for dear life. This can mostly be attributed to just not having enough time to get up to speed with what is considered modern mathematics. Most courses in mathematics at the undergraduate level are about math from 50-100 years ago (if not older).

Secondly, undergraduates do not often have the mathematical experience to know what the right plan of attack is when faced with an abstract and new problem and they may not know how to check their work thoroughly to make sure there are no major oversights or blunders. A lot of mathematics involves lateral thinking and it takes a lot of time to build those connections. The hardest part of a pure math PhD (in my opinion) is learning how to attack a problem no one has considered before. Standard techniques that others used may not be useful at all to you for one reason or another. An undergraduate won't have the creativity to navigate this kind of issue because the kind of creativity that is needed comes with a lot of experience. Even when an undergraduate student thinks they've proved something, the nuances of their argument likely will not be apparent to them. (This is especially true when it comes to functional analytic/measure theoretic arguments - the devil is in the details.) Thus a proposed proof may not even be close to being right.

Lastly, not many undergraduates in pure math do research because the gap they have to overcome between coursework and modern mathematics is pretty substantial. Those that make contributions in pure math are those that are very, very talented and have very thorough backgrounds (backgrounds that rival master's/PhD students).

Undergraduates in pure math are not expected to make contributions. That is not what research is about for them. Introducing an undergraduate to research serves a couple of different purposes: it introduces them to more advanced topics and it gives them a taste of what research is like so that they can make an informed decision about whether or not graduate school is right for them. As such, the theses are more like surveys of a specialized topic in mathematics. There is a lot of independent learning involved and there may be some unique examples, insights, and connections contained therein. They may not be presenting "original" work, but poster sessions are there to present what they've learned regardless of whether or not it was original. So yes, it is kind of like a lecture. They are undergraduates and far from being experts in their field.

Note that I am not saying that no undergraduate ever produces new results in pure math (there are some high school students that are better than most PhDs), but it is not a common occurrence and is not expected or considered the norm.

It is possible to obtain two PhD degrees (various fields) on the basis of one interdisciplinary PhD dissertation?

It is possible to obtain two PhD degrees (various fields) on the basis of one interdisciplinary PhD dissertation? Is this something feasible (in Europe)?

Or maybe there must be two different 'physical' doctoral dissertations?

Answer

No, at least the regulations that I am aware of require that the dissertation be a novel contribution to the respective field and that it has not been submitted before.

If you write a dissertation at the crossroads of different fields, you have to decide for a field in which you want to formally graduate and obtain a degree. It may be advisable to look for supervisors from different fields or with an interdisciplinary background.

publications - How to force a journal to address an associate editor's scientific misconduct?

My manuscript, submitted to a high-rank and very respectable journal, has been rejected by a referee. From the referee's report one could make a conjecture that the referee is one of my competitors, whose results are far inferior to mine. A second referee also rejected my work by giving an absurd argument. It is not an emotional exaggeration, the absurdity of the second referee's argument should be obvious to anybody graduating a university. The editors agreed with such reports, despite the fact that all my arguments have been completely ignored by the referees. I appealed and my manuscript was considered by one of the associate editors. And now is the most interesting part.

The associate editor agreed with the referees and added his own argument against my work. But in this case his real name is known. He happened to be a very famous scientist. Knowing the name, it is very easy to find out his own works on the topic in question. Surprisingly, at the same time I submitted my manuscript, he (associate editor) published two papers in this and higher-rank journals where he stated exactly the opposite to what he wrote in his report to reject my work. Even after he had written his report, he continued to publish and give talks where he states the same point of view (which is the opposite to that of he wrote in his report). If my conjecture concerning the first referee's identity is correct, he is a coauthor of some of the associate editor's works and the associate editor just wants to help him to reject competing superior results.

I collected all these facts, presented them to the editors of the journal and accused that associate editor of scientific misconduct (because what he wrote in his report is a deliberate lie, supposedly in collusion with the referee, or even with both referees). After two months, I received a short message that the Editor in Chief will decide what to do in this case. Up to now there is no reply. It seems that the editors simply want to hush this incident up.

This journal is one of the oldest and most respectable journals in its field. Is there a way to change this situation and force the editors to report this incident and disclose the identities of the unfair referees?

How should I state a 'PhD dropout' in my CV?

I was a final year PhD student (into the last quarter of year 4) in cancer research (passed my qualifying 2 yrs back) but was let go thereafter due to 'unsatisfactory progress' as my data is not sufficient for a PhD thesis. I have to admit here that I've gradually lost my enthusiasm in the project and kinda burnt up after year 3. I've completed all required modules with a decent GPA (4/5). My supervisor was lenient enough to recommend me to graduate with a MSc instead but am facing some 'cross-deparmental red tape' at the moment to say the least (no news of my MSc transfer after 2.5mths of appeal). I'm in the midst of preparing my CV for future job hunt but decided I should just state my current qualification as a 'BSc'. How should I address this 'failure/ 4-yr gap' in my CV? I have no intention of applying for any academic research jobs but felt it's best that I stay in a relevant field (bio/pharma?). Any advise given would be greatly appreciated. Thank you!

conference - Should the slides in a presentation be self-explanatory or be as minimal as possible?

When you do a research presentation, what is usually the focus that you take.

Some professors tell me to make the slides as self explanatory as possible, and I quote:

Someone should be able to understand your slides without you being there

To me, this approach seems counter intuitive to the principle of a "talk". After all, you already wrote a paper that meets that objective.

Other people, for example in things like TED talks or (please bear with me) presentations by Apple, have very bare bones slides, where they only focus on transmitting the main message of the talk.

What is your take, should the presentation be made as didactic as possible or just a cold transference of information?

Answer

I would say the two most important points are to make slides you are comfortable with and not to limit your oral presentation to reading your slides.

Furthermore, if you are presenting a research paper, i.e., where more written material is available to the audience, then the objective is usually to make people want to read your paper, instead of explaining the entire paper in 20 minutes.

Some people prefer to have full slides, arguing that when members of the audience are not understanding English very well, it can help them to have both the oral presentation and the slides, especially when the speaker does not speak a perfect English. It is also helpful for members of the audience who got distracted at some point, and who can quickly read where the speaker is. Other people prefer minimal slides, arguing that having both the full text and the oral presentation might confuse the audience. In particular, whenever a slide is displayed, the audience tends to read it immediately, and during the reading, to be less receptive of any spoken words.

In other words, the only "bad" presentation would be to have full slides, and to limit your presentation to reading them, because you become basically useless. However, you can have long slides, as long as you consider them as an aid for the audience who haven't followed what you said (for whatever reason), and not as your script to read. You can also minimal slides, containing only the key points. In the end, you need to be comfortable with your slides, and to give a presentation like one you would like to attend.

phd - Is it acceptable to ask a professor who is not your supervisor to give you M.S. thesis topic?

I'm currently a M.S. student. My supervisor give me freedom to choose thesis topic. Since it is so hard for me, I decide to ask another professors whom I consider to be their PhD candidates in future. I have written an email to ask them. Is it a good idea to do so? And is my email appropriate for this purpose?

Dear Professor xxx,

I am a M.S. student at University of xxx-the most prestigious university in xxx- with a major in information technology- multimedia systems. I will graduate on September 2016.

I had the chance to read your publications and some of your articles. I really enjoyed them, and it gave me many ideas for my future research. Due to my strong interest in your research area and considering the experience I have gained from my relevant courses, I believe I can be a beneficial part of your research group, if I get a chance. Since I haven't chosen the topic of my M.S. Thesis, I prefer to ask you to give me some information about the topics you are currently working on, in order to get a higher chance to be your PhD student in future. I know you’re very busy so I appreciate any time you can give me.

Thanks very much,
Sincerely,
xxx

Answer

I do not think it is a good idea to ask this other professor to give you your thesis topic, either asking by email or in person. If you want to be this professor's PhD student in the future, the best thing you can do is do a good job on your thesis and complete your Masters degree. Doing your thesis on a topic of his choice does not increase your chances of being his PhD student, and may decrease your chances because you aren't demonstrating independent judgment.

Both Masters and PhD students should do the work to pick their own topic. (Narrowing down my dissertation topic has been a multi-year exercise -- working part-time.) As a Masters student, you don't have to break new ground or advance the state of the art. But, by picking a topic that is at the state of the art, you demonstrate that you understand, in general, where the state of the art is.

Instead of asking some professor to hand you a topic, you should investigate why picking a topic is hard for you. Do you lack ideas? Do you understand what qualifies as a good idea? Do you have trouble selecting from alternative ideas? Once you've pinpointed the problem, you can ask your adviser or anyone else for help on this aspect of the problem.

botany - Help ID this plant, quite possibly a weed

I found this plant near my South Indian home in Kerala, India. Most probably it could be some sort of weed. Anyhoo, is this plant of any medical or commercial value? Is it a remedy for something?

• It has a white tap root with little veins off the main root


• It has a really small yellow flower


• It's leaves are similar to that of a clover, except for that it has three to five leaves

Merci d'avance!

(P.S. Forgive me if this is some very common plant that I should know about, I'm in 7th grade.)

Answer

I presume it is Cleome viscosa, the Asian spiderflower.

It is commonly found in rainy season.

Medicinal uses:

The crushed leaves have been investigated as a treatment on stored seeds of cowpea, to prevent weevil infestation.

The leaves are use as external application to wounds and ulcers. The seed are anrhelmintic and carminative Juice of leaves is used as remedy against discharge of puss from the ear.

Identified by the following features-

1. 
   

   Palmate leaves

   
   


2. 
   

   Colour of flower especially the brown part at the base

   
   


3. 
   

   Herbaceous habit

   
   
   

References:

1. Wikipedia


2. Flowersofindia.net

What part-time jobs are suitable for PhD students?

I know PhD is unsparing in terms of available time, but at times there may be situations that demand some extra income, for example, family situations or some medical emergency.

In such cases, are there any specific jobs PhD students could take up? This could be at some place within a university (a library, say) or somewhere in the city (assume it is a large one like London or NY). The desiderata are minimal time consumption and a sum of useful money which could be used to manage the unexpected expense.

Answer

1. 
   

   I know of a few graduate students who successfully made money doing consulting in their line of work. Most of these were engineering students, where the knowledge gained during graduate school is easily transferable, but I've seen others as well.

   
   

   If you're interested in this, talk to as many people as you can and network, network, network. It can be a fun side project with the potential to become a full-time job if you're interested.

   
   


2. 
   

   Another very useful skill that some graduate students may be able to do is grant writing. While you may not realize it, this skill is necessary in many, many industries, and if you're good at writing, you can make earn some good income contracting out your skills.

   
   

publications - Uploading a revised version of published journal article on arXiv

I uploaded a pre-print of an article on arXiv 1 year ago. The article was accepted in SCI journal and currently available online. However, I found a typo mistake in one equation and want to add more discussion related one figure (On researchgate I am receiving a lot of queries regarding that figure).

Should i upload a new version of pre-print on arXiv? (How citations will work in this case? as arxiv version is more advanced compare to Journal version) Or
I may upload a short document on arXiv as an errata/correction with extra discussion?Or
I may address errata and discussion in online page of journal?
Actually this journal allows the registered users to comment and start discussion related to published article.

phd - Professor refusing to write recommendation letter to make student work longer

My friend is on his way to graduate with PharmD (outside US). He wants to apply for PhD program in US, and have asked his professors that he has worked with in the lab for recommendation letters. However, his professors refused to write him a recommendation letter unless he stays in the lab for 1 more year after graduation to work with the current on-going project (2 of them refused, another one has written him a recommendation letter).

The professor also belittled him when he asked for the recommendation letter, saying things along the line of

Am I, or this university not good enough for you? You must be pompous for wanting to go to another university.

That particular professor has also shared the rumor in the department that he thinks he is too good to be part of this university. In the past, they have offered him PhD program with scholarship, but have later retracted the scholarship so he rejected the offer to stay with them. He needs the recommendation letter to apply for PhD program.

What can he do when professors refuse to write recommendation letter for him unless he works with them longer? He definitely do not want to stay in that toxic environment anymore.

EDIT (12/19): All professors have agreed to write the recommendation letter, as long as my friend writes the draft of the letter himself. He has decided to go with this proposal and wrote three recommendation letters for himself, and gave it to his professors.

Answer

1. 
   

   Your professor is not obligated to write you a recommendation letter.

   
   


2. 
   

   You should think about getting a letter from someone who will write a good recommendation for you.

   
   
   


3. 
   

   Your professors' attitude is highly unprofessional and needs to be exposed to their academic community. When you're clear, file a complaint through proper channels to the dean/HOD. If possible, keep any record of your conversations/emails with the faculty members. Given the fact that such unprofessional behavior exists in your university (that they will ask you to work for them for 1-2 years after graduation as a condition for a recommendation letter), may be the human resource, dean office etc. themselves are unprofessional. So, tread carefully if you plan to expose their behavior. Maybe do it after you have received your degree etc. However, such behavior needs to be exposed in any academic institution for the sake of future generations.

   
   


4. 
   

   If your foreign university asks (e.g., in future) why your own advisors didn't write you a recommendation then there is no harm in telling the truth. However, tell only the truth not your version of the truth. It's common for students at a certain phase in their career to panic, act hysterically, and believe that everyone is out to get them.

   
   

Letter of recommendation from Post-Doc or Professor

I was guided by a Post-Doc for my undergraduate thesis, but the one responsible for all and offering the thesis was a Professor, who I only talked to when discussing the thesis, agreeing to it, and the explanation of the grade in the end. Who of both would be the one to ask for a letter of recommendation? More general, should you always ask the person with who one was mostly in contact during work, or the person responsible for it all, if they are not the same person?

Understanding the strategy of Sanger DNA sequencing

The Sanger sequencing method creates large numbers of sequences of all possible lengths, ending with a specific nucleotide, by terminating with a tagged (fluorescent) nucleotide at the end.

But if you already have fluorescent nucleotides of a specific base, why not just do regular PCR with them, create a huge number of full length copies of the original sequence, and then simply see the locations where the nucleotide fluoresces to determine all the locations of that base. Why do we need a large number of copies ending at each possible location, as with the Sanger method?

Answer

If you mark the full length strand of the DNA with the fluorescent labels, you will get a lot of signals from the same nucleotide without the possibility to discriminate where the actual nucleotide is located on the strand.

Sanger sequencing doesn't end with the preparation of the terminated and labelled DNA strands, the following step is crucial in discriminating where the labelled base actually is. After labelling, the sample is run through high resolution capillary gel electrophoresis to sort them by size. The smallest fragment comes out first, then the one with one base more and so on. The detector which then identifies which fragment is coming through is located at the end of the capillary.

This works like shown in the schematic image (from here):

If you would mark a complete strand, no dicrimination by size is possible (ideally, all DNA would run on the same height of a gel) and all flourescent signals for all positions would come on the same spot. Not very helpful.

ethics - When is it acceptable to report classmates who cheat on an exam?

So for one of my computer science classes, we have a WhatsApp chat among all students in the class to network and help each other out with questions regarding homework, or if we have any confusion on assignments. It's a given that we can get help on these types of assignments.

But exams are proctored online, and getting help on them is strictly forbidden. However, some students in the chat have posted to the WhatsApp chat during their proctored exams, posting photos of the exams, the questions, and receiving help from others during their exams.

Why would I care about this? So normally, when a student cheats on an exam, it would have no effect on another student because the two overall students' grades are unrelated. However, the exams are curved. So these students that cheated on the exams **not only have an unfair advantage, ** but they also put other students at a disadvantage. Them doing exceptionally better than they would have has the potentiality to reduce other students grades by up to 10-15% of what it would be. So if Student A would normally get a 65 because they don't know the content, they now get a 89, thus, throwing off the entire curve. However, student B who actually DID try his hardest and studied got an 74. Their grade would have been higher with the curve, but student A cheating disrupted the curve. As a result, student B gets an 79, where they would've had an 84 without the several cheaters with almost perfect exam scores at the top.

Personally, I hate to be 'that girl' that reports someone else like a snitch... But I worked so hard in this class. I studied for 6 hours every day before this exam, and got an 83... and these people admit in chat that they would probably fail if they didn't use WhatsApp (have it screenshotted-saying that exactly). So I worked so hard and got an 83. They cheated and got a solid 90, doing no studying, no hard work on their own part. They work full time, so they complain they don't have time. But how is that my fault, or the fault of the other students that the cheater makes different life choices, or chooses to put less time into school, and we as a result should suffer? That's my rationale for wanting to report them. I play fair, so why should we suffer because they don't?

vision - What gives things their colour?

My 6 year old daughter asked me 2 biology-related questions yesterday and I tried my best to answer them with the aid of YouTube videos. One of the questions (I may post the other one too) was

How do we see colour?

I showed her a video on YouTube where it was explained that light hits an object and if that object is a tangerine then that object will absorb all colours except orange and will reflect orange and that's why we see it as being orange. I then repeated this explanation and she said.

But how do we see different colours?

I then showed her a video describing corneas, vitreous humours, lenses, optical nerves and so on. I think I lost her. I got a bit lost too.

Now I have two problems, which I'd like to ask to you all as questions

1. 
   

   I do not know how to explain to a 6 year old how we are able to perceive colour. Does anyone know how this can be explained?

   
   


2. 
   

   I have never quite understood this idea that an object has a colour depending on the light that hits it. Okay, I understand that in low light objects have a different colour because there is a not much light hitting it and that different objects absorb different wavelengths of light and therefore appear as different colours. What I don't understand is that if I place a bar of gold a bar of silver side by side in the same lighting conditions they do have different colours, so therefore there must be something inherent in these object that give them different colours. What is that something?

   
   

Answer

I do not know how to explain to a 6 year old how we are able to perceive colour. Does anyone know how this can be explained?

Well, depending on the depth you want to introduce her to, it can be difficult to explain to adults - much less children. You explained the basics well enough. Without going to the molecular mechanisms, here's a useful diagram:

Light will pass through the eye and Retina until it hits the Cones and Rods. That produces a reaction (which I'll address next) - which then causes signals to either resume or cease (Rods are, ironically, shut off by light - not turned on). These signals pass through Ganglion cells, through the Optic Nerve, and interpreted by the brain. When some cells are switched on, like a 3-Way traffic stop, they will prevent the information from other cells being transmitted.

A simple way of explaining it might be that inside our eyes are millions of teeny-tiny molecules that act like light-switches, and the brightness and color of light determine which of the "light-switches" are on or off.

If you want to go further into the actual mechanisms (or just have the background knowledge for future reference) the next diagram shows the mechanism itself (and the original in full-size since the one shown is squished if you prefer):

The big things to note above is the change from cis-Retinal to trans-Retinal which occurs after a Photon is absorbed. This causes signaling molecules to go a bit wild, open ion channels, and the depolarization of the membrane propagates the charge down the cell - much like a neuron.

I have never quite understood this idea that an object has a colour depending on the light that hits it. Okay, I understand that in low light objects have a different colour because there is a not much light hitting it and that different objects absorb different wavelengths of light and therefore appear as different colours.

Well, let me stop you here. Low-light is a different situation than colored-light. Let's get the basics down:

Photons are absorbed by the electrons of the atoms that compose the molecules of an object. Whatever Wavelength of light is not absorbed by the electrons is reflected, and it's this Wavelength that we perceive as the color of the object as our Cones absorb the reflected light.

Photons can also be emitted when an electron moves to a lower-energy state. The Wavelength emitted by the electron is directly related to the difference between the High and Low energy states, as this diagram shows fairly well:

The emitted photons are the object's "Incandescence" - which is when an object produces a color of light by itself. The color you perceive is NOT going to change if the object emits incandescent light because the object is generating its own light. Neon signs are a great example: The gases being subjected to a current emit light, and will appear whatever color it's supposed to be whether or not it's a blue moon or sunset.

Photons which are reflected and not emitted - i.e. almost everything that doesn't have a power source - as I said above, are then absorbed by our Cones and our brain interprets the signals to produce a color.

The reason why objects that reflect light can change color is because not all environmental light is the same. Red objects will appear Black under Blue light because Blue light doesn't contain Red Wavelengths - there's nothing to reflect, so the object absorbs all of the available Wavelengths - the very definition of Black!

A lot of our color perception depends on ambient light, and most of the time - thanks to the Sun - that is a full-spectrum white light. Which brings me to answer the last bit of your question:

What I don't understand is that if I place a bar of gold a bar of silver side by side in the same lighting conditions they do have different colours, so therefore there must be something inherent in these object that give them different colours. What is that something?

Yes, there definitely is something inherent in both objects. That is: Their electron configurations absorb different chunks of the spectrum, and accordingly reflect different chunks of the spectrum. Although that's still a bit simplistic, since metals have some unique properties that other Elements do not. Their electrons exist in more of an "ocean" than around central atoms, but that's a whole other question.

As a fun bit of Trivia to impress your daughter when she's old enough, it's always a fun fact to know that the color Yellow is completely constructed in your head.

The human eye only has Rho (Red), Gamma (Green), and Beta (Blue) color receptors which have the following absorption pattern (from photo.net):

What everybody sees as "Yellow" is actually when both the Green and Red receptors are activated at the Wavelength where they intercept above, which your brain interprets as "Yellow":

Because your brain does a lot of processing, despite having only three color receptors we can perceive millions of colors (and shades/tones). Now for a while everywhere you look you'll be utterly amazed at what's going on, and you rightfully should be. ;-)

citations - What address to put in bibliography for Springer (and others)?

Some publishers like Springer appear variously with different addresses. Sometimes (in the case of Springer) it's "Berlin, Heidelberg", sometimes it's "Heidelberg, New York", or even "Berlin, Heidelberg, New York, London, Paris, Tokyo".

Should I, eg. in a thesis, just settle for one address per publisher and stick to it, or is there a different correct address for each publication?

Answer

It's better to put what is on the copyright page of the book in question. If you don't have it, then you may have to punt, but wherever you can use the full reference, you should.

Edited to add: The goal in a citation is to allow your reader to find the exact work that you used, so you need to be as precise as you can. If there are different editions, etc, they may have different publication locations, so make sure you described the physical volume you have precisely. If you don't have the physical version, then be sure to give your reader 50 years from now the ability, as best you can, to track it down.

physiology - Why do small organisms make faster movements than big organisms?

I hesitated to ask this question because it seems so obvious and intuitive. However, I am not able to explain this tendency.

Background

It seems to me that small organisms make faster movements than big organisms. I don't mean that they are able to travel at higher speed (the cheetah is a big animal and is the fastest terrestrial species) but I mean that their movement are fast, quick and their members undergo high acceleration.

Examples

I would guess for example that the legs of a tiger beetle (clade of fast sprinter beetles) (see movie) undergo much higher acceleration than the legs of a cheetah (fastest terrestrial organism on earth) (see movie). To avoid taking the extreme, I would think that the legs of a Drosophila (see movie) undergo higher acceleration than the legs of a dog (see movie). The organism that is able to create the fastest acceleration is the mantis shrimp. Wikipedia says:

Both types (smashers and spearers) strike by rapidly unfolding and swinging their raptorial claws at the prey, and are capable of inflicting serious damage on victims significantly greater in size than themselves. In smashers, these two weapons are employed with blinding quickness, with an acceleration of 10,400 g (102,000 m/s2 or 335,000 ft/s2) and speeds of 23 m/s from a standing start. Because they strike so rapidly, they generate cavitation bubbles between the appendage and the striking surface. The collapse of these cavitation bubbles produces measurable forces on their prey in addition to the instantaneous forces of 1,500 newtons that are caused by the impact of the appendage against the striking surface, which means that the prey is hit twice by a single strike; first by the claw and then by the collapsing cavitation bubbles that immediately follow. Even if the initial strike misses the prey, the resulting shock wave can be enough to stun or kill the prey.

Finally, note that Gabel and Berg (2003) show that the flagella can rotates up to 270 Hz.

Questions

• 
  

  Am I right to think that small organisms tend to make faster movements than big organisms?

  
  


• 
  

  If yes: Why do small creatures make faster movements?

  
  
  
  
  • Does it has to do with time for chemical diffusion?
  
  
  • Does it has to do with mechanics? ($F=ma$... But muscles are smaller as well).
  
  
  • Does it has to do with the resistence of biological tissues?
  
  
  
  • ...
  
  
  
  

---

Answer

It's a general phenomenon that the time scale correlates with the size scale of complex systems. Energy consumption is the main concern dealing with the speed for biological organizations. In the absolute sense, a turtle has a higher speed than a small bug. But based on their sizes, the bug seems much quicker and faster. So we need to normalize the speed with the size scale which we can temporarily call 'fastness".

Here is the relationship between the fastness and the mass:

Where u is speed of the organism, M is mass, alpha is a constant which we assume that the metabolic energy is related to the body mass of the organism with a power law.

The final equation says that if alpha > 1.67 then the larger would be faster. But our observation tells us that the smaller the faster. Therefore, we know alpha < 1.67. In fact Kleiber's law tells us that the alpha is about 0.75.

You can check some numbers related to some animals here

Are the referees of a journal allowed to reveal the title of the papers they review after the review process?

I am wondering if a referee can reveal the title of the papers he/she has refereed for a journal (either by talking about it in the pub, posting it on facebook or another mean) after the decision has been made.

The reason for my question is that I have seen some people revealing titles of the papers they referee but I have not found an authoritative reference for judging this behaviour.

Answer

Don't do that.

Everything related to reviewing is confidential.

You will certainly upset some editors if you reveal your identity to the authors without the editor's permission. (Remember that the authors usually know who was the editor. Perhaps the editors did not want the authors to know that they asked you to review the paper?)

More generally, there is nothing to gain by doing this, and everything (= your reputation) to lose. You do not want to do anything that someone might interpret as a violation of the confidentiality of the peer-review process. (Even if you had both the authors' and the editor's permission to publish this information, others might not know that.)

species identification - Questions about insects eating flour and living in the cracks of a wooden cutting boards

I have a large wooden cutting board which is used in my kitchen mainly for preparing egg pasta. The wood type is Populus (poplar or aspen or cottonwood).

The main ingredients used with the cutting board are: flour (mainly soft wheat flour), hens' eggs, white sugar, butter, and baking powder.

After the food preparation, the cutting board is cleaned by scraping away the ingredients remains.

The board has some cracks and some small unknown insects are living inside the cracks.

The board has also a lot of holes due to woodboring beetles but I think the woodworms operated long time ago and they no longer live in the cutting board.

The unknown insect has an approximate length of 1 mm (along the direction of their movements) and a width of 0.3 mm. The unknown insects do not have wings, they just walk. I am not able to see how many pairs of legs they have.

The color of the insect is pale brown.

The cutting board was free from these unknown insects some months ago but then they appeared.

My questions:

1. What insects are they?


2. Are these insects poisonous to humans?


3. How can I get rid of them?

Update

The unknown insects could be Acarus siro, I will try to get a picture of the insects.

Update 2

Here is a picture. The bottom part of the image is a one Euro coin, the top part of the image is a caliper (each bright area is one mm tick).

Some more pictures:

Answer

This is a species of psocid (of the family Psocoptera, AKA booklice).

Species are best differentiated by their abdominal structure and antennae. Without a better (more magnified) image and info about the OP's location, identification to species is not possible. Though its small size will definitely narrow the options.

If I had to guess based on the limited detail (and my limited knowledge), I'd say it's a species in the genus Liposcelis or related genera. See Oklahoma State's ENTOPLP ID key for examples and info. I've included 2 random images of Liposcelis species for reference: the (TOP) is Liposcelis brunnea and (BOTTOM) is Liposcelis corrodens.

You can find info about prevention and removal from Oklahoma state, King's College London or the Orkin man.

UPDATE: Though I, myself, cannot identify this psocid to species, according to this KCL article, Liposcelis bostrychophila is the most likely candidate. [See here for ID notes].

From the KCL article:

Liposcelis bostrychophila is the principal psocid pest species in the UK and in Europe. This single species, which is mainly an inhabitant of households, is responsible for virtually all of the psocid related complaints in the UK (Turner & Ali 1996)...Recent estimates are that 30% of households contain this species.

Several other small (about 1mm long), flattened, wingless liposcelid species (eg. Liposcelis corrodens, L. pearmani and L. brunnea) can become quite common in industrial sites, particularly in the summer months but are uncommon in domestic premises.

job search - Leaving PhD program to apply for industry job - better to apply while still officially enrolled?

I am going into the fourth year of a PhD program and my research, which is in a STEM field, has clear applications in the tech industry.

I have my Master's degree, but have decided not to finish the PhD.

Is it important to be enrolled while applying for jobs rather than be unemployed? Will the people hiring view me differently?

Note: being enrolled brings some significant demands on my time.

Answer

Being unemployed can significantly decrease your likelihood of successfully landing a job. The preceeding link is one of many stories covering that angle. The best graph describing how bad it is comes from this Atlantic article:

The upshot of most of these is that employers have a psychological bias towards employed people. Whether this is "fair" or "appropriate" or even "smart" not is really not the question, the finding is pretty difficult to refute: you are far more likely to land a job if you are currently gainfully employed.

To bring this back to your original question, I would strongly recommend you begin your job search before you leave the program.

molecular genetics - Do cell walls prevent cancer?

To my knowledge plants do not have an uncontrolled growth disease similar to cancer. Is the function by which they avoid uncontrolled growth related to their cell wall and preventing damage to DNA/RNA? Is their telomerase special in some way in that it does not indefinitely replicate?

Answer

Plants do have uncontrolled tumorous growth. Though in almost all known cases, it is pathogen induced; such as in the case of the bacterium- Agrobacterium tumefaciens. Viruses can also induce plant tumors. Theoretically, the cell wall will pose a mechanical barrier to cell division. Also, cell wall synthesis is an extra biochemical step during cell division. Surely, the presence of a cell wall will disallow any metastasis if it might occur. There is an old article which says that cell wall structure differs between the normal plant tissue and the crown galls (tumor). However, this is with respect to Agrobacterium adsorption sites.

I am not aware of any natural plant tumor or the role of telomerase in plant tumorigenesis. However, there is one paper that says that telomerase dysfunction leads to disorganized growth.

publications - My paper was too revolutionary - reviewers at a top journal rejected it "by simply reading the title". What now?

Some days earlier, in the hour of contemplation, I made an extremely critical and paradigm-shifting breakthrough in my field and then, I started writing on it for a publishing and many times checked through the paper and finally submitted it after many days of proofreading.

The paper was committed to the biggest and most popular journal for my field, and I waited for a reply. And the reply was saddening, my paper was mysteriously rejected. As I contacted the reviewer, I was told that he and others "rejected it by simply reading the title".

And my title was very professional, in the sense that it was not something like "X proven wrong and Y revolutionized!".

Now I am confused on what I should do, this paper needs to be published. If not for myself, then atleast for the thousands of other researchers who have hopelessly comitted their lives to this field.

I must add here, as my advisor congratulated me and hugged me on this great discovery, he was skeptical of my paper being published because it is simply too outstanding to be true. And big journals who receive thousands of paper each day will most likely reject it in quickness, and this paper needs to be read with a lot of thought and concentration to be believed. He advised that I should submit it to a lesser known journal whose reviewers he is great friends with, so that he'll tell him to take a good thoughtful look at it. He assured me that my paper would be accepted there. However, I might have naively not considered this and simply went for the biggest journal out of extolment.

So what should I do now? And is rejecting a paper because it is too good even a valid reason?

paper submission - How can I withdraw a publication from a predatory (fake) journal and resubmit to a legitimate journal?

I have published a paper in a fake journal. I want to withdraw the paper from that journal.

After successful withdrawal from the fake journal, can I can submit the same paper to a legitimate journal?

research process - Collaborating (online) with researchers from other institutes/countries

I am a first year graduate student in a completely theoretical field. How does one go about collaborating online or otherwise with researchers from other institutes/universities? In particular, if I am interested in a problem or an area which is not very well represented at my current institution, how do I approach researchers from other institutes to start a collaboration assuming I have the basic background to start research? Should I have a very particular problem/idea in mind while contacting a potential collaborator, or is it unusual if I approach a researcher just because I am interested in his work and would like to learn more and work on it with no particular problem in mind?