chemistry - ACS Style image citation

I'm trying to cite an online image that I am using for a chemical literacy review. It is required to use ACS style, but the style guide makes no mention of images per se. I therefore tried to cite it using the "General web site" format. Is there a correct way to do this?

Wikimedia Commons. https://commons.wikimedia.org/wiki/File:Slaapbol_R0017601.JPG (accessed April 15, 2016).

Answer

From the ACS Style Guide, regarding the correct format for citations of websites (quote slightly reformatted):

Recommended format for general web sites:

Author (if any). Title of Site. URL (accessed Month Day, Year), other identifying information (if any). Use the title found on the Web site itself; add the words “Home Page” for clarification when needed.

...

ACS Publications Division Home Page. http://pubs.acs.org (accessed Nov 7, 2004).

Chemical Abstracts Service. STN on the Web. http://stnweb.cas.org (accessed Nov 7, 2004).

International Union of Pure and Applied Chemistry Home Page. http://www.iupac.org/dhtml_home.html (accessed April 24, 2005).

...

Recommended format for documents retrieved from institutional or agency web sites:

Author 1; Author 2; Author 3; etc. Title of Document, Year. Title of Site. URL (accessed Month Day, Year). If an article is contained within a large and complex Web site, such as that for a university or a government agency, the host organization and the relevant program or department should be identified before giving the direct URL of the article and accession date.

Chou, L.; McClintock, R.; Moretti, F.; Nix, D. H. Technology and education: New wine in new bottles: Choosing pasts and imagining educational futures, 1993. Columbia University Institute for Learning Technologies Web site. http://www.ilt.columbia.edu/publications/papers/newwine1.html (accessed Aug 24, 2000)

In your case, I would considering citing it as a document, so it would become:

KGM007, Opium pod cut to demonstrate fluid extraction1, 2006, Wikimedia Commons. https://commons.wikimedia.org/wiki/File:Opium_pod_cut_to_demonstrate_fluid_extraction1.jpg (accessed Feb 17, 2018)

You could cite it as a web page - that would look like this:

KGM007, File:Opium pod cut to demonstrate fluid extraction1.jpg - Wikimedia Commons. https://commons.wikimedia.org/wiki/File:Opium_pod_cut_to_demonstrate_fluid_extraction1.jpg (accessed Feb 17, 2018)

In your citation, you gave the name of the site, not the title. The title (as defined by the HTML title tag) is what shows in the top of your web browser when you visit the page:

If you intend to submit this for publication, the publisher should check and confirm the format during production anyhow.

conference - Multiple paper submission deadline extension (three times in few days)

Important Announcement – Paper Submission Deadline Extension

The paper submission deadline has been extended to May 25, 2015 June 1, 2015.

This is the third extension of the deadline for the meeting where I have submitted my paper.

1. To May 1, 2015 May 18, 2015.


2. To May 18, 2015 May 25, 2015.


3. And now, to May 25, 2015 June 1, 2015.

I do not know what think. I have submitted the paper on the afternoon of May 18, 2015. That evening I saw the second extension (like Cinderella, not at midnight but close). Now I have seen another extension, and I am concerned because I have worked very hard in this project.

The question is: there is a concrete risk that the conference could have had a few submissions and could be canceled?

Answer

Typically, I have seen two cases of deadline extension:

1. Some venues have a "customary" extension, which always happens, and thus all regulars know that the de facto deadline is slightly later than the initially stated deadline.


2. The other main case of extension is when a venue wants a few more submissions and is hoping an extension can drum them up.

Multiple deadline extensions sounds to me like desperation, and you might well be looking at an event that will either be cancelled or accept a lot of trash. Unfortunately, there's not much you can do about it right other than withdraw your paper if you are nervous, which might not help you much either.

evolution - Why does the apex of the human heart usually point to the left?

In the majority of human beings, the apex of the heart (left ventricle) points towards the left side of the body. Sometimes however (approx. 1/12000 births), a person is born with a condition known as "Dextrocardia", in which the apex of the heart points to the right side of the body instead.

Is there an evolutionary reason as to why the human heart usually points to the left side as opposed to the right side of the body?

(Note: Please don't answer with, "because there is a notch in the left lung", because I will simply reply with, "is there an evolutionary reason for the apex of the heart AND the cardiac notch being on the left as opposed to the right side of the body").

Answer

From a quick look at the paper @ChinmayKanchi links to (Palmer, 2004) it seems that:

All living vertebrates possess a heart that is conspicuously asymmetrical and normally displaced toward the left (Fishman & Chien, 1997).

So the heart orientation seems to be evolutionary conserved in vertebrates (as are many fundamental traits), and no specific explanation is needed for humans.

This is said with the reservation that human anatomy is not my subject field, and the refered paper also digs deeper into the molecular basis for the orientation/symmetry of organisms. For instance, it also says that:

Second, the molecular pathway directing hearts leftward—the nodal cascade—varies considerably among vertebrates (homology of form does not require homology of development) and was possibly co-opted from a preexisting asymmetrical chordate organ system.

so the molecular mechanisms governing this seems to differ between species. This could indicate that there is a selective pressure molding species into the same heart orientation. This is pure speculation on my part though.

I also want to mention that evolutionary outcomes doesn't have to have a "reason" (i.e. a selective advantage). Much depends on chance events and evolution can only act on what is present at the moment (i.e. is restricted by earlier evolutionary history).

molecular biology - Negative feedback loop and oscillations

According to the textbook Alberts Molecular Biology of the Cell (5th ed., p. 902), negative feedback loops cause oscillations when they are long delayed. I just can't figure out why.

Except for that, in case of short delayed feedback, the inhibition doesn't seem to be full and to go down only mid-way, according to the attached plot. Why?

graduate admissions - Role/importance of letters of recommendation for PhD-applications in Europe?

In the US PhD prospects apply to several universities and those select an amount of applicants from that pool according to how many open spots the universities have for that term. Criteria for admission are GPA, GRE/SAT and research experience documented by 2-3 letters of recommendation.

In Europe the application process is often times quite different in the way, that not a selected number of applicants get admitted each year, but each available research/teaching assistants position is treated individually. Because the requirements differ vastly, a lot of the times the only formal requirement for application is a 'good' or 'very good' masters degree and/or experience in field x or with technology y.

I wonder, are letters of recommendation expected, if so how many, and how important are they actually?

Answer

We can distinguish two different kinds of doctoral graduate studies in Europe:

• Programs through "graduate colleges" and "graduate schools" with centralized admissions policies


• Individual PhD positions in the research group (or institute, chair, etc.) of an individual professor

In the first case, everything is essentially along the lines of an application to a US-based graduate program, and letters of recommendation still carry the same weight.

For an individual position, letters of reference may be important, but as you suggested, it depends on the individual professor doing the hiring. For some research groups, the posting of an application is a formality, as they're only interested in hiring "internal" candidates (that is, people who have already worked in the group as bachelor's or master's students, and who thus can be "directly" evaluated). For people doing real searches, however, letters of recommendation are also important, because they can provide information about a candidate's research abilities in a way that is not possible just looking at a transcript or set of certificates.

citations - Conjugation: Do we cite authors or papers?

When referencing to another work in a scientific paper, do we cite the paper or its author(s)?

This question is intended to clarify the conjugation of the verb that follows the reference -- especially in these cases:

• 
  

  One author, two papers:

  
  

  
  

  Jane Doe (2015a, 2015b) list-s the very specific conditions under which...

  
  

  
  

  -> lists (singular: referencing to Jane Doe) or list (plural: referencing to both papers)

  
  


• 
  
  

  Several authors, one paper:

  
  

  
  

  John Doe, et al. (2015) claim-s this and that.

  
  

  
  

  -> claim (plural: referencing to the multiple authors of the paper) or claims (singular: referencing to the single paper).

  
  

Answer

I would say that it depends of the citation format, and the point is to look what is the subject of the sentence. In the examples you present, the conjugacy would be with the authors and the parenthesis only provides a precision about which paper is concerned.

In math we usually cite like that:

It is proved in [Doe15] that ...

---

References

[Doe15] Jane Doe, "paper name" Journal name, 2015

Therefore, we tend to cite the papers. However I often write

In [Doe15], Jane Doe proves that...

where the conjugacy is obvious.

neuroscience - Is it possible to process electrical signals from the brain and interpret the results as exact thoughts?

If the brain uses extremely low voltage signals to communicate (from what I understand around 100 mV), what sort of breakthroughs would be necessary to intercept these signals and interpret them as exact thoughts? I know we interface with the brain's electrical field through already at a much higher level, but what is stopping us from being able to interpret it more precisely?

Answer

The brain activity is electric and chemical. The male adult human brain contains about 86 billion neurons (Azevedo et al). There is about 100 trillion connections between them. Solving a puzzle like that is not easy..

what sort of breakthroughs would be necessary to intercept these signals and interpret them as exact thoughts?

What you are referring to would be called solving the neural code in neuroscience. With today's methods, it is probably not possible.

Consider electroencephalography (EEG). It records the electrical activity of the brain. Ag/AgCl sensors are placed along the scalp (typically 64-256 in research settings). When about 50,000 parallel neurons fire simultaneously, a change in a recorded signal can be seen. While the time resolution is about 1 ms for EEG, the spatial resolution is several centimeters (it is not easy to find which areas produced the recorded signals; it is an inverse problem). A newer technique, called magnetoencephalography (MEG), is becoming more and more used but is expensive. It records the magnetic fields related to the electrical activity and allows better localization.

Is there other complications? Well... lot's of them. Blink your eyes during the recording and there will be a major artefact masking the brain signals in most channels (10-100x greater in amplitude than the brain signals).

Anyway, you would probably be interested in the new research involving the use of machine learning techniques: it has been possible to decode the contents of dreams, reconstruct what a subject is seeing, etc. The best papers have been published by Science, Nature, and PNAS, so using their search engines with the keywords decoding and brain should allow you to explore the topic easily.

PS. I did not have time discuss fMRI; someone else can may be do that..

In what ways would co-authoring a graduate research paper as an undergraduate help me?

I have been working on a graduate level research project, with the bonus of being listed as a co-author if I make a significant contribution (which I likely will). I am still an undergraduate, but have significant experience (professional and educational) in the field.

My question is: Is this a big deal? If I go to grad school in that field, would this allow me to obtain a PhD quicker?

What if I don't go to grad school, but choose to work in the field, would being listed as co-author on a research project of this level hold enough weight to warrant listing on my resume?

Answer

It doesn't exactly "allow you to get a Ph.D quicker". However, you would have more experience in academic writing than if you hadn't contributed to the writing in the paper. Writing a paper isn't just "writing" a report - a lot of analysis, interpretation, and technical work goes into papers and these are skills you want to have as a Ph.D student. Being a co-author on a paper will make your application stand out.

If you go into any job, you can list this as a project that you have worked on. If you are familiar with the contents of the paper, then you can talk about it as if it was another project that you've worked on. Having your name on the paper is verifiable and can look pretty impressive especially if you are familiar with the details.

coursework - When and how should you talk to a professor if you think you deserve a different grade?

I recently was returned a midterm I wrote. One question I interpreted differently than what was intended. As a result I got 0.5/3 marks, which isn't a big deal but considering the test was only out of 15, it adds up. Due to timing conflicts I'm unable to meet the prof during office hours, but have scheduled to talk to him after next class.

I'm getting a bit stressed out, I'm uncertain what to say and what to ask for. If I had interpreted the question he intended it to, then I'm sure I could have gotten full marks. Any suggestions? This is the second time it happened but the first was only for 0.5 mark, so I let it slide.

The question had to do with output of a program and asked "what are all possible outputs of the program?" and I wrote down the correct answer, but what he was getting at was if the program was rerun the output may be in a different order so he wanted the answer to have all possible permutations.

Does anyone have recomendations on how many marks to ask for or have a policy on when to talk to the prof when you think you deserve more marks?

botany - Can galls be formed from mutualistic relationships?

According to Wikipedia, galls (cecidia) are formed by parasitic insects and mites like gall wasps (Neuroterus albipes). At some metamorphic stage, these organisms alter cell division processes in meristematic tissues of their host plants, which creates a tumour on (typically) the surface of leaves, branches or roots. These organisms use the galls as their habitat and/or food source (exploiting the sugars present).

However, I also know that bullhorn acacia and ants form an interspecific mutualistic relationship (with galls), so apparently galls don't need to be parasitic. Are there any other specific plant-insect pairs that have the same type of mutualistic gall relationship as the acacia-ant system?

Answer

Yes, pollinating fig wasps are gall inducing and mutualistic at the same time, and actually essential for the pollination of figs (see e.g Martinson et al., 2015). During the very intricate mutualism, fig wasps deposit eggs in some of the flowers and leave others. The flowers with eggs and later larvae will develop into galls that will produce new wasps but no seeds, while the flowers that lack wasp larvae will produce seeds. However, the hatched females that leave the figs will pick up pollen before leaving, and are essentially the only vector for cross pollinations between fig plants.

(with the aim of expanding the answer later...)

funding - What are interests of a country to fund international PhD students?

I would like to understand positive and negative effects for a host country and for a home country of a student.

Answer

To the host country:

Positive: A host country that is able to import top talent from other countries has a greater chance of keeping them in the country after graduation. This, undoubtedly, is an effort to promote national interests in a specific field (typically, scientific). Often, importing students to to do research is low cost (in comparison to hiring full time scientists or professors) and typically yields lots of deliverables (e.g. research papers) in a short time.

Negative: A host country takes a lot of risks when it invests in a foreign student. There no guarantee that student even graduates, much less that he/she remains in the country after graduation, or in any way promotes the host country's national interests.

To the home country:

Positive: A home country that can produce top talent gains a reputation international level for its education system (for better or worse, regardless of whether this is actually true or not).

Negative: A home country has the potential to lose its top talent to other countries, which is often counterproductive to its national interests (especially scientific interests).

In addition to the countries, i feel it is important to discuss the benefits and risks that this presents to the student as well:

To the student:

Positive: The student can gain a high quality education, typically with no strings attached. When they graduate, they are free to choose their destiny (assuming that they even have the option of staying in their host country).

Negative: The student effectively becomes low-wage, indentured migrant labor to the host institution. Students are often not promised jobs or citizenship in their host country, but are often led to believe that "it is possible if you work hard enough". This will often lead to foreign students out performing their domestic counterparts, but sadly offers little pay, benefits, or guarantees to the foreign student. As J.J. points out, if a foreign student screws up in some way, they lose (potentially) their only chance of a better life outside of their home country.

publications - A manuscript I refereed gave me an idea for a paper, not sure how to proceed

So, last week I refereed a paper for a journal. The paper in question is a reply to a previous paper by a different author: it points out a serious problem in the original paper and then proposes a solution. The evaluation I sent back to the editors is that, while the problem is real (to the extent that a different researcher has independently identified it), there are a number of reasons why the proposed solution is not going to work.

Over the weekend, I started thinking about the paper in question again and suddenly realized that I know how to solve the problem (in a nutshell: you need to use a technique originally developed to solve a mildly related class of problems, but which nobody had yet thought of applying to this particular domain). Right now, I have a bunch of handwritten notebook pages with everything I need to write a paper, and all I have left to do is to find a couple of hours to sit in front of my computer and type it up properly.

The question is, how should I proceed now? On the one hand, given that I've developed my own solution, I'm not plagiarizing the paper I refereed (in fact, I intend to give it proper credit for discovering the problem). On the other hand, if I hadn't been asked to referee this paper, I wouldn't have put enough thought into it to come up with my own solution. More generally, to what extent is it acceptable to write a paper that directly builds on a paper you've been asked to referee?

Answer

I think there are two questions that need to be answered first.

• 
  

  Is it important to you (e.g. for career reasons) to publish solo, or would you consider publishing with the other author? Keep in mind that publishing jointly may have extra benefits: the two of you together might come up with an even better solution, or it may lead to future collaborations on other projects. Or do you perhaps not care about getting credit at all?

  
  


• 
  

  Is the manuscript public? Has it been posted as a preprint on arXiv or a similar server, or on the author's website, etc?

  
  

Depending on the answers, there are a few cases:

1. 
   

   You don't care about getting credit. Write your report on the paper: "The approach to agrobaric frobotzim via PDQ analysis is unworkable because of foo, bar and baz. However, this could be fixed by using QPM analysis instead. [Sketch your idea here.] Pending this fix [and any other suggested revisions], I recommend the paper for publication." Expect that when the paper is published, there will be an acknowledgement: "We thank the anonymous referee for suggesting the approach used in Section 5."

   
   


2. 
   

   You want to publish jointly. Contact the editor: "The author's approach to agrobaric frobotzim via PDQ analysis is unworkable, and as such I cannot recommend the paper for publication as it stands. However, I have some ideas about how to resolve the problem, and I would be interested in collaborating with the author to work them out. Would you be willing to put me in touch with her?"

   
   
   
   
   1. 
      

      The editor says yes. Great!

      
      
   
   
   2. 
      
      

      The editor says no, and the manuscript is public. Submit your report pointing out the flaws and recommending rejection. After a decent interval contact the author: "I saw your preprint, and had an idea to improve the results using QPM analysis. Would you be interested in working together on this?" Opinions vary on whether you should reveal that you were the referee; it is possible the author will guess anyway.

      
      
   
   
   3. 
      

      The editor says no, and the manuscript is not public, but you know who the author is. Submit your report pointing out the flaws and recommending rejection. The next step is a bit controversial. Some would say you should wait until it is public, so as not to break the anonymity of the reviewing process. Others think it is fine to reveal yourself and contact the author directly to suggest collaboration. I am not sure what to say here.

      
      
   
   
   4. 
      

      The editor says no, and the manuscript is not public, and you do not know who the author is (double-blind reviewing). You have no choice but to wait until the manuscript is made public (maybe until it is published somewhere else), since that's the only way to find the author and suggest collaboration. If you think you should give up on finding the author and publish solo instead, see below.

      
      
   
   
   
   



3. 
   

   You want to publish solo. Write and submit your report. Now, is the manuscript public?

   
   
   
   
   1. 
      

      The manuscript is public. You may write your paper, citing the other author's preprint and giving her due credit for noticing the problem. This is ethical, but if you meet the author at a conference, don't expect her to buy you a beer: she was hoping to solve this problem but you beat her to it.

      
      
   
   
   2. 
      

      The manuscript is not public. You may not proceed. As a reviewer, you received the manuscript in confidence, and to write a solo paper based on it would be to take unfair advantage of that access. You must wait until the preprint appears publicly. (This might be when it is published in another journal, or maybe never.) It's possible that in the meantime, the author will discover your solution independently; those are the breaks. This would be a great time to reconsider seeking joint authorship.

      
      
   
   
   
   
   

In case 2, if your field has a notion of "first authorship", that would be something you'd need to negotiate with the other author, based on your field's norms. (Mine uses alphabetical ordering almost exclusively, so this issue wouldn't arise.)

neuroscience - Understanding the brain: how are neurotransmitters released in the brain?

I have a basic knowledge of how neural networks work. A potential difference is created that forces sodium, potassium, chloride, and calcium ions to flow which carries an electrical signal to the end of a synapse. From there, the presynaptic neuron releases neurotransmitters creating a potential difference to the postsynaptic neuron.

What I don't understand yet are the mechanics of which neurotransmitter will be released. Do the vesicles of each type of neurotransmitter have an energy threshold? If yes, when the highest energy threshold of a vesicle is achieved, does this mean all the other vesicles will release the encapsulated neurotransmitters?

job search - What "Applicant Confidential Data Form" has to do with tenure-track positions?

The data collected using "Applicant Confidential Data Form" will be used by US-based universities to monitor University’s Affirmative Action/Equal Employment Opportunity Programs as required by the US government.

I have seen that in (some) cases, faculty job applicant seeking academic job in US-based universities are asked to submit this form after they successfully submitted their initial application. The point is that, typically there is no instruction in "call for faculty member note" to fill this form and submit along with application. But the faculty search committee asks after while.

So it raises a question:

Do the faculty search committee sends this form to ALL the applicants or particular applicants who are allegedly suitable for the job. Is receiving this notification from the committee can be considered a positive sign in recruitment process?

Answer

I've received this form from hundreds of employers that later rejected me. I think schools that use it will send it to every applicant. So it doesn't mean anything except that your application was received.

I believe the reason for it being a separate form, rather than part of the application, is that it's meant to be for statistical purposes only, and should not affect the hiring procedure. The best way to achieve this is to ensure that the hiring committee never sees it. So they send a separate form, to be returned to a separate office within the institution, which holds it confidential.

postdocs - University rank/stature - How much does it affect one's career post-Ph.D?

What I'm trying to understand is, to what degree does the status/rank of the University (where one completes his/her Ph.D) matter while shaping his/her career after graduation? I would like to know the weight given to one's school in both the following cases:

• While applying for post-docs/faculty positions in academia


• While applying to industrial research labs

For instance, I've read on some forums (I can't locate the link now) that while considering prospective applications for tenure-track faculty positions, very few Universities accept a candidate who has completed his/her Ph.D from a lower ranked school having a lesser "brand" value, irrespective of the fact whether he/she has published equally original work as his/her counterpart from an Ivy league college. How much truth is in this statement? It would be really great if someone already in academia, either as a newly-accepted faculty or someone on the Faculty Hiring committee could share their experiences/statistics on this regard. I'm simply interested to know the answer, without commenting at all on whether such a practice is justifiable.

Similarly, what about recruitment to internationally acclaimed research labs (like IBM T.J.Watson lab or Microsoft research lab) - what importance do they place on the pedigree of a candidate's college, before taking into consideration what they published ?

I'm personally interested in answers related to the field of Computer Science (theory), but the question is applicable to any prospective grad student in any discipline in my opinion. Feel free to share your personal experiences post-Ph.D in detail, as that would give me (and future viewers of this question) about what its like to carve a career once you are out of school!

Answer

Let me answer as a theoretical computer scientist with former PhD students in tenure-track academic positions and many years of experience on faculty hiring committees. (However, my understanding is that the selection process at industrial research labs like IBM T.J. Watson, Microsoft Research, Google Research, AT&T Research, etc., is really not that different from academic recruiting.) As always, take my advice with a grain of salt; I'm as guilty of confirmation bias as any other human being.

Nobody in theoretical computer science cares where you got your degree. Really. We. Do. Not. Care. We only care about the quality and visibility of your results. Publish strong papers and give brilliant talks at top conferences. Convince well-known active researchers to write letters raving about your work. Make a good product and get superstars to sell it for you. Do all that, and we'll definitely want to hire you, no matter where you got your degree. On the other hand, without a strong and visible research record, independent from your advisor, you are much less likely to get a good academic job, no matter where you got your degree.

(This is less true in more applied areas of CS, in my experience, mostly because it's significantly harder for PhD students in those areas to work independently from their advisors.)

But. Faculty candidates are necessarily judged by people who are not experts in their field. Without the expertise to judge whether your work is really good, those people must look at secondary data that correlate strongly with successful researchers. One of those secondary characteristics is "pedigree". Did you get your degree at MIT, Berkeley, Stanford, CMU, another top-10 department, or somewhere else? (What's an "Ivy League"?) How good/famous is your advisor? If they're really paying attention: Where did your advisor's other PhD students get jobs, and how well are they doing now?

Fortunately, most good departments do make a serious effort to understand the quality and impact of applicants' results, instead of relying only on secondary data. Also, secondary data matters considerably less once you actually have an interview.

And. In my experience, where you get your degree is strongly correlated with successful research. I got my Master's degree at UC Irvine in 1992 and my PhD at UC Berkeley in 1996. The biggest difference I saw between the two departments was the graduate-student research culture. Every theory student at Berkeley regularly produced good results and published them at top conferences. When the FOCS deadline rolled around each year, the question I heard in the hallways from other students was not "You know the deadline is coming up?" or "Are you submitting anything?" but "What are you submitting?", because "nothing" was the least likely answer. Everyone simply assumed that if you were there, you were ready and able to do publishable research. Publishing a paper wasn't exceptional, it was just what you did. That cloud of free-floating confidence/arrogance had a huge impact on my own development as a researcher. I've seen similar research cultures at a few other top CS departments, especially MIT, Stanford, and CMU. (Caveat: This is an incomplete list, and there are many departments that I've never visited.)

tl;dr: Yes, getting a PhD from a top department definitely helps, but more by helping you become a better researcher than by making you look better on paper.

evolution - Is local equilibrium a reasonable assumption for evolutionary processes?

Whenever I look at discussions of fitness landscapes (in particular, Kauffman's NK model) the questions tend to resemble:

The population is at a local equilibrium, but another equilibrium of higher fitness exists, how will the population cross the fitness valley between these equilibria?

These sort of statements assume that the population has reached a local equilibrium. Although, the local equilibria must exist, why do the people working in this field believe that they can be found before environmental (or other external events) change the fitness function? Are the timescales required to go from a random initial population to one that is at a local equilibrium compatible with the typical time-scales on which a fixed fitness landscape is an appropriate approximation?

If we switch to the polar opposite model of complete frequency-dependent selection (say replicator dynamics in evolutionary game theory) then limit-cycles (think rock-paper scissors game) and chaotic-attractors are common and it is possible for the population genetics to be constantly changing and never at equilibrium.

In an experimental setting, it also seems like although beneficial point-mutations are much more rare than deleterious, they do exist. This would suggest that experimentally, organisms are not at a local equilibrium. Do model organisms tend to be at local fitness equilibria?

In general, is the local equilibrium assumption in fitness landscapes research a reasonable assumption?

teaching - Ethics of conducting research on a class

I'm a repeat Teaching Assistant in a fairly large (100-200 students/semester) core, required CS course at a large, private US research university. I'm very interested in researching what factors influence success in the course, possibly with an eye toward SIGCSE.

I'm concerned about how to ethically conduct research on students.

Yes, I know a little about IRB, and I assume at some point I'd need to get IRB approval. However I'm so unsure about this, I'm not even sure what to ask the IRB yet. I'm hoping y'all can provide me some guidance and advice as I begin to plan for next year.

I assume I have to ask for explicit, opt-in consent? Obviously, participation or non-participation couldn't affect their grade. However, if only a very biased subset bother to opt in, the research might not be worth conducting. Can I compel students to choose to opt in, or opt out?

Additionally, the course is very similar year to year, so the extent that it would be very useful to be able to include previous semesters. I imagine this is even trickier.

I have the full encouragement and cooperation of the faculty member, but working with human subjects, much less students, if totally outside their expertise.

This is similar to this question, but slightly different and, I think, more difficult.

Answer

I conduct biology education research at my large, state research university, so I have experience with this process.

An IRB is necessary if you plan to make the results public. Educational research is considered "exempt" research under IRB regulations, but this really just means you have fewer flaming hoops, not NO flaming hoops. You will likely be able to convince your IRB that students do not need to sign consent forms, since you will post a study information sheet and they have the opportunity to opt out to someone else without it affecting their grade. You may also be able to get student data from previous years with a retroactive IRB.

An additional hurdle is that you will probably need the approval of your FERPA specialist in addition to IRB approval, as FERPA is very concerned with the sharing of private student information. Our FERPA guy is in our registrar's office.

As you can see, I'm being a bit vague. Every institution interprets the human subjects regulations a bit differently, and sometimes schools are relaxed... and sometimes they are not.

So, it's doable, but not at all trivial. If you still want to move ahead, I recommend you call your institution's IRB office and say you are considering education research and would like to meet with an analyst. And the first question to ask the analyst is, "who else on this campus has ever done education research?" and get the real skinny from that research group.

Then, the basic steps will be:

1. Design the experiment, do a lit review, write up the IRB proposal and study information sheet


2. Send the proposal and SIS to the IRB analyst, and they will help you make changes



3. Send the proposal and SIS to the FERPA specialist and they will send an approval letter to IRB (in a month?)


4. Wait for the IRB subcommittee to approve the proposal (another month?)


5. Post the study information sheet on the class website, and get another grad student or postdoc to be the "safe" researcher that students can contact to opt out. This researcher will make a short announcement on the first day of class.


6. Teach using your fabulous new technique


7. Ask the registrar for grades for previous years (if you've worked this out)


8. Do analysis, write it up, present it. Fair warning - most of the time we find that the first try is the beta test, and the SECOND try generates better results.

publications - Is it better to have a single-author paper or a joint-authored paper?

I am a new graduate student and I am about to start writing my first paper. Some of my adviser's other students have been working on similar topic to what I have been working on and he has been pushing us to combine our results into one paper. However, I feel my results could be a paper on their own. I want to start beefing up my CV so that I can get extra funding and, hopefully down the road, a research position but I am afraid that if I am only a coauthor on a paper it won't look as good as if I am the sole author (especially since I worked completely on my own for my section).

So my question is: would it be better to try and publish a paper in which I am the sole author or would it be better to try and publish a slightly better paper in which I have 2 or 3 additional coauthors? Do funding selection committees and the like give precedence to people with papers that they are sole authors over ones who have coauthors?

Edit: My field is math, in case this matters.

publications - Adding co-authors after acceptance

I am writing a paper, need some review. I want to send it to IEEE, without the name of my co-authors. I might get acceptance. I need to know, in that case, will I be allowed to add my co-authors or not?

bioinformatics - Machine learning for light microscopy -- problems to solve?

I would like solve some biological problems that would improve the state-of-the-art of biology or bioinformatics. In particular, I want to apply machine learning on light microscopic images. The equipment and experience I have are:

• Bright-field, dark-field, and phase-contrast microscopy


• Modern laptop


• 56-core super-computer with >100 GB of memory (on request)


• Intricate knowledge of machine learning algorithms and signal processing


• PhD-level research skills


• Programming skills that would get me to work at Google


• Limited knowledge about biology, bioinformatics, and microscopy (yet)

I want to do some publishable research free from all academic hassle. I will do this solely on my own time, without hurry to publish, in an attempt to do something good for the mankind. I can throw a few hundred dollars on the project every two months (or abour 1000 USD per year).

Much of the biological research published in Science, Nature, PNAS, Cell, etc. are so specialized that I find it difficult to detect important problems I could have a good chance of solving given my skill set. Thus, I am asking your help:

• What kind of software you always wanted for light microscopic research, but did not know how to build?


• What are some important biological problems you would like to get solved? (For machine learning, problems with a binary decision task are particular well suited -- e.g. "does this person have malaria or not"?)


• What are some recent, high quality reviews on open problems in biology?


• Something else?

While my question is a bit broad, I think this goes under the "good intention" (or whatever it is called) SE policy.

graduate admissions - Summer Schools and academic career

There are some prominent summer schools in CS (ML in particular) like MLS (Machine Learning Summer School).

What is the impact of attending such program on academic careers? (or applying for graduate programs)

For example, LxMLS (Lisbon Machine Learning School) this year has ~ 150 selected participants from all over the world.

The summer school offers the following things:

• Lectures (from basics to advanced topics)


• Lab sessions



• Talks


• Poster Session (based on which the students were selected)

Would it be a worthwhile investment of 1000-1200$ (Assuming I have the means to fund myself) or are such opportunities common and easily funded in US and I should be looking at not attending and saving money?

What else would this summer school bring forth for a recently graduated undergrad student?

Some of the summer schools have courses which can be treated as university credit equivalents. Is this true for all summer schools?

• Background: A student interested in Machine Learning and Natural Language Processing and has taken online courses in these subjects.

Answer

I'm a PhD student in my final months, I'm in a different field (geophysics), but I've been to some summer-schools that I found very valuable. One lecturer even stated that summer schools are the best forum for scientific exchange. The summer schools I've been to didn't have as many participants as yours, but still, besides from the obvious point of acquiring knowledge and skills, summer school permit you to:

• Meet and talk to senior people in your field


• Meet other students, who may be going to be the future senior people in your field

The bottom line is: A summer school is as good as its lecturers are. Look at the list of lecturers, and ask a senior scientist you know to look at the list. Are there many famous names? Go for it. Are those mainly lecturers who spend most of their time teaching at not so well known institutes? Then you can probably spend your time and money better elsewhere. Depending on what's included (lodging/meals/...) and on how long it takes, 1000$ is not bad, although of course it's better if you can find someone else to pay it for you ;).

copyright - Creative commons for academic library

I am building an online library, where professors will be submitting academic work (text and multimedia).

I want to find the right CC license. The work provided by the library can be shared and anybody can build upon it for commercial or non-commercial purposes, as long as they give credit to the professor. But the original work must remain un-edited. So, CC-BY-ND fits this description, but there is a part that worries me. If anybody can "remix or transform" the material, what is stopping them from changing the article and re-share it as their own, or claim that is the original?

Is there any way that CC-BY-ND protects me from this danger, or should I use another copyright licence?

Thanks

Are you allowed to copy text from your Master's thesis into your PhD thesis?

I wrote a Master's thesis a couple of years ago (which is available to view from my University's online service; so it's out there) and am now doing a PhD. Some passages from my Master's thesis is relevant to my PhD and could be used in my PhD literature review. If it matters, the masters thesis is not published and I am studying in a UK university.

Am I allowed to copy chunks of text from my masters thesis into my PhD thesis?

Answer

No. It's called self-plagiarism. You can of course cite results from your Master's thesis, and even quote it, but only if you clearly indicate the source. That it wasn't published doesn't make a difference.

funding - Is offering to use personal funds for research a good idea?

I'm at an engineering department at a public US university, and I'm somewhat new to writing proposals. The call I'm submitting to wants know if the project budget is higher than the amount of the grant, what other sources of funding the PI will use, presumably to ensure the success of the project.

First, I'm not rich. But this leads to me to think, is it okay to use personal funds to do research? For example, if a piece of equipment costs $4000 and I only have $3950 left, can I supplement it with personal funds?

What might end up happening is that I might convince a colleague to lend me his instrument. But I don't want to say this in the proposal. Also, I'm not sure saying the project will be "supplemented by personal funds" is a good idea.

advisor - Is it appropriate to buy a "thank you" gift for a PhD supervisor?

I am nearing the end of my PhD and I would quite like to buy a "thank you" gift for my supervisor (although, she's the socially awkward type who I'm sure will be greatly embarrassed to receive one).

I'm just wondering whether a gift is the done thing? And if so, what sort of gift seems appropriate? I suppose a bottle of wine would be a safe choice?

Answer

After your defense, and final submission to the university; you can give the gift, with a thank you note. Right before your defense is a big no, in my opinion.

citations - How to deal with sources whose authors I don't have good relationship with?

I used to have a good relationship with an author, but now it's broken. However, my work is heavily based on the work of that author, and I'm not sure if citing it without informing them is OK here. Would there be any potential trouble from this? What if they explicitly tell me to not cite theirs? I just don't want to make the relationship worse, because they may not want to have any affiliation with me. But this is just my thought, I really don't know what they really think.

Answer

Yes, cite the other author's papers regarding any data or ideas on which your own work is based. It is crucial to do so; you MUST acknowledge the other author's contributions to your field if your own work builds upon those. As mentioned by others, unless you are writing a rebuttal, keep a neutral, dispassionate tone in your writing and refer to the other author's papers in neutral terms. Be specific in your citations. And yes, try to avoid having your paper reviewed by this author, at least for now.

The bigger problem was somewhat glossed over. Can you reach out and attempt to repair your relationship with the author with whom you've had the falling out? Ultimately that will be the best for your career, and maybe for your health. You can say, "I perceive we've had this 'time out' but I'd like to apologize if I've caused some problem. Can we meet for coffee and see if we can find some common ground?". Or something like that. It takes courage to go back to someone who has become hostile, but it could be that your load will be much lightened by such an effort. There's the possibility that some misunderstanding can be resolved. And even if you are rejected, you have at least tried. Life is short. I'm hoping for you!

If supervisor has no expertise in your research work, is it possible to do a PhD under that supervisor?

In my PhD, I am assigned mathematical modeling topics and my supervisor's work is related to mathematical biology. But I don't want to work in mathematical biology. Because actually there is not so much real application of that and I don't like biology. Instead, I want to work in fluid dynamics. But my supervisor's research area is totally different. Is it possible to do independent research work without supervision of supervisor?

mathematics - How should one acknowledge assistance received via sites like SE?

I have been working for some time on a paper that I hope to submit to a mathematics journal. Buried deep in the guts of the paper is a technical lemma that I struggled with for some time before finally posting the question to MSE, where it promptly received an answer. What is the proper way to acknowledge this assistance in the submitted manuscript?

Answer

In your case, the user who helped you participates under his real name (he's from my hometown :)). I would include his proof, with a footnote at the page bottom "This proof is due to ...", and additionally thank him where you usually thank people (I've most typically seen this as footnotes on the page of the abstract, but whatever is normal for you). To cover all bases, I'd finally contact Hagen by simply leaving a comment under his answer with @(name) either linking to this question, or outlining what you intend to do, and getting his sign-off to do so. I think in any case where you can identify a user by name, mention of MSE is optional.

The same generalizes for those participating not under their real names. You should then just discuss in your @(name) message under which name (if any) user would like to be quoted. If user agrees to using their proof but prefers to not be mentioned by name, then thank an anonymous user of MSE.

publications - What are the strategies for getting feedback on articles?

As an academic, one has to publish. Often, an article is drafted, and you need feedback of a colleague. I see that quite often some perspective articles are often written by long-term collaborating pairs of authors.

What are some strategies people use to get feedback on their articles (outside of immediate boss; and in the case that none of the friends in the field of work in the specific domain of the article, and one needs specific (not general) feedback)?

How do you approach a colleague to simply read your article. Or do you just mention it at a conference to the most suitable colleague - would you like to read an article and give me feedback? How do handle the co-authorship or acknowledgement? Do you establish the limits at the "approach time"?

What are some strategies to establish a "publishing" duos (buddies).

Answer

When I have a manuscript nearly ready to submit, I send it (by e-mail) to colleagues who I think would be interested in it. I politely ask them to read it and send me any comments they have. Sometimes they do, and sometimes they don't; it's understood that there is not an obligation. Of course, some of them send me their manuscripts too, and they're more likely to read mine if I have read and commented on theirs.

The colleagues I send the paper to (usually about 2-4 in number) may include:

• Senior people who have mentored me


• Past coauthors and collaborators


• People I don't know but whose work is essential to that in my manuscript

People in the first two categories are usually willing to assist based on our existing relationship; those in the last category are generally pleased to see their work being cited and built on.

I don't usually need very specific feedback at this point in the process. If I was concerned, say, about the correctness of some part of the work, I would have worried about that long before I wrote the article. Occasionally I may have a specific question about, e.g., suitability of the manuscript for a particular journal. In that case, I would send the article to one of the editors of the journal or to a colleague who often publishes in that journal, and ask specifically.

Any colleagues who provide substantial feedback will be acknowledged at the end of the paper. Providing this kind of feedback certainly wouldn't qualify one for co-authorship.

publications - How to identify top researchers and landmark papers in a field?

I am currently a student doing research in Neuroscience, and as you can imagine it is a pretty big field. I am trying to better familiarize myself with my own subfield and other fields such stem cell research and genetics.

What is a good way to find some landmark papers and authors who are highly regarded in a certain field?

Answer

To identify landmark papers, you can also consult the bibliography of your textbook if you have already taken classes that cover (even briefly) your subfield of interest. If your textbook is one that is used by a lot of university professors, then it probably covers landmark papers well. You can often identify the most important papers in a textbook because they'll possibly:

• be referred to multiple times and in multiple chapters


• appear near the beginning of a chapter when a topic is first introduced


• explicitly be acknowledged in the text by the author of the textbook as a seminal paper

A disadvantage to this approach is that, depending on when your version of the textbook was last updated, it may miss important developments in recent yeras.

Identifying highly-regarded authors can be harder, but you can try looking up authors (especially last-named ones, who are often supervisors/professors) of important papers on, for example, Google Scholar, to see what else they have produced and whether they have a lot of highly cited papers.

conference - Does giving an easily-understood talk make the audience think you did something simple?

Alice and Bob both go to a conference. Alice gives a great talk, and most people understood it. Bob gives a much more technical talk filled with jargon which almost everyone failed to understand. Do people walk out of the talk thinking Alice must've done something simple while Bob did something profound?

I get the feeling that this happens - after all given two concepts, one which I understand and the other which I don't, it's intuitive that the one I understand is the simpler one. It also feels like the easier-understood the talk is, the more questions Alice receives that aren't directly related to her work. For example I once attended a talk where the speaker talked about aggregating samples of the sky, and someone asked "why do you use square samples? Why not circles or triangles?". This kind of non-specialist question is obviously hard to see coming, and the you-either-know-it-or-you-don't result is uncomfortable.

On the other hand, if it's indeed true that giving easily-understood talks makes people think you did something simple, it would imply that giving comprehensible talks is a bad thing. That not only sounds silly, it's also counterproductive.

Answer

I will tell you what I've observed in Math. Similar to what Jordan Ellenberg says in How not to be wrong, one can think of depth and technicality as two orthogonal axes, so one has 4 rough categories of results:

1. 
   

   Deep and simple (technically easy)

   
   


2. 
   

   Deep and hard/technical

   
   



3. 
   

   Shallow and simple

   
   


4. 
   

   Shallow (unimportant) and technical

   
   

Some people like things that are more technical and some people like things are simple, but deep. For instance, Atle Selberg thought that the most profound ideas in math are simple and said all of his ideas were simple ones.

Correspondingly some people are more easily impressed by technical talks and some people are more easily impressed by simple talks. So my answer to:

Do people walk out of the talk thinking Alice must've done something simple while Bob did something profound?

would be, while it of course depends on the audience, I think this depends largely on the talk. If you can explain a simple idea that lets you solve long-standing open problems, I think most people will agree this is deep. However if your talk doesn't make it clear you're solving long-standing open problems, then people will be unsure. And you certainly want to avoid giving a talk that is shallow and simple, as no one will be impressed.

I myself generally prefer (giving and listening to) understandable talks, and here are a couple other pieces of advice:

• 
  

  Even if you don't want to present technicalities, make it clear to the audience that technicalities are present, and maybe make a few comments to the experts as to how you handle them.

  
  


• 
  

  What may seem simple to you, who have been thinking about these things for months or years, may not seem simple to others. I've many times given talks and worried that it was too simple for the experts in the audience, and found out later that many of them didn't completely understand what I said beyond the introductory material.

  
  
  

application - What is the most accepted time for a pre-tenure move?

I am a second-year assistant professor who is hoping to make a pre-tenure move to a school/location that is better for my family. It is not a situation where my current department is bad or toxic, but I think my partner (job) and kids (schools, time with relatives) would be happier elsewhere.

I read a lot of advice which suggests that it is best to make a move before tenure rather than after. However, no one seems to specify when pre-tenure one should be looking. I am inclined to begin looking even before my mid-tenure review because the departments I would be looking in are typically small and I can't rely on the fact that they would have an opening in any particular year.

Is there a "normal," "accepted," or "typical" time to be make a pre-tenure move?

Here are some related questions:

What is a better point in an academic career to move to the U.S.: as an assistant professor or after tenure?

Job search when coming up for tenure

Answer

There’s no such thing as a normal or typical time to move. Faculty move when the right opportunity presents itself. So long as you’re upfront with everyone, I wouldn’t worry about the timing. The only caveat is to try not to leave your old department in the lurch when you go—if possible, give them enough notice that they don’t have to scramble to replace your teaching load and other assignments on short notice.

Note that those arrangements could be through adjuncts or reassigning the load among the existing faculty, or anything else. I agree waiting for a TT hire is unreasonable—the process just takes too long. However, if you've been there a year or two, you should already have a sense of when teaching assignments are being decided for the following year and can plan accordingly.

embryology - Can a chicken really be hatched outside of the egg?

This YouTube video (screenshots attached) claims to show Japanese schoolchildren breaking an egg into a kind of clingfilm "hammock in a cup", and then growing and hatching a chick from it in an incubator.

Is this really real?

My first immediate thought is, "If this can happen, why don't the eggs in my cupboard at home sometimes hatch? Why do I never see an embryo in my frying pan?"

Obviously the egg has to be fertilised, but depending upon where you get your eggs (like an "organic home farm" or something) this might happen.

If it's more a matter of temperature, how warm do the eggs have to be? For how long? (ie, Could a warm kitchen cupboard in a hot summer do it?)

What other biological requirements are there to make this work?

---

Answer

Yes it is real, in the sense that this protocol has been through a peer reviewed journal.

Note that the embryo is developing outside the shell, not outside the egg. It is the fertilized egg that develops into the embryo. The shell only provides protection and allows exchange of gases. You can replace the shell with any other material that does the same job. Embryos of non-placental animals can grow in a petridish as well. Someone seems to have done this back in the 1980s (Scadding, 1981).

You can see a video along with the detailed protocol of this process in this article published in the Journal of Visual Experimentation.

Why do I never see an embryo in my frying pan?

Because it has probably become an omelette.

how warm do the eggs have to be?

37-39^oC is the ideal temperature and usually hen eggs hatch in 21 days (common poultry facts). However, the incubation time can depend on other factors (including temperature) such as humidity and air composition.

evolution - How scientists can be confident that human embryo tail is really a tail?

From Wikipedia:

Human embryos have a tail that measures about one-sixth of the size of the embryo itself. As the embryo develops into a fetus, the tail is absorbed by the growing body.

How are we sure that it is a real tail and is not a superficial resemblance of something else?

I ask this because some creationist guy challenged me in this regard.

How to respond to intentional lack of citation?

I work in a field that heavily uses arxiv.org and posts papers before submitting them to journals, so it's common for people to send a citation request when they see a preprint that they think has overlooked their work. I do this pretty rarely, because I think it's often abused by people looking to pad their citation count by asking for citations from work that's only marginally related. Still, when I see work that very closely resembles something I've done, I generally send an email.

My question is what to do when a paper appears that is very closely related to my work, has not cited me, and it was clearly intentional. In this case one of the authors had a previous paper that followed up on--and cited--one of my papers, so I know they were aware of my work in the past. Furthermore, in their current paper they use a technical term that I introduced. There is no possible way that they could have written their current paper without being aware of its close relationship to my work, but they haven't cited my papers.

In this context, the usual email of the form "I have read your interesting new paper and wanted to make you aware of my related work" would be so disingenuous as to be ridiculous: they are clearly already aware of my related work. I can only conclude that they have intentionally chosen not to cite it. All of my encounters with these authors in the past have been friendly, at least from my perspective, so I can't imagine any interpersonal conflict that's behind the omission.

A similar thing happened to me once before when some authors wrote a paper that had enormous overlap with one of my papers, which they cited, and they corrected, in passing, a minor technical mistake that didn't change any significant conclusions. Subsequently they built a minor industry on this work but never again referred to my previous work, with the result that their papers that were only a very minor improvement on mine have been cited several hundred times more than my paper has. So I may be overly touchy about this sort of possibility.

At the moment I'm inclined to do nothing, because any message I could imagine sending them would come across as either disingenuous or combative. But I wonder if anyone has a suggestion for dealing with this situation.

phd - Getting the best out of a book-reading exercise

A doctorate involves plumbing the depths of a problem and often this involves a lot of knowledge breadth-wise in related areas. Though the latter is provided by coursework, education about a precise "tool" that a doctorate may need during solving his problem is unlikely to have been provided by the courses. Often the PhD may run into huge tomes of material which he has been introduced to by Wikipedia. Intuitively he/she may feel that somewhere in those volumes lies a theorem or an idea which can provide vital keys to solving his own problem. So I come to my questions:

• What should a student do to get the best out of a book-reading exercise? The question in turn assumes the student has arrived by some means at the best book for serving his purpose.


• There is a trade-off involved in reading books tangential to your field: you may spend a lot of time groping in the dark looking for a bounty which may never be there. How does one gauge the potential applicability of a book to his work? When does a student decide to pull the plug on such an effort?

Related Question: Skimming through a paper

Answer

First, I would like to comment on some of your sentences. Then I will answer to your 2 questions.

• Often the PhD may run into huge tomes of material which he has been introduced to by Wikipedia: I am not sure that I understand this sentence well. Are you using Wikipedia for bootstrapping and then proceed from page to page in wikipedia, hoping to find something useful, or do you use another source of idea, but jump to wikipedia to understand in a faster way the entities/concepts you find in the first place ? BTW, in most cases I am not sure Wikipedia is something we should use at the research level. The quality is clearly increasing, but this is far from perfect, and some essential intuitions are missing sometimes (almost always ?).



• Intuitively he/she may feel that somewhere in those volumes lies a theorem or an idea which can provide vital keys to solving his own problem. This sentence makes me think that you maybe focus too much on a specific problem.

Now, my answers :

• 
  

  When I read a paper or a book, I proceed the same way: First I quickly go through the whole thing (for a book, the whole thing is generally a chapter). Then I try to understand the key intuitions and results. At that point I don't try to understand how they are proven. Then I switch to other things. When I am thinking of a problem, or when I am on other concepts, sometimes a flash occurs and I have the intuition that something I have read can be useful, then I go back to the paper/book and try to totally understand the result. Here, this means more or less homework like in the old days ;)

  
  


• 
  

  Reading tangential materials is a necessity. I proceed as stated above, and to make sure that I will not spend all my time on this, I decided to always spend the same amount of time reading on other fields. For me this is roughly 1 day a week, which is 1/3 to 1/2 of the time I can use for research.

  
  

zoology - Help Needed Identifying Corvids

I'd appreciate some help identifying these three corvids I photographed in Austria during the Summer:

I know identifying corvids can be difficult and I'm not an ornithologist -- just an amateur bird watcher. After looking through many images of various crow species and their hybrids, I've tentatively identified these as:

1. Carrion crow (Corvus corone)



2. Carrion crow × Hooded crow (Corvus corone × Corvus cornix)


3. Carrion crow × Hooded crow (Corvus corone × Corvus cornix)
   I initially believed this to be a Hooded crow (Corvus cornix), but the broken coloration on the wings made me think it might actually be a hybrid as well.

Can someone here either confirm my identification or provide a more informed identification?

Answer

The plumage of carrion crow is black with a green or purple sheen, much greener than the gloss of the rook. The bill, legs and feet are also black. It can be distinguished from the common raven by its size (48–52 cm or 19 to 20 inches in length as compared to an average of 63 centimetres (25 inches) for ravens) and from the hooded crow by its black plumage

ashy grey bird with black head, throat, wings, tail, and thigh feathers, as well as a black bill, eyes, and feet.

^Hybrid

At first glance, #2 looked somewhat like a Western jackdaw (Corvus monedula) because the grey feathers travel fairly high up on its neck and because the bird appears to be somewhat smaller.

Measuring 34–39 centimetres (13–15 in) in length, the western jackdaw is the second smallest member of the genus Corvus...The cheeks, nape and neck are light grey to greyish-silver, and the underparts are slate-grey. The legs are black, as is the short stout bill.

However, C. monedula has fairly conspicuous grey eyes and its feathers travel up the neck/head almost as far superiorly/anteriorly as the eyes. Neither appear to be the case in your specimen.

All three species are common in Europe.

citations - How to mention a completely rewritten article in PhD thesis?

First of all, I am from Europe. At my university are hardly any regulations of the form of my PhD thesis, especially nothing that concerns the following question:

I published a paper as a first author together with my supervisor. I have rewritten my work of the paper, the structure, each sentence, and all images, because I didn't want to give a Journal the copyright of a part of my PhD thesis. However, the original methods and ideas are still the same. Currently, this rewritten paper is one chapter of my dissertation and I have not cited the paper.

Would you recommend to let the reader know that the ideas of this chapter have been published in a journal?

---

Edit: Thank you for the answer, here are some remarks that didn't fit in the comment section:

1. 
   
   

   I asked the journal, they responded:

   
   

   
   

   Permission is granted for you to use the material requested for your thesis/dissertation subject to the usual acknowledgements and on the understanding that you will reapply for permission if you wish to distribute or publish your thesis/dissertation commercially. You must also duplicate the copyright notice that appears in the Wiley publication in your use of the Material.

   
   

   
   

   However, I didn't want to duplicate the copyright notice of the journal in my thesis.

   
   


2. 
   

   I will now mention that the chapter is based on the publication. I thought its fine to not cite yourself, because it was mentioned in the first comment of the question How to reuse complete paper for my thesis? that it is common in UK to rewrite the article so heavily that citation is not needed anymore.

   
   

Answer

because I didnt want to give a Journal the copyright of a part of my PhD thesis

Have you checked the copyright agreement? Various academic publishers explicitly make an exception of their exclusive right of publication of the material (although graphics might be a different question) for the author's educational theses.

Would you recommend to let the reader know that the ideas of this chapter have been published in a journal?

Yes, this is absolutely required. Otherwise, you are committing self-plagiarism, which is considered a form of academic fraud. This could have severe repercussions during your later career. The reason is that if no citation is given for something non-trivial and substantial, the reader will assume it is new and has not ever been published before it appeared in your thesis.

A good idea to handle this is to add a remark in the beginning of the respective chapter(s) that says that the following text is partially/largely based upon your journal article.