Nowadays, in almost every scientific field, there are hundreds of conferences. Many call for papers emails fill our mail boxes.
Freedom of choice is great, but, how to choose to which conference send a paper?
Should I choose one...
based on the scientific relevance?
based on the scientific vicinity to your paper theme?
based on its prestige?
because of some official ranking?
because it provides the best food?
Is it okay to discuss personal experiences or observations in literature review as long as they are relevant and contribute to the presentation of the summary of literature?
In other words, I am not intending to reference or cite any of my experiences as a source, but rather, I am seeking to use my experiences to essentially add to the research story.
For instance,
The Blah Blah theory by Smith (2010) suggests A, B, and C. I experienced event M and I observed event N, which may potentially be manifestations of the phenomenon described in the Blah Blah theory, with event M being a possible example of A and event N being an example of C.
Something to this extent.
Many of the papers I have read primarily use examples from their studies or hypothetical scenarios to explain models/theories, but I have only ran across personal experience examples in textbooks and not in academic review papers or theses.
Answer
Although you didn't quite ask it this way, I see two parts to your question, and I will offer answers accordingly: "Is it okay to discuss personal experiences or observations in academic writing?" and "Is there any difference when it comes to literature reviews?"
Is it okay to discuss personal experiences or observations in academic writing?
Although it is controversial (some people will tell you never to include personal experiences), I think there is a place for personal experiences. But first, you need to understand why this is generally frowned on.
Everyone has personal experiences and everyone has different ways to interpret them. Anyone can write a magazine or blog article sharing their personal experiences. That's just their opinion, which the reader could take as good or bad. What separates an academic article from such opinions is that academic writing is usually expected to be fairly objective (tries to take a disinterested third-party perspective) and critical (takes nothing at face value, but tries to dig under the surface to understand what is really going on from multiple non-obvious perspectives). (One notable exception to this is critical social theory, which does not necessarily try to be objective, but nonetheless strongly emphasizes being critical.)
So, where do personal experiences fit in here? Most of the time, they are not objective (by definition) and all too often, they are insufficiently critical. This is why they are often frowned on. However, I believe they could be helpful and acceptable if the writer considers their own personal experiences this way: "What makes my personal experience more outstanding than other random personal experiences related to this phenomenon?" If there is nothing particularly outstanding about it (e.g. it merely serves to illustrate the point, as do other people's experiences), then it is best not to mention it, since such a mention would weaken an otherwise strong academic argument. But if it is unique or original (e.g., the entire study is propelled by the fact that the writer's personal experiences contradict the dominant scholarly discourse), then it is definitely worth mentioning. However, in such cases, the writer should try to describe their experience as objectively as possible and should be critical in not accepting their own interpretations of their experience at face value. When presented properly, such personal experiences can strengthen the credibility of the writer.
Is there any difference when it comes to literature reviews?
I believe the principle I laid out for academic writing in general also applies to literature reviews. However, there are two levels or two aspects to a literature review that you need to distinguish in this case:
Including your personal experiences as part of the "literature" being reviewed: NO. Your personal experiences are not "literature". "Literature" means published works (by "published" I include grey literature such as working papers; I also include non-scholarly practitioner publications). It does not include unpublished, unwritten anecdotes. That is at best to be considered primary research, which is never part of "literature" being reviewed in a literature review. (Don't misunderstand me; you are certainly free to supplement a literature review with original primary research if you want to, but you just have to clearly distinguish that from the "review" part of the article or chapter.)
Including your personal experiences as part of the introduction or discussion of your literature review: In this case, since you are clearly not presenting your own experiences as part of the "literature" being reviewed, then my comments above apply. I see no problem with this if it is done properly. But again, this is controversial; "controversial" means that your supervisor or journal editor might disagree, and so you might have to drop it regardless.
What is the probability of conception in situations when sperm isn't directly ejaculated into the woman's vagina, like:
In all these situations, it seems possible that a tiny amount of sperm is eventually transferred into vagina indirectly. And since just a single cell is enough to fertilize, it seems that there is non-zero probability of conceiving. How much care need to be taken to prevent conception in such situations? Does simply washing sperm away with water (+ soap perhaps) eliminate it?
If you think of similar situations that are similar, please don't hesitate to add them.
I managed to successfully publish my old bachelor thesis in a good quality national journal in my country. However, I am thinking of retracting the article due to certain circumstances. First, I felt really embarrassed by the low quality research methodology used in my bachelor thesis. I only used simple correlation in my research. After it was published, I realized that the journal editor team forgot to include a reference in that article because they were rushing me throughout the editing process. I informed them about their mistake and it seems that they have done nothing to fix the problem. I became a bit annoyed because the editor team has never made this problem in the past.
I felt that it would be better for me to simply ask for retraction to solve this issue, but I am a bit afraid of negative consequences in the future. Is it okay to do this? I am really interested of entering the academic world in the future.
I am a PhD student in Europe and also TA for some bachelor's degree classes for my supervisor. Just by chance, I have found an open Facebook group (normally, the group aims to create an interaction between students and opened by students as well.) in which people in class insult me very harshly about the way I do the tutorial and my personality. (How I look etc.)
How to react or not to react, really? Any suggestions in order to be objective in evaluation of those students? Because, I don't want to introduce any personal judgemental issue for those who insult when I grade midterms.
I'm currently uploading my MRes thesis to my university website, but I have some doubts regarding the permanence of the link as it may change after I graduate. I do not have many illusions over who may want to read my thesis in the future, but I would like to have a link to give to people or to put on papers in the future without fear of the link breaking in the near/mid/far future. Additionally, I know that having it available in a place spiders are more likely to look makes it (marginally) more visible to web searches and thus more discoverable.
A quick search turns up a good bunch of PhD theses, but it doesn't say how many there aren't very many MSc or BSc theses in there. My reading on this is that it is OK but by no means a standard practice.
Before I upload it though, I would like to know if there are reasons not to put it in such a public place. I am after all a bit of an arXiv fanatic and there may be factors I'm not considering. Any thoughts?
Answer
There doesn't seem to be any real restriction on publishing theses of any kind to arXiv. Therefore, whether you choose to do so is a decision that should be made between you and your advisor, taking into account any regulations your school may have. If your work has been funded by an external agency or company, you should also take their requirements under advisement.
However, so long as your topic falls under arXiv's category guidelines, and there are no restrictions preventing you, there isn't much to lose by submitting the final version of your thesis to a public repository. It would ensure far greater visibility for your thesis than if it's left on your university's website alone.
I have a pure mathematics problem which I formulated after years of research in signal processing of audio signals and years going into formulating a problem on precise mathematical terms, which is a provable/disprovable mathematical statement. (I avoid using the term conjecture as I am not qualified enough)
My belief is that it has very important applications in real world signal processing. I want to solve this math problem, and I need funding, research environment, collaborators, and access to mathematicians for discussions. All this I believe is provided by a PhD position in a University that is serious about path breaking research. My goal is to solve this particular problem and not any other problem.
How can I go about achieving this goal?
Edit : summary of problem
In effect i have proposed a new formula for inverse fourier transform with no assumption on its jumps except that they are finite and absent beyond a certain point. This new formula ensures not only pointwise convergence but also convegence of variation. Classical Fourier formula does not have convegence of variation in the presence of jumps.
I have to request a faculty member outside of my department to be on my thesis committee and I was wondering how I should go about doing this. To be frank, I don't really see why someone would be willing to be on the thesis committee for someone outside their department and even field - apart from the altruism of wanting to help others in academia and all, but I assume professors are busy! Therefore, I imagine that it's hard to convince someone to do this?
In any case, I was wondering:
what information about myself should I aim to include in an email request to a potential thesis committee member outside my department?
In addition, while I need to find someone to file my candidacy papers, but I have only a vague idea of what my final thesis will look like (I know the field, but not the particular question it will address.)
Some things I have come up with include:
Answer
From my experience, having cross-department committee members is very common, and can actually be very beneficial to the student, as you gain access to expertise and perspective you might otherwise miss. There's usually at least some connection between the research being done and the expertise of the faculty member. To use myself as an example, my research involved behavioral neuroscience, but I had both an electrical engineering faculty with signal processing experience and a psychology faculty on my committee, and they both gave very useful advice with my project. That being said, I had a committee member who was completely unrelated to my work (my focus shifted midway through my PhD career), and he requested to still stay on despite the lack of direct research connection; he was happy just to give advice and provide feedback.
You can find potential committee members by talking to other graduate students, and by looking at what theses professors have worked on (as you suggest above). I definitely recommend talking to other students; some professors are more difficult to work with than others, and you likely won't get that type of information from your advisor.
Regarding how to go about talking to the professor, I would just send a simple email asking for a meeting about this topic. If they're simply not interested, they'll say so, and you'll save yourself time. If they are, meet to discuss the following:
Shortly before his untimely passing, the computing pioneer Alan Turing published his most cited paper The Chemical Basis of Morphogenesis (1952).
The central question for Turing was: how does a spherically symmetric embryo develop into a non-spherically symmetric organism under the action of symmetry-preserving chemical diffusion of morphogens (as Turing calls them, an abstract term for arbitrary molecules relevant to development)? The insight that Turing made is that very small stochastic fluctuations in the chemical distribution can be amplified by diffusion to produce stable (i.e. not time varying except slow increases in intensity; although also potentially time-varying with 3 or more morphogens) patterns that break the spherical symmetry.
The theory is beautifully simple and abstract, and produces very important qualitative results (and also quantitative results through computer simulation, which unfortunately Turing did not get to fully explore). However, even in the definition Turing discusses some potential limitations such as ignoring mechanical factors, and the inability to explain preferences in handedness. The particular models he considers -- a cycle of discrete cells and a circular tissue -- do not seem particularly relevant. As far as I understand, the key feature is his observation of symmetry breaking through small stochastic noise and instability.
What was the most important contribution of Turing's paper to developmental biology? Is his approach still used, or has the field moved on to other models? If his approach is used, how was the handedness problem resolved?
Answer
This is a very interesting question. Many people have researched this topic, and many still are. But regardless, I had never heard of Alan Turing's contributions, so thank you!
First of all, I cannot actually find who first coined the term morphogen. Though people had hypothesized that chemicals could play a critical role in development through much of the 20th century, I cannot actually find the first person to use morphogen. But the most important paper really came from a guy named Lewis Wolpert, who came up with the model of a gradient of morphogens leading to differential cell fates. The idea being that if some area of an embryo produces a morphogen at a very high concentration, then as you move away from that area, the concentration goes down. So if this morphogen is required at or above a certain threshold for activity, then only those cells with that concentration will have a certain cell fate, while at lower concentrations, the cells can become something different.
But this does not really answer your question. You are asking how a single cell, which is spherically symmetrical, can determine a particular axis. Though most organisms do this is in slightly different ways, the most common feature is that sperm entry point breaks the symmetry. The best way to explain this is to show you a diagram of Xenopus (frog) eggs.
Image from: http://studentreader.com/nieuwkoop-center/
The Xenopus egg, first of all, is inherently not spherically symmetrical. There is a black animal pole, and a white vegetal pole. The sperm can only enter a marrow region of the egg about 30˚ north of the animal/vegetal line. Upon fertilization, an event occurs where the pigmented areas turn toward the sperm entry point, leaving a gray crescent. Nearby the gray crescent, in the vegetal pole, a structure called the organiser develops. This organiser creates many of the morphogens that then pattern the rest of the embryo.
Researchers have studied this a lot in many different organisms, but a few things really remain constant: eggs are not exactly spherically symmetrical, and the sperm entry point provides asymmetry.
I am currently writing a paper for the thesis work I did last year along with my advisors. (I successfully graduated last year and currently work in a software company.) I am confused regarding what organization I should mention in the author's section. Should I mention my university name since I completed my thesis work when I was a university student or the name of the company I currently work for?
Answer
I will take a somewhat different view from @jakebeal's answer.
The primary question is: when did you work on the paper? Did you do all of the work while you were a thesis student, and then the paper has slowly made its way through the system? Or did you actively work on it as part of your new job? Did you use institutional resources from your new position to do any part of the paper?
If the answer to the latter is no, then you should only list the old institution in the actual affiliations, and then list your new job as a "present address", if you so choose. If you worked on the paper as part of your new job (beyond rote submission and minor edits), then you should list both workplaces as "active" affiliations.
In academia in the US, the dominant name format is [firstName lastName]. And in APA citation format you typically cite by referring to the last name. So e.g. if John Doe wrote a paper in 2014, you might cite it as Doe (2014).
More generally you'd cite by referring to the family name. So e.g. if the Chinese basketball player Yao Ming wrote a paper in 2014, you would cite it as Yao (2014), since Yao is his family name and Ming is his given name. But there is typically no confusion anyway, because when East Asians publish in Western academia, they simply give in to Western convention and reverse the order of their names. So Yao Ming would typically simply have his name printed as Ming Yao. And so we're back to the [firstName lastName] format and there is no confusion.
My question is: What about patronymics? E.g. if Osama bin Laden writes a paper in 2014, should he be cited as Osama (2014) or bin Laden (2014)? It seems that unlike with East Asians, people with patronymic names have been less inclined to give in to Western convention and reverse the order of their names. So his name would still appear as Osama bin Laden on the title page.
Suppose I notice that everyone simply cites his paper as bin Laden (2014). (Indeed, in the real world, this is how Western media outlets often refer to this historical figure, even though this makes as much sense as referring to George W. Bush as simply George.) If I want to cite this paper, should I simply follow what is now the convention and cite it as bin Laden (2014), even though this is mistaken? Or should I cite it as Osama (2014), at the risk of my peers having no idea which paper I am talking about? What is or should be the proper convention?
Note that this 'problem' is not limited to Muslim names. Even in Europe there are e.g. Icelandic names. There are also some cultures where people go by a single given name (i.e. no last name/family name/surname) but which may sometimes be composed of more than one word (e.g. sometimes in Mongolia, Burma, South India, Indonesia).
there are similar questions on how to list on CV publications that have not passed the accepted or in press stage when applying to junior research positions ( PhD/postdoc).
I am not clear if such publications should include the journal name or not, and what would be the reason for either choice.
Answer
Everyone I know feels that "accepted / in press" is just as good as appeared: the delay between acceptance and publication has nothing (or anyway, too little) to do with you. You should certainly list them on your CV, no matter who you are. I don't even list these as in a different category as the ones which have already been published: the only difference is that (roughly speaking; electronic publication and DOIs complicates this somewhat) I can't tell you the bibliographic information if it hasn't appeared. I think it is very important not to list a paper as accepted without listing the journal, because therein lies the route to verifiability that your paper has been accepted.
In my opinion, you should list submitted articles on your CV no matter who you are. (I would be interested to hear why @aeismail feels differently about this.) This advice comes from someone who works in a field (mathematics) for which recently submitted articles ought to be freely available: if you want to get credit for having submitted an article, then whoever you are trying to get credit from ought to be able to see the article. Ideally they don't have to ask for it specifically (because maybe they won't), so you should include a weblink to submitted papers on your CV. (This last part is more for people who are in a potential-hire situation...which is not restricted to grad students and postdocs. Nowadays, lots of academics are in a potential-hire situation or would like to be.)
In mathematics, each paper takes a long time: the period between when you say "Aha, I can prove the theorem" -- and e.g. start to give talks about it -- and the period which it gets accepted is probably over a year in many cases, and closer to two for serious, important work in many cases. Who is reading this part of your CV and isn't interested in what you've been working hard on for the last year or two?!?
Whether to list the journal submitted to is a well known question mark. I do not put this information on "external" documents -- i.e., the CV and the publication list which are on my professional website. I do usually list it on "internal" documents -- annual reviews, grant applications, job applications (well, it's been a little while). There are a lot of nuances here: one is that it is really hard to know how much credit to give someone for submitting a paper to journal X. After all, anyone can submit a paper to the most prestigious journal in their discipline, and in many cases they will spend a nontrivial amount of time before rejecting you. So you want to be careful about this. Nevertheless, where you submitted a paper is an important piece of information about how you feel about the paper, which is worth including in various cases (e.g. grant applications, where the panel will be suitably skeptical). Another issue is that one commonly submits to more than one journal (not at the same time, but in sequence) so the information about where you submitted a paper is likely go out of date, so is less suitable for a sporadically updated CV and more suitable for a CV guaranteed to be complete up to such-and-such a date.
Note also that in my discipline, many people -- especially young people but not always -- also include papers which are "in preparation" on their CVs. This is, frankly, a little shaky: I have papers on my own CV which have been "in preparation" for getting on a decade. But the above philosophy still applies: if you've been working on something for five years and you're 75% done, then shouldn't you say something about it?
One last piece of advice: it behooves you to make absolutely clear the distinction between all these categories. I get annoyed as a hirer when people use categories that don't fit easily into any of these boxes: e.g. some job candidates list papers as provisionally accepted, conditionally accepted, or accepted pending revision. What a hiring committee litmus test that becomes: their proponents will insist that these be counted as actual publications, their detractors will insist that they don't count as any more than submitted, and people in between will get a headache.
(I don't mean to imply that it's necessarily the candidate's fault. Sometimes the journal tells me that my paper has been provisionally accepted, and when I need to create a CV for a grant application that gives me the very same headache: please give me a paper status that has a clear, unambiguous meaning! They do enjoy their little games, the journals...)
I recently deleted a response on Academia.SE because many people thought my response was supporting the idea of a 'diploma mill'. My understanding of the matter was that a diploma mill is simply a business that provides a piece of paper, and possibly some kind of shady verification service, for a fee. That's it. Money in, diploma out. This does not seem to be the case for many of this community, however.
I've done a bit of research, cursory to be fair, and the most clearly defined line that I can find between a "real" school and a "fake" school is that of regional accreditation. Beyond that it appears to be a subjective melange of opinions, ultimately boiling down to the idea of 'second class schools'. Clearly, I am out of touch with the general consensus on this matter so I put it to you SE.
What are the defining characteristics of a 'diploma mill'?
Answer
We should start with the Wikipedia definition:
A diploma mill (also known as a degree mill) is an unaccredited higher education institution that offers bogus academic degrees and diplomas for a fee. These degrees may claim to give credit for relevant life experience, but should not be confused with legitimate prior learning assessment programs.
If a student doesn't have to do any academic work for a degree, or the student is given credit based on "life experience," it qualifies as a diploma mill. Another key indicator is whether there are actually any teachers that work for the business. While it is probably not illegal in most cases to claim a degree from such a company (and I deliberately do not use the term "institution"), there have been many cases of employees being disciplined or fired for using the degree to either get a job or to obtain a higher salary based on claiming a degree from a diploma mill (esp. teachers whose salaries are based on the level of a degree).
As the Wikipedia article notes, there are legitimate schools that have a system for awarding credit based on other formal education, such as military education obtained while on active duty or in the reserves (see, for instance, this guide to transferring credit). This type of credit transfer is rare for graduate work, although certain rigorous post-baccalaureate programs in the military, such as the U.S. Navy's Nuclear Power School, may qualify for some post-B.S. programs. This type of credit should not be confused with work obtained at the military's post-graduate schools, such as the Naval Postgraduate School or the Air Force Institute of Technology.
Diploma mills should also not be confused with for-profit education, such as the infamous University of Phoenix. Arguments over the merits of for-profit education are not really within the scope of academia.stackexchange, but for what it's worth, degree-granting institutions of this type do require students to follow a curriculum, take actual classes (many times online), and give grades based on assessed performance (and charge a good bit of money per credit-hour).
Bottom line: if you have to pay a nominal fee for a "degree" that requires no official classes or research, you got your degree from a diploma mill.
I am admittedly an undergraduate so I do not have very much experience yet in finding resources.
When I have an idea of something I would consider worthwhile to research (in my case for a proposal to a supervisor about an undergraduate research opportunity), assuming I do extensive research online to see what has been found out about the subject and end up concluding that what I want to look into has not been investigated yet.
How can I ensure that it actually hasn't, and it isn't just a case of me not finding the information that is already available somewhere?
Answer
This is of course always hard to protect oneself from. However, I would say the best way to ensure that your research proposal hasn't been investigated before is to get in contact with an expert in the field and ask him or her this.
Of course, you should investigate the topic thoroughly before approaching the expert. One tip to do this is by using a citation index. This enables you to track how a certain paper has been cited, meaning you can follow the trail and more effectevly find out what has been done. For example, if you have located an old seminal paper in your field, finding out which papers have referenced this one should give you a fair chanse of finding what you're looking for.
Throughout high school, I remember learning about Darwin's theory of evolution as if it were near-fact. But something always seemed wrong about the ideas presented.
All of these things seem to account for some margin of evolutionary progress, but I always remained skeptical that the extremely complex features of life could have formed from these methods alone, even after hundreds of millions of years.
Here's what I notice:
Any time a species has needed the development of a specific feature to survive, it has developed that feature, and that feature precisely.
I'm going to use this example:
Turtles on an island where shrubbery grew higher up developed longer necks, to reach the leaves.
I imagine that turtle looking up at that food, and sub-consciously wishing to get to it, constantly straining, for its entire lifetime.
It seems plausible to me that we (advanced life) could have a biological mechanism to "write" needed alterations into either our own DNA or our reproductive DNA over time, triggering the very specific evolutionary developments necessary to our survival without relying on random mutation.
My question:
Is this possible? Does any similar mechanism exist that we know of? If not, how can so many specific (advanced) evolutionary leaps be otherwise explained?
Answer
This entire answer will be long, so read the short part first, then read the rest if you (or anyone else) is curious. Citations are included in the long section. I can include additional citations in the short section if needed.
Long Story Short
Your question touches on some common misconceptions about how the evolutionary process. Organisms don't "want" to evolve traits. Traits evolve through the biological processes of random mutation and natural selection.
Organisms do not "want" to evolve traits. (Well, OK, I'd love to evolve an extra pair of hands but that is not possible.) Natural selection works by modifying existing traits. Your turtle can stare all she wants at food out of reach but she will not evolve a longer neck. Instead, natural variation exists among neck lengths of the turtles because of variation of the genes that determine features related to overall boxy size. Those individuals with longer necks may be able to get a bit more food, live a little longer, and reproduce a little more. They will pass along their genes to their offspring, so perhaps more of their offspring will also have longer necks. Over many generations, the turtles may have somewhat longer necks.
A common misconception is that the traits of organisms are precisely adapted for a specific need. They are not, for a few reasons. First, natural selection occurs relative to the current environment. Adaptations that work well in one environment may not be so useful in another environment. Environments are rarely stable over evolutionary time so traits are subject to constant change.
Next, as mentioned above, natural selection can only work on what traits are present. While an extra set of arms would be handy, I am a tetrapod. My four appendages, along with the appendages of all other tetrapods, trace back to our common ancestor. The appendages of all tetrapods are modifications of that ancestral trait.
Finally, organisms haven't "sampled" the entire realm of possible mutations and combinations of mutations. In other words, a certain mutation or set of mutations might actually be able to adaptively improve a particular trait in the current environment but, if the mutations never occur, then the improvement can never happen.
We only need to look at ourselves to realize how imperfectly adapted we are. We get bad backs and knees because our bodies weren't designed to walk upright. We evolved from quadrupedal organisms. This has happened so recently that changes in the structure of our knees and backs haven't yet evolved (and may never). Search the internet for the "blind spot" eye test. We have a mass of blood vessels in front of the retina of our eyes, which reduces our visual accuity. We often have to have teeth pulled from our jaws because the flattening of our face (relative to our australopithicine ancestors) has shorted our jaws. We don't have as much room for our teeth but we have not evolved a reduced number of teeth.
As for human technology being able to make direct changes to our DNA to improve our adaptability, I would say no. While I do not have the ability to see into the future, the complexity of our genome, and more specifically how genes are regulated, suggests to me this would be a very daunting if not impossible task. See the long answer below for more on regulatory genes but the gist is that a small set of regulatory genes control most of the other genes (including other regulatory genes). The interactions are extremely complex and we have a detailed understanding of very few of these interactions. I speculate that affecting one such gene in a "positive" way is very likely to have many unintended negative consequences.
Below are some simple math and other ideas to show you how mutations can lead to the many adaptive traits that you see among the diversity of life on earth.
Long Story
how can so many specific (advanced) evolutionary leaps be otherwise explained?
Mutations occur at random throughout the genome. Most mutations will be neutral. That is, they are neither bad or good from an evolutionary viewpoint. The mutations are neutral because the genome for most organisms is non-functional. Mutations that occur in the functional regions of DNA (i.e., protein-encoding and related regions) are more likely to be detrimental (bad) because the mutation may negatively affect the function of the protein or even the ability to produce the protein. However, some mutations are beneficial. The mutation may actually enhance the functionality of the protein or even produce new proteins.
A couple of factors have to be considered regarding mutations. The mutation rate is very low. For example, Kumar and Subramanian (2002) compared the DNA sequences of 5669 protein-encoding genes from 326 species of mammals. Their results suggested that the average mutation rate among mammals is 2.2 x 10$^{-9}$ per base pair (bp) per year. This means that, on average, a point mutation has changed each DNA nucleotide position in the mammalian genome slightly more than twice (2.2 times) every billion (10$^9$) years. That's a lot of time!
However, this same rate occurs in every individual in the population, so you have to consider the population sizes of the organisms. So, let's do a simple exercise. Consider a species like the rock pocket mouse or another small mammal that has a very short generation time. For this simple example, let's assume the generation time is one year. That means that the mutation rate of 2.2 x 10$^{-9}$ per bp per year would then correspond to 2.2 x 10$^{-9}$ mutations per bp per generation. Generation time is important because new mutations are inherited only through reproduction.
Assume the average mammalian diploid genome is about 6 billion (6 x 10$^9$) nucleotides in size. The number of heritable mutations that occur in a single offspring is
$$(6 \times 10^9) \times (2.2 \times 10^{-9}) = 13.2.$$
Next, assume that about 2.5% of the mammalian genome is composed of functional, transcribed sequences that may affect the phenotype (the traits of the organism). That means that, of all the mutations that occur in every offspring every generation, about 2.5% could potentially affect the phenotype. That is,
$$13.2 \times 0.025 = 0.33.$$
Still a small number. But, now we have to account for population size. Small mammals, like mice and voles, generally have large population sizes. Assume that the population of rock pocket mice contains 100,000 reproducing individuals. If so, then
$$0.33 \times 100,000 = 33,000,$$
which is the number of new heritable mutations that could occur in the population. Most of these mutations will be detrimental and removed from the population by natural selection but, if even a small fraction of these new mutations are beneficial, then natural selection can cause these beneficial mutations to increase rapidly in frequency in the population during future generations.
In humans, Nachman and Crowell (2000) estimated that the average mutation rate was 2.5 x 10$^{-8}$ mutations per bp per generation (not year), by comparing the genomes of humans and chimps. If we assume the same genome size and effective human population size of 500,000 individuals, then applying the same math suggests that 1,875,000 new mutations that potentially affect phenotype occur in the human population every generation. Again, only some of these will be beneficial but that is still the possibility of a number of new beneficial mutations. In evolutionary terms, a mouse or human generation is the blink of an eye.
How long would it take for a beneficial mutation to spread through a population? That depends on two things. How beneficial is the mutation (called the strength of selection, s) and the population size? To estimate how long it would take for a beneficial mutation to spread through a population, we can use the formula,
$$t = \frac{2}{s}\mathrm{ln}(2N_e),$$
where $t$ is time in generations, $s$ is the strength of selection, and $N_e$ is the effective population size (number of reproducing individuals). For the strength of selection, let's assume $s=0.01$, which is weak but positive natural selection. Going back to our rock pocket mice with $N_e = 100,000$, then the beneficial mutation would be spread throughout the population in only 2441 generations (remember, we're talking evolutionary time so 2000 years is nothing). If $N_e = 10,000$, the mutation spreads in only 1981 generations. If we increase the strength of selection t 0.2, then the times are 122 and 99 years for population sizes of 100,000 and 10,000 years, respectively.
These "back of the napkin" calculations show just how quickly even weakly beneficial mutations can appear and spread throughout a population. Yet, this doesn't include other types of mutations like gene duplications that can also allow new proteins to evolve. For example, human ability to see red colors is due to a simple gene duplication (Nathans et al. 1996 and references therein). This duplication also explains the common form of red-green colorblindness.
Whew!
There's yet more to our mutational story. Consider humans and chimps, which are nearly identical from a genetic standpoint (between 96-99% depending on how you calculate it) yet they appear very different. If humans and chimps diverged from their common ancestor within the past five million years, how could they differ so much? This question was initially posted by [King and Wilson (1975)]. They argued that mutations to structural proteins (like those that compose bones and muscles) would not be enough to explain the phenotype differences between humans and chimps. The proposed that regulatory genes are the key to understanding the big differences. Regulatory genes are those that control other genes, by turning them on or off and other important functions. Changes to the regulatory genes can cause fairly rapid changes to the phenotype.
This understanding has led to the broad (and fascinating) field of evolutionary developmental biology. This field focuses on how mutations in regulatory genes associated with development (from embryo to adult) have had a long-term evolutionary impact. The field is rich with examples, but one cool one is associated with duck feet and bat wings. Let's begin with the embryo. Most vertebrate embryos have membranes between the digits (fingers and toes) during an early stage of development. For most vertebrates, the membranes are lost later in development. The small flaps of skin you have between your fingers are the remnants of your embryonic membranes.
A set of regulatory genes called BMPs (and a couple of others) are responsible for causing the loss of the membrane in vertebrates. However, through different sets of mutations, the BMPs are not able to function in duck feet and bat hands. Thus, they both end up with membranes between their digits (Weatherbee et al. 2006). Thus, two different mutations block the same set of developmental genes, leading to novel adaptations in two very different types of vertebrates. One final example is the evolution of bird feathers from scales. As you may know, birds are evolved from dinosaurs. It turns out that bird feathers and alligator scales (alligators are birds closest living relative) use the same regulatory genes to develop. The genes are BMP2 and SHH (sonic hedgehog for fans of the old computer game) (Harris et al. 2002). Other regulatory genes underlie the different types of feathers, like downy feathers and flight feathers (Harris et al. 2002).
Literature Cited
Harris, M.P. et al. 2002. Shh-Bmp2 Signaling module and the evolutionary origin and diversification of feathers. Journal of Experimental Biology 294: 160-178.
King, M.-C. and A.C. Wilson. 1975. Evolution at two levels in humans and chimpanzees. Science 188: 107-116.
Kumar, S. and S. Subramanian. 2002. Mutation rates in mammalian genomes. Proceedings of the National Academy of Sciences USA 99: 803-808.
Nachman, M.W. and S.L. Crowell. 2000. Estimate fo the mutation rate per nucleotide in humans. Genetics 156: 297-304.
Weatherbee, S.D. et al. 2006. Interdigital webbing retention in bat wings illustrates genetic changes underlying amniote limb diversification. Proceedings of the National Academy of Sciences USA 103: 15103-15107,
In order to build an intelligent design such as a bridge or a mechanical watch, you need a series of non useful steps.
As far as I understand, in random evolution theory, the "intelligence" involved is the process of natural selection.
The problem with this is that natural selection requires that each step be advantageous right away. If I want to build a bridge, I need many steps which would be disadvantageous until the final product which would be advantageous. This would be like trying to write a computer program where each line of code must be advantageous to the program. An intelligent design just cannot be done like this.
How does modern biology deal with this problem? To say it all happened at once, is not possible since the probabilities against this are simply outside the capabilities of a random system. Furthermore even if by some freak monumental event it happened, it would need to happen again many times since there is a huge diversity of intelligent designs in life forms such as lungs in birds vs gills in fish, or sexless reproduction in bacteria versus male/female reproduction in animals (which are fundamentally different).
(Also, as side question has there been ANY experiment demonstrating that such a thing is even possible? I mean for example, to have a computer simulation of random self-replicating molecules, then having an intelligent human being picking out the best version and eliminating the others, then repeating, etc. until you have an intelligent design.)
I need an advice about returning to academia as a visitor/post-doc after working for a year in finance.
I finished my PhD in summer 2013 with a good record of publications (3 papers in high impact journals). Both my bachelor and PhD were in applied mathematics and theoretical physics. Towards the end of my PhD I felt burned out and was unsure if I want to continue the same line of research.
Furthermore, almost all my colleagues who finished their PhDs around the same time struggled to find positions and all moved overseas, which was not an option for me at that time.
During this time a have kept in touch with my supervisor and colleagues. I also kept reading and searching for new interesting ideas. Recently I started to feel enthusiastic again and full of fresh ideas.
My question is do you think it is acceptable to approach my supervisor/colleagues and ask for a position and what is the best way to go about this?
Answer
Sure, why not? What you write makes me think that you could tell them exactly the way you tell it here: Being recovered from the PhD and full of fresh ideas.
It is not unheard of that PhD students need to recover from the PhD by doing some different kind of work for a while (such as a couple of years in industry, I've even heard of running a store in a completely different retail sector).
Personally, I think that it should be taken as a warning sign if this happens regularly. However, that consideration doesn't have anything to do with your position, but I think it is worth while remembering when you enter the side of PhD supervisors.
Regardless of how much enthusiasm you've gained back I think it would be a good idea to sit down and recall what exactly drove you away and what caused you feel (close to) burned out - in order to avoid getting there again. I somehow think it unlikely that a postdoc position would be more calm than a PhD.
With supercomputers doing calculation in petaflops ($10^{15}$ Calculations per Second), have we crossed the speed of Human Brain?
Answer
There's a very big difference between doing the calculations needed to simulate the human brain (or any animal brain - we can do a fairly decent job on C. elegans), and doing computations. While a basic leaky integrate & fire model is fairly simple, to accurately simulate a single neuron in real time takes a pretty fast computer. See e.g. these links for more, http://www.neuron.yale.edu/neuron/, http://bluebrain.epfl.ch/ http://www.artificialbrains.com/darpa-synapse-program.
Brains do well what computers do poorly, and vice versa. The HP12C calculator on my desk, made in the early '80s, can do many sorts of mathematical calculations faster than I can, because brains aren't really optimized for doing, for example, compound interest calculations. But my brain, or my dog's brain for that matter, can do all the 'calculations' needed to process a stream of images, recognize that they show a ball, predict its path, and catch it - while simultaneously processing visual, auditory, olfactory, and kinesthetic inputs for obstacle avoidance and threat recognition, and (in my case, anyway) perhaps thinking about how to solve complex programming problems.
Maybe I should add that there are basically three different things that a computer can do in this context:
(1) is what we mostly use computers for, and they're way better at it than human brains. (2) is a special case of (1), which we do because we don't have much of an idea how to do (3), and having a simulated brain we can alter at will might help in learning how real brains do what they do.
The title basically says it all. At which point in the refereeing process does it become acceptable to mention on my list of publications (e.g. the one on my website) that a paper has been accepted for publication at Journal X? Specifically:
Answer
I'd do it when getting the final acceptance letter. Before that, you can say "submitted" or "under revision".
I have many friends who are interested in Biology and want to know more about the subject in general (like a history of biology, from Darwin's theory, to DNA structure discovery, to the human genome project). Of course, I cannot suggest to them to read Alberts or Lenninger. Do you know whether such a book exist? I guess that a book that covers most fields of biology cannot be compiled, but even more focused book would do.
Let me try to narrow it down: something like the greatest discoveries in the field of biology (like this article) would be an interesting book to read.
I am not sure how appropriate this question is for SE, but I am sure that I will get the best answer here. Besides, it would be great if lay people can be more excited about biology and contribute to the site growth.
Answer
It doesn't have very many reviews, but The Epic History of Biology sounds like it's perfect.
Flipping through the first chapter in the preview, it doesn't seem overly technical in any way, so secondary school-level knowledge is probably enough. If your associates have absolutely no biology experience, perhaps a run through a popular press book would provide all of the background necessary.
I mean there are lot of caterpillars or hairy caterpillars to be more precise when we touch those hairs we get extreme itching on that area i want to know why we got that itching? Ok i know that it must be some chemicals but which? And if one has got itching how to remove it?
Answer
It would seem that you're referring to caterpillars that have urticating hairs, such as the goldtail moth caterpillar.
Erebidae similis 
.. when we touch those hairs we get extreme itching on that area i want to know why we got that itching?
In this case, the itching sensation is the effect of a hair-specific, soluble protein known as Thaumetopoein. According to this publication, in where they studied the urticating hairs of the Thaumetopoea pityocampa moth caterpillar when applied to guinea-pig skin:
The hairs are hollow inside with sloping spikes toward the distal end. There are no holes or pores on the hair and the irritating factor can only be obtained by crushing the hair. This suggests that when stinging occurs the hair is broken in the skin and the substance [Thaumetopoein] is released.
More information about this immunological reaction begins on page 5 (numbered 350).
And if one has got itching how to remove it?
Poison.org - Caterpillar Stings
In my Google Scholar profile, I have a paper which I uploaded to ArXiv a while ago, which has a few citations. Since then, that same paper has been accepted for a peer-reviewed conference. It was only uploaded to ArXiv to bridge the gap between the paper submission date, and the release of the official conference paper after the conference.
How can I merge citations for my ArXiv paper and my conference paper, such that there is only one entry in my Google Scholar profile, where that entry is listed as the conference paper rather than the ArXiv paper?
Answer
"My citations", then tick the square boxes next to the papers you want to merge, then click on the "merge" button that just appeared.
I have gathered online that SpringerPlus is legit. thing and not some scam. But they emailed me (a PhD student) and called me a Professor and asked me to review an article which was accepted in some other journal.
I feel like i should do the review because it's good for one's career, but this seems very strange. What to do?
Answer
You should immediately inform the editor and let them decide how to proceed further.
If this is indeed a double publication, reviewing it is a waste of time for you, other reviewers and the editor. In the unlikely event that there is some good reason for this (e.g., the other journal is a scam), the editor should be able to find out quickly or already know about it and tell you.
As for your reputation as a reviewer: If you see something very suspicious, reporting it is the proper action and is a job correctly done.
You should also ensure the following:
I am a young resercher from bangladesh. I have submitted a muniscript to SPGbiomed and the articale has been accepted. Now I have to pay the APC (article processing charge). Is there any grant who can provide the charge on behalf of the author?
I previously asked this question in the physics forum (tag soft-question), but was convinced that it better suits in the academia forum. So I deleted it and posted it here.
I was recently asked to review a paper for a well-established physical journal, but as I have a lot to do in the moment, I'm tempted to refuse it. This is even more the case since I quit my scientific carreer roughly a year ago.
Thus my question: particularly outside physics, what are the benefits of being a referee? [beside the idealistic attitude of "bringing on physics" -- this is a valuable point in principle, but in reality, I've been long enough in the business to know that this is hardly the case for most papers. In contrast, most papers originate due to the need to continuously publish, a thing which I consider to be wrong].
For people in science, I see a clear opportunity in being a referee.
First, it gives you a connection to the journal editors and contributes to your authority.
Second, by concentrating on the paper, you are forced to learn something on your topic which might help you later. Further, you might be able to add citations to your own work and thus increase your influence.
Third, from a global point of view, you have to do it since you also expect your own papers to be reviewed (although this point is somewhat of a social dilemma, since [neglecting the previous points] it would be better to review as few as possible and concentrate on your own research).
However, do you see any personal advantages once you have quit physics? Are there maybe some if one plans to return some day?
Answer
To me, refereeing papers in subject X is a non-negligible part of being a professional academic in subject X. So the premise that you want to referee a physics paper having "quit science" seems moderately self-contradictory: using your expert level qualifications to evaluate a scientific work is being a scientist, isn't it? I'm almost sure it is. :)
So I guess you haven't "quit science" completely, or -- and this may come to the same thing -- the physics community is not fully aware of this fact. One thing I might do if I were you is to make sure that the editor who asked you to review the paper knows that you are no longer employed as a physicist. If I were an editor, that would be useful information, and unless I knew you rather well and knew that you retained a special expertise in this particular area, I would probably select someone else.
I think it's clear that you no longer have any kind of ethical obligation or professional expectation of reviewing papers. I also suspect that once the community understands that you really are doing something else now your referee requests will come rarely or cease altogether. So this is probably a decision that you need to make more for any particular paper than as a general life decision. I would say: if you feel just as qualified to referee the paper as before and if you want to referee the paper, then do it. For instance, if you see something valuable in the paper that you think that some other qualified person might miss, then it might be a nice parting gift "to science" to speak out for the worth of this research. On the other hand, if it's just business as usual (or worse, motivated by "the need to continuously publish"): well, you don't have to clean the bathrooms in the apartment that you're not renting anymore, do you?
If you have thoughts of breaking back into science later on, then I think you need to think seriously about how to keep your connections and your intellectual life, um, alive. There are many aspects to this, and making sure that you continue to referee papers is not, so far as I can see, especially close to the top of the list. If I'm looking at the CV of someone who left academia for a while and is trying to come back (and it does happen), I will look to the work they have done recently and their plans for work in the near future. I don't really care whether they've refereed some papers in the meantime.
After you have finished a PhD when does it become inappropriate to ask your advisor for advice, read over a manuscript, or do any other "advisor things"? Presumably if every student an advisor ever had continued to act as if the former advisor was still his/her advisor, the professor wouldn't get anything else done. Basically how should one interact with the former advisor once the PhD is finished?
Answer
My advisor, at two different points in my academic career, said:
I took away from this that your advisor should always be available at some level, it's part of the point of taking on students. You are part of their scientific (or otherwise scholarly) contribution. At the same time, post-PhD you have to develop your own network of support, which is part of your growth as a scholar.
But how do you know when to do this? I think the best answer is simply to ask your advisor (see, they're always there to answer the hard questions). Hopefully they'll give you an honest opinion - either to keep asking them for help or that they think you're ready to fly on your own. Either, if you don't feel confident that you have enough peers to count on, it's probably a sign that you both can still ask your advisor for help and that it's time to put some more energy into expanding your professional network.
I have a learning disability where I can only learn through seeing (not seeing and hearing). As a result, I need to have headphones in class to block all sound. Should I just tell the professor this?
I was confronted by this question:
Biological evolution of life on Earth, from simple prokaryote-like cells to large, multicellar eukaryotic organisms,
Answer: A
However, I do not understand. Biological evolution does cause the system (living organisms)'s entropy to decrease. So, by the second law of thermodynamics, the entropy of the universe (in this case Earth), must have overall increased.
I would answer D... Where am I going wrong?
I'm not an academic, but I notice a trend in the top journals where replication studies aren't taken with the same glamour as original studies. Considering mountains of recent research show the majority of studies in many fields may in fact be irreproducible 1 2 3 4 etc, how can journals as a whole be taken seriously?
As a scientist, surely the scientific method must be respected, and one tenet of that method is reproducibility. This fundamental part of science seems to have taken a backdoor seat, and is not taken too seriously it seems. Be it due to funding, lack of prestige, or whatever. The end results are tainted/irreproducible studies that are cited many hundreds of times, distorting the truth of the world.
I respect there are individual initiatives recently to replicate large numbers of studies, but replication should be the norm, not the exception.
My question is, why are prestigious journals relied upon in terms of status, knowledge and information exchange, when in fact the replication rates of their studies are quite low, and there is no guarantee of any study you publish, cite or rely upon actually being accurate unless it's been replicated?
I have been offered and have accepted a position at a university. The position is not advertised yet, but they will advertise it because they are required to. Is this something common in academia? To be more clear on what happened, prior to the offer I sent my CV as a respond to another similar position which they advertised, but it was to be filled immediately and so I was ruled out. I guess after looking at my CV and having further conversations with me they were keen for me to join them and so they offered me this new position. But because they are required to, they have to go through another round of formalities.
I did ask the head of department how he could be sure that I would be the most suitable person for the job and told him that others might be better candidates, to which he said something to the effect that he saw me as suited for the group. But since I have not signed any contracts yet, how can I guarantee that I will eventually get the job? From the time I accepted the offer, I have stopped looking for other jobs, and have withdrawn my other applications, but since there are no contracts signed yet, I am a bit worried.
Perhaps another question I should ask is why are universities required to put up advertisements and to go trough all the formalities if they already decided on someone?
The pectoral fins of a whale and a shark. Are they analogous organs? I was looking at this question, and I saw that the two answers defined the range of 'same origin' differently. One said that sharks and whales have the same origin as jawed animals, (therefore they are homologous) and the other said that they had different origins, namely cartilaginous fish and mammals(therefore they are analogous). Now here's the question.
How large is the range of 'same origin' when determining whether two organs are analogous or homologous? Is it as large as a Kingdom or a Phylum? Class? Order? Family? Or is there another criterion?
I am a Masters degree holder in Computer Science. Where I live, the most popular way of receiving research grants is from the government. There are two problems with that.
First, You have to be enrolled in a Masters or doctorate degree program at the time of applying for funding.
Secondly, the researcher only gets a small amount of pay from the grant(Like about 2 or 3 percent). About 10 to 15 percent is for research supervisor. And remaining is equipment and other costs.
So is there any way of applying for research funding as an independent researcher? I am currently enrolled in a Masters program and am very close to getting a grant for my research. But I would like to continue work as a researcher after completing my Masters and would like to apply for funding independently.
Answer
Having only a MSc (and not doing a PhD) it might be hard to get an official research funding (although, there are many different programs and maybe there is one for someone with your status; especially if in some way you are still affiliated with an university of institute).
Sadly, (as Paul Hiemstra pointed out) there no such thing as a scientific freelancer. Science market is very far from an unregulated, free market (and the supply is higher than demands, so it is not a place for freelancer jobs).
However, there are two options which may make sense to you:
How much value do I acquire if I complete an online master's degree in CS and I plan to apply for doctoral study?
For example, Georgia Tech seems to offer an online master's program. Does this type program puts up anything to apply for a Doctoral program?
In short, if somebody wants to get a PhD degree in Computer Science, do Online Master's degrees aid in their ambition?
I have recently published an article in a "renowned" open access journal which cost us 2000 USD. I say 'renowned' - not to brag, but to highlight that the journal is not the kind of new age OA journal from which I would expect questionable practices.
Another group of researchers now started the process of submitting a comment to our article, to which we crafted a reply. After review, the journal now wants to charge them, as well as us another 2000 USD each for the publication of the comment/reply pair. This comes as an absolute surprise to me.
In my opinion, this practice is actively discouraging scientific exchange, and it seems simply excessive to ask for another 4000 USD. Furthermore, should the reply not be considered part of the comment, therefore, if anyone, the commenter should pay for the publication cost?
I am wondering if anyone has heard of something like this or has experience with publishing comments/replies in Open Access journals?
I am applying to neurobiology Ph.D. programs in the US that focus on disease research.
I am seeking opinions on my personal situation regarding the decision to include either a resume (1-2 sides) OR a CV (multiple pages) in my graduate school application for the schools that don't provide me much space to write about research. I also want to know about whether or not I can include research experience blurbs in the CV.
Originally, after being told by most schools that allow up to 5 recommendation letters to only submit 3 and after being told not to upload anything in the "optional and additional uploads," I felt a resume would be better for my application. Less writing and easier to read for the admissions faculty. However, I know many Ph.D.students that have submitted CVs, and almost every school I'm applying to states that I can submit a CV.
I don't have that much to discuss, aside from 3 significant 2+ year teaching experiences as an undergraduate student and 3 research experiences (2 summer internships + home university research since I was a freshman). Unfortunately, I won't have a paper out for at least another year due to an ongoing study. I am also active in several clubs/honors societies. Thus, my current "resume" is 3.5 pages long. I could probably get it to 2 pages, but this is where you come in.
Would you suggest to expand even more, possibly elaborating more on my research experiences so that my CV is around 4-6 pages, or would you recommend to keep it as a brief resume? For the CV, can I include 4-5 sentence research descriptions after I list the knitty-gritty stuff (e.g. program, what I did in that research program in regard to career building, etc.)?
The main reason I ask this is that I'm slowly starting to figure out some schools give me absolutely no room to discuss research experience. For instance, Johns Hopkins allows me to write a single page personal statement while answering quite a few other large points; thus, elaborating on research is hard. Also, I just contacted Duke who had a similar case in their application, and the Ph.D. admissions advisor for neuroscience told me to include details about my research experiences in the CV or the optional supplemental uploader. Harvard told me not to utilize the optional supplemental uploader to further discuss my research, although they allow CV uploads.
Regardless, for some of these schools, I will need to at least include a few extra sentences about my research whether that be through the optional file uploader or a CV. Has anyone had this internal debate or has a strong opinion on the better option? Thank you!
I have an idea that I would like to publish. However, the idea is so simple that basically everyone in the field could reproduce the experiment that shows its benefit within a day or so.
What can I do to ensure that my idea is not stolen during the review process by a reviewer, for example?
If the reviewer holds back my paper and publishes it himself somewhere else, is there something I can do to prevent this?
Answer
Assuming the journals you publish in allow it, you can submit your work to a preprint archive such as ArXiv.org. You can also put it up on a personal website.
Even if someone tries to scoop you, if you work is ever published, the date it was submitted for review should appear in the final article, giving your work precedence on any other. As for your concerns about reviewers stealing your work, there is not much else you can do besides the above. The peer review system is based on good faith, and hopefully you end up with ethical reviewers.
I use the online tool citeulike to manage my bibliography. The main tool to organize the library is tags (functionally equivalent to tags here on this site). One problem I seem to be having is I do a very poor job of initially choosing tags, so I need to continually re-tag my library to keep it organized.
Is there any advice on choosing an intitial set of tags? Or will it be necessary for me to continually maintain my library to keep it organized/updated as much as I would like?
Answer
Tagging is only useful if you use it with discipline. Look at Wikipedia or Stackexchange, most articles can be determined by 5-6 categories (science - math - geometry - euclidean geometry - metric). Stackexchange has a max. of 5 tags, often you only see 1-2 on questions, which is often pointless, as those tags will appear often in the question/paper title and abstract too. Wasted time.
So, if you decide to create a tagging system, use at least 4-6 tags depending on how interdisciplinary and specialized your paper/link collection is.
Also consider to not only tag by topic but also kind (review, letter, peer-reviewed, experimental results, theoretical analysis, explanation of new measurement method, meta-discussion...), year, personal rating (very interesting article you learned a lot from and should read again from time to time), rarely/often/top cited, new theory/model, strongly discussed in the research community
A last note. I use myself Copernic Desktop Search as a supplementary tool, I download all papers of possible interest (disk space is cheap ;) ), papers I read, will read or maybe will never take a look at. The point is that Desktop Search software often has more powerful search operators and sorting mechanisms than Google Scholar & Co. If you know how to use them, you can save a lot reading and tagging time or tagging at all. You know, if you are smart in using Google & search operators and have a good vocabulary, you don't have to ask a lot questions on internet boards.
Conclusion:
Don't use tagging for creating a pure thematic and linear directory structure, if finding again your papers or bits of information can be done by learning a good Desktop Search software. Use your tags in a personal way and remember, the point is not to structure your bibliography like a folder directory for categorized files, the point is to find again the bits of knowledge and most memorable papers, which will rather look like a strongly interconnected nonlinear tag cloud. If you look how people tag sites on del.ic.ious, often only 2 or 3 tags, sometimes using up to 10 pure thematic redundant tags, they are doing it imho wrong and waste a lot of time.
I am writing a paper in game theory. It is almost ready and I would like to submit it to an economics journal. Meanwhile, I would like to present a part of it in a computer science conference which is also interested in game theory. This will probably not be a problem from the journal's point of view, since the journal version contains much more results than the conference version. It is common to send to a journal, an extended version of a conference paper. But, I am not sure if it is allowed from the conference's point of view. In the "multiple submission" policies of two conferences, I found a similar statement:
I understand that I am not allowed to submit to the journal BEFORE the submission deadline, and not allowed to submit BETWEEN the submission deadline and the acceptance/rejection decision. What I don't understand is: am I allowed to submit to a journal AFTER the decision (assuming it will be an "accept" decision) but BEFORE the conference itself?
The rules do not say explicitly that it is forbidden, but, I thought that it may be "obvious" that it is forbidden, since the conference organizers want to make sure that the paper is fresh and new when it is presented in the conference.
Answer
If I understand your question correctly, you're planning to submit the journal paper after receiving the decision from the conference. In that case, if the journal is ok with considering an extended version of a conference paper, the conference organizers are probably not in a position to say anything against that. However, you have to follow the standard referencing rules when finalizing the journal paper:
Yesterday I had a tearful encounter in office hours with the most avid participant in the math class I teach, in which she related the following situation.
She is an international student whose parents are well off by local standards but have made significant financial sacrifices for her to study abroad at the university where I work. Part of the plan was that she should have a scholarship, but it has recently been denied on the grounds her grades are not strong enough, and as a result she will have to switch to a nearby university in the fall. Part of why her grades aren't strong is because she is a very specifically focused student: professional mathematics is all she really wants to do with her life. She already knows. When she is able to do what she wants, she just studies math. She works extremely hard, but at end of the day she couldn't care less about her other courses and views the struggle to get good grades as a distraction from what's important to her.
Her parents disagree that there is any future in math for her. They tell her it's not worth it and that she's bad at it. They're medical doctors in a country where teachers are treated poorly, viewed as people lacking the talent to do anything better, and are worried that a career in math would be both unremunerative and undignified—which might be the case in her home country, but my student also doesn't hope to return home. Nevertheless, for because her parents are footing the bill and because she's not willing to openly defy them, my student will finish a pure CS major when she enrolls in her new university, and won't be allowed to enroll in any future math courses during undergrad.
I watched her just crumble as she told me this, weeping and apologizing for it, unable to make eye contact. She's about to embark, without any choice in the matter, on a course that's going to make her miserable for years, if not longer, and moreover, from what I know of her, she is just the kind of person who should be in math.
I've told her there's nothing anyone can do to stop her from learning on her own, and that absolutely no instructor would refuse to let her sit in on whatever math course she wants, so that at most this will be a hiccup resulting in her getting a sort of bachelor's degree she doesn't really want at the expense of what she'd rather do, and that at the time she's financially independent, she can really study what she wants, but one could tell she's not completely buying this. She's devastated, and I can hardly blame her.
What can I (or anyone) do to help in this situation?
I am most of the way through my freshman year at Washington State University, pursuing a BS in Computer Science. Going away to school has been rough, and I have been pretty depressed for most of the time there. Right now, I am leaning towards not wanting to continue my education, but my parents are strongly opposed.
One of the main factors that is pushing me away from school is the fact that I already spend plenty of time working on my own software projects. On my own, I have gained extensive knowledge and experience with web application development, using platforms that are far too new to have a undergraduate class that teaches them. These are platforms used in real workplaces and production software, and I would not gain these skills in school.
Second, I have lost a lot of faith in my school after seeing so much incompetency from people who are meant to be educating me. The professors outsource a majority of their work to their TA's, who I feel I know more than. My Computer Science class is really just an entourage of TA's parroting the words of the professor, with embarrassingly little of their own understanding.
Another big reason is that for 10 weeks this summer, I will be travelling to Silicon Valley to take part in a 'startup accelerator program'. This is a program where already-established tech entrepreneurs and investors help people who are new to the game with building their product and starting their company. At the end of the 10 weeks, investors decide how much they want to put into each company, in exchange for some equity. Of the companies that go through these kinds of programs, a very high amount succeed. I feel that if the developers I am working with and I do well here (no, it is not guaranteed that we will make money), college is pointless for me.
College has been hard for me. Not because I am not capable of understanding the material, and not because I don't have enough time to get all my work done. I have been suffering in my classes because instead of going to class or finishing assignments, I work on my own projects.
Of course, if I forced myself to put time and effort into this work, I would achieve satisfactorily. However, that is much easier said than done.
In order to start caring about school, I would need to drop all my other software side-projects (or at least greatly limit the time I spend on them). Essentially, this is a choice, and right now I will always pick my own projects over school.
After all that I have seen about the limited job market (even for degree-holders) and all that I have experienced in school, I am really questioning whether I need to stay in school. Convince me whether or not I really need a BS, or any other advice you can give about the subject.
Thank you so much for taking the time to read and answer this. I normally feel bad taking time away from other people for my own benefit, but this is a major life-decision, and I cannot properly come to consensus on my own.
Answer
I know from all too personal experience that it the easiest thing in the world to say "I could totally ace these assignments if I tried, but I can't be bothered to try." Talk is cheap. You may be different, but when I said stuff like that I was completely deluding myself.
You may be being too hard on your profs and TAs. CS departments generally don't cover specific development platforms in their classes because platforms come and go, sometimes in a shockingly short period of time. A good CS department is going to try to educate you in the foundations of CS and software engineering. Stuff that is not in the tech headlines now, but is more likely to still be relevant 10 years from now. Still, it may be that they aren't very good, in which case the solution is not necessarily to drop out, but to find a better department.
That said, if you aren't applying yourself in school, and aren't getting much out of it, then you probably should't be in school. However, if you are not going to be in school, you still have to move forward with your life. You can't just hop on the bus back home and let your parents support you. The accelerator sounds great, but it's a roll of the dice, so you need a backup plan. The obvious choices are joining the military and finding a job. I've never been in the military so I can't advise you about that. If you find a job that pays all your expenses, then your parents may be upset, but they can't really stop you. They probably will be less upset with you if you have a job in hand as you announce that you are leaving school. If you can't find a job that will support you, then that's a pretty critical piece of information, and it means you've either got to suck it up in school or join the military.
My suggestion would be to completely put aside your personal projects for the rest of the year. Focus on your schoolwork, and prove you aren't just blowing smoke, when you say you could excel at it. Prove it. At the end of the school year, start looking for a job. If you find a job that will pay all your living expenses, or if your accelerator works out, then take a leave of absence. If you prosper in your job or startup, great. If it doesn't work out or seems like a dead end you can go back to school. If you really want to pursue your projects as an entrepreneur, then live on Ramen, save every penny, and bankroll yourself for a couple of years.
What do different people in the department expect from a postdoc? By different people I mean the advisor, graduate students and PhD students.
I know it mainly depends on the job description but there are few basic things that a postdoc must be expected to do. How aggressive (proactive) must one be? This question is important since a postdoc cannot just wait for the adviser to give him/her inputs. Rather the postdoc must take the project(s) as another PhD research of his own but be completely accountable to the adviser in terms of what he/she is doing and how is he/she doing that.
The above are my thoughts. My question is divided into the following sub-parts:
Answer
You'll very quickly learn that being an academic involves more than just writing research papers. Your time as a postdoc is when you can start learning about these other aspects, while building your own profile.
A postdoc needs to do the following:
Be as proactive as humanly possible, without being annoying. Talk to everyone in the department, especially people whose research interests are close to your. Go to conferences and sit down and work with interesting people (not necessarily the superstars).
