publications - Copyright issue regarding creating an image by using other images taken from a website

I need to use images related to "cricket umpire signals" in my paper. I want to create a new image by putting some of these small images together along with graphs and comments next to them. But my concern is the copyright issue when i take those small images from websites.

I found the images on many websites such as BBC or WordPress blogs.

http://news.bbc.co.uk/sport2/hi/cricket/rules_and_equipment/6135798.stm https://paulsaekiblog.wordpress.com/umpire-signals/

But BBC says that they don't own all of the images on their website, and they don't reply back fast. and on other websites, there is nothing specifically said regarding the copyright license.

Also, i asked someone who has used such images in his paper about the issue, and he replied back "they are in the public domain and a permission is not required" along with the following link. http://123coolpictures.com/cricket+umpires+signals.
But I'm not sure how acceptable/reliable is his answer regarding this issue.

I'm writing the paper for an ECML/PKDD workshop (computer science) in europe and I live in Germany.

Answer

Any image is copyrighted unless the author releases it into public domain or some special circumstance apply (author dead long ago, image below threshold of originality, etc.). You can't reuse the image or make a derivative work from it without consent of copyright options.

As far as I can see you have three options:

• Ask the copyright holders to give you permission to use the images. First you would need to identify who are the copyright owners.


• Look for an equivalent image already released under a free license - free enough for your intended use - and abide to the license (that may include acknowledge author, release under similar license or refrain from commercial use). Wikipedia Commons may be a good place to search for such image.


• Create your own version of those images. Images are not free but information is. You can adopt the positions depicted in the images and ask a friend to photograph you. This way you (and your friend) will be the copyright holders and you can do whatever you want with the image.

In some academic settings, you could use an image and cite it, but I'm not sure about something different than citing (and reproducing) and image from an academic journal in another academic journal.

And of course, I must admit people very often copy images in the Internet without abiding to copyright and nothing happens, but I wouldn't do it in a paper. In fact, I doubt any editor would let you to do so.

In summary, taking in account how easy would be to create equivalent images (by drawing or by photograph) I would create new images unless I could find free equivalent ones.

publications - how to stop working for other people's thesis?

Last semester, I took a course with my supervisor and he assigned me a project. This project is part of one of his student's theses. I did the project and passed the course.

Later, I was asked to upload my code for use in a paper. It turned out that the data the grad student had generated was not appropriate, and he needed to do other experiments. It later turned out there were other problems with the underlying model, and I redid a lot of that work as well.

The problem is that this other student is not really contributing at all.

• Sometimes he does not come to work at all


• On one occasion the professor assigned us to do something, and he immediately told me he had no idea how to do it


• In one of our meetings with the professor, he talked 2 minutes with the prof with no slides; I talked for the other 58 with slides.

What should I do in this situation? I could not work like this, I have my own project and my thesis and stuff. I cannot dedicate my self for another student's thesis.

Question 1: how should I make this student understand this is his thesis and he should work more than me?

Question 2: How can I get off this project? I am taking another course with my supervisor, he again assigned me a term project with the same system and same grad student. I do not want to keep going like this. What should I tell to my supervisor Due to the problems we found, I think this current system is a bit of a dead end. But, I do not want to lose my connection with my supervisor; he is a good man.

Answer

how should I make this student understand this is his thesis and he should work more than me?

You don't.

what strategy should I take?

You talk to the professor. Tell him clearly that there are two issues:

1. Working with the other student is untenable, and


2. Your have technical concerns about the project.

Try to agree on a strategy where either:

• the other student is removed from the project completely, or else


• you and he are working on two totally separate things, and the requirements for "your piece" are well-established and entirely within your control.

If you communicate this clearly (hopefully more clearly than your post here!) and the professor is still uncooperative, you should look for another supervisor.

How to write abstract for conference when you have no results yet?

This situation is not uncommon; in my case, I have to submit abstract for conference in September by the end of January already. But the problem is I have no results yet. I'm pretty sure that in those 8 months I will get pretty interesting results. But..

How to write smooth abstract without reporting results?

I started something along these lines:

1. This and this is an important factor ...


2. However, few studies on this topic have been done ...


3. In our study, we compare this and this



4. ??

Now the problem comes in point 4, where I should report some results.

• How should I go around that?


• What formulations should I use?


• Shall I speak in present, future, or past tense? The studies are usualy written in past tense like "we analysed, we compared...", but in this case I would tend to present tense.

Thank you for your help. Examples are welcome!

P.S.: this is an interesting discussion however didn't give me actual guidelines of how to write it.

Answer

Don't write results you don't have. Neither in the present, past or future tense. Just don't do it. Yet, I agree with you that there are circumstances where you do need to write an abstract on on-going work. For example, many big conferences in my field now ask for abstracts to be submitted up to 10 months in advance of the conference itself! If you are a post-doc staying on a 12-month project, you want to present something but you might not yet know how things will turn out. So, two techniques I propose:

1. 
   

   Just write about the methodology, and present your goals in a general way, without “predicting” particular results but insisting on the importance of the topic. That is, emphasize strongly your points #1 and #2, and then describe point #3 as you would your “results”. Things like:

   
   

   
   

   In this particular study, we compare the efficiency of methods A and B on given subsets of a reference database. We use a large number of different criteria for measuring efficiency, including …, … and … We also discuss in detail the implementation of subprocess X in method B, because its has not been specifically optimized in the existing literature.

   
   

   
   

   I know it sounds vague, but that's the best you can achieve honestly, without pretending to know what you expect to find.

   
   



2. 
   

   Bait and switch: if you have existing results in a closely related study, you can incorporate them as part of your results. Mix this approach with above, so that you have at least a few specific results to list in your point #4. Then, when you will make your presentation, just present your new results alongside the old (some people would remove completely the old results, but that makes it too much of a “bait and switch” for my taste). It is, after all, quite common for people to include newer results in orals/posters that they obtained after the original submission. It is not frowned upon, as long as you keep a decent agreement between the original abstract and the final content.

   
   

plagiarism - What should I do when someone's falsified information based on governmental connections to accuse me of academic ethical misconduct?

It was about three years ago that I have started my M.Sc. degree. I was a top student at our department. I have graduated with honors and with several journals and conference papers. Everyone knew who I was and I was really popular in our department. In the first year, a supervisor asks me to work on a data that he said the data was his own and he had worked on it along with a draft written originally in another language. The data he had given me was based on a project in our class. Every student had to take part in the project as an assignment. There was a student X.X. he was so bad with me and always showed negative behavior through me. Our supervisor decided to put us on a team to make us friend! eventually, we were the only people that have finished the project and decided to publish it as an article. The calculation made by X.X. was wrong therefore our supervisor had told him that we have to go with my calculations for the journal based on the propositions that I have made. At that point, I have changed many things within the initial draft. With the insistence of Mr. X.X. our supervisor agreed to a conference submission of early stages of our project BUT he said that Mr. X.X does not have to be on the Journal paper because he didn't do any of new calculations and the writing process has been done by our supervisor. Therefore he told me to finalize the project without his name in the paper. Also, he told me that I could be the first and corresponding author because he doesn't have any time to work on the project. So, We have published the paper in English in a reputed journal. It is also worth mentioning that few weeks after we submit the paper to the journal, the conference has emailed us that the abstract along with a text has been accepted in the conference for a poster presentation. Our supervisor has shocked! because the paper that was available in the inventory of the conference proceeding was the semi-final paper in the native (foreign) language and the conference had sent us the final acceptance letter. Our supervisor has sent them an email and explained the situation that the paper that has been sent is not spouse to be online because he does not agree to sent this paper and the acceptance was based on only a poster presentation, not a manuscript text! they said OK and the argument was done.

It was in March that we have found the conference paper have been forged and indexed in the conference proceeding that we said not to publish. This proceeding was indexed after 1 year and a half after the conference! Our supervisor had three other proceedings in this conference and they were published at the time in 2015. BUT the conference paper that Mr. X.X. was working on published in 2018 which obviously they have forged the date. Because I have printed all the proceedings in 2016. I have gathered that Mr. X.X is a son of a very powerful man in a governmental organization. Himself Mr. X.X works in as a government employee and he has many and many connections.

Exactly a week after we saw the proceeding my supervisor has sent emails to the conference explaining that this article has been sent without his permission and we have once told them to withdraw the paper. He has also included the technical report on the paper that have problems. Consequently, they have removed the paper from the indexing website.

Two weeks after this the journal that we have sent our paper contacted us that someone emailed us that this paper has been published in a conference proceeding and the policy of journal said that the translation of such is a redundant publication and it is marked as plagiarism.

We have answered their email that Mr. X.X have forged this paper and sent it to the conference and they had published the paper based on his lobbying and concoctions. We explained that at that moment (April 2018) there was NOT a single proceeding available with that information and we have sent the journal complete information about that. We have told them that Mr. X.X is a very well connected man to the government and everything is possible in this country because it is a dictatorship in a middle east (you guess!).

Since then there was not a single email have came to us from the journal. BUT two weeks ago July 2018 the proceeding have been uploaded once again in the same database with a forged date that indicates it had been uploaded in 2015 !!!!

I don’t know what to do.

This man is very well-connected and powerful within the government.

I am really scared that the journal won’t believe this and someday Retract the paper due to duplication or redundant publication.

I have told this story to my main supervisor who supervised my thesis he told me that Mr. X.X is linked to the dean of our department and it would not have any effect if I told him. Also, the head of our department is a woman that works for his father.

I don’t know what to do, and I am really scared that at this point that I have made this far and took this much effort in order to be an academic and to continue my studies as a Ph.D., retraction of this article with such accusation and falsification ruin my career and my life. Because we can't do anything about the conference proceeding that is not even in English!

What do you think I should do?

How to prepare for being a TA (Teaching Assistant)?

I start my graduate program next week, which includes spending some of my time as a Teaching Assistant. It is my least favorite part of job, and I do not want to teach in my career after that. I don't want to become professor but get a job in a company.

Nobody told me how to teach and I don't even know what classes I have. I have little time to prepare, and probably don't know the professor (professors?) well. So what can I do to prepare, until I know what courses I have and can go over the material? I'm quite scared right now.

Answer

Be honest and be yourself. Students will latch on to your discomfort and will use it as an excuse for their performance. I have found that if you are honest with them with a statement along the lines of "I am new to teaching, so please be patient while I work out my teaching style and get more comfortable. If you have any concerns about how class is going, please speak to me as soon as possible." they are much more forgiving of your mistakes which you are bound to make. There is nothing worse than students who feel they cannot pass the class due to your teaching, so allowing them to voice their opinions early can both help in your teaching (i.e., "You stand in front of the board too often." or "It would be more helpful if you spent a little more time going over X.") and in your students attitudes towards you. But be careful on this front, make no instantaneous decisions. I always will say something like "I will think about it and get back to you next class if the policy X needs to change." Always get back to them about it, even if it is a no.

Additionally, talk to other grad students and faculty if you are finding you are having problems with teaching. I would be surprised if your department or university had people did not staffed just for training of instructors for teaching duties. Talk to them and voice your nervousness, they are there to help. Even think about all your classes and what the professor did that you hated or liked and try to emulate the best attributes as best you can. But don't try to be these people, just be yourself.

The key here is talk to everyone, do your best, and be yourself.

Since you're just starting out, I don't believe that they would throw you in cold into a classroom and say "teach" without any forewarning or even knowledge of which class, but they might depending on where you are (and talk to other people about what to do quickly if possible). You will probably start out grading and/or doing recitations/review sections a few times a week until you are more capable/comfortable with maintain your own class.

Good luck in teaching and studies! I always think being able to explain what you know to other people is a true sign that you know it yourself.

Addendum: The books that earthling suggested will always help. If you are in mathematics, I also suggest How to Teach Mathematics by Steven G. Krantz. Even though it is written for those teaching math, it is also a good read for almost any new instructor, particularly in the sciences.

presentation - When should I stop including talks on my cv?

When I was applying for grad school, I felt that my CV was pretty empty and so I included all my research related presentations (posters/talks) from conferences/competitions/etc (11 of them at the time). However, I am not sure how much of a role they played in my acceptance at that time (I feel I mostly got accepted based on my papers and two very strong reference letters).

Now I keep a semi-complete (semi- because of infrequent updates) list of presentations on my website; this is mostly so I can post slides. However, I feel the list has gotten too long for a CV (~25 items; about a full page) and other more important parts of my CV (such as publications) have grown to need that space more.

When should I start omitting or shortening the talks on my CV?

If I include a 'selected' talks section: How many talks should I select? Should I select them based on prestige of venue, or uniform-covering of my interests, or uniform-covering of my time (show that presentations are a regular activity)?

More context: I am at the graduate-student level in my academic progression. A related question: Do presentations given during interviews count as invited talks?

Answer

First of all: note that there is a difference between an academic CV and a resume.

• An academic CV typically lists everything you've done related to academia; every talk, every conference paper, every award, every grant, every mentored postdoc, grad, and possibly undergrad.


• A resume is a two-page document that summarizes your work/academic experience.

(Terminology may differ, some may refer to the first as a resume also; semantics aside, there is a distinction between the two documents.)

That being said, the answer to your question depends on which document you want to complete. The first should have everything, no matter how old. The second should list your most important, more recent accomplishments, in the interest of space. Regarding the second, the answer to "when should I remove stuff" is simply "whenever you have newer and better things to put in it's place".

industry - Transition from PhD to project-manager position

I’m approaching the end of my PhD adventure and I’ve started looking around for job opportunities. Recently, I found a job posting that fits my career goals quite nicely, but it has more managerial ingredients in it than pure research. It is concerned with managing/coordinating multiple research teams – something I’d like to do eventually but maybe at a later stage after gaining some more research/management experience as a postdoc.

Yet, I found the job description really encouraging:

Requirements: experience in project management or a strong desire to learn it.

That’s why I decided to try my chances anyway. Lucky enough, I'll be interviewed for this position.

In the past, I have had students (BS, MS) who did their theses and semester projects under my supervision. Additionally, I’ve had a graduate-level course on general management and took the lead role in a small research project. Even though these experiences were valuable, this job would arguably require managerial skills at a higher level.

So, my question is as follows: What type of difficulties/changes should I expect from this transition that I may undergo: from a technical PhD to a research manager/coordinator?

Answer

If you've taken Project Management classes and have taken lead roles in regards to projects and BS and MS students, you'll find Project Management to be a more intense version of that. For example, you'll be needing to ensure everyone is working at the pace they should, getting the needed work done, and be prepared to figure out ways to remedy issues that occur. You will be working closely with stockholders, include managerial people, customers, etc, and you need to have the ability to answer any questions they may have regarding your project, even though you yourself are not the one directly creating that content. You'll need to figure out how to effectively communicate with people under you to get a sense of what they're doing and how things will impact the project. Be prepared to do scheduling of the project, which includes figuring out things in terms of Man Hours required for project in contrast to what you have available as resources. A lot of these things are similar in respect to what you've done in school, though to a higher degree: there's more riding on it, and these people aren't grading you, they're expecting it to be done right the first time.

As far as difficulties, if you have done all the above in classes or with your BS and MS students, then just be prepared for the faster pace and higher volume of stockholders. It can be a bit overwhelming, but doable.

Having a technical PhD will help you in these situations, because you'll have a better understanding of what your workers need to complete their tasks, how fast it will take them, and what it is exactly that you're working on. In fact, it will give you a leg up on other candidates or PMs that don't have technical backgrounds. If you can listen to a technical explanation of what's happening, and relay it to stockholders in a way that non-technical people can understand, you'll be fine.

immunology - Could bone marrow transplants help make xenotransplants viable?

So the immune system doesn't calibrate (for want of a better euphemism) to recognize it's own cells until fairly well along in fetal development & the major components of the immune system (antibodies, white blood cells, etc) are all produced by the bone marrow.

Those are the known details that cause me to wonder if this (below) might not be a viable approach.

Introduce the patients cells to a pig fetus before it's immune system has been set & it will be born with an immune system that recognizes both it's own cells & the patients cells as it's own.

Kill the patients own marrow (as per a normal bone marrow transplant) & transplant the pigs bone marrow into him giving him an immune system that recognizes both his cells & the pigs as it's own.

If my understanding is correct you should then be able to transplant any other organs from the pig into the patient without any tissue rejection issues.

I am only interested in the science so (any legal & moral issues aside) are there any major factors I'm unaware of to suggest this approach is a non-starter?

See Xeno: The Promise of Transplanting Animal Organs into Humans By David K. C. Cooper M.D., Robert P. Lanza M.D. Published 23 March 2000 by Oxford University Press, specifically the section on "The Induction of Chimerism Before Birth" from page 117 onward in this link.

That talks about my suggested first step (though in reverse), creating a human with immunity to cell rejection of a donor animals cells, which isn't much use to anyone who's already been born.

So I flipped the idea.

A Thymus transplant might be needed as well.

publishers - Can someone really be assigned to review in the APS’s editorial system for over a month without reacting at all and if yes, why?

From observations as an author and reviewer that I made myself and that have been reported to by others, it seems that the editorial system of the American Physical Society (which in particular publishes the Physical Review journals) works as follows:

1. The editor selects a reviewer.


2. The reviewer receives an invitation to review, which he can accept, decline or ignore.


3. If the reviewer declines, inform the editor to select a new reviewer (i.e., go back to step 1).


4. Otherwise, wait approximately one month for a review.


5. If nothing has happened, inform the editor to select a new reviewer.

This means in particular that if the reviewer does not react at all (for an extreme example, because he died years ago), it takes one month until another reviewer is selected. In contrast, with all other publishers, step 3 seems to be instead:

3. If the reviewer declines or does not accept the invitation within a few days, inform the editor to select a new reviewer.

which seems much more reasonable to me, as a reviewer who does not accept to review (which usually is little work) for whatever reason is very unlikely to review a paper.

My questions regarding this are:

1. Does it really work like this?


2. If yes, why is the system not switched to one, which requires the reviewers to give some positive response within a few days?

---

Note: Just in case, somebody mistakes this for some disgruntled bashing: Apart from the above, my experience of publishing with APS journals has been rather positive. I am just puzzled by this seemingly nonsensical mode of operation.

human biology - Do we actually get more sick (flu/cold) during winter?

The word flu derives from the Italian phrase "influenza de freddo" meaning "influence of the cold".

Indeed it is that time of the year when my colleagues seem to have the flu/cold more often than not. I remember during university, winter lectures would be riddled with people coughing and sneezing - the so called "freshers flu"

Questions

• Is there statistical evidence for this claim?


• If so, what are the causes/factors involved?


• Another post asks why our noses get runnier during cold whether, is this related?

Answer

The combination of these two reports from the CDC give information about the comparative prevalence of flu infection in the winter (September '12- May '13) and summer (May '13 - September '13). I'm going to assume that 2012-2013 was a fairly representative year as far as the level of detail of "do we get sick more in the winter" goes. Particularly striking are the graphs linked to in both documents of the number of flu-infected respiratory specimens per week:

Winter (infected specimens out of 311,000 tested):

Summer (infected specimens out of 52,000 tested):

Together these two figures cover data Sept '12 - Sept '13. Note the difference in scale on the vertical axis. Forgive me if I don't run any statistical tests, but I think you can spot the trend.

The sum of all the Winter cases represents 23% of the 311,333 specimens tested from Sept '12 to May '13, and the sum of all the bars in the Summer figure represents 3.9% of the 52,150 respiratory specimens tested from May '13-Sept '13.

Still left to answer: Why is this the case? In my preliminary research it seems like we still don't fully know the answer to this one; I'll leave someone else to speculate.

---

Edit: Some tentative answers to why is there a seasonal flu outbreak:

This review (1) does a nice job of laying out some of the current ideas about the cause of the seasonal flu. One interesting note is that seasonal flu is a phenomenon of temperate climates: in tropical regions flu outbreaks occur on a much less regular periodic schedule. Some possible causes mentioned by the authors (paraphrased from the article):

• It takes time for virus to mutate enough to be infectious again to people who were already infected with it.


• The efficacy of the immune system may vary seasonally, say, due to changes in daylight hours/vitamin D and melatonin levels (which have been shown to affect immune system function in hamsters)


• Flu is transmitted better in more crowded conditions + in winter people are more crowded together. This is a popular explanation, but the authors claim that it has not been satisfactorily tested. It has been argued convincingly that the 1918 flu epidemic was exacerbated by the crowded condition of army barracks in WWI (see citation in paper).



• Indoor heating encourages air recirculation, which allows virus to persist in the air around you longer.


• Viruses survive/persist better in cold, dry conditions. This may allow them to spread in the atmosphere longer during the winter, and be more easily transmitted from person to person via "bioaerosols" (sneezes).

Ultimately, as I said before, we don't really know yet. Reading that list you can imagine several ways in which a few of those factors are not at all causal and are rather just strongly correlated with the "true" cause of flu seasonality.

(1): Lofgren et al. Influenza Seasonality: Underlying Causes and Modeling Theories. (2007). J. Virol. 81(11): 5429-5436. doi:10.1128/JVI.01680-06

natural selection - Why do heterozygous individuals have increased resistance to malaria?

I am aware that there is such a thing called heterozygous advantage, which is due to the presence of a certain single allele, and that an example of this could be with "sickle-cell anemia". I am quite curious as to how exactly this heterozygous advantage is created.

Could the increased resistance against malaria be due to natural resistance or natural selection?

Answer

The heterozygous advantage generally lowers natural selection against the carriers of mutated alele, because it helps them to survive some specific conditions (which have to have some major impact on the survival rate). This means these individuals have bigger chances of reproducing, which means spread of the alele.

Sickle cell anaemia is one good example in countries with big incidence of malaria (caused by a protista plasmodium falciparum). This parasite reproduces itself in human Red Blood Cells (RBCs), destroys the cells and releases its sporozoits (which can infect other RBCs and the cycle continues). This massive destruction of RBCs is called haemolytic anaemia. Without enough RBCs and haemoglobin, the organism isn't able to function properly (falls ill in malaria).

Individuals which are heterozygous for HbS alele (which in homozygous state causes sickle-cell anaemia) can catch the parasite, but the chances are bigger, that the infected cells will be phagocytized by macrophages and the parasite will be unable to reproduce in them. Illustration Therefore the chances are bigger that they will survive the infection by plasmodium, therefore they can pass their genes (containing HbS gene to the next generation. (The whole process is a bit more complicated by presence of other genes, some details can be found here, but this mechanism seems to be the most important one.)

In general, many homozygots for "normal" Hb alele die as a result of malaria infection, most homozygots for HbS alele die for sickle-cell anaemia. So the winner is heterozygous conformation, which is saved from both. This influences the frequency of HbS alele (it makes it higher until this effect gets balanced with the effect of selection against HbS alele because of too many homozygous individuals with sickle-cell anaemia)

Another good examples in European population are heterozygozity for CFTR mutated alele, which helps during epidemics of cholera. Vibrio cholerae which causes this disease modifies the effects of G protein pathway for release of some ions (and water) into the lumen of intestine, which causes massive diarrhea. Specific mutations in CFTR gene deplete its function (the transport of Cl-) which in heterozygous conformation lowers the loss of water, which is the main cause of death in cholera, therefore helps the individuals to survive. Homozygous conformation however results in cystic fibrosis.

Hope this helps. :)

publications - Why use version control systems for writing a paper?

I am following the advice of @Piotr Migdal in Is there an internet Git-like repository for collaboration on a paper?, and I want to ask about version controls: how beneficial are they (specially under LaTeX settings) for writing papers compared to Dropbox and SugarSync?

I have been using SugarSync for almost a year with no pain. Usually, I create the paper folder and invite other authors to join, so we can see and edit the last version of the paper.

Answer

tl;dr: Version control is harder to set up, but makes it safe to work on the same file, and makes it easy to track history (i.e. previous versions).

Pros and cons of syncing files

Yes, the biggest advantage of things like Dropbox (I use it as well for backuping and synchronizing my files) and SugarSync is their easiness.

They may work for collaboration on files, but:

• they are not meant for two people editing the same file at once (no merge functionalities - so one guy changing a file can overwrite changes made by other guy, even without knowing that),


• you get no history, i.e.:
  
  
  
  
  • did anyone worked on that file I want to work know?
  
  
  • did anyone added or modified any other files?
  
  
  • which changes were made?
  
  
  • can I go to a previous version, the one I sent to my supervisor?
  
  
  
  

Depending what you do, it may not be an issue. For example, if only one is editing tex file, while others are only reading or uploading figures - it's perfectly fine.

And also, look at my answer on Simplest way to jointly write a manuscript? with a not technically-inclined collaborators.

Version control

Version control systems require some technical skills.

Two the most common version control systems are Git and Mercurial (with the second one being more Windows-friendly and, arguably, easier to start).

Both by standard comes only with command line access, but there are some graphical interfaces as well (I really recommend starting with SourceTree).

So, if the collaborators are techie, just teach them how to use it. If not - there is a way around.

You can keep track of version control by yourself, without engaging others (I'm doing it just now with 2 collaborators).

Just you start a repository inside folder you share (the examples are with Git):

cd ~/path/to/the/folder
git init                    // start git repository inside this folder
git add .                   // say git to track all files inside it

Now, every time you or your collaborator make some changes (e.g. add some files, correct typos, revise a chapter, ...) you do:

git commit -a -m "Fixed typos in Seciton 3"

Later, you will be able to go back to this version; and also compare, e.g. the current version of your file with the previous one (by default - by line, here - by words):

git diff HEAD~1 --color-words my_file.tex

See also:

And real world example from using diff (it makes my life so much easier :)); commit messages in Polish, but I guess you get the idea:

Otherwise (a strip from PhD Comics):

phd - How to stop feeling guilty about unfinished work?

My biggest challenge as a PhD student is best summarized by the following from PHD Comics:

_{"Piled Higher and Deeper" by Jorge Cham www.phdcomics.com}

A consequence of working in research is that the end is never in sight - unlike other jobs, there is always more work for you to do.

I am pretty good at making sure to take care of myself, because I know it's important. I can force myself to go for a run, get something to eat, participate in a regular activity that's not related to academia. But I can't turn off the voice in my head that keeps nagging me about the work that's waiting for me back at the office.

This is especially true when there are deadlines and people relying on me to meet them. On top of my research, I have mentees I should be spending more time with, students we won't be able to hire if I don't get my grant-writing act together, collaborators who keep asking when I'm going to write up that work we did together last summer. If I don't do this, nobody else will; it's not like a normal workplace, where your boss can reassign an important task if you are too overloaded to handle it.

So, my question is:

How do you avoid feeling guilty about all the unfinished (and unfinishable) work in academia?

I am looking for specific, practical techniques based on research and/or personal experience, not suggestions that you just thought of but have never tried.

One technique I've tried with limited success is to make a daily to-do list that is limited to three items, and tell myself that I'm not allowed to feel guilty about not doing things that aren't on the list. It works when I'm not terribly busy... but most of the time it doesn't.

Related questions:

How to avoid thinking about research in your free time is related, but I'm not trying to avoid thinking about research in my free time. I'm just trying to avoid feeling guilty about research in my free time.

Also related is How should I deal with discouragement as a graduate student? but those answers seem to address how to convince yourself that your efforts are worthwhile. I (usually) realize that my efforts are worthwhile, I don't know how to convince myself that I'm putting in "enough" effort (whatever that means).

Answer

tl;dr: Keep forgiving yourself and keep working.

I am having the same problem, and only recently it got better. I have it only for open-ended work (scientific projects, other personal projects - everything which is of type "I should have it done" and the same time it is not closed; even worse when others are waiting for results). It seems to be very different from "normal" work (when someone gives me a particular task) and work with an expiry date.

The wisest (and most successful) piece of advice I found is this one (from Smart Guy Productivity Pitfalls - Book of Hook, which has more good points and is definitely worth reading):

6. Do not overpromise to make up for poor productivity. There's a tendency when we're falling behind to try to overcompensate with future promises. "When I'm done, it'll be AWESOME" or "I know I'm late, but I'm positive I'll be done by Monday". By doing those things we just build more debt we can't pay off, and that will eventually lead to a catastrophic melt down when the super final absolutely last deadline date shows up. Just get shit done, don't talk about how you're going to get shit done.

Also, somewhat related is forgiving yourself for being not productive enough (constantly feeling guilty does not help; not only for me, but it seems it does not work for most of people):

The key finding was that students who'd forgiven themselves for their initial bout of procrastination subsequently showed less negative affect in the intermediate period between exams and were less likely to procrastinate before the second round of exams. Crucially, self-forgiveness wasn't related to performance in the first set of exams but it did predict better performance in the second set.

And from a bit different angle, from Elizabeth Gibert's TED talk on genius (it's about treating inspiration, but it is similar for everything - no matter how good you are, you won't do everything; so why should you be bothered by missing a few things?):

And [Tom Waits]'s speeding along, and all of a sudden he hears this little fragment of melody, that comes into his head as inspiration often comes, elusive and tantalizing, and he wants it, you know, it's gorgeous, and he longs for it, but he has no way to get it. He doesn't have a piece of paper, he doesn't have a pencil, he doesn't have a tape recorder.

So he starts to feel all of that old anxiety start to rise in him like, "I'm going to lose this thing, and then I'm going to be haunted by this song forever. I'm not good enough, and I can't do it." And instead of panicking, he just stopped. He just stopped that whole mental process and he did something completely novel. He just looked up at the sky, and he said, "Excuse me, can you not see that I'm driving?" (Laughter) "Do I look like I can write down a song right now? If you really want to exist, come back at a more opportune moment when I can take care of you. Otherwise, go bother somebody else today. Go bother Leonard Cohen."

And from my personal stuff (I mean things that I found helpful):

• using to-do list only for task (i.e. things I know I can do in a few hour max), not projects (it's depressing to have "finish this paper" on the same list for long months, cf. relevant PhD Comics strip),


• underpromise and overdeliver to oneself; i.e. committing to do each day less task than expected (this way, with the same results, it's "wow, I did things from the list plus 2 extra" instead of "I only made almost half of the first point out of 7"; extrapolating one's maximal efficiency does not work...).

productivity - Scientifically meaningful sources of bibliometrics

Whether we like it or not, modern academia is increasingly being measured, in some vain attempt to get objective measures. Although it is unwise to fight 'being measured', it is at least possible to steer the measures away from meaningless ones, backed by peer-reviewed research that establishes this unrefutably.

There are a lot of different metrics that have been defined - I am not looking for those. What I want is pointers to the research behind the scientific validity of those metrics.

So the question is: where should I look for scientific assessments of bibliometrics?

Answer

Johan Bollen and Herbert van de Sompels are two researchers to follow in this area. Bollen did an analysis of 39 different citation-based metrics which is a good place to start. However, it's crucial to note that there are serious errors in trying to use citation-counting methods as some sort of ground truth. Citation counting is problematic because:

• Different fields have different citation practices. In biology it's common to have 10 or more authors on one paper, whereas in math you often have only one or two.


• Citations take a long time to accumulate, penalizing early-stage researchers.


• Citations only tell part of the story, leaving out the useful contributions made by researchers in the form of code written and datasets released.


• Citations often mutate over time.

It's now possible to get more information about a paper than just who cited it, and it's possible to get this information before several years have passed and before the information about the impact of the paper becomes old and less useful. The Public Library of Science makes detailed article-level metrics available and Mendeley has an API from which you can collect real-time data about how many readers a paper has, as well as social metadata such as tags and annotations and reader demographics. These metrics are being consumed by services such as Total Impact and combined with data from Github, Twitter, and traditional citation metrics. My bet is that if you're looking for a meaningful set of measures, you're going to find it in these richer sets of aggregated data.

graduate admissions - PhD opportunities when lacking publications

This question in some sense, complements this question. Suppose a good student completes his master's degree in a less-than-top-ranked university. He has excellent academic grades both in his bachelor's and master's, but unfortunately has not experienced the best research 'atmosphere' in his post-grad and so does not have any publications thus far in his career.

It is a hugely relevant practical issue: low-ranked universities woo good students by providing them full funding plus scholarships for their master's, so there are many cases where students prefer them to top colleges where funding is not assured. After completion of graduation, these students desire to go for a PhD in top universities. So the question is this:

• How does a bright student with excellent grades but lacking in publications secure an admit in a top school?

One obvious answer is to formulate an excellent research problem and to convince professors of his research ideas pertaining to the problem. Any other useful suggestions?

Answer

You have to make the case that your research potential outweighs your lack of research output.

The only places to make that case are your research statement and your letters. Both your statement and your letters should make it clear that you are an active researcher, even though you are not yet published. Your statement should describe the specific research problem(s) that you are pursuing, promising and specific partial results, and a specific and well-informed plan of attack.

Similarly, letters from faculty at your MS department should describe your independence, stubbornness, intellectual maturity, and so on, in specific and credible detail. When you ask for letters, ask your references specifically if they can write a strong letter about your research potential. Ideally, your references should admit that their department doesn't provide you with the environment that you need to thrive as a researcher. And it really hurts to write “[Bravo] can do better than us,” so it better be true.

Admissions committees (at least the ones I've been on) do take applicants' previous institutions into account when judging research records. We know that applicants from most 4-year liberal arts colleges don't have as many opportunities for computer science research as applicants from (say) MIT, so our expectations for MIT applicants are higher. So your lack of publications may not hurt you as much if your MS department is known to have a weak research atmosphere.

However: Do not suggest in your application that your lack of publications is your MS department's fault. You may believe it's their fault, and you might even be right. But if you actually write that it's their fault, you'll come across as someone eager to blame others for your weaknesses. No matter how good you are at research, nobody will admit you if they think you're a jerk.

teaching - What makes a good chalkboard?

I've encountered lots of chalkboards through my career, and they vary widely in quality. Some write smoothly and erase cleanly; for others, the chalk squeaks and the eraser just smears.

I assume there are differences in the materials they use, the construction techniques, how the surface is prepared or treated, and so on. But I'm clueless as to what these differences might be, and how they affect the quality. If I'm looking for a "good" one, what questions should I ask?

(Academics are one of the few groups these days that use chalkboards on a regular basis, so I hope this question is suitable for this site. Please note that I'm not asking for specific product recommendations, just general information.)

evolution - Is there evidence that some non-human species perform sexual selection based primarily on intelligence? How do they do this?

I'm a biology amateur, but it seems like sexual selection is almost always performed based on physical characteristics, the outcome of physical contests, or some sort elaborate courtship. But do any non Homo-Sapiens perform sexual selection based on intelligence factors, like problem solving abilities? If so, how does the species accomplish this? I know natural selection as a whole would definitely favor intelligent individuals, but I'm curious if any species actually takes this into account when choosing mates.

Answer

Very intresting question. The problem is that animal intelligence is hard to measure not only for scientists, but probably also for the potential mate. Paradoxically, that is why selection for intelligence, if it occurred, may be very strong. One has to be smart in order to recognise smart behaviour, so preference and preferred feature are strongly connected. But that's only my opinion.

Boogert et al., 2011 1 reviews the current knowledge about animal preferences for cognition skills. They conclude that there is very little data on this subject. The given examples are:

1) Preference for elaborating birds songs (as songs are not inborn and have to be learned)

2) Spatial abilities:

In meadow voles (Microtus pennsylvanicus), males with better spatial learning and memory abilities were not only found to have larger home ranges and to locate more females in the field (Spritzer, Solomon, et al. 2005 2) but were also preferred by females in mate-choice tests, even though the females did not observe males’ performance on spatial tests (Spritzer, Meikle, et al. 2005 3).

In guppies (Poecilia reticulata), males that learned faster to swim through mazes to gain a food reward were found to be more attractive to females (Shohet and Watt 2009 4). However, females were not able to see the males’ performance in the mazes. Although male learning ability was weakly correlated with saturation of the orange patches on his body (a sexually selected trait (...)), orange saturation surprisingly did not correlate with female preferences. Thus, the cues leading female guppies to prefer faster learners are unknown.

It is possible, that females base their choose on some factors that correlates with cognitive skills or on total wellness, what may depend on intelligence.

3) bowerbird's abilities to build bowers (courtship constructions):

Comparative studies across bowerbird species have shown that relative brain size is larger in species that build bowers than in closely related nonbuilding species (Madden 2001 5). In addition, relative brain size increases with the species-typical complexity of the bower (Madden 2001 5), and a comparative study on the relative size of specific brain regions showed that species with more complex bowers have a relatively larger cerebellum (Day et al. 2005 6).

4) foraging performance

A recent experiment by Snowberg and Benkman (2009) 7 using red crossbills (Loxia curvirostra) showed that, after observing 2 males extracting seeds from conifer cones, females associated preferentially with the more efficient forager of the 2. The authors were able to exclude female choice for correlated traits by experimentally manipulating foraging efficiency, such that fewer seeds were available in the cones of one of the males. The males were also swapped between treatments (i.e., slow vs. fast forager) so that male identity could not explain the females’ preferences for the most efficient forager.

---

Another way that intelligence may be favored by sexual selection is "cheating" during courtship. For example most frog species call to attract females. But this signal may also attract aggresive rivals or predators. Some males, especially the weaker ones, do not call but stay near calling individual. This allows them to avoid confrontation and wait for approaching females [8]. The successfulness of this strategy may depend on how "smart" the individual is (only my opinion).

[1] Boogert, N. J., Fawcett, T. W., & Lefebvre, L. (2011). Mate choice for cognitive traits: a review of the evidence in nonhuman vertebrates. Behavioral Ecology, 22(3), 447-459.

[2] Spritzer MD, Solomon NG, Meikle DB. 2005. Influence of scramble competition for mates upon the spatial ability of male meadow voles. Anim Behav. 69:375–386.

[3] Spritzer MD, Meikle DB, Solomon NG. 2005. Female choice based on male spatial ability and aggressiveness among meadow voles. Anim Behav. 69:1121–1130.

[4] Shohet AJ, Watt PJ. 2009. Female guppies Poecilia reticulata prefer males that can learn fast. J Fish Biol. 75:1323–1330.

[5] Madden J. 2001. Sex, bowers and brains. Proc R Soc Lond B Biol Sci. 268:833–838.

[6] Day LB, Westcott DA, Olster DH. 2005. Evolution of bower complexity and cerebellum size in bowerbirds. Brain Behav Evol. 66:62–72

[7] Snowberg LK, Benkman CW. 2009. Mate choice based on a key ecological performance trait. J Evol Biol. 22:762–769.

[8] Bateson P. 1985. Mate choice. Cambridge University Press. 181-210

biochemistry - Why do the humans become sleepy after meals?

I don't know about all the mankind, but I know enough people, who becomes sleepy after their meals. Also, I'm not sure, what kind of food do they consume, but I personally get sleepy almost from any food: sweet, fat, spicy, salty, liquid, tasty, not tasty, etc.

Is this phenomenon well known? And, if yes, how does it occur?

bioinformatics - In Sanger sequencing, why do we resort to cloning? Why doesn't PCR suffice?

I understand that in Sanger sequencing we can clone our fragments with the help of e.g. bacteria to make multiple copies of our fragments for further analysis.

I also understand cloning can be a bottleneck in Sanger sequencing - and partly prompted the development of NGS methods.

But doesn't PCR do just that, make multiple copies?

What am I missing?

Answer

You can use PCR products in Sanger sequencing; it is very common. Using PCR products instead of cloned genes does raise a set of problems that are less of a concern than with cloned sequences, such as the presence of incomplete or incorrect PCR products, but there are standard and simple solutions for most of these concerns.

phd - Having children while at graduate school

I am finishing my first year of Masters and have always thought of going for a PhD in North America. I and my girlfriend are going to have a baby which is totally unexpected. The due day will be somewhere this december which I am still half year away from finishing my Masters degree.

I don't know under this circumstance should I still, or am I able to, apply for PhD positions overseas. This would mean I will have to leave them or bringing them together for my study. I am not super rich to afford a family personally and would need to rely on studentships, but I don't think graduate studentships are sufficient to afford the living expense and future education fees of my coming baby.

Taking on a PhD and a research career are definitely my dream and situation seems very difficult for these to come true. Anyone knowing someone carrying kids along grad school, or any suggestion to me? I just don't have a clue how to take care of everything.

Why is human vision restricted to 400-700 nm?

Across the electromagnetic spectrum, 400-700 nm is a narrow spectrum of frequencies and focused in the region of short wavelengths. For example, radio waves cover a large range of frequencies unexploited by the visual system. So what biological reason is there that evolved us to use such a small frequency bandwidth for vision?

Answer

Short answer
The visible spectrum has the highest energy in sunlight at the earth's surface, explaining the gross location of the visible spectrum in life on earth. The specific frequency range varies across species and can be explained by species-specific survival strategies.

Background
When you look at the solar light spectrum at the earth's surface the visible spectrum has the highest intensity (fig. 1).

^{Solar irradiation. Source: University of California.}

So it makes sense to use the range of frequencies that is represented most in sunlight as a starting point.

Then the question becomes, why do humans utilize approximately 400 to 700 nm, and not infrared or UV? That can be explained because we do not need it. Our range has been hypothesized to be related to foraging behaviors and our visual system is particularly sensitive in the frequency range of the coloring of (ripe) fruits, which is thought to have been of great benefit to our hominid ancestors (Osorio & Vorobyev, 1996).

Why then do animals extend their vision into UV? Many fish, amphibian, reptilian, avian, and some mammalian species use UV vision. Many birds can identify UV-reflected nectar and berries, and UV-reflecting plumages in birds, and scales in fishes are used for recognition (Shi & Yokoyama, 2003). Moreover, some arthropod species are know to use UV vision to reduce light-reflection distortions under water, such as in the mantis shrimp that features 12 photoreceptor types (as opposed to four in humans) (Thoen et al., 2014).

Why then do animals extend their dynamic range into the infrared? A notable beneficial effect of perceiving infrared is the detection of body heat. The generation of heat is accompanied by the generation of infrared light. The detection of this emitted light is highly useful for nocturnal predators, like the rattle snake (Hartline & Newman, 1982).

<sub>References
- Hartline & Newman, Sci Am (1982); 246(3): 116-27
- Osorio & Vorobyev, Proc Roc Soc B (1996); 263(1370)
- Shi & Yokoyama, PNAS (2003); 100(142003): 8308-13
- Thoen et al., Science (2014); 343(6169): 411-3</sub>

<sub>Further Reading

1. Is our color vision calibrated to sky, vegetation, and blood?
2. Is there a physical reason for colors to be located in a very narrow band of the EM spectrum?</sub>

Is the human body composition real?

In Fullmetal Alchemist when Ed goes to disprove to Rose the Sun God's "miracle" to bring humans back to life by proving that science (in the form of Alchemy) can create people by saying

Water (35 L), Carbon (20 kg), Ammonia (4 L), Lime (1.5 kg), Phosphorous (800 g), Salt (250 g), Saltpeter (100 g), Sulfur (80 g), Fluorine (7.5 g), Iron (5 g), Silicon (3 g) and trace amounts fifteen other elements.

I am wondering, is this composition true in real life? if so what are fifteen trace elements?

PhD dropping out and funding reimbursement

What happens if one has a PhD scholarship and drops out in the second year of the PhD program? Should he pay back the money that he got in his first doctoral year?

population genetics - Ways to distinguish between purifying selection and selective sweep

When looking a population genomic data, regions of low diversity (lower than expected; such as in a region of high recombination) can indicate either purifying selection of deleterious mutations or a selective sweep of an adaptive mutation. What are some ways one can tell which one occurred?

One way I've heard of is to use an outgroup that did not live through the same events as the main group. If the outgroup also has low diversity, it means nonsynonymous mutations in that region are deleterious regardless of events, and so those homogeneous regions likely underwent purifying selection. If the outgroup has high diversity in those regions, the main group likely went through a selective sweep.

What are other ways to distinguish between the two?

career path - Why do research faculty pursue administrative positions, such as dean, provost, president, etc. ? Do such positions spell the end of one's research?

At a recent seminar talk, I was amazed to note that one of the two coauthors (not the presenter) was the president of a large and well-known university, since I had always assumed that taking on such a position would necessarily mean the end of a research career.

• 
  

  Are there m/any examples of people that continue to do substantial amounts of research when in a senior administrative position, such as dean, provost, president, etc.?

  
  



• 
  

  Do research faculty often become deans, presidents, etc.? Why do faculty usually do this? (I understand that there might be a pay increase, but does it usually indicate that they no longer want to do research as intensely?)

  
  

Answer

In these positions, one gets to influence the direction of the whole university, rather than the direction of the research of 1 to n individuals. At such magnitude, one can effect more change.

Often people get disgruntled with the way things are run at the level they are currently working. The only way to fix things is to move to more managerial positions. Don't like the way the Masters program is run? Become Coordinator of the Masters Programme. Don't like the way the faculty is being run? Become Dean.

publications - Found a severe error in a conference paper after presentation but before the proceedings

I am a final year undergraduate student and had worked on a very fundamental project(there is no available literature on this field presently) during my sophomore year. The results obtained were quite interesting but there was no available literature to back up my results. My supervisor suggested me to submit it to a conference and get reviews on the work.

I did the same and when I submitted the final paper, I got a strong accept with quite positive feedback. I presented the paper at the conference and was also appreciated by my conference chair who said that it was an interesting finding. However, while working on the journal version recently, I discovered a severe error in my paper which completely invalidated the claims I had made in my work.

The conference was highly reputed and delegates from all over the world were present. I feel really ashamed of presenting the wrong work at such a big stage. I discussed this with my supervisor and he told me that we will decline for publication by stating the reason when they will send the copyright form for inclusion in the digital proceedings. This gave me a sense of relief.

However, I cannot stop thinking about having presented the wrong work and seems like I should not have gone for it in the first place. Please suggest me what should I do. I have a deep interest in research but I am in constant fear that my habit of premature celebration will land me into trouble someday.

Answer

Let's see:

• You wrote a paper of sufficient writing quality that it was chosen for presentation at a conference and publication.


• None of the peer reviewers noticed anything wrong with it.


• None of the people in the audience questioned it.


• Your supervisor saw nothing wrong with it.


• You gave an excellent presentation.


• You found a flaw in a paper that had already been accepted for publication.



• You had the integrity to withdraw your paper from publication.

That's a long list of things to put on your "plus" list. Most undergrads don't achieve even one of them. None of them should be seen as a negative.

---

Be warned that you'll become more jaded as you progress.

I remember as a grad student being asked by my supervisor to review a paper that had been sent for him to review. It was well written and obviously the result of a lot of hard work, but I found a fundamental oversight that would have allowed the entire problem to be reduced to something very trivial.

We told the publishers about this, and they wrote back requesting that we recommend it for publication anyway. My supervisor said that the author could publish another paper later that would re-analyze the problem and present it differently.

That's one (of many) reasons I eventually didn't bother finishing my own PhD.

statistics - Appropriate statistical test for a student lab?

I am a HS Bio teacher and doing a microevolution lab involving candy. Essentially students use four candy types and push them together until one cracks (Nat Sel). They also do simulations of migration, mutation and genetic drift. They then calculate the "allele frequency" of each type per generation and look for changes. I want to have my students do a simple statistical test to see whether the change was significant or not from each evolutionary factor. I was going to do a chi square test, but someone told me that is not appropriate to this type of experiment. So, can anyone confirm, is chi square inappropriate, and if it is.. Can anyone point me to a more appropriate test. These are high school kids with no stats background (and I have forgotten virtually all the stats I learned 20 years ago)...

copyright - Does publishing a paper on arXiv prevent me from submitting it to a non-open access journal?

If I publish a pre-print paper on arXiv, how can I guarantee exclusive rights to the publisher afterwards? Am I unable to publish on non-open access journals after I publish a pre-print on arXiv ?

Answer

You are generally allowed to publish even in a non-open access journal even if a pre-print is on the arXiv. Most journal copyright agreements explicitly allow the authors to post the article online. Here's an example of a fairly generous one:

The ASL hereby grants to the Author the non-exclusive right to reproduce the Article, to create derivative works based upon the Article, and to distribute and display the Article and any such derivative work by any means and in any media, provided the provisions of clause (3) below are met. The Author may sub-license any publisher or other third party to exercise those rights.

and a less generous one which still allows the author to post a copy online:

I understand that I retain or am hereby granted (without the need to obtain further permission) rights to use certain versions of the Article for certain scholarly purposes, as described and defined below (“Retained Rights”), and that no rights in patents, trademarks or other intellectual property rights are transferred to the journal.

The Retained Rights include the right to use the Pre-print or Accepted Authors Manuscript for Personal Use, Internal Institutional Use and for Scholarly Posting; and the Published Journal Article for Personal Use and Internal Institutional Use.

I've seen examples where the journal actually did some genuine copyediting beyond what the referee did where the author wasn't allowed to post the version that benefited from the copyediting, but could still post the earlier version.

So, for most journals, the answer is that you're allowed to post the article online because it's specifically allowed by the document they ask you to sign. But it is possible that posting on the arxiv will rule out particular journals that have more restrictive policies.

evolution - How does natural selection favour large body mass and size (or so it seems)

I was walking through a park this afternoon and observed a few birds having fun flying around and it got me thinking why would natural selection favour birds with flesh at all if it hinders their flight.

We started first with single-cell and micro-organisms flourishing the ponds and then they evolved into massive dinosaurs. It therefore seems, there are some unique reasons for growing to such a large size.

However, I thought it's counter intuitive because the large body slows down locomotion, requires lots of food and energy upkeep, is a big flesh target for predators, makes hiding ineffective.

Although it is obvious that the flesh protects the internal organs, but it seems like a chicken and egg problem because without a massive body, perhaps then there is no need for the internal organs.

On a different perspective, perhaps those animals that evolved without flesh are called plants.

That sums up my naive train of thoughts.

So, any expert can shed some light?

Answer

Well first of all I don't know if natural selection favors larger animals - most of the living things in the world are single celled.

Still there are advantages to being larger. I don't know if I can list them all! In no particular order:

1) Living things that are large are more metabolically efficient. The amount of food required goes as a 3/4 power of the size of the animal. Thus a cat 100 times the mass of a mouse requires only 31 times more food. I don't believe that it is not known how this works.

2) r vs K selection: larger animals have greater individual "value". Smaller animals tend to live by r-selection - they are cheap and reproduce in large amounts, then lead short and highly competitive lives where most offspring die without reproducing. Larger animal tend to live longer and reproduce offspring with a greater chance of life. In the extreme case you can compare a cockaroach to an elephant here. This is not a hard and fas rule, but cheap offspring do tend to be small.

I seem to remember that there are lots of other surveys done and body size correlates to life span and any number of other attributes, which I will try to add after I get some sleep unless someone slips in and lists them all.

3) Cope's rule - an observation as much as a rule that size must convey some advantge because most animals become larger the longer they are around. Not always true, but there is a trend that the longer evolution works, the more likely a large animal will show up. This might be because as niches for smaller animals are filled, niches for larger animals become more accessible?

authorship - What should the chemist who synthesized a drug expect regarding coauthorship of papers on clinical trials?

Should the industrial chemist who conceptualized , first synthesized , characterized and patented a novel drug , transferred the synthetic technology (at the 3 Kg scale ) to a CRO for preparation under cGMP conditions,substantially helped in drafting the CLINICAL TRIAL INVESTIGATOR BROCHURE , and provided advise throughout the trial be granted coauthorship of the paper reporting the trial ?

Do PhD courses in engineering fields in European non-English speaking countries require knowledge of the native language?

Can a Ph.D. student who only knows how to speak English study in a European non-English speaking country (e.g., Austria, Netherlands, Switzerland, Italy, etc.) without any problems? Does applying to these universities require knowledge of that country's language?

human biology - Where does the 'C' in exhaled CO₂ mostly come from?

When a human being exhales CO₂, what is, by the numbers, the main source of carbon atoms exiting the body in this way? I mean what class of cells, or which tissues are the biggest on a pie chart of where carbon atoms breathed out in the form of CO₂ molecules came from?

Answer

CO₂ is a product of Cellular Respiration, which generally takes Glucose and molecular Oxygen to produce Carbon Dioxide, water, heat, and allows ADP to be regenerated into ATP (or other various oxidation reactions). The Carbon comes from wherever the acetyl-CoA used in the Citric Acid Cycle came from - either carboyhydrates or fatty-acids (saturated carbon chains).

Simplified reaction:   C6H12O6 (s) + 6 O2 (g) → 6 CO2 (g) + 6 H2O (l) + heat

So, you are correct. CO₂ transferring out of the lungs is mostly the result of burning sugars (or fats) for energy (the regeneration of ADP/GDP with respect to human biology).

To that end, the tissues that produce the most CO₂ will be the cell-types which constantly require energy. Nominally, muscle tissues.

Per your comment, broken down fat, or rather, the process of Fatty-Acid Catabolism, results in the production of acetyl-CoA, which is a primary player in the Citric-Acid Cycle. The Citric Acid Cycle, which you should recognize as the Cycle that Pyruvate - the end result of Glycolysis (the breakdown of Glucose into 2x 3-Carbon Pyruvates) - also goes into after being converted into acetyl-CoA by Pyruvate Dehydrogenase.

The sum of all reactions in the citric acid cycle is:
Acetyl-CoA + 3 NAD+ + Q + GDP + Pi + 2 H2O → CoA-SH + 3 NADH + 3 H+ + QH2 + GTP + 2 CO2

So, for a basic breakdown with respect to CO2:

• 
  

  Carbohydrates (Sugars, Starches) → Glucose → Pyruvate + ATP + NADH

  
  


• 
  

  Pyruvate → Acetyl-CoA

  
  



• 
  

  Lipids (fats) → Lipolysis → Acetyl-CoA

  
  


• 
  

  Acetyl-CoA + ... + H₂0 → ... + CO₂

  
  

Is it reasonable for me to expect an official and timely response to my PhD application?

I recently applied for a PhD position with a major university in Europe. However, I haven't heard back from them even though the dates for the interviews have passed. This somewhat provoces me since I've put a lot of work into my application (it feels disrespectful to not get back to me) and since it makes me unsure whether I have been rejected or merely forgotten. I've already got a response (possibly automately generated) that my application was received by them.

Answer

I think it is perfectly reasonable to expect a timely response, however it seems to be the case that many graduate schools are overwhelmed with applications and underestimate the time it takes to deal with them. A slightly more cynical view would be that many graduate school admin departments are understaffed and don't have the resources to cater for expected number of applicants. In my case I submitted my application on 28 Feb and was informed that interviews would take place "during the week of the 19 March". This date came and went and I assumed I had not been successful, so I called the Faculty Graduate Office the following week and was informed that the process was taking longer than expected but I would be notified of the status in due course. On 5 April I received an email saying I had been selected for interview and "we will contact you shortly with an interview date and time". On 25 April I was given the interview date (for the middle of May).

I would recommend that you just call them and ask to know the status.

learning - What is the best way to retain learned materials

No matter who you talk to, students or professors, they all say that the materials they once learned can be quickly forgotten without further experiences that utilizes or enhances on that prior experience.

I fondly remember a professor once telling me that his final year in undergrad was the happiest year in his life, at time when he felt he could do anything, from nuclear physics to parallel programming to electromicroscopy to constructing an audio amplifier...then one year later he has forgotten almost everything.

This is more noticeable in students, where it is often exaggerated to the cliched phrase "you never actually use anything you learn in school".

This is problematic for students who aspire for higher learning because much of the material or understanding is accumulative. It amazes me how people manage to get all the way to the top of the academic ladder (PhD, Post-Doc) without losing previously gained knowledge along the way. I'm sure there were important theorems, relations or techniques that I once learnt, maybe was even an expert in, the question is how do I unlock these memories so I can be more effective in tackling the problems I have today?

How do people deal with the inevitable loss of knowledge from years of disuse? Do you start from scratch? Can someone offer good ways for retention of class room materials?

Answer

This is problematic for students who aspire for higher learning because much of the material or understanding is accumulative.

Actually, that's precisely why it's not problematic. If you had to memorize random trivia, it would become more and more difficult as you had to remember more unrelated things, but academic studies work in the opposite way. Because it's accumulative, you are constantly practicing and applying what you learned before, which helps you solidify your understanding. Furthermore, the more you learn, the more connections you can see, and these relationships help you organize and retain knowledge. Of course you'll still forget some details, but you'll forget less than you expect and recover it more easily.

My impression is that severe forgetfulness in students typically occurs when they are studying ideas in isolation and setting them aside as soon as the class is over. Instead, it's important to play with ideas constantly. How are they related to your past studies? To other interests of yours? Can you think of further applications or connections? This can help bridge the gaps between how you learned these ideas. This sort of exploration is almost essential if you want to do research, and it's a useful study technique in any case.

genetics - "Same" DNA vs genes

It is often cited that humans share 99% (or 98%) of their DNA with chimpanzees.

On the other hand it is stated that siblings share only half of their genes.

What (if any) is the difference between DNA and genes; or, how can the above two claims be reconciled? (I am assuming of course that chimps and humans are more different from each other than two siblings are from each other.)

(I am asking this question as a layperson, who had a little biology in school but not much more.)

June 2015 Addendum: Here is a nice YouTube video just released by MinuteEarth; I do not know how accurate this video is, but as a layperson I found it insightful.

Can I request the code behind a research paper from the author?

I am in the field of computer science. It is often the case when I am reading a paper I start to wonder, "Wow stunning results, however, I would like to prove that." or "How exactly did he get these amazing results? He/she just wrote a rough overview of the real methodology used in this paper.". As you can see, a lot of times the small things have a huge impact on the overall performance of the underlying methodology. Often they are not part of the paper or not revealed at all.

My idea would be to contact the paper writer, to ask for his research programs to recreate them and understand them. Can/should I do that?

I personally think that there are probably not a lot of researchers, who would let somebody else "look at their cards". What's your experience with that?

Answer

Ask for the code. Please do, however, explain why you want it and what you intend to use it for.

Personally, I would be quite happy if someone contacted me about my research, and would try to give all the necessary tools to recreate my data. Especially so if I am not currently working on a follow up piece.

That said, I've asked for parameters, codes, procedures etc. several times from the authors when the description in a paper has been vague. I've had a lot of different responses: Some have plain ignored me, others have given me everything I asked for, and yet others have only obliged when I've suggested that I might be willing to put them as co-authors if I built upon their code in a way that leads to a publication. Finally, some have refused my request. This has happened for a number of reasons, for example those discussed in this question.

If you ask for code and say that you just want to verify some of the conclusions of the authors or use it as a reference for your own implementation, you can most typically expect a refusal or no reply. This, at least, is the experience I've had.

What types of industry positions favor PhD over a masters?

I'm coming from a biomedical engineering background, and I'm noticing that almost all job postings ask for either an MS or a PhD, and from speaking with my friends with masters it seems that masters are often favored, because they demand less pay. In fact, the only positions that specifically seek out PhDs seem to be research positions in industry.

Based on that, I'm curious to see if this exists beyond just engineering. Are there any non-research industry positions that actively seek to hire PhDs over masters students?

Answer

High-tech engineering companies, for one. A friend of mine works at a small system-on-a-chip designer company, and they supply highly specialized chip designs to other businesses which utilize embedded systems -- think leading automotive, aerospace, consumer electronics OEMs. The company is small and every engineering employee has at least a MSc, most of them have PhDs or higher (that would be associate professors and professors).

Another example is automotive R&D -- mechanical engineering. Companies are financing new development of new methodologies in product development -- particularly structural optimization, design automation, manufacturing process simulations. Virtual prototyping is the name of the game for top manufacturers currently, and the demand for highly-skilled experts is great, even in these uncertain economic times.

In the country where I study, PhD projects are financed jointly by interested private companies as well as research organizations, and the companies have a vested interest to receive not only the direct results from the research, but also trained individuals that can integrate the research outcomes into their product development or manufacturing process.

Obviously YMMV by country and research field. PhDs in in mostly theoretical projects might have harder time finding a good position after graduating, while hands-on graduates whose projects were conducted in collaboration with industrial partners are much more likely to secure a senior technical position even before their dissertation.

human biology - Why would taking antibiotics increase stamina and energy?

I often hear that people who are taking antibiotics experience wild fluctuations between feeling full of energy and completely alert but soon after feeling impossibly fatigued and sick.

Does this have anything to do with the antibiotics being used by the body as anything? For example as a hormone or as a source of nutrition? Is this this a reported side effect when used for other infections?

Answer

I have never heard about this phenomenon from my patients or professors at the Medical School, but this is a possible mechanism that comes to my mind.

One of the classification for antibiotics takes consideration the effect on bacteria. Two possible effects are either stopping the proliferation (and letting the immune system to kill those that are currently present in the body) or killing bacteria directly.

The second approach is obviously more effective but has one big disadvantage: massive death of bacteria leads to the massive release of their toxins that are normally trapped within they bodies (so-called endotoxins). The symptoms you describe as "impossible fatigue" match exactly the symptoms of bacterial intoxication -- and this can increase upon the antibiotics intake.

Depending upon the bioavailability and pharmacokinetics some antibiotics might not kill all bacteria "on the first run" and the symptoms of intoxication recur several times with decreasing severity of manifestations.

publications - Things to do before submitting a manuscript

After having written a manuscript and formatted it to the publishers specifications, are there any additional things you do before submitting it (or right after submitting it) that make the review process easier. For example, for journals that I know the approximate time it takes to review, I make a note in my diary to check on the manuscript around that time. I also print out a hard copy and move the digital files into my lab notebook. Are there other things that I should be doing?

Answer

Putting together also some advice from the previous answers, here is my suggested checklist:

1. Run a spellchecker :)


2. Prepare a cover letter. If the manuscript has a previous history (e.g., it is a modification of a rejected papers; overlaps partially with a conference proceeding), you should state it. Some may want to suggest possible referees in the cover letter; I find it ethically dubious, so I never do it. In case, you may want to suggest referees to avoid. (maybe we should have a separate question on this point).


3. submit a preprint, either at your institute or on arXiv, or at least think about it. Check the terms of the journal you are submitting to (this is a great resource) to make sure you can; often the submission is the best moment to do it, since the journal can have no reasonable copyright claim on what happened before it.


4. Even if you don't submit a preprint, make a backup copy of the .tex and .pdf files. If you use source control, tag the latest version as "submitted". This way it will be easier to recover that exact version when the referee report mentions "line 4 on page 2".


5. Send a copy to your co-authors, for backup and self-archiving.


6. Relax and celebrate.

You speak about applying the journal style in the manuscript; I suggest not to do it at this point. Referees won't care; it is really needed only after the manuscript is accepted, or if an over-zealous editor asks you to do it. You might spend lots of time without reason, resizing figures and line-breaking formulas that will be dropped after the referee comments.