zoology - Do animals other than humans have different blood types?

Humans have the ABO and Rhesus blood typing systems. I have two questions about it:

• Why have we evolved these blood types?


• Do other animals have different blood types as well?

botany - What does "chlorophyll photosynthesis peak" mean in relation to photon wavelength?

When reading about how green / leafy plants work, I saw that they have chlorophyll A & B, which allow the plant to use the energy from light by capturing and transforming.

When reading about Chlorophyll, I saw some charts showing "peak points" for each type for light wavelengths. Apparently, each chlorophyll type has both peak points.

Since from further reading I learn that plants can use all the light in the visible spectrum for photosynthesis, I'm wondering (my questions >>):

• What do "peak points" of wavelength correspond to / stand for?


• How does light peaking in red spectrum (say around 630nm) differ to (or affect plants) compared to light in red spectrum peaking at 680nm (which I gather is Chlorophyll A peak-ish)?


• When same amount of radiant flux is projected to leaves on different wavelengths, one far from a chlorophyll peak the other near, which one gives more energy to plant and why?

journals - What is the benefit of 'voluntary page charges'?

There are quite a few journals which ask for voluntary page charges. Some may do for the whole journal and most for the first couple of pages.

Take IEEE Transactions on Forensics and Security for example.

Voluntary Page Charges. Upon acceptance of a manuscript for publication, the author(s) or his/her/their company or institution will be asked to pay a charge of $110 per page to cover part of the cost of publication of the first ten pages that comprise the standard length (two pages, in the case of Correspondences).

Mandatory Page Charges. The author(s) or his/her/their company or institution will be billed $220 per each page in excess of the first ten published pages for regular papers. [...]

Surely $110/page is not a charitable amount for an average author. What is the benefit the author/institution receive for agreeing to pay these voluntary charges?

Answer

The benefits of "voluntary" page charges are much the same as for "mandatory" page charges - you are paying them in order to support publication of the paper. The only difference is that, technically, you don't have to, and you can avoid it if you wish.

Why do we have such a weird situation?

There is a long and complicated history here; what follows is mostly a precis of this paper, which is an interesting read.

This particular journal seems to be using an unusual holdover from an old-fashioned way of handling page charges.

Page charges date back to the 1930s. (You may want to remember this the next time you see someone saying that paying publishers is a shocking modern development.) The majority of journal subscribers at this time were individual members of scholarly societies, rather than libraries, and so there was a fairly low limit to how much you could reasonably charge for a subscription.

However, particularly in physics, the amount of stuff people wanted to publish was growing dramatically - Physical Review doubled in size during the 1920s, and even then still had a growing backlog. Printing and mailing larger issues more often obviously costs more, but subscribers would balk at rapid subscription increases, and the societies were already (mostly) losing money publishing the journals to begin with. The solution by the American Physical Society (followed by many others) was to shift part of the cost onto the authors, allowing the cost charged to subscribers to stay the same even if they now got more pages in their journals, or if the amount of papers dramatically fluctuated in a given year.

But not everyone had the money to pay the charges. For the first couple of years, a generous benefactor paid for everyone who couldn't; after that, unpaid charges mounted up. Some institutions and funders were asked for donations to help cover the gaps, but, critically, authors were not penalised for failure to pay, nor were they chased for the money. The sense that these were "optional" charges became quite well entrenched, and while most authors paid, many avoided doing so without complaints. The US government gave tacit support to the emerging model in the fifties, when it was decided that federal agencies could pay page charges as long as they were the same assessed on non-federal authors, and they were voluntary. (You have to love the logic of "we'll pay if voluntary, but not if mandatory")

By the 1970s, page charges were well established in the scholarly landscape, and almost 40% of US-published articles were in page-charge journals - higher than 80% in some fields. (It was much lower outside the US.)

In the 1970s, the US Postal Service got involved. They took the position that a page charge was essentially a fee to distribute advertising about your research, which would mean that the journals got hit by much higher postage charges than if they were simply distributing public-good information. The IRS made a similar argument about payments being commercial and threatened to increase taxation. The negotiated solution was to very clearly emphasise that page charges were a voluntary contribution, rather than a mandatory one, neatly evading some of the legal issues.

Page charges mostly died out after this. American society journals were always the major users of page charges, but during the 1980s, most of them were absorbed by commercial publishers (who almost without exception stopped levying page charges). Many of the remainder, presumably, found that they could shift away from page charges by taking advantage of the very dramatic increases in subscription charges during the 1980s and 1990s (the famous "serials crisis").

But you'll still find a few today - eg PNAS, or the AGU titles. Most of these now structure page charges as mandatory - I suppose the complex financial issues from the 1970s have now been solved in other ways, or else the fact that you can ask for a fee waiver means they still technically qualify as "voluntary". Not quite sure how this circle got squared... but, regardless, that's where we originally got the "voluntary" text.

genetics - What test to apply to detect genomic signatures of selection?

I would like to ask you for your sugestions for selecting a test to detect signatures of selection in the following mouse model:

We have three groups: animals exhibiting trait A, trait B and controls. These animals were selected over the last 4 decades (controls were mated randomly and do not show any of the traits). That is total 170 generations (~4 generations per year).

We want to detect the genomic signatures of selection for trait A and B.

I am new in population genomics, but according to this paper (http://www.ncbi.nlm.nih.gov/pubmed/21218185), showing a desition tree (fig 1). I should apply a the Fst and a Linckage 'Desequilibrium test, given that the time scale would be short (40 years, 170 generations) and there are multiple populations.

Could you corroborate if this is the correct approach?

Thanks

Answer

I am assuming in this answer that you do not have any information about what environment is affecting the selection pressure so that methods like Bayenv2 can't be used.

The standard algorithms are:

• Lewontin-Krakauer test


• fdist


• BayeScan


• FLK



• PCAdapt

Whitlock and Lotterhos 2014 showed that most often FLK and Bayenv2 perform better than the the three others. A number of articles (Meirmans 2012, Bierne et al 2013, De Mita et al 2013 and Fourcade et al 2013) have also shown that fdist and BayeScan suffer from high false positive rate. I would therefore recommend to go with FLK but I am probably not good enough to give very good advice.

Note that you should learn a bit about how these algorithms work and not using them blindly.

etiquette - How do I tell my advisor about mental health problems?

I'm an undergraduate student (20f). I have 2 academic advisors - one in the Honors College & one in my department. I met with the Honors advisor recently to discuss study abroad and we somehow got on the topic of me not ever taking breaks. My GPA had fallen the past semester, and she warned me that if I don't start taking care of myself, I could burn out before getting my PhD (which is my goal).

I've suffered from anxiety/depression for years and recently begun to see a psychiatrist and counselor when I stopped eating, starting passing out, and developed repeated thoughts of suicide. All of that happened this past semester when I took an independent study with my Dept advisor, and I don't think he noticed. I want to be able to continue my research, so I'm trying to take care of myself. Unfortunately, that means I need to diminish my work load some.

I've been working with my Dept advisor closely for 2 years. He's helped me go to undergrad research conferences, get published, get grants etc. Always there for me academically, but the relationship's still very professional. We're officially starting my thesis work in the fall, but I told him I would start the readings this summer (halfway through the list). However, if I'm going to slow down the pace, I feel like I ought to give him reasons so he doesn't just think I'm slacking off. At the same time, I don't want to make it overly personal and make things awkward between us. He always asks how I am and it's a joke between us that I always say "tired" and he says "me too." I know that he pushes himself incredibly hard and never gives himself a break.

I would really appreciate examples of how I could word the email. I was thinking of asking him to meet some time (we're both in town over summer) to discuss and then tell him. Would it be better to do it over email? How do I tell him that I can't handle my current workload and still expect him to respect me as an academic?

Answer

Good for you for recognizing your illness and for getting professional help.

My answer has two parts.

Regarding how to tell your adviser, I suggest that you can write a short, factual, but non-personal email that contains all the information you want him to know. Something like this:

Dear Professor X,

I need to tell you about a health condition that I have struggled with for some time. I have a psychological condition involving anxiety and depression, and I am receiving professional medical treatment for it. We have a course of treatment that is appropriate but it will take some time to be effective.

One consequence is that I will need to be more careful about the amount of stress I am experiencing, including avoiding a stressful work load. I have decided that my past work load (including X, Y, and Z) is too much and not healthy for me.

Considering the alternatives, I have decided to focus my effort on X and Y, and to discontinue (or cut back on) Z. I remain committed to academic excellence and my career goals, and I believe this new work plan will be more likely to be successful than my previous work patterns.

I will be happy to meet with you to discuss this decision and alternative suggestions you might have. However, there are aspects that I hold private and will not be open to discussing. Thank you for understanding.

Best regards,

Student

You only need to meet in person if the Department adviser requests a meeting.

The second part of my answer comes to me intuitively based on the way you have written your question and the background.

I sense that you might have a belief in perfectionism -- that the only acceptable level of effort is 110% and the only acceptable level of results is perfection. You might have a very negative association with being perceived as "lazy" or "slacker" if you take any vacations or breaks. You might also believe that any error or misstep is a sure sign of unrecoverable failure.

If these resonate with you, then they need to be addressed to avoid recurring patterns of overwork, exhaustion, and eventually burnout.

Since you are seeing a professional psychologist and counselor, I suggest that you raise these questions and your responses with him/her. No need to respond here (in public).

---

EDIT: Anticipating some objections, I know that making explicit mention of "psychological condition" and "anxiety and depression" may be risky and may go against cultural norms. As a matter of ethics and morality, I believe it is important and necessary for all of us, individually, to act against those cultural norms that are harmful and counter productive. In this case, it is prejudice against mental illness, but I hold the same views regarding racism, sexism, and other cultural dysfunctions.

Of course, each individual needs to weigh the potential consequences of going against cultural norms. If you can't bear the potential consequences, then don't do it. You'll have to leave it to others to push for changes to cultural norms.

evolution - Why did humans become bipedal?

Somewhere in evolutionary history homo started walking upright and became bipedal. You hear these hypotheses that, by walking upright, they could see better across the grassy savannas to escape predators, find food, find fellow humans etc. However, the most parsimonious way to accomplish looking farther across the grassy plains is by growing taller - much less adaptations necessary and hence more favorable from an evolutionary perspective. Other hypotheses say homo freed his hands to carry things. Quite fine, but some apes are known to carry around stuff. Moreover, walking on all fours increases running speed (you don't have to see far if you can escape faster) and apes climb trees better (what's a better place to hide from predators?). Hence my question: Why has bipedalism been favored in evolution?

Answer

As already pointed it out, there is no scientific consensus on the answer to this question. This is because it is hard to test proposed explanations and it's likely that several factors interacted.

All of these have been claimed to be the explanation for the evolution of bipedalism:

1. 
   

   Freed hands for increased tool use. (Encyclopedia Britannica)

   
   


2. 
   

   Freed hands for the use of weapons in hunting or the use of containers to transport plant foods obtained by gathering. There are three variants: the “man the hunter” version which sees male hunting as the key stimulus (Washburn 1967 in Haraway 2013); the “woman the gatherer” version which sees women needing their hands free to carry gathered vegetable foods as the stimulus; and the “man the provisioner” version, which stresses males carrying food (either meat or plants) to provision females and offspring. All of these explanations are probably flawed because they invoke present utility to explain the origins of bipedalism.

   
   


3. 
   

   Bipedalism was created by female sexual selection of males with large, visible genitals. Although unlikely, this may be correct, but it is impossible to test. (Encyclopedia Britannica)

   
   


4. 
   
   

   Bipedalism evolved to aid in avoiding predators. Higher head allows you to see longer distances over the grass. (Encyclopedia Britannica)

   
   


5. 
   

   Bipedalism evolves because it allows energy efficient locomotion between forest patches in an increasingly open environment.

   
   


6. 
   

   “Radiator theory”: Natural selection favored bipedalism in open environments because it decreases exposure to the sun and helps keep the brain cool. (Wheeler, discussed in Haviland 2007 and Encyclopedia Britannica) Brain is highly sensitive to heat stress. This allowed hominins to be active in mid-day, when competing predators are less active. (Essentials of Physical Anthropology, p. 165). Since the same carnivorous animals with which hominins were in competition (both would scavenge dead game) could attack hominins, hominins were probably safer from predator attacks during midday as well.

   
   


7. 
   

   Terrestrial bipedalism may be a continuation of an upright body posture inherent in a tree-climbing/brachiating adaptation. Gibbons, the most arboreal of the apes and the best brachiators, walk bipedally on the rare occasions they come to the ground. (Encyclopedia Britannica)

   
   
   

The earliest hominin fossils appear to have been bipedal, with no clear evidence of a transition through a knuckle-walking stage, the principal mode of locomotion of modern African ape. (Kivell and Schmitt 2009, here's a secondary source, and here's a primary source that disagrees, Richmond and Strait 2000)

If this is true, then the modern African ape mode of locomotion (knuckle-walking) is a derived trait, and vertical body posture may be the ancestral trait in the African hominoid evolutionary lineages. In other words, if this is true, the ancestor of all great apes including humans was already bipedal, and modern African apes have evolved to knuckle-walk since then. Also if this is true, the previously mentioned factors would reinforce and refine bipedal locomotion in the hominin lineage.

It is likely that explanations 4, 5, 6 and 7 all interacted to select for bipedalism. They correspond best to the paleontological and ecological data. Numbers 1 and 2 are unlikely, because bipedalism appears long before evidence of tool use.

ethics - Hugely important database replete with errors

I am about to finish my PhD in bioinformatics. I am trying not to give out too many details, so I won't be very specific.

In the field I am working in, there are two extremely important databases being used. During my MSc internship, I chose one of the two databases, decided to stick with it and never looked back. However, as my PhD approaches its term, I find more and more errors in this database.

I only contacted the database team once to tell them I thought I had spotted an error and to ask them whether my reasoning was correct. They took more than 2 weeks to reply and only said they had fixed the error without providing other explanations. Intrigued, I looked more closely at the data and started "reverse engineering" the database: I don't know how everything is internally articulated but I start getting a pretty good picture of how they do it. It's a very old and big database that keeps getting bigger and richer. The scientists behind the database are constantly trying out many new things to enrich the data. They keep some changes and discard others.

Now here's the problem: these attempts at enriching the data are badly integrated. The database is never checked for internal consistency. It is highly inconsistent, and I can prove it with a systematic approach. I can point out actual problems and potential problems, with suggestions to discard dangling references.

They also license their data. Some of it is freely available and some of it can be obtained with an academic or a commercial subscription. If they sell their data they might as well sell clean and coherent data!...

Many database maintenance operations seem to be handled manually and with no regard to existing data. Their enrichment methods seem to be based on in-house scripts that the team praises in different publications and that can be used in web forms, but for which the source code is never available. The whole database seems to use a very old and messy design and I have the feeling they never had engineers in their team. The team itself and their research... well, they are not really transparent. The website only has a feedback form. One can never know what problems have already been reported and fixed. There is no changelog. They can change what they please, when they please and in any way they please.

My PhD adviser encouraged me to pursue this investigation and warned me not to contact the database team any more because we will need to figure out what to do. According to my adviser, even though I'm right, this investigation alone does not warrant a publication. In any case, it will at least make a chapter in my PhD thesis.

What I want to obtain is to get these problems fixed. What I would like to obtain, but I don't think it's likely to happen because of the aforementioned lack of transparency, is to get a paper co-published with the authors behind the database, or at least a collaboration for my lab.

Side note: my PhD research is utterly uninteresting and advances a boring method of doing something nobody wants to do and that will therefore never be used. If I manage to link my name to updating and correcting this database, then my PhD will have served a purpose.

Do you have any experience and advice on how to best handle this delicate kind of issue?

EDIT: I want to thank everybody for their contribution. I will select the most helpful answer. The answers and comments I received pointed me to the right direction. I want to make the issues known once I finish writing up my tool on consistency checking. How exactly I will go about making the errors known is something I still need to decide on. A few final notes:

• As one of the comments pointed out, it is only fair for the bioinformatics community depending on this database that such errors be known. Maybe making them public will lead some research groups to reevaluate the degree of this dependence.


• I did not mean to start a stir on computer science vs engineering.


• My PhD is valid and defend-able as it is; it's just not innovative, but that is another story. Pointing out inconsistencies in a public database is not what my PhD is about and will not be used to "save" my PhD as it doesn't need to be saved. :-)

Answer

There are many critical scientific resources out there that have massive known flaws, but are still useful because the flaws don't prevent people from getting high value from the resources. GenBank, for example, is the predominant source of genetic information in the world and is also known to have many mislabelled sequences.

From what you have written, it is not clear whether something like this is also the case with the resource that you are dealing with. The course I would recommend you take depends on 1) the degree to which the flaws are known and 2) their degree of impact on scientific conclusions derived from the database. The key cases that I see are:

• 
  

  The flaws are well-known and researchers are able to work around them: Here, there's nothing you really have to do, and the maintainers are unlikely to be particularly responsive to your complaints, since their system is "good enough" and they likely have other priorities.

  
  


• 
  

  The flaws are well-known and difficult to work around: This seems the least likely case, as why would people use this database and not the alternative that you mention? If it is so, however, you should probably just finish your thesis and move on: a paper on the flaws isn't interesting if they're already well-known, and while you should report your problems to the maintainers, you'll just be one more instance of the issues they already know about.

  
  
  


• 
  

  The flaws are not well-known and likely to cause serious problems in most research: In this case, a publication about the flaws is likely to be of interest and worth doing. It might or might not cause the database to be fixed, but it is likely to be important to alert researchers using the database to the problems in their work, creating pressure for the database to be fixed or people to migrate elsewhere.

  
  


• 
  

  The flaws are not well-known, but not likely to have a serious impact: This is likely to be the case if you are using the database in a very different way than most others, such that your research is more strongly impacted. In this case, talking about it in your thesis seems sufficient. You should document the problems you had and the flaws you discovered, but you are unlikely to get them corrected because you are not their target market.

  
  

Notice that in all of these cases, I assume that the database is unlikely to get fixed. That is because the persistence of the problems over time and the non-professional curation that you report indicate an organization that is probably missing either the resources or the incentives to make the fixes you would like, even in collaboration---although you might turn out to be pleasantly surprised.

publications - In peer-review, is it common for a reviewer to be shown and asked to comment on other reviewers' reports?

Some months ago, I was asked to review a paper for a computer science conference. I submitted my report about a week before the deadline, and I strongly recommended acceptance subject to a few minor corrections.

Just after the deadline, I was contacted by the programme committee member who originally asked me to review the paper. He sent me another reviewer's report (without a name or other identifying information) and asked for my opinion of it. The other reviewer had recommended rejection on the grounds that an example in the paper supposedly contradicted the claim of the main theorem. I explained that the other reviewer has misunderstood the example (in fairness, the authors of the paper could have stated it more carefully), and I see that the paper was ultimately accepted.

I have never before seen or been asked to comment on another reviewer's report, but my field is primarily mathematics, where there is often only a single reviewer for a paper, and I have only reviewed a few computer science papers.

So my question is this: in fields where it is usual to have multiple reviewers, is it common to be shown and asked to comment on other reviewers' reports?

A secondary question would be: if it is not uncommon, does it mainly occur when reviewers take opposing positions on a paper, like in the situation I describe?

thesis - How to find relevant and new open research topics?

How can one find relevant and new open research topics?

When working on my PhD thesis, I find it hard to find open questions in my very specific research area. Which approach do you take to find new and relevant topics?

Answer

Try to find papers giving a state of the art review on your field. They'll be easy to find, they generally have a lot of citations and written by the experts in the field. Some of those review papers (ones I've read at least) provide suggestions to researchers as to what needs improvement in the field. Good luck.

May they delay for a long time the decision of a submitted manuscript of someone that already sent a paper which didn't pass plagiarism check?

As I already shared in this question, I have submitted a paper in January of the last year to a high-rank journal and they decided on my paper with reject and resubmit. I worked very very hard and prepared a revised version of the manuscript which significantly improved the paper with a near 50 pages response letter to reviewers.

Unfortunately, in this university which I am getting my Ph.D., they have an obligation that advisor, must be the corresponding author. Two students of my advisor, which I don't know personally, submitted a paper to the same journal a short time after the decision of my manuscript. After less than a week, journal sent a letter to my advisor which is also the corresponding author of their manuscript that their paper didn't pass the plagiarism check. By my investigation, I found out that they copy-pasted some parts of their introductory paragraphs from other papers. My advisor sent a letter to EIC telling him that this problem was due to not having plagiarism checker software. He is the second author in my paper and third author in the other paper and corresponding author for both of the papers.

I have now waited a long time for the decision of my manuscript. One of the professors in this university, yesterday told me that they may not have sent the paper to the reviewers and make you wait for a long long time. Then if you mail them, they will reject your paper. It is a punishment for your advisor. Otherwise, they will make you wait for 12 to 15 month just for punishment and then without review reject it.

It was a nightmare for me as I am under immense pressure for my job and my graduation. I agree that my advisor is an irresponsible and ignorant person. But I didn't do anything wrong. Just honest very very hard work.

May they delay for a long time the decision of a submitted manuscript of someone that already sent a paper which didn't pass plagiarism check? Is there any such policies or behavior in journals? What should I do?

Answer

I know of no such policy - but editors are humans, too. On the other hand, an editor has to deal iwth hunderts of submissions per year. Plagiarism check is usually done automatically. At least I would not have the mental capabilities for remebering those issues and playing such games. But you never know.

Rejecting a paper without review after a year of letting it sit and then returning it without review would be malpractice and a reason to complain about the editor behaviour.

writing - Software to draw illustrative figures in papers

I would like to have suggestions of good software for drawing illustrations in research papers. I already know about Xfig, but this works only on Linux and is at times, clunky when it comes to text. Moreover the resolution is not always perfect making it difficult to manoeuvre the objects. Besides it is tough to learn and master, with all its weird click procedures.

I would love to know about better alternatives. Not talking about graphs here, just block diagrams and explanatory illustrations.

Answer

As drawing software, I use OmniGraffle which is much more modern that Xfig, but based on similar principles. It's only available for the Mac and is not free, as far as I know. With little effort, one can produce very attractive diagrams.

I also use Tikz/PGF. It produces very nice diagrams and is very flexible. On the other hand, it requires that you specify the diagram in LaTeX and it has a bit of a steep learning curve.

mathematics - Is it possible to attend graduate school in pure math after undergrad in CSE?

I am a Bangladeshi student studying CSE in the best university of my country. At the beginning of my second year in my university, an interest towards pure math grew in my mind. But my university does not offer courses in Abstract algebra, Real Analysis, Topology, Complex Analysis, Algebraic geometry, etc. I have seen this related post, but the advice there doesn't help me because there is no computer scientist in my university whose research interests lie between CS and Pure Math.

I met a few of my professors to discuss about my situation. Some of them asked me to study math by myself and also to try to study a paper by mathematicians under whom I want to work, then to write a paper which demonstrates I understand all (at least most of) the things written in the paper, and later send it to them asking if they are interested in taking me as student. They also asked me to get prepared for Math GRE. But is it possible to switch to pure math if I do so? If not, how I can go to a pure math grad school?

Answer

As Dave mentioned, what you want to do will be very challenging. One possibility would be to change to a different university that offers the math classes you mentioned. However, I will assume that switching schools is not an option for you. If you are very dedicated to this goal, here is one possible route.

• finish your current studies in CSE


• get a job in a town with a university that offers the math classes you desire


• start taking one class each semester as a non-degree student. I don't know about policies elsewhere, but many school in the United States have less strict admission requirements for non-degree students. Your goals for these classes should be two-fold. (1) Learn the material as well as you can. Your understanding of this material will be important for both getting into and succeeding in graduate school. (2) Impress your professors with both your ability and your desire. When you eventually apply to a masters program, you will ask some of these professors for letters of recommendation.


• apply to a masters program in mathematics. Ask for letters of recommendation from both your current professors in your CSE program and from those who know you from the math classes you take after you finish your BS.



• as you near the finish of your masters (where you have worked hard to prove yourself) apply to PhD programs

I know this is a long-term plan, but with hard work and dedication you could make it work. Here is another question Advice - MS in mathematics to increase competitiveness for PhD programs? that you may find to be helpful.

phd - Choosing your research area

I am considering pursuing a PhD in computer science one day. What I am deciding now is what I want to...I guess specialize in (is that the way to put it)? What I want to focus my research efforts on.

A couple of things I am interested in are:

1. Something involving manned/unmanned space exploration (writing guidance/navigation systems for the next Mars rover, etc).


2. Using Computer Science to find cures for diseases (folding @ home).


3. Computer models of climate change, as I am very much a person that thinks "Global Warming is real and needs to be dealt with yesterday".

But this questions isn't "what should I do research in" but more of "how can I decide what I should do research in."

I know a lot of people will counter with "if you don't know what you want to research then you shouldn't be considering getting a PhD", but I don't believe in that line of reasoning. I know I want to do research. I know I want to be involved with something that expands the boundaries of Computer Sciences as we know it. Just because I am not exactly sure what avenue I should go down in doing so, doesn't in any way change how much I know that I do want to do it.

So my question is, where to start with figuring out what I should eventually specialize in? What are my theoretical options? Where can I see if "getting my PhD to write software to guide probes to Jupiter" is even a viable option? Must I choose a area that is currently being researched at the university I attend, or am I free to come up with my own? Can/should I be reading recently released papers on Computer Science topics for some inspiration, and if so where do I go to find those?

Answer

This is one of the harder questions you'll have to ponder, and one of the most useful. First off, realize that your choices are not (completely) irrevocable. Many researchers shift areas every 5-7 years or so - the changes are not dramatic, but over time you can make useful contributions in a number of different areas.

Having said that, what you are looking for is a broad topic that will presumably take you through the 5-6 years of a Ph.D. To look at your questions one by one:

Where can I see if "getting my PhD to write software to guide probes to Jupiter" is even a viable option?

Do you know of people working on this ? maybe at NASA ? Where did they do their Ph.D ? what kinds of topics do they publish in ? What I mean is that one way to figure out if "Ph.D in X" is viable is to see if there are people doing X, and then figure out what their trajectory was by looking at their publications, CV etc

Must I choose a area that is currently being researched at the university I attend, or am I free to come up with my own?

It depends. You're in an MS program, and you haven't mentioned whether you're planning to apply elsewhere for a Ph.D. An MS is a good time to explore your options with people at the university, burnish your research credentials, and build some background in areas of interest. Obviously it helps if your area of interest is covered, but even if it's not, figure out related background that you need, and maybe look for someone doing research in a related area. Also see which places/people you'd like to do a Ph.D at based on the area, and that will give you a sense of what kind of extra reading/prep to do.

Can/should I be reading recently released papers on Computer Science topics for some inspiration, and if so where do I go to find those?

But of course ! but you should try to focus your search a bit. There's a large body of work in each of the topics you listed, and google is your friend. Once you find even a few papers, you can figure out where they were published, and then look at other papers in those venues, and repeat.

About embryonic and genetic evidence of evolution?

My question here is about evidence for evolution from Embryology and from Genetics.

1. 
   

   Mammals do have similar Embryos, but is it the case that for each species there is an embryonic development that occurs in earlier species, has such relationship been observed?

   
   

   What I mean for example if we generally conceive of having species$Sp_1,Sp_2,...,Sp_n$ where each $ Sp_{i+1}$ being evolved from $Sp_i,$ then is it the case that the embryonic development stages of $ Sp_{i+1}$ contains some of the embryonic development stages of all of its ancestor species.

   
   


2. 
   

   Similar question to 1 but regarding Genetics, is it the case that every species has a genetic thumbprint of its ancestors that lie there in the non-functional sections of its DNA, i.e. is it the case that all the genetic history of our evolution is recorded in the non-functional section of our DNA. So do human DNA have some portions of the DNA of some dinosaurs for example?

   
   

Answer

Question 1 asks whether ontogeny recapitulates phylogeny. It is striking that the when observing e.g. human embryo development, the embryo seems to go through stages that its ancestral species would go through, but where those 'lower' species would terminate at a specific stage. In other words, embryonic development seems to recapitulate a species' evolutionary lineage.

This is the recapitulation theory, which is outdated and incorrect, but a great example from the history of science. The most prominent of these was Ernst Haeckel's biogenetic law and the Meckel-Serres Conception. There were many problems with this, especially because they focused on noting similarities rather than differences, and several exceptions exist to the rule. They were not very scientific. It also incorrectly presumes that complex organisms have more predecessors. However, it is a compelling piece of evidence to elegantly show that evolution acts incrementally on existing embryological processes.

Question 2 asks whether there is evidence of ancestral DNA in our genome. The answer is yes. Where to begin? We share almost all of our genes with close relatives (e.g. chimpanzees and bonobos) and progressively fewer with more distant relatives. 50% of a banana’s genes (and indeed most other plants') can be found in the human genome. But remember, logically, that doesn't necessarily mean that 50% of human genes are found in bananas, though, because of the way divergence works. The human genome also contains a record of many viruses that have inserted themselves over tens of millions of years. Though they are not ancestors, they have been added 'horizontally' as opposed to the 'vertically' that ancestor DNA is modified over a species lineage.

It's very possible to answer your questions from many, many different angles, and present countless pieces of evidence in favor, but I think this should suffice.

publications - What's the point in a "list of figures"?

What is the point in a "list of figures" in the following cases?

1. Masters thesis


2. Ph.D. thesis


3. Academic (text)books

Answer

A list of figures allows one to find the figures contained in a book. This could be useful, for example, when you want to quickly find one of the figures you recall seeing in the book, but you can't remember which page it is on. You could also use the list of figures when buying the book to see whether it has lots of figures or only a few.

citations - What does YEAR: NNff means in research papers? eg 1965: 47ff

I am reading a book called Foundations of Statistical Natural Language Processing, in which there is a section called further reading. It states the following:

Chomsky (1965: 47ff, 1980: 234ff, 1986)

I am not able to find any paper of Chomsky written in 1965! Any help?

Sending non-fully translated academic transcripts for US PhD admissions

I am currently applying to PhD programs in the US and got my undergraduate degree from a German university. My university issues English transcripts of records, yet for special (graduate) lectures, the description is often still in German. Instead, a generic english name is used for the name of the lecture. For example, a generic entry might look as follows:

Course Name: Mathematics V
Description: Statistische Inferenz für Netzwerke
Grade: ...

Of course, I would much rather the transcript said "Statistical Inference for Networks". What is the etiquette in such cases? Do I take my German transcript and receive a certified translation, even though technically my institution issues "English" transcripts?

Some universities have an additional upload section, where I can describe the most important courses in more detail (including their content). In such cases, it would not be a problem. Yet, other universities only ask for a pdf of the transcript. Would it be OK to include my own descriptions at the end of the transcript pdf file, so that the committee can take these into account? Or would this rather upset the admissions committee?

Answer

It sounds like this is for only a couple of courses in your transcript? I'd submit the official English transcript issued by your institution and append in the same PDF a short note with the translations. I think I'd be grateful if I were to review your application.

zoology - What kind of creature is this?

I saw this on Facebook today and have tried researching it myself, but I have had no luck.

graduate admissions - Is omitting a school with blank transcript considered unethical in academia?

Suppose one was accepted to a school of higher education, but due to personal reasons withdrew three weeks after the beginning of the first semester without registering for and attending courses. Suppose he is now reapplying to other schools and has to submit all transcripts from the universities attended. Is including information about such a school relevant on an application? There is no transcript to submit, and no grades.

students - How do you respectfully give a teacher feedback about their teaching?

My teacher's teaching style isn't working for me, and he asked for feedback about the class and how he could teach it better. He teaches with powerpoint and gives quizzes that are all about rote memorization of the slides. Most of the class finds these quizzes to be of little help in understanding the information, but nobody knows what to say to the teacher about it.

ethics - Is it ethical to do paid literature searches of research journals for other students?

Is it unethical to research journals for other students?

For example, a student is researching gifted students and their subsequent ACT/SAT scores. Then:

1. 
   

   Would it be unethical for me to research educational journals and give the student the title of articles that pertain to their research?

   
   


2. 
   

   Would it be unethical for me to charge for this?

   
   

ethics - Conflict with department chair

I am a new faculty member. My chair is simply crazy in my perspective.

1. 
   
   

   I am an assistant professor. However, my teaching assignment is "offering individual statistical consulting/workshops", not "teaching any classes". This was indicated in my job description when I applied for this job. However, several times, she says, "you are not teaching" - so she says that I need to do what she asks me to do because she pays my salary (I really do not know why she pays).

   
   


2. 
   

   What she wants me to do is to write research/funding proposals and articles, then put her as the PI/the first author although they are my research ideas/works. She has taken three studies so far. More seriously, when she took the first one, I refused it. Then she sent out an official letter including some other faculty, saying that she took my research proposal because it was originally her idea and I stole it. Worse still, she then forced me to write the paper for her.

   
   


3. 
   

   My Ph.D. is in statistics. She said that I couldn't get tenured unless I change my research field into an education field which she wanted to do. Her point was again "paycheck" - I should do something because I am not teaching.

   
   


4. 
   

   Worst of all, she claims I am a bad person and faculty member because I refuse her unethical requests as a researcher. Furthermore, she talks about me to all the other faculty members, causing them to hesitate to be friends with me. Whatever I say goes to the chair.

   
   
   

I am preparing to leave this crazy medical school. However, my concern is the possibilities the chair could ruin my future career by using her connections. What should I do?

phd - Etiquette for reaching out to previous students of advisor

I have a question that isn't immediately relevant to me, and I'm not sure will be important in the future as I am quite happy with my situation. It is however something I have thought about at length and I've yet to come up with a set of general guidelines. I am a graduate student in the United States studying Mathematics, and am currently working with an advisor who has graduated ~10 students in his career. He has in the past mentioned a couple of the students, both in the context of research and current careers.

Is it appropriate to ask my advisor's former students questions regarding my relationship with said advisor? If this is a normal practice (as the question below would suggest), what is the etiquette to use in this situation? In particular, I am asking in the case where the previous students have all moved on and already graduated so email seems to be the best method of reaching out. Also, given that these conversations could contain sensitive information (i.e. questions regarding funding options given to the student, or grievances with said advisor) what would be the "kind" way to prevent the "sensitive" parts of the conversation from being relayed back to the advisor? Finally, would it be wise to reach out to some of these former student's at some point in my studies just for introduction and networking purposes? It is unlikely that our research interests would line up exactly, but it is an opportunity to contact people who have been through the same experience.

A specific case that is could become relevant in the future:

One of my advisor's recent students went into industry, and if this was something I considered in the future, would it be intrusive to email them and ask about their transition from graduate school to industry? In particular, would asking questions specific to my advisor's thoughts on this transition be appropriate? Also, related to the sensitive part, if for whatever reason I didn't want the advisor to know this was something I was considering would it be okay to ask the former student to keep this between us?

Note, I thought there would be many threads with a similar question, but the closest thing searches brought up was this link.

copyright - Why does academia.edu reserve the right to sell, modify, and "exploit" my papers if I post them there?

In academia.edu's terms of service, it says

By making available any Member Content on or through the Site or Services, you hereby grant to Academia.edu a worldwide, irrevocable, perpetual, non-exclusive, transferable, royalty-free license, with the right to sublicense, to use, view, copy, adapt, modify, distribute, license, sell, transfer, publicly display, publicly perform, transmit, stream, broadcast and otherwise exploit such Member Content only on, through or by means of the Site or Services.

This seems crazy, and posting anything there would clearly violate even the most lenient publisher agreement (for instance, many math publishers allow me to post the final paper on the internet, but not to sell it). Furthermore, these terms seem potentially very harmful to the users. What is their rationale for employing such terms? And why would anyone in their right mind even consider posting a paper there?

Note (as of July 2016): this part of the terms of service have changed and seems slightly less horrific. Though other parts seem more insane, and also in contradiction with each other, like they own all your intellectual property rights.

Answer

It's not necessarily crazy for academia.edu to ask for these things (although, as I say below, I certainly don't think users should agree to these terms). I imagine their lawyers advised them to use an agreement that covers all possible use cases as their business model evolves. For example, if they decided to charge their users membership fees, and only users who paid the fees got access to the site and could view profiles and download papers, then that would be tantamount to selling the papers and other user data (so they couldn't do it unless they had permission to sell this content). Posting ads on their web pages could be considered a form of commercial exploitation of the data, so they want to make sure they can do it. They might someday want to change file formats, such as converting PDFs into future super-PDF formats, and having permission to modify content submitted by users guarantees that they could do this. Even if they intend to take things down upon receiving requests from users, having irrevocable permission to post them means users cannot sue them for failing to take them down quickly enough. Basically, this agreement says they can do anything they want, which is obviously very convenient for them.

For comparison, Harvard's model open access policy also retains very broad rights (although not the right to sell papers for a profit). I believe the motivation is that universities can be trusted, and it's better for them to retain more rights than fewer, in case they need them someday. See the notes to line 7 in the model policy for more discussion of this point. Of course, the difference is that academia.edu is a commercial website, and even if they are trustworthy now, they might become less so in the future or be bought by someone untrustworthy.

On the other hand, even if it's not crazy for the site to ask for these rights, it's certainly crazy for users to agree! I'm amazed that these terms of service are being used, and I assume just about nobody using the site has actually read them and understood that they are permanently granting the right to sell arbitrarily modified versions of their papers. I hope you send them a complaint, as well as publicize this on the internet, because they need to change these terms as soon as possible. In addition to being completely unreasonable, they clearly conflict with a large majority of copyright agreements for papers, as you point out.

publications - How to cite a conference paper in an "extended" journal version?

I recently presented a paper at a conference which was published in its proceedings. Now it is time to submit an "extended" version with "30% new content". The new content isn't a problem, I've added several figures, a couple of genuinely new findings and some helpful illustrations that I developed while preparing my talk. However, the instructions from the publisher state:

In the extended paper clearly cite the conference paper and list it as one of the references.

In my opinion, this can be interpreted in one of two ways:

1. Write a new article that assumes knowledge of the proceedings. This is kind of a scary option because it implies that it really has to be a new work.


2. Explain that an earlier version exists and what's new here. This is a comforting interpretation but seems kind of uncharacteristic for the style in most journal articles.

What's the best path to follow here?

undergraduate - Why would a student go to a lecture at all if everything was in the book already?

Why would a student go to a lecture at all if everything was in the book already? The lectures make sense if and only if the lecturer tells more than in the book(s) and in more detail (or at least, in a better/more clear way). [not my comment]

Especially in light of the Internet in general, what is the added value of a lecture over a (hypertext)book?

Reasons I can think of:

1. 
   

   spoken word might stick better, because our language is not primarily based on text,

   
   


2. 
   

   the possibility to ask for clarification,

   
   


3. 
   

   some material might not translate well to media

   
   
   

I dislike those arguments, because a huge class can neither run at a comfortable speed for all at once nor answer everyone's questions. The expectation seems to be that the students should be homogeneous and everyone nonconforming should be filtered out.

4. personal contact affects us on a deeper level, role models are important

Depending on the class size, even that is doubtful.

5. to form communities,

which would substitute or supplement the professors, but obviously at a different rate.

This is a trick question, because it depends on the style of the lecture. In my experience the lecturer is acting as a medium and I'm watching them half the time writing on the board, or someone is asking obvious or distracting questions.

molecular biology - Why mutations in genes involved in general processes like DNA repair increase the risk of developing specific types of cancer?

For example, mutation in MHS2, which encodes a protein involved in the repair of mismatches that occur during DNA replication, dramatically increases the risk of developing colon cancer. (There are many other examples, like the RB gene which encodes a tumor supressor protein and is correlated to retinoblastoma, thus its name)

My question is: how a gene like MHS2 which participates in a general mechanism of DNA repair increases the risk of a specific type of cancer? Why doesn't it increase the risk of developing cancer in other tissues as well?

Answer

I can't fault @WYSIWYG for mentioning the cited Vogelstein article in providing an answer. You point to what seems like a great explanation for why certain cancers arise in some tissues but not others. However, for those who look closely this paper has some serious errors in its derivation of the model, and for good reason it has come under strong fire in the last couple of months.

See this for a really important rebuttal: http://ameyer.me/science/2015/01/02/vogel.html

Unfortunately, the paper provides an elegantly specious explanation for, in part, the longstanding paradox of why cancers more readily arise in some tissues like the intestines and from seemingly identical mechanisms, but do not seem to arise in other tissues. My favorite example, though @El Cid you do list some good ones, are inactivating BRCA1 mutations which normally play a role in repairing double stranded DNA breaks. And yet even when mutated in the germline this only seems to increase cancer risk in the breast, and really only in one gender (females).

So the answer is still quite certainly that the field does not understand this paradox, and the cited Vogelstein paper was a total tragedy of a publication. There have been a number of officially submitted critiques of the paper and the Vogelstein lab has been trying to defend it as best they can. This is however a great example of how big name labs can seem to get anything published in Cell/Nature/Science.

Another thing to consider and @El Cid points to a good example, is the pRb mutations (in a very central tumor suppressor pathway for all cells) cause retinoblastoma and not for instance intestinal or blood cancers very readily, and the retina is not a rapidly dividing tissue. So the Vogelstein paper cannot explain this.

What Proteins Are Universal To All Life Forms?

According to National Geographic, there are 23 proteins that are common to all life forms:

All species in all three domains share 23 universal proteins, though the proteins' DNA sequences—instructions written in the As, Cs, Gs, and Ts of DNA bases—differ slightly among the three domains

According to NCBI there are 324 proteins common to all life forms.

How many proteins are common to all life forms, and what are their names?

publications - How to know whether a journal is indexed by Thomson Reuters or Scopus?

I am preparing to submit my first article to a specific journal. How can I know if a journal is indexed in Thomson Reuters or Scopus?

publications - Is there a difference between "forthcoming" and "in press"?

Once a paper of mine has definitively been accepted for publication, I typically list it on my CV and in citations as "forthcoming". Other people seem to use "in press" for the same category, and an author once asked me to change my reference to his paper to use "in press" rather than "forthcoming". Do you feel that there's a literal difference in what's conveyed by these two terms, or some difference of connotation? I suspect it simply has to do with conventions in different disciplines.

(Personally, I'm a little bit uncomfortable with "in press", since it suggests that the publisher is at least close to the process of printing the paper. Apart from the fact that that doesn't make sense for online-only journals, I feel funny referring to a paper that I know will appear in a journal issue dated a year and a half into the future as "in press". Actually being printed is a long way off.)

(On the other hand, I suppose that "forthcoming" might be confusing to someone who doesn't know its standard meaning in academia. In theory, someone might interpret it as implying no more than "This is something that I'm planning to write, when I get around to it, and this is the journal I expect to publish in." Obviously, that's not what most academics take "forthcoming" to mean, but any thoughtful person would understand that "in press" implies that you can count on the paper being published.)

EDIT: Obviously, given some of the answers to my question, the way that I thought that nearly all academics obviously interpret "forthcoming" was not correct (assuming that there's not too much weirdness in the sample I've drawn by asking the question here).

Answer

I don't agree with most of the answers so far in one point: The answer depends on your field / area of research, so there is no universal truth about them.

For example in economics I have never seen "in press" and "forthcoming in [journal]" means that it is accepted. If the issue of the journal is already clear some people change it so that it looks like was already published (with a date in the future). (However, most people don't care after that point.)

The only thing where I have seen "in press" is when talking about a book.

So the main point (at least for me) is to clearly state by whom it is "in press" or where it is "forthcoming", as this adds credibility to your claim that it will be published.

However, from your question it is clear that both are common in your area of research and therefore I would just stick with the most commonly used. If you add the journal / conference where it is going to be published it should be clear that it was accepted.

grammar - Academic Writing: Numbered points in text etiquette

I am writing a computing conference paper, it's for a high quality conference, and my friend and I have a mini dispute. The loser pays for drinks, so no pressure!

Which of the following is better/appropriate/there is no difference?

The loser will: 1. get laughed at, 2. pay for drinks and 3. have to run outside naked.

vs

The loser will: 1) get laughed at, 2) pay for drinks and 3) have to run outside naked.

In all seriousness though, is one more formal/acceptable than the other?

Also, I think I remember that maybe a ";" should be used instead of the ",".

Thanks for reading!

Answer

They're both acceptable, nobody except very careful English fanatics are likely to care, but the latter is preferable. Reasons:

1. 
   
   

   Periods are more "final". They indicate the end of the sentence. That implies that you should instead use capital letters if you stick with periods:

   
   

   
   

   The loser will: 1. Get laughed at, 2. Pay for drinks and 3. Have to run outside naked.

   
   

   
   


2. 
   

   Because periods indicate the end of the sentence, one doesn't expect to see multiple periods in a single sentence. Using ) avoids this problem.

   
   

As for whether or not to use a semicolon, again it's up to you, but the comma is fine here. That's because the three things listed are all pretty related, short phrases, and on an equal footing. Semicolons are better when a sentence is complex or has other punctuation symbols. Example of something where I'd prefer the semicolon:

This new year, I resolve to: 1) cook 100 breakfasts for my wife - she deserves it; 2) set tests such that 50% of the class fails to shake my reputation as an academic Santa Claus; and 3) run for president.

t7 promoter - What determines a successful protein expression in E. coli?

Some proteins express well in a heterologous host; others- don't. A few requirements are known to determine the protein expression, like a strong promoter (like T7) for transcription and a strong ribosome binding site for translation. I am working with a protein, which consists of 2 subunits - alpha and beta. Both of them are on a plasmid with T7 promoter in front of the beta subunit (i.e. the construct is T7 promoter, CDS for beta subunit, CDS for the alpha subunit). The beta subunit expresses well, but the alpha doesn't. Do you thing this has something to do with the local environment (promoters, RBSs, etc) and how much does it depend on that? How can I increase the protein expression?

Answer

I found a very nice paper: Designing Genes for Successful Protein Expression, which covers most factors that determine protein expression. I post parts of it, because I am sure it will be useful to some of you.

Translation can be controlled at the level of initiation and elongation. Initiation of translation is primarily dependent on the sequence of the ribosome binding site (RBS) and early mRNA secondary structure. Other determinants of protein expression are less well understood but equally potent.

1. Initiation of translation

A key component affecting initiation of translation in prokaryotes is the RBS that occurs between 5 and 15 bases upstream of the open reading frame (ORF) AUG start codon. Binding of the ribosome to the Shine–Dalgarno (SD) sequence within the RBS localizes the ribosome to the initiation codon... Affinity of the RBS for the ribosome is a critical factor controlling the efficiency with which new polypeptide chains are initiated. This interaction is in competition with possible base-pairing interactions involving the RBS region that may form within the mRNA itself. Thus, SD sequences with weaker base pairing to the ribosome are more susceptible to interference from mRNA structure. However, some experiments suggest that SD sequences with too strong affinity can be deleterious, particularly at lowering temperatures, by stalling initial elongation. Also critical is the distance between the RBS and the start codon with 5-7 bases from the consensus SD AGGAGG being optimal.

Numerous lines of evidence suggest that the initial 15–25 codons of the ORF deserve special consideration in gene optimization. Studies have shown that the impact of rare codons on translation rate is particularly strong in these first codons, for expression in both Escherichia coli and Saccharomyces cerevisiae. In E. coli, peptidyl-tRNA drop-off during translation of the initial codons appears to be accentuated by the presence of rare NGG codons. These effects appear to be independent of local mRNA secondary structure. It is also true that expression may be recovered by 5' sequence replacement even for sequences that do not show especially strong mRNA structure or contain rare codons or other obvious deleterious elements in this region.

2. Codon bias

The second way in which host codon frequencies can be used is to match the host codon frequencies in the designed gene. This can be done simply by choosing each codon with a probability that matches the host codon frequency...Using sets of genes broadly varied in gene design features, Welch et al. found that variation in synonymous codon usage frequencies had a profound effect on the amount of protein produced in E. coli, independent of local 5’ sequence effects. Variation of at least two orders of magnitude in expression was seen due to substitution beyond the initial 15 codons of the ORF. This variation was strongly correlated with the global codon usage frequencies of the genes, although the codon frequencies found in the highest expressed variants did not correspond to those found in the genome or in highly expressed endogenous genes of E. coli. Multivariate analysis showed that the frequencies of specific codons for about six amino acids could predict the observed differences in expression. It is not clear what the biochemical basis is for this correlation.

3. mRNA structure and translational elongation

While much evidence suggests that mRNA structure can interfere with translational initiation in both prokaryotes and eukaryotes, the effects of structure on elongation are less well understood. This in part may be due to intrinsic helicase activity of ribosomes, which allows translation through even very strong hairpins and may preclude many structures from limiting the translation rate in either prokaryotes or eukaryotes. Perhaps more importantly, mRNA structure is difficult to predict, particularly for actively translated messages which are in continuous flux between various folded and unfolded states.

4. Protein-specific factors providing additional complexity

The protein may be particularly unstable in the host, especially if it is poorly folded due to inherent instability, lack of sufficient prosthetic factors, or improper post-translational modification... Expression of secreted and membrane proteins may be limited by mechanisms for directing these proteins to the membrane. It is even possible that the protein amino acid sequence may limit translational efficiency. For example, proline is thought to be slowly translated in E. coli, regardless of which codon is used.

Expression of the protein may be toxic to the cell leading to instability of the expression vector or host suppression of protein synthesis...A common strategy to reduce toxicity is to lower expression to tolerable levels. Promoters varied in strength can be valuable tools for finding an optimal expression rate for maximal yield...One potential way to avoid toxicity of some proteins is to direct expression to the periplasm or media. This may be accomplished by N-terminal fusion of a secretion signal sequence.

For more information, please read the whole paper. I also recommend reading Design parameters to control synthetic gene expression in Escherichia coli.

What's the expected level of paper for top conferences in Computer Science

What's the expected level of paper to be submitted to top level conferences in theoretical computer science (FOCS/SODA/STOC)?

I think there should be four main concern:

1. Is it a novel results?


2. How hard is the paper?



3. Generality and extension of the results.


4. Is it an interesting topic?

But actually I cannot imagine how reviewers are going to measure above concerns, e.g, If in some paper there is 10 mediocre result means is good? ...., also I don't know is there any other important thing that we should be careful about it for top conferences.

Actually someone can try to send the paper to the FOCS/SODA/STOC and see if is rejected then send it to some other conferences, but IMHO this is not appreciated. It's good if referees to related conferences help to understand what did they expecting for top conferences?

P.S1: Actually one of an important things in all the conferences is writing style, but suppose all preliminary stuffs like writing are OK.

P.S2: I could talk about this with my adviser, but also it's very appreciated to see other top conferences reviewers/participants/... opinion about this.

P.S3: Also experience of reviewers in similar fields would be very appreciated.

Answer

What's the expected level of paper to be submitted to top level conferences in theoritical computer science (FOCS/SODA/STOC)?

Top. The top level.

My experience on program committees for STOC, FOCS, ITCS, SODA, SOCG, etc., is that there are FAR more submissions of publishable quality than can be accepted into the conference. By "publishable quality" I mean a well-written presentation of a novel, interesting, and non-trivial result within the scope of the conference.

For example, I was on the STOC 2013 program committee. We accepted 99 out of 361 submissions. Program committee members were specifically instructed to limit the top rating to only the top 20% of the papers we reviewed; at least for me, that meant some very hard choices. Most of the discussion in the last week of the review cycle revolved around papers that were clearly very strong, but were not obviously "competitive" with other papers that were already accepted.

There are several questions that come up over and over in the FOCS/STOC review cycle:

• How surprising / novel / elegant / interesting is the result?


• How surprising / novel / elegant / interesting / general are the techniques?


• How technically difficult is the result? Ironically, FOCS and STOC committees have a reputation for ignoring the distinction between trivial (easy to derive from scratch) and nondeterministically trivial (easy to understand after the fact).



• What is the expected impact of this result? Is this paper going to change the way people do theoretical computer science over the next five years?


• Is the result of general interest to the theoretical computer science community? Or is it only of interest to a narrow subcommunity? In particular, if the topic is outside the STOC/FOCS mainstream—say, for example, computational topology—does the paper do a good job of explaining and motivating the results to a typical STOC/FOCS audience?

As a general rule, for a paper to be accepted to STOC/FOCS, at least one person on the program committee must be willing to pound on the table and demand that the paper is accepted, with strong answers to all these questions. Which means that as a minimum, the authors must have compelling answers to all these questions, even if professional modesty forbids writing those answers into the paper.

Specific criteria vary between different conferences, and not only because of the obvious differences in topical coverage. A well-written paper that combines existing techniques is a surprising way to obtain an elegant proof of a novel and interesting result, but does not introduce new techniques or require much technical sophistication, is much more likely to be accepted at SODA than at STOC or FOCS. (I've seen more than one paper rejected from STOC and accepted to SODA with precisely that review summary at both conferences.) ITCS favors conceptual contributions — new approaches, new models, new problem areas — over technical difficulty.

But at its core, conference reviewing is a random process. (As Baruch Awerbuch put it: "...whose expectation depends on the submissions, and whose variance depends on the program committee.") Every submission is a gamble. Your chances of winning the lottery may be small, but they're infinitely larger if you actually buy a ticket than if you don't.

• Write the best papers you can.


• Keep your target audience in mind when you write.


• Especially if you're submitting to a conference for the first time, get feedback on your paper from a community expert well before you submit.



• If you believe you have a reasonable chance of acceptance, submit it. Be respectful but brutally honest with yourself. Do not listen to the Impostor Syndrome.


• Regardless of the outcome, take reviews and other feedback seriously. Don't just revise your paper; also revise your writing habits and your mental model of the audience for future submissions.


• Rejection is not the end of the world. It's only one paper; you'll write dozens more.

Actually someone can try to send the paper to the FOCS/SODA/STOC and see if is rejected then send it to some other conferences, but IMHO this is not appreciated.

It's a bit more subtle than that. Submitting a paper that might get in is fine. What PCs really don't like is being asked to review submissions that are clearly below threshold, especially papers that were previously submitted to comparable conferences but were not updated to respond to previous reviews. (Even when a paper is submitted to several different conferences, it's not uncommon to have overlapping sets of reviewers. I've been asked to review four different submissions of the same paper.)

conference - Fee discounts for full time PhD Students; is this discriminatory?

In computer science many conferences provide a fee discount for graduate students. This is ok, but many times these discounts are limited to full time PhD students, and not available for part time ones.

Now, part time students many times are less lucky than full time ones, as often they don't have any scholarship, so ideally they have less resources than a full time student; so why these discounts are only for full time students? It would seem more natural the opposite..

presentation - Is it acceptable to take photos of slides at a conferences for private use?

Is it accepted/appropriate to take pictures of presentation slides at conferences for private use?

I am not talking about putting those pictures out in the public afterwards, I know this is illegal without consent of the presenter.

Should it matter, I am talking about math conferences. And I am asking because I don't see anyone taking pictures.

career path - Is it more difficult to score a Tenure Track position in the US when applying from outside?

I am currently located in central Europe. When I was hunting for an assistant professor position some months ago, I was also planning to apply to some US institutions for Tenure Track positions. However, one senior professor with some experience working in the US told me pretty much straight-up that this will be a waste of time, as "US universities do not hire people from outside the US/Canada on Tenure Tracks". Relativizing somewhat, stated that "of course exceptions exist, especially if they personally know the applicant, but generally you will get onto the reject pile immediately as they don't know your school well enough.". I was counselled to apply for a postdoc at an US institution first, if I really wanted to get into an US school.

Looking over the CVs of some existing assistant professors in good schools the statement could be accurate (almost nobody with the job title Assistant Professor seems to come directly from outside the US - many graduated somewhere else, but the last position before was almost always an US institution).

In your experience, is this sentiment correct? Does it even make sense to apply for a TT position in the US from outside (under the assumption that your CV is reasonable for a TT in the first place, of course)? Computer Science is most relevant to me, but any information from any STEM fields would be interesting as well.

Answer

While the "I don't know your university" element can have an influence on whether your application gets summarily dismissed to the reject pile, it's less of an issue than one might think. We all travel to Europe and Asia for conferences now, and meet colleagues who come from different countries. I can probably name the top few universities in my field in many European countries, as well as personally know people in each of them.

But there's a more mundane logistical reason for potentially avoiding applicants from other countries: expenses. There's always a risk in getting someone to come for an on-site interview, but with a foreign candidate the expense and logistical work (visa processing, payment methods and so on) are more onerous. We always want to find strong candidates, but when there's a large pool of highly qualified candidates in the US, it can be convenient to focus on those that we expect have a chance of actually making it through the interview process and coming.

There's also the question of whether someone from Europe (as opposed to someone working there) really does want to come to the US, or is just casting a wide net. But that can be addressed in candidate statements or even conversations.

None of this means that foreign candidates are disqualified. Far from it. But it creates a moment of doubt.

How to deal with unavoidable failure in my first year of tenure-track applications?

I got my PhD recently. I applied to many tenure-track positions and got selected for several onsite job interviews. Yay. However I have actually been told in no uncertain terms by several trusted people that this year, my chances are extremely close to zero, considering my short track record.

I cannot help but get my hopes up. How do I deal with this upcoming unavoidable failure and put a good spin for myself on my situation?

It may sound stupid but like many people in academia, so far I have been quite successful and have not had to deal with professional failure much... (Consider this: good in school, good in university, graduated with honors, got accepted to masters, got accepted to PhD, got the PhD - most people in academia follow this kind of path. I hope this does not come across as immodest, I am very aware that I am just a cog in the grand (grant?) scheme of academia. I am good at what I do but not at the rest.) Of course I met failure very often in my private life, but this does not feel the same.

human biology - Are all the atoms in your body replaced with others over a 30 year period?

I was reading Creation - Life and How to Make It by Steve Grand. (This is the book that inspired Jeff Bezos to start the AWS initiative. ) In it he makes the following statement:

Anyhow, by now I hope you have thought of an experience from yoru childhood. Something you remember clearly, something you can see, feel, maybe even smell, as if you were really there. After all, you really were there at the time, weren't you? How else would you remember it? But here is the bombshell: you weren't there. Not a single atom that is in your body today was there when that event took place. Every bit of you has been replaced many times over (which is why you eat , of course)....

That didn't sound quite right to me. How could the atoms in your bones be replaced? Aren't your nerves pretty much fixed in place?

My question is: Are all the atoms in your body replaced with others over a 30 year period?

What is the relationship between sexual and natural selection?

In Evolutionary ecology: Novelty makes the heart grow fonder, they say:

Thus, it seems that the diverse coloration in this species is promoted by both natural and sexual selection.

I had always thought of sexual selection as a subset of natural selection. What's the right way to think about the relationship between the two?

How important is it to note, in a citation, where a book/paper was published?

Citation systems often specify writing down the location (e.g. London) that a book/paper was published, how important is this, and if it is important, then why is writing down the publisher/journal name not enough?

Reference for annual journal subscription costs paid per university?

Is there any resource that lists how much each university pay in journal subscription fees? I am mostly interested in US universities (E.g. Harvard: $3.5M/year in 2014, MIT: $4M/year in 2006 for science and engineering journals alone), but still curious about other countries (e.g. French universities paid 172M EUR/5years to Elsevier, Finnish research organisations paid a total of 27 million euros in subscription fees in 2015).

Answer

There is, in fact, a resource with the information you asked for, for institutions in the United States.

Detailed information on individual academic libraries' expenditures (by university) is available from the National Center for Education Statistics in the United States, as part of their Libraries Statistics Program.

The data from these surveys, including the individual responses from each university, are available for download in plaintext format at this link. The most recent year available is 2012.

To take your example, according to that data, Harvard's expenditures for library resources in 2008 included $9,248,115 for serial subscriptions. In 2012, this number was up to $16,391,638 (the most of any library in the survey).

If you're interested, a set of related information on amounts paid by selected public universities to specific major publishers can be found in

Bergstrom, Theodore C., et al. "Evaluating big deal journal bundles." Proceedings of the National Academy of Sciences 111.26 (2014): 9425-9430.

(see especially the supporting information for the latter.)

Why is DNA replication performed in the 5' to 3' direction?

DNA replication goes in the 5' to 3' direction because DNA polymerase acts on the 3'-OH of the existing strand for adding free nucleotides. Is there any biochemical reason why all organisms evolved to go from 5' to 3'?

Are there any energetic/resource advantages to using 5' to 3'? Is using the 3'-OH of the existing strand to attach the phosphate of the free nucleotide more energetically favorable than using the 3'-OH of the free nucleotide to attach the phosphate of the existing strand? Does it take more resources to create a 3' to 5' polymerase?

Answer

Prof. Allen Gathman has a great 10-minutes video on Youtube, explaining the reaction of adding nucleotide in the 5' to 3' direction, and why it doesn't work the other way.

Briefly, the energy for the formation of the phosphodiester bond comes from the dNTP, which has to be added. dNTP is a nucleotide which has two additional phosphates attached to its 5' end. In order to join the 3'OH group with the phosphate of the next nucleotide, one oxygen has to be removed from this phosphate group. This oxygen is also attached to two extra phosphates, which are also attached to a Mg++. Mg++ pulls up the electrons of the oxygen, which weakens this bond and the so called nucleophilic attack of the oxygen from the 3'OH succeeds, thus forming the phospodiester bond.

If you try to join the dNTP's 3'OH group to the 5' phosphate of the next nucleotide, there won't be enough energy to weaken the bond between the oxygen connected to the 5' phosphorous (the other two phosphates of the dNTP are on the 5' end, not on the 3' end), which makes the nucleophilic attack harder.

Watch the video, it is better explained there.

ethics - May a man attend a workshop entitled “Young women in [domain]”?

The Max Planck Institute for Mathematics at the University of Bonn hosts workshops such as 'Young Women in Harmonic Analysis', 'Young Women in Geometry' and 'Young Women in Mathematical Physics' biannually, I think.

I am very interested in attending such a workshop as they are seldom found within the topics I am interested in. However, the title of the workshop begins with "Young Women". Moreover, the description on their page states that "the workshop provides a platform for female graduate students and postdocs in mathematical physics..."

Now, before you lambast me for even considering it, note that they also write "everybody is welcome to attend the workshop. We encourage all participants - male and female".

My worry is that male participants are technically permitted so that they do not break any discrimination laws and that if I were to attend such a workshop, I may find myself in the awkward situation of being the only male there facing the scowling looks of my female contemporaries.

Thus, my question is: can I apply (from a common sense, ethical, moral, situational point of view...because technically, I obviously can)?

heat - How and why can cold inflict pain?

I was carrying a can of very cold liquid, had something heavy in my other hand so couldn't switch hands. After a few minutes, I started to feel very intense pain. I was very surprised. cold is just atoms moving slower. This makes more sense if you think about how heat, or burns can cause pain. But heat can cook tissue and disable it, it makes sense it would hurt.

research process - How can I improve the effectiveness of my literature searches?

OK, I know this is a pretty basic question but I haven't been able to come up with any really satisfactory solutions. (I have searched around on this site, but none of the related questions precisely answer my problem.) I'm a first-year PhD student working mostly in evolution, phylogenomics, and conservation biology. I'm looking for basic tips on how I can become more effective at finding papers when I need to research a subject for any of the usual reasons like developing a methodology or drafting a proposal.

Right now I seem to be pretty bad at this. My search strategy pretty much consists of putting likely keywords into Web of Science and Google Scholar, and then looking at whatever papers appear that seem like they might be relevant to my query. Frequently this fails to yield satisfactory results, even when the subjects that I am researching seem like they ought to have a significant body of existing work behind them. I know I must be able to do better, because I see other people coming up with papers that I don't seem to be able to find.

What are some basic best practices for conducting a literature search? I feel like this is a big gap in my existing skillset, and something that will really hold me back if I don't get on top of it soon. Again, I realize that this is a pretty remedial-level question and I appreciate your patience and guidance here.

Answer

Literature search, to me, is like the recipe of potato salad: everyone has at least one, and they always claim that theirs is the best. In fact, we just use what we feel comfortable and, so far, has not caused any major meltdown. So, bear in mind that these are just what work for me, and you should modify them along the way.

Schedule a meeting with a librarian, now

Talk to a librarian at your institute. In our school we have a medical librarian and perhaps you may find one specialized in your field as well. They are trained to locate useful information and are up to date with related technology. Give them a clear field of study and even a gist of your research, and ask for a good list of databases. I may go so far to say that a good database list is half of the game. Apart from the list, learn Boolean and learn them well, pick up a good electronic reference manager software. Your library should have these resources.

Also, ask your library if they have any library consortium. Some major institutes have large amount of subscriptions which open the gateway to many full articles. If your institute is tight on budget, a lot of the time you can just find abstracts sans full text. Having a consortium library card may grant you access to other bigger institutes' library, in which you can print or photocopy their articles. On the same note, ask for an introduction on doing inter-library loan and how much you're supposed to pay.

Learn systematic review

Systematic review, simply put, is performing literature review as a scientific research. It's problem-based, protocol-focused, and the process is meticulously documented and hence readily replicable. There are plenty of publications about this skill. I have been using Booth's Systematic Approaches to a Successful Literature Review and so far it serves me well.

Focus on the chapters about question formulation and ways of collecting data. I think even we are not heading for a formal systematic review, learning how to keep a clear search records, draft a conceptual framework, and maintain a paper trail would still be very beneficial.

Understand the cataloging system

In biomedical field (where I work) we have MeSH (Medical Subject Headings) which shows the hierarchy and grouping of keywords. Consult the librarian and see if such thing exists in your field.

Read a few systematic reviews or literature reviews in your own field

To get the general picture, I actually first start from Wikipedia and encyclopedia. If you already have some background knowledge, you can probably skip the first phase. After meeting with the librarian, use the new-learned technique to find a few literature reviews or systematic reviews (hereafter "review") in your field. Review articles provide general scopes and a rich pool of keywords for your later use. You can also perform a reference tracing technique on these articles because they usually have unreasonably nice and comprehensive bibliography.

Spend some time with the online search engine and really read the "read me first" and "how to use this site" links. Learn how to massively download cited articles from a hosted article and export them to your manager software of choice.

Another good reason to start with these articles is that they are all required to report the information retrieval in details. Which engines were used, how articles were screened, what were the criteria, etc. You can get a good sense of how researchers do it (or appear to want to be seen doing in order to look trustworthy.)

Start casual

Through this snowballing technique, a small body of articles should start to form. Pay attention to their use of words, keywords, etc. It's still somewhat a toying phase but you should start using your tools seriously. The only recommendation from me is at least one electronic storage/manager software should be used. Make sure you can integrate this software into the word processing software in a harmonious manner, and be able to export a formatted document on the fly. For the rest, it's personal choice: index cards, Post-it notes on the wall, writing on a poster size paper, etc.

Now, many fun tools are available... mind map allows you to cluster the ideas and words, citation map allows you to trace the ancestors (cited) and offspring (citing) articles of any indexed articles, word cloud allows you to identify the most frequently used words, some of these functions are also embedded in manager software such as Qiqqa, which is largely free and powerful.

Then get serious

After a week or so, you should have a good command of the tools, the software, the databases, and the keywords. Now you just need a question. Personally, all literature review should be problem-based. If someone asked you to "go and understand the field," that is just simply absurd. It's like searching an encyclopedia without anything to search; while there may be people who enjoy randomly reading wikipedia entries (I do, to confess), but that's not the best use of PhD time. Isolate the questions from your study before doing any literature search.

Now, what to search? I work in biomedical field so your and my paradigms may differ. For me, I usually go by this sequence as a starter:

Definitions: How does my field define XYZ? What are the controversy of the definitions?

Operationalization: How does my field capture/measure different contexts? How do we approximate "poverty"? How do we call a good "user experience"? etc.

Data source/Research design: What does my field do when they study the phenomenon of XYZ?

Analysis: What is some specific analysis for a certain type of design?

In a way, use the first literature review to solidify and fortify the understanding of every single phrase in your research questions and specific aims. Then expand to other questions (you WILL have branching questions along the way, trust me. It'd be hard to suppress them). Stop when you feel you have somehow exhausted the answers, and/or you're happy with the results.

Never start a literature review without a question, or you'll find yourself still only reading paper 18 months into the PhD, and that is probably not good.

PhD is not a between-people competition

You mentioned that sometime you saw others finding stuff that you did not. I'd suggest just ask them how they did it. Just because you asked them doesn't mean you're worse than they are. If they found something you didn't, get the references, read them and incorporate them into your manager, and instantly you're as well informed, if not better informed.

Talk to experts

Find some prolific faculty members and researchers, and ask them for tips. Collectively you should be able to get something more out of just talking to the librarian. Experienced researchers also tend to know more about the seminal work. And if you can get that list, compounded with the ability to trace the work's offspring, you can pretty much recreate the family tree of a particular key research theme.

Use crowd-sourcing

Websites like Mendeley and Research Gate utilize social bookmark approach and you can refer to other people's collections of articles/citations. If you have a good peer in your team, you may also divvy up the work and then evaluate the findings together, exchanging references, etc. Also some young researchers may be on other social sites such as Reddit (but refrain from checking funny videos) or crowd sourcing sites such as GitHub... you may consider setting up an account and set up a chat thread or a project for others to contribute.

Exploit all services of journals

There are at least a few services that you should see if your field's prime journals provide:

1. Mail alert: Some journals or search engines will send you e-mail when an article containing any of your preset keywords is available. Get like a weekly notice from them, and you can keep yourself somewhat up to date.

2. Twitter: Same as above, but through Twitter.

3. Digest: Some journals may boil down their published works into short pieces then feature them in the form of an online billboard. Occasionally a third party may do that as well for a nominal fee. For example, MDLinx summarizes key medical journal findings and e-mail them to subscribers as a 5-minute digest every day.

Pay attention to "grey literature"

Notice that in some fields there is a tendency to favor publishing results that are statistically significant. Relying solely on literature database is only unbiased in the domain of the published literature. Sometimes, grey literature such as conference abstracts, documentaries, unpublished papers, white papers, proof-of-concepts, blog posts, grant proposal archives, trial registries, patents, personal communications, and general mass media may needed to be explored as well. Each field has their own literature graveyard and atypical channels of documentation, you'll need to talk to some specialists in your field.

Be always on

To me, literature search is really more of a lifestyle change rather than an activity. Now I have camera to take snapshots of posters, take verbal and written notes. I bring index cards for writing. Etc. When talking to people I often drive the topic to what cool papers they recently found. That's my best way to deal with potentially tricky water cooler conversation; either I'll learn something or they'll leave me alone.