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What to expect as a supervisor's first PhD student?
Very much as the title states; what should I expect being my supervisor's first PhD student?
I understand that there are likely both pros and cons to this - however I'm looking to hear the experience of others, and how this compares to experience of those who have had a supervisor with previous students.

He/she is very interested to get you graduated as soon as possible to be able to get promoted to tenure.

Pro: your supervisor will have much more time than in a later stage of his career, will care more about your topics, and will also give you ideas and topics that he had for a long time without having time to work on them.

Please clarify: "first PhD student" as in, the first PhD student the supervisor was officially the supervisor for, or the first PhD student the supervisor has ever remotely counseled? In any case, a hard transition from never having advised a PhD student to being fully responsible for one seems unusual to me.

I'm voting to close this question as off-topic because it is a broad request for experiences, not a concrete answerable questoin.

@DavidRicherby: "Too Broad" and "Off Topic" are separate things. This is much too broad though.

@einpoklum I should have edited the default text more.  I'm voting to close because this question is: 1. too broad; 2. a request for experiences, not a concrete answerable question.

@Seeda The concept of "tenure" is not universal. It doesn't exist in the UK, for example.

I was my supervisor's first Ph.D. student and I survived the experience...
Although your advisor is almost certainly trying to do a good job, the simple fact is that neither you nor your advisor has ever done this before so mistakes are likely.
My advice would be to make sure that your dissertation committee includes some more experienced faculty and get them involved in the process (e.g. by having meetings with your full committee, having the committee review dissertation proposal and attend presentations that you might give on the work) as early as possible.

"nor your advisor has ever done this before" - maybe that is location-specific, but I have seen various postdocs who got very gradually involved with supervising PhD candidates, very smoothly taking them from never having done that before to almost completely having done that before by the time they became professors.

@O.R.Mapper may I suggest that's almost an answer? My conclusion from your comment would be that the OP should try to talk to the students in the group where the new supervisor was most recently a postdoc. (I also suggest that the process starts earlier in the career, with experienced PhD students training/looking after new starters)

My favorite "pro" would be the exciting experience of helping to put a lab together from an empty room, if the PhD is in the sciences and the mentor is building her first lab. The value of such an experience can be huge.
As with many things, this can be a pro or a con.  The "con" side is that this is a frustrating procedure.  Things will take longer than if you walked into an established lab.  You and your mentor will make mistakes.  Some of the money spent will be wasted.
The "pro" side is that you will have the experience of building a lab.  You will understand the whole lab much better than somebody who walks in to a developed lab.  You will have more input into the final product, and thus, more ownership.  You'll get to help spend startup money.  You'll learn how choices are made.
In the balance, I think this is a positive aspect.

Some people see this as a risk: https://academia.stackexchange.com/questions/84586/what-are-the-time-demands-on-a-phd-student-who-is-helping-set-up-a-lab/

@JayFromA As with everything, there are high points and low points.  I'll edit the post

I agree that this is overall a "pro". I just posted the link because the answer there adds another viewpoint. I think your edited answer covers this aspect well now.

How is this in the question at all? (i) There are plenty of PhDs in the sciences that do not require setting up a lab; (ii) it is perfectly possible for OP's supervisor to be embedded in a larger group that already has a lab; and (iii) the situation you describe could equally well happen with an experienced supervisor who has recently changed institutions. If the difficulty of setting up a lab from scratch were a factor, the OP would most likely have mentioned it. As it is you're answering a question that's entirely uncorrelated with the one posed.

@E.P.  edited to add the conditional you seem to want.

@ScottSeidman I guess that makes it off-topic in a tangential sort of way, as opposed to completely unrelated, but you're still answering a completely different question that is not what the OP asked. I hope this gets overtaken soon by the several great answers that do answer the question.

I was the first PhD student of a mathematician who was already a very strongly established researcher at the time.  It was an extremely valuable and positive life experience for me and I consider my choice of the advisor a major hit of luck.
You can expect the first-time tutor to be more motivated to help you succeed than one who already leads several students.  That's a definite plus.  Motivation is one thing, ability another.
You should look closely at where the potential advisor themselves are before you start, and whether it would be a huge step forward for you to ever get professionally to where the potential advisor already is.  Consider their past projects, publications, collaborators, funding, their position in the department where you will be a student; also their skills and values that appeal to you personally, especially their skills to explain known things and stimulate curiosity about the unknown.  Expect that they will teach you achieving just a subset of what they already achieved themselves; and only if they are a good teacher.  Spend enough time with the potential advisor and their closest collaborators beforehand to make sure you've tasted what you will be getting if you sign up, before you decide.
Did the potential advisor lead any undergraduate students in research related projects before?  Do you know of any PhD students who are already benefiting from working with your potential advisor, although their primary or formal advisor is someone else?  How is your potential advisor successful as a course instructor?
While you will be part of their future research, many technicalities will likely be similar to what they achieved in their past research, or to what's generally achieved in the department they are starting to work in, by researchers of a similar track record.

I was my supervisor's first PhD student, and honestly I would not recommend it.  The main downsides were

He did not have grant funding, and I have had to TA almost every semester of my PhD, even though this is very atypical in my department.  He said he was going to get grants, but he just never did.
He was a terrible manager (in several ways) and kept switching management styles.  I didn't find this out beforehand because he had no other PhD students to warn me about this.  However, it is probably pretty common for new professors to be poor managers, because they don't have a lot of experience in managing students.  (It is probably common for older professors to be poor managers too, since professors get very little management feedback from their students.)
In general, you have no idea whether the advisor will be good or not because there is no track record and no lab alumni you can talk to.

Any upsides? Also, your points 1 and 2 are not restricted to new advisors; i.e., more experienced advisors may also not have funding for their advisees or may not be very good managers.

Sorry, but none of your points is valid: (1) is true for many people not just young people, and you should have discussed the funding with him beforehand, no matter whether he's experienced or not. (2) is true for many people as well, moreover, if you're the first, the supervisor is more likely motivated to do his best, if you're #12, you're often simply #12 and nothing more. (3) is a problematic point, because people do change, and they do change a lot, so any information from his former PhD students has to be considered carefully.

I would argue that 1&2 are just as possible to occur with any professor, and in terms of having other people to warn you, well, a lot of that depends on personal styles too. You may clash with an advisor but that doesn't mean they are a bad advisor: it only means they may be a bad advisor for you.

Well, the same as you should expect from any supervisor: guidance, support, constructive critique, one-on-one meetings of appropriate frequency, and some insight into how the internal process at your institution works (he/she might have to familiarise him-/herself with that).
One aspect where lacking experience with PhD students might have an impact is the "proper calibration" around what constitutes a PhD-worthy topic and what constitutes a sufficiently comprehensive body of work. Likely the supervisor only has his/her own PhD to extrapolate from, and particularly when the supervisor has moved after the PhD and entered a significantly different academic culture, some adjustment may be needed (that was the case for me). Because of that I would hope that the supervisor is open to engage with some sort of mentor (a more senior colleague with already some PhDs under the belt) to talk about this. You might consider to have such a person as a co-supervisor.

Let me also add an answer to this question, but notice that I'm not a PhD but a Master's student now.
My supervisor for bachelor's diploma and research was a very well-known scientist who also was a head of the department. At first I thought that it was a great choice because of experience but then I realised it wasn't. When going to some famous person be sure that he or she would have enough time for you (answering your questions, explain some theory that wasn't cover in general courses, etc), especially if he or she is busy with some kind of administrative work. That leads to the situation where de jure my advisor was a famous mathematician but de facto I was supervised by his PhD student.
As opposite to this experience now I am working on my master's thesis under supervising of recently graduated PhD holder (just to be more precise, he is only 28 years old when I'm 22). This choice was a major hit of luck since firstly I didn't consider this opportunity and joined only after some other professors recommend him as a good and wise expert in my area of interest. I am very satisfied with my supervisor and till this moment have only pros. He really takes care about what I do, give quick answers to emails, always able to explain something unclear to me and looks very interested in good quality of my research.
So as my personal experience I would suggest not to be afraid of being someone's first student. Your advisor would probably have more time and motivation to work closely with you.


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Using parts of previous work in dissertation
I'm currently getting towards the end of my Master's year, and so I am working on my dissertation.
I completed a couple of projects for a module (assessed by report) in my third year that are relevant to my Dissertation, which include the geological/geophysical background to the region, and also the background theory of the methodology. These, however, are not published pieces; they are written coursework reports.
So these sections for my Dissertation are essentially written in different reports.
My question is whether it's acceptable to assimilate this information in my Master's write-up? (Mainly the methodology, there aren't many ways to concisely convey the information and theory, c1000 words.)
This probably matters, and my dissertation supervisor is the same person who marked the other pieces of work.
Thanks for your help.

By dissertation you mean your master's thesis?

Yes, that's correct

Cite the reports correctly as unpublished reports and give credit to the co-authors of the reports.

The only correct answer here is: Ask your supervisor!
You are not exempt from rules about self-plagiarism just because your previous work was unpublished, but without knowing the material, there is no way for us to be sure what side of the line you are on. Since your supervisor is also the person who previously graded this, it is natural to ask. Your supervisors job is, after all, to supervise.

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What should I do if my professors don't reply to my email for recommendation letter
I'm applying to an undergraduate research program and I'm gathering recommendation letters. I am currently studying at a different university as an exchange student. The applications were not open before I left my home university but I spoke to two of my professors, explained the situation to them and asked for a recommendation letter. They both agreed to write me a recommendation letter and they told me to send an email to them when I needed the letter. So, I sent an email to both of my professors with reminding them who I was and mentioning that I've talked to them about this matter before. It has been almost a week but one of the professors still didn't reply to my email. The other professor first sent me an email saying that I should come to his office to talk about this and then he didn't reply to my following email where I told him that I am not able to come to his office.
What do I do in this type of situation? Should I just write a follow up email to them or should I start looking for other possible recommenders?

look for someone else or call them

Keep trying to contact them.  It's possible they've changed their minds about writing you a letter, but if so they should tell you, not ignore you.  More likely they just forgot to reply.

Bombard them relentlessly, as they have no lives outside of academic responsibility and should in no way have anything else to do with their lives. /sarcasm  by the way, giant paragraphs are annoying

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Can I use an independent research to get a master degree?
I have an undergraduate degree, and I do some of independent research on my own, so I was thinking if universities have some kind of offer where I can use it, and I mean in exchange for my research I'll get the master degree without following the course, or anything that looks like that, any resources or references where I can look ?

It may depend on the field, but I think it's very unlikely that any reputable university routinely offers such a thing.

"(...) I'll get the master degree without following the course, or anything that looks like that (...)" I wouldn't hold my breath.

You're essentially asking for a degree without doing any work

If you are capable of doing independent research on your own, why bother with a master's degree? Go ahead and start publishing. If you are in industry and capable of publishing papers on your own, I would think that would look more impressive than a master's degree. However, if you want to get into academia you would likely have to conform to the usual requirements (i.e. a traditional master's and PhD)

There are some cases I heard of (mostly universities in Japan),  when respectable institution accepted independent research for PhD, however I heard tons of predatory business pretend to offer the same. So I would be very careful in your case, and also wouldjoin @haff and ask myself why I need this degree in the first place.

Following from @haff, you should seek a research-based degree (e.g., PhD) rather than a taught degree.

Well, not exactly a Master but a PhD.  In Norway, there's an option at University of Oslo called "Dr.Philos. degree" which may be awarded to academics who have qualified for a doctoral degree on their own, without formal supervision. Such candidates have no formal affiliation to the University of Oslo until their application for the doctoral examination has been approved and shall be an independent scientific work. It shall contribute to the development of new scientific knowledge and must be of sufficiently high quality to merit publication as part of the scientific literature in the field.
Source:  http://www.uio.no/english/research/phd/drphilos/

There is the possiblitity to get a research-oriented Master, which is the thing closest to what you asked for. Here is the link to one example course that I found during a quick search:
http://www.findamasters.com/search/masters-degree.aspx?course=15956
You didn't state which field of study you are interested in and in which area of the world, so this is probably not precisely what you are looking for. However, as Nate Eldredge already wrote, you can't expect to spend only a single day at your Master's University. They will want to make sure that you meet their standards, and typically, this involves at least a moderate course load for a Master's degree. Also, the degree of independence in research that you are asking for is probably not the same than the one that you get there.

In Canada, many Master's programs are research based, and in general act as miniature PhDs. In addition, they are also often funded. There is usually a course requirement, but at least your second year will be primarily research.
So while this isn't exactly what you're looking for, if you're wanting to do research, get paid for it, and get a Master's degree, you might consider a Canadian Master's program.


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Is it possible to obtain a second PhD degree in Europe?
As I have heard it is not possible to get a second PhD in Europe if you have obtained first PhD in Europe. Is it true? My 1st PhD is in Theoretical Physics which I won't find a fair job related to that. so I am trying to apply for second PhD in Mechanical engineering or applied Physics.

Related: http://academia.stackexchange.com/questions/1836/when-does-one-go-for-a-double-doctorate

I know someone who was doing a second PhD in Europe (first one was Asia), only to run off to the USA halfway through when he got a post-doc offer.  I think his second supervisor will henceforth think twice about accepting PhD students for second PhDs.

I am most familiar with the situation in Germany. There it is in fact possible to get more than one PhD degree. Different departments award different types of PhD degrees, depending on the academic field. In physics, you will typically earn a "Dr. rer. nat." (PhD in science), while in engineering you will get a "Dr.-Ing." (PhD in engineering). While most dissertation regulations will explicitly exclude the possibility that the same degree can be awarded twice, it is of course possible to earn a "Dr.-Ing." degree even if you already have a "Dr. rer. nat." or vice versa. Then you would have two PhD degrees.
In addition, there are honorary PhDs, which are awarded independently of and in addition to real PhD degrees. But I assume that your question wasn't aimed at those.
However, that it is possible to get two PhD degrees does not mean that it is a wise thing to do. To others, it may just be a sign that you didn't take the next steps in an academic career after getting your PhD, but didn't leave academia either.

As a further comment, note that not every PhD is recognized in Germany/Europe. One could thus get a second PhD ('Doktor') in Germany after having obtained a non-recognized PhD from somewhere else.

I encountered multiple people who refer to "Habilitation" as a "second PhD". It is very typical that you go for a "Habilitation" after your PhD in many countries in Europe and Central Asia. It is not a PhD though, earning a Habilitation degree will change your title to Dr. habil. XXXX YYYY
Unlike a PhD thesis, a Habilitation thesis covers a topic in breadth rather than in depth. Typically it is in the same field but covers a different topic than the one covered in your PhD.

In Germany, "Habilitation" was necessary to obtain the license to teach, i.e. only PhDs who also habilitated could become professors. This also informed the spirit of the "degree": you would have to present at least one worked-out lecture and, afaik, do some teaching. Nowadays, the "degree" has all but vanished in favor of "Junior" professorships in Germany, but it may yet come back.


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How to interpret quality of computer science journals that charge publication fees?
I usually publish my research work at conferences in the field of Computer Science, I do not have so many papers and the question that I am doing here it might sound foolish for some (or maybe a lot) of researchers in different fields. A situation has arosen when a colleague of me wants to publish a co-join work that we have done in a CS journal. For my experience conferences charge a fee for authors when their work is accepted, but I have some doubts about the fees that I found for some journals in the field:

Some journals I have seen are free and have an open access so that everybody could read or access a research work
Other journals charge some fees for accepted works that range from 200 USD to 600 USD, they are indexed in Scimago
Other journals that are indexed in Scimago in quartiles Q1 and Q2 can charge like almost 2000 dollars for accepted article, I have seen those in an Elsevier table, or maybe am I wrong?

I mean according to some PhD students that I have talked, they told me that usually good journals do not charge publication fees, but why for example the aforementioned editorial does that? I mean sometimes a journal could be accused of predatory because it charges for publishing, but it is not almost the same with some respectable journals in the field that do the same?
Bottom line, should one aim to publish only on free fee for publishing journals? Or one should better look out for the quality of the articles accepted within a journal instead of the fees charged for publishing?

While some people may use the existence of publication charges as a criterion by which to judge predatory or not, it is worth noting that Beall does not. He only mentions fees in regards to copyright restrictions.

See my answer to a related question, which begins "I have never paid...".  Also, in my experience, CS conferences don't charge authors when a paper is accepted, but rather when they register for the conference.

thank you @JeffE, I have a doubt with this journal: http://journal-bcs.springeropen.com/submission-guidelines/fees-and-funding do you think that is commandatory to pay the fee for publishing? I just don't know why a lot of q3 journals charge publication fees

From a comment of yours, you seem to be specifically interested in the Journal of the Brazilian Computer Society.
From the website it appears that this journal is part of a set of Springer journals with an open access policy (Springer Open). This is also clearly stated in the fees and funding page:

Open access publishing is not without costs. Journal of the Brazilian Computer Society therefore levies an article-processing charge of £695/$1085/€885 for each article accepted for publication.

Among the reputable journals there are usually three different publication policies:

Closed-access journals. Authors don't pay a dime, or they pay only if their paper is longer than a certain number of pages. Here the publication fees are covered by those -- typically libraries -- who subscribe to the journal. Only the subscribers can access the journals' content. Actually, many publishers require institutional subscribers to buy the subscription to a large number of journals, with very high subscription costs (can be in the range of 30 k$/yr).
Journal with mixed access. Here the authors choose what type of access they want. If they opt for closed access, they don't have to pay, but their paper will be accessible only by subscribers; if, instead, they opt for open access, their paper will be accessible by anybody but they have to pay a fee, which can be as high as 2-3 k$. The fees should, in principle, pay the article-processing costs (something that is questioned by many people).
Open-access journals. Here authors have always to pay a fee which covers the article-processing costs. The articles are however free to access to anybody.

I would highlight two points from the fees and funding page that may be of interest to you. First:

If the corresponding author's institution is a Member, the cost of the article-processing charge is covered by the membership, and no further charge is payable.

And the final paragraph:

It is the wish of the JBCS team that all quality articles will be
  published in the journal independent of the funding capacity of the
  authors. Thus, if the authors are unable to pay the APC charge, we
  recommend that they contact the editors. The JBCS team will provide
  support to find alternative ways of funding. In particular, a grant
  from the Brazilian Internet Steering Committee helps sponsoring the
  publication of many JBCS articles.

Regarding point #1, standard page charges (not length-dependent and not linked to OA) still exist in some journals - the most prominent example is PNAS - though I'm not aware of any in CS specifically.

This is less a response to the main question than to one of the answers, which says, "[At full or non-hybrid OA journals] authors have always to pay a fee which covers the article-processing costs."
It's not true that all OA journals charge publication fees. In fact, it's not even true that most charge publication fees. On the contrary, most (about 70%) peer-reviewed OA journals charge no fees at all, and about half of all articles published in OA journals are published in the no-fee variety.
To find no-fee OA journals in CS, go to the Directory of Open Access Journals < http://www.doaj.org/ > and look for journals in CS < https://goo.gl/imUOGt >. To learn whether or not a given journal charges a publication fee, just click through to the DOAJ record on that journal.
BTW, even when OA journals charge publication fees, the fees are seldom paid by authors. They're usually paid by the author's funder (59% of the time) or the author's employer (24%), and only 12% of the time by the author out of pocket. See the SOAP study < http://arxiv.org/abs/1101.5260 >, Table 4.

I wouldn't suggest such a directory: many of the journals there linked appear in the Beall's list of "potential, possible, or probable predatory scholarly open-access publishers". Moreover I didn't say "authors have always to pay a fee which covers the article-processing costs.", but I said that reputable journals usually require a fee to have open access.


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What strategy should I follow for lecturing a course in which I have only a basic background?
I am currently working in a faculty where among the courses in CS there is one about Computer Graphics. That course was taught last year by a professor who actually has retired, and who was a specialist in the field. The thing is that the Dean has talked to me for putting me in charge of that course in the undergraduate level, mostly because the other lecturers are with no available free time at all; and it will take some time to hire another professor.
The problem that I have is that even I hold a MSc in Computer Science, the knowledge that I have about Computer Graphics is basic. Only what I have followed in my bachelor's a long time ago.
Actually I am little scare of what to do, I have started compiling material for read and prepare my upcoming lectures, but I am afraid that maybe I will not be able to make a good course. In short, what strategy should I follow for lecturing a course in which I have only a basic background? Should I be completely honest in the first session and mention the students that this area is mostly new for me?

Related (possible duplicate): How to teach a class that I've never taken?

Can you get help, such as lecture notes, from the retired professor?

I have a few additions on top of the related question.
I don't think you should be too concerned about your abilities. Your domain knowledge will be beyond the vast majority of the undergraduate students, and thus you will acquire knowledge very quickly. It is inevitable that you will miss some of the obscurities and fine details in the first time running the course, regardless of your graphics background.
Specifically about Computer Graphics: I had a lecturer who had no background in computer graphics. She was taking the course for the first time, and it was one of the best courses I've experienced as an undergrad.
Factors contributing to success:

She took material from the previous lecturer (who had experienced success) and adapted it to her needs.
She used many illustrative, well-commented code examples
The assignments were fun, the results were impressive, and there was much opportunity for creativity and your own modifications. (bonus marks awarded for 'extension' tasks such as rain, fire, shadow effects)
Lectures were absolutely full of practical examples. She wrote code on the spot and demonstrated how they affected the graphics. She solved mathematical equations on the spot and connected them up to code examples.
The ideas taught facilitated graphical effects that were impressive and instructive, and with simple code examples. For example, a rain effect is constructed very concisely by randomly generating 2D rectangles, and you can teach billboarding with it. A realistic tree is constructed concisely with a lindenmayer system.

The course website is open to everyone.
I think you should mention that it is your first time teaching it, and ask the students for feedback during the semester (early in the course). They will be more forgiving and more inclined to offer helpful suggestions.

Re: the last paragraph, it's okay to say you haven't taught the course before, but you probably don't want to put your students under the impression you don't know the material (you should prepare thoroughly so you know it well enough before they do).  So I wouldn't say you're new to the area, but if someone presses you with a lot of questions you can't answer beyond the scope of the course, it's okay to say, "I don't know, I haven't worked on such things."

I suggest that you plan for a self-study program in Computer Graphics before you start the first day of this class.  If you can't plan a self-study program for your self, then you do not have adequate mastery to teach the course.
You should do all of the exercises and projects yourself.  If you can't or won't do this, then you shouldn't teach the course.  As you do all these exercises and projects, you should take copious notes on what questions and problems arise, and what you find confusing.  Computer Graphics is a well-established branch of Computer Science, so if you find yourself unable to explain the basic concepts clearly, then you shouldn't teach the course.
Finally, you should put some attention to your written communication. Your question has many grammatical mistakes.  E.g. "Actually I am little scare of what to do, ..." should be: "Speaking frankly, I am a bit scared regarding what I should do."  No matter what you are teaching, speaking and writing well is a vital skill.


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Does emailing a journal to ask if my article is within scope hurt chances of getting published?
When I started my "quest for knowledge" several years ago I began in an already ill defined-field which was on the borders between science and philosophy but as I progressed I drifted further and further into something I can only classify as "something pertaining to many sciences but not really a part of any one field". It became some even I-can-not-tell-what field of science and although I have completed my quest and came with a sound paradigm it doesn't really pertain to the scope of any of the journals in my area which I use in my references. Or to be more precise, it pertains to all of them but only "a little bit", this is why selecting the proper journal seems so difficult now.
In order to solve the problem, and actually thinking this is a solution, I decided to write a small e-mail to journals explaining my situation and what I have done. It was something like a 200-300 word abstract so they know what my paper is about and then asked if this is within the scope of their journal. None have answered me!
Has anyone had a similar experience? Did I do the right thing writing their editorial boards these e-mails? Did I shoot myself in the foot by doing this? Any suggestions what the effect of these e-mails could have been (e.g. they think I am a crackpot, they just deleted them, they put me in a "forbidden list")? Am I doing something terribly wrong here? Can anybody give me advice as to how I can handle the situation from now on? Do such e-mails effect my chances of publishing there negatively or outright stop them?

Thank you for the edit. I am still new here and may be this is the reason why I make so many mistakes. I will try checking spelling and grammar better next time I write a question.

Not a duplicate, but possibly of interest: http://academia.stackexchange.com/questions/61712/how-to-publish-a-paper-that-does-not-seem-to-be-within-the-scope-of-any-journal

The solution is to start your own journal, of course ;-)

Actually, gerrit, I am sometimes very tempted by the idea to say the hell with the peer review and write a small book on the questions I have delved into. I will organize it accordingly and provide with reference, write it under the creative commons license, go to one small book printing business located near where I live, go to some torrent tracker and push it there to see what happens :) I have really thought about it. This business offers the service of "small number books publishing"(I can't translate it correctly)for a modest amount of money.But then will I be considered a real scientist?

The point is, I can't claim I have discovered anything without going through the peer-review. Am I right?

@YordanYordanov: freedom of speech, go ahead. The problem is not making the claim. Plenty of pseudo-scientists do it all the time. Your problem is that you don't want to be lumped with those. That's why you often see the strongest scientific rigor on the edges of respectable science.

Actually, you are even more than right! If I wanted to just publish it, I am sure I just need to add the word "quantum" in some paragraph and I can easily find many "universities for holistic medicine", "energy healing schools" and other "alternative scientists" but then who would I be? I have quite the experience with those guys! When they learn you have a degree in anything and your ideas aren't trivial they all come cheering down but once you get to know them you realize what they are full of sh*t! I have seen plenty of it!

Peer-review for all its evils is the best way to "stay in reality"! Otherwise all we will be doing is creating new religions with some "grain" of reality in them. And we all know how they end up!

Don't worry.  There is nothing bad about what you have done, and it will almost certainly have no impact on consideration of any manuscript you may submit to any of those journals.
Most academics divide their time between large numbers of obligations, and they receive many unsolicited emails; this is even more true of those who are on the editorial board of a prominent journal.  Many of them will not reply to an unsolicited message from someone they don't know.
They have not put you on a "forbidden list" or labeled you as a crackpot (unless the content of your message was such as to warrant that -- but even then they probably don't remember your name).
Let me add that it is sometimes a good idea to contact an editor before submitting your paper, and I have done so on occasion.  This usually requires that you know the editor, or that someone who knows them can introduce you -- or that you can manage to bump into them at a conference.  Asking informally if your manuscript is a fit for their journal can be helpful when the work falls between disciplines, and an immediate answer saves time for you, for the journal, and possibly for potential reviewers.  When doing this you should usually contact the particular associate editor who is most likely to handle a manuscript like yours.

Thank you very much. I feel relieved now! I still just don't know how the system works. That is why I ask here.

The assumption that a 200 to 300 word abstract of the OP's work would not give the impression that he is a crackpot is a strong one. Based on his description of his work in the question I would say there is at least a 50% chance he is a crackpot, and the question doesn't even go into any details on his work.

I'm somewhat surprised at the other answers labeling this an unusual practice, since some journals invite pre-submission inquiries. For example, Current Biology says:

The editors strongly encourage authors who are interested in submitting work for potential publication in Current Biology to send a presubmission inquiry prior to any formal manuscript submission. Presubmission inquiries should include a clear abstract and a cover note explaining the significance of the advance and the potential general interest to the broad readership of Current Biology.

Nature does them, but a less formally, as does Neuron. Theodora Bloom, a editor from PLoS Biology, has a longish post describing how and why PLoS Biology uses these inquires. In general, this should help you determine if your paper is in scope and sufficiently "newsworthy" (for journals that care) before you rewrite and reformat your manuscript for a particular journal. It certainly can't guarantee anything, but it may save you some time and frustration.
However, if you are doing this, you should follow the journals' procedures (if any are published). Nature, for example, wants a specific format (essentially the first paragraph/summary of your paper), while Neuron wants the emails to contain "presub" in the subject line.

Based on your description I think it's indeed possible that your email, or maybe even the content of your article itself, makes you appear somewhat like a crackpot - it's impossible to say without knowing what you wrote. But that is neither here nor there; a single email should not get you blacklisted or affect your chances of getting published, so I don't think you need to worry that you caused yourself irreparable harm.
With that said, the email doesn't sound like an effective strategy, and it doesn't seem very surprising that you are not getting any responses. Journals are busy enterprises and they like to work according to a specific workflow to maximize their efficiency. That workflow is quite simple and looks like this:

The author submits the paper by following the instructions for submission on the journal's website.
The journal processes the submission, gets the paper reviewed and eventually informs the author of the decision.

(In some cases there are extra steps involving revisions, but such complications are irrelevant for the current discussion so I'll ignore them.)
To summarize, you didn't get any responses because you didn't follow the instructions for submitting your article. Follow the instructions, and then the journal editors will have the information they need to make a decision about whether your paper is a good fit for them, and they will let you know (hopefully soon). Simple.

I am sorry if you think my question can be off-topic, but can you recommend me a question on this SE section dealing with first publication. Has this question ever been discussed here? About the troubles one may get if trying to publish in a journal for the first time?

@YordanYordanov can't help you with that, sorry. Use the search feature of the site.

This question and its answers may be at least a bit helpful to you: How to write an academic paper for the first time?.  Writing a good paper is difficult, and the input from more experienced colleagues and an advisor are invaluable - without this help, submitting a publishable work is going to be even harder for you.  Kudos to you for giving it a try.

I don't think those emails will hurt you. But they won't be any good either, I think. The problem is that journal editors don't really act as an editor, in the sense that they are not expected to work with the author to improve the manuscript and/or define its scope. Most scientific journal editors receive (many) manuscripts, they find suitable referees for them, and then eventually decide whether the article will appear in the journal or not.

This is only one part of the definition of the word editor. What editors of academic journals do is indeed acting as editors.

Regarding the question

Is it OK to send an abstract to an editor asking if the corresponding article could be considered for publication in the journal?

(my rephrasing).
My answer is: Yes, it is ok, but this is unsusual and I am not surprised that you did not get a response.
To give some advice: You can do a similar thing, but, instead, send the whole paper and not only an abstract to an editor and ask if this article is within the scope of the journal. I did this, and I got a reasonable response from the editor very quickly (a few days - the paper got rejected finally, but on the ground of well found reviews). I guess that just sending an abstract would not have gotten any response in my case, too. This is because it is virtually impossible for an editor to judge the content or contribution from an abstract without the paper - well, you can describe some contribution, but an abstract is much too short to argue in a proper way.
Regarding your further questions:

Am I doing something terribly wrong here?

Not terribly wrong, but unusual.

Can anybody give me advice as to how I can "handle the situation" from now on?

My advice: Write your article with a specific audience and journal in mind, then send it to the (associate) editor of said journal that fits best and ask if the paper would fit the scope of the journal. If he or she says no, rewrite the article for another journal and repeat (or find a journal for which you think that article does not need rewriting). If he or she says yes, but do take it for granted that the paper is accepted. The chance of acceptance is not changed by asking in advance.

Do such e-mails effect my chances of publishing there negatively (or outright stop them)?

No, it would not get you blacklisted for the journal (I am not sure if such a thing actually exists) and your chances to publish an article are most likely not changed (unless you send multiple requests for an opinion of an unfinished work and really annoy any (associate) editor).

I would guess that very loose and informal 'blacklists' exist, which are probably nothing more than records of people who have either submitted umpteen papers disproving the Riemann Hypothesis and for whom further articles will not typically be sent to reviewers, or who tend to respond to rejection letters with vexatious and persistent challenges, and with whom correspondence will not be entered into.

I have two suggestions for you.
1) For books, authors are encouraged to submit a "proposal."  Here are some sample instructions:

Submissions Guidelines
Please be sure to include the following items in your submission. Your proposal should not exceed 30 pages and should preferably be in the form of a Microsoft Word document.

A title and a subtitle.
A one-paragraph overview that explains the premise of your book, why you wrote it, and who you see the audience being (with any relevant demographic data you might have about the potential size of the audience).
A brief author biography (1–2 pages) that focuses on why you are uniquely qualified to write your book and what kind of platform you have to reach a wide audience.
A table of contents that outlines the book, with chapter and section titles, as well as brief descriptions of the material each chapter and/or section will cover. It should be no more than ten pages total.
A market analysis of the potential readership for your book, including a comparison to similar books. When comparing your proposal to other works, please briefly explain (just several sentences) how your proposed book differs from these titles. Please limit yourself to 3–4 books.
A sample chapter that is representative of the style and content of the larger work.

I will suggest that you take this as inspiration for how to pitch your article to journals.  Try to reduce the 200-300 word pitch down to a more manageable size.  Maybe your pitch will be a little bit longer than the sample I included.  Imagine that you are writing to someone you know pretty well in one of these near-fields.  Explain to this friend why your article will be interesting to its target audience.
Interestingly, when I have gone through this exercise, I have ended up with a clearer idea of what I'm trying to accomplish with my article, and it has enabled me to improve my article!
Your pitch may be a bit different depending on which area the journal you're submitting to covers.  For example, if you submit to a chemistry journal, your pitch would be different from a submission to a physics journal.  You would need to explain to the chemistry journal why your paper would be interesting and important to chemists.  And for the physics journal, why it would be interesting and important to physicists.  (Physics and chemistry are just examples.)
The pitch is written in a more down to earth way than the paper itself.  And note that the pitch is not the same as an abstract.
The pitch is kind of like those short blurbs you hear as ads in the Fresh Air podcasts, where the advertiser tries to give you an idea in 25 words or less what kind of book is being advertised, so you can form a very quick idea of what kind of book it is.
Your pitch will function as a pre-submission query.  As others have noted, this is unusual.  The better you can prune this down, and really focus it, I think the better your chances will be.
If you are going to introduce a completely new animal to your circus, you need to describe this animal to people, so they will be receptive to it.
2) Find at least one person with a strong publication list of his or her own to put in a good word for you -- in whatever way that person is comfortable doing.  In other words, do some networking.  This person will not be recommending that the journal accept your article.  Rather, this person will be requesting that the journal seriously consider your submission, despite its unusual nature.
Make sure that you and this person (~mentor) are on the same page about the thrust of your pitch, so that s/he can underscore some important parts of it, in a way that matches your description.
Last note.  Please don't be tempted to start with the first paragraph of your question here, or anything like that.  It was fine for Academia SE, but it wouldn't be an effective way to start your pitch.
Edit:
To clarify, adapt the above sample instructions to suit your needs.  Specifically, I would enclose the manuscript itself along with the thing I have called the "pitch."

I think this is bad advice. 'Pitching' as a form of advert for an as yet unseen paper does not seem either a good idea or necessary. Journals believe that they will accept any paper which is correct, on-topic and sufficiently interesting. Such a paper should sell itself rather than need to be sold. Similarly, getting someone well-connected to 'recommend consideration' may be counter-productive and should certainly not be needed. Journals review papers by unknown authors all the time.

The difficulty here is convincing the journal that the paper is on topic. // Edited answer to correct misimpression.

-1 Don't "pitch" to journals. If you are worried that your manuscript is not within scope, email an editor with the abstract. Articles are not written the same way as books and you should not try and take lessons from one to the other.


text:
Does posting my work on the Internet protect me if someone else tries to publish it with peer review under their own name?
I'm in a very unique situation. I have ideas of something potentially valuable for science and I want to get it published but I haven't been able to go through the peer-review process, yet. That is why I'm thinking about simply putting all I have on the Internet and leaving it be there to see would any "real" scientist (with the equipment and the position) be interested in them. I don't work in anything related to science and although I have a degree I don't have PhD so it's like I'm nobody.
What is my "protection" if one of those experts (who obviously know much better how to publish) just takes it and puts his/hers name on it even if I manage to show files containing the same ideas loaded on the Internet for public access (so I have the site administration to verify my publication dates) much before his/her work was submitted to a journal?
Does such obviously public documents have any weight against peer-reviewed paper or is the fact that s/he managed to go through the process but I didn't make these ideas his/hers? Is any value in the fact that a document is publicly displayed before the submission date or does the fact that it's publication anyways make it "the real deal" while the other document, even if it can be shown to be earlier by outside source (like the administration of the web site)? If I just "publish" it on the Internet under the Creatice Commons license does it give it any authority in any way measurable to a peer-reviewed publication or anybody who has one can claim ownership over the ideas?
P.S. Can the entire issue be "dissolved" quickly if the one who got it published in a peer-review journal just mentions my work in the acknowledgements and says these ideas were mine and s/he just "used" them. Then is the authorship of the ideas automatically transferred to me and the issue is non-existent? But what if I ask him/her and s/he refuses. Then, can I claim authorship of the ideas or are they out of my reach now and I would just have to be satisfied with the fact that at least now they have gained some form of recognition (although I'm not their author in the eyes of the community)? (The issue is I just want scientists to view my work seriously, I don't do it for the money, the job or the fame. I just want to know am I right or wrong, so what if someone just uses and claims authorship-should I be satisfied only with the fact that I was right all along or should I try to pursue him/her for non-proper use of my ideas.)

Why would an 'expert' do that?

Because I propose something original no one has proposed before and although I have no Ph D the paradigm and the methodology it produces can still be useful for a researcher. If you just stumble on an interesting methodology someone with no background in science proposes but you think it can help you design new experiments and explain your results would you consider pursuing it, although it isn't peer-reviewed?

How about discussing potential collaboration with researchers near you! perhaps they can help you with writing a nice paper that can be published in a good journal.

There are sites like arxiv.org where you can publish something, which isn't peer-reviewed yet, but which becomes public and stakes a claim to the idea.
However, that's usually what some people (usually at universities, not companies) do when they have a full-fledged paper to release. In your case it sounds, if I read this correctly, like you have some general ideas you have not yet had a chance to pursue in depth.  You're considering putting them out and inviting others to run with them, but want some credit.  I would say that if you simply put out a general idea, that is worth an acknowledgment in a paper, not co-authorship.  Being an author means actually doing some of the work -- writing text, doing experiments, etc.  I don't think what you describe rises to that level.
One thing you might consider doing is putting out enough information to tease people into inquiring for more information, then trying to work with anyone who inquires to be more directly involved in the work as it proceeds.

Actually, you're on the top @FredDouglis ! This is exactly my case. I want to put something and one journal may want to publish it (I actually managed to find a journal that is pure reviewed and can accept my manuscript-I wrote to them but they have $2000 fee and I just don't have the money-little and poor country) so the more I think the more the Internet is my only option. This is why I'm thinking about the authorship issue here. I just want to gain some recognition, not get into courts and copyright issues. An acknowledgement will be fine. My question is can the ArXiv be sufficient for it?

I've never used ArXiv myself so I don't know enough about it.  I've seen citations to it occasionally.
I don't know your field, but in computer science, there are a number of journals that do not charge, unless you want to make the article available via open access.  Otherwise to access the article people must pay to download, or have some form of subscription.
Perhaps you can find a different peer-reviewed journal or get them to waive their fee due to your circumstances.
Of course, it still has be something a journal would choose to accept for publication.

@YordanYordanov To post it on the arXiv, it will need to be on topic for some part of the arXiv (and you need to pick which one, which seems to be one of your problems). Further, you will need someone who already has a record of posting papers in that topic to endorse you, which will involve sending them the manuscript, and this seems to be something you are very afraid of doing. That said, if you can satisfy these conditions, the arXiv is a good place for preprints and certainly establishes priority.

Two comments for you:

You commented that you found a journal that wants your paper but is asking you for $2000. Take care that this is not a "predatory journal," that is to say, a fake website imitating an academic journal in order to take your money.
If you really need to get credit for this idea ASAP, you can always post it to viXra. This is virtually the same as uploading it to your personal website. At least it will be time stamped, which is proof you publicized your idea at a specific time.

It is up to you if you want to risk publicizing your idea on one hand, with the benefit of establishing precedent for yourself on the other hand. That is really an individual choice.

No, putting it on viXra is not virtually the same as putting it on your personal website. If you put it on viXra, many people will decide to not look at it any further based solely on that fact. It will still establish priority in case of a dispute, but simply posting it there will label you as a crank to many.


text:
Extent of reuse and reanalysis of data published by others
There are a number of questions about accessing the data corresponding to publications. In the recent years, many journals have improved their data availability policies and this is less of an issue. On the other hand, I do not find much about the extent of exploiting these data that is thought acceptable.
Firstly, I believe most scientific communities accept that other's data are replotted along with similar data acquired by the authors (showing repeatability) or along with similar data from yet other groups (meta-analysis type of figure). Still, I have the impression that in many communities people rather plot only their own data and comment that this is the same behavior as reported by so & so. So is there a policy? Should one ask for author's permission? Should one specify exactly what data of theirs will be shown along with what other data?
Then, there's the question of data re-analysis. For instance, say authors have published the time evolution of several variables of interest, and Methods make clear that these were acquired simultaneously on the same sample. Is it OK e.g. to publish separately from them a figure which plots one variable from their dataset against another? I guess the answer to this question can be yes or no, depending on the way this is done. I expect that in most cases, having this plot with only their data as my Fig 1, possibly overlaid with a model prediction, and being the main result of my paper, will be judged problematic. Is it? If yes, what is the red line between acceptable re-analysis (e.g. I've already seen data re-plotted in log scale, but the figures with this data were in supplementary materials only). And of course, same questions as above apply.

You can do anything with previously published data without consent from the authors. Problem is finding something interesting and new enough that warrants such a publication.

@MaartenBuis: That's a very strong statement to make, and in this generality, I would guess it's most probably wrong. Understanding the applicable laws and contracts would be complicated enough if one knew the jurisdiction, but it seems like we don't, so a sweeping statement like that is unlikely to stand.

@RQM Legally your are right, we can't know the legal position of any specific jurisdiction. However, culturally MaartenBuis is completely correct. Once something is published it is regarded as pubilc domain and you are free to do with it as you wish, as long as you cite the original publication.

@IanSudbey: I don't know what "culturally" is supposed to mean in this context, but your last sentence is most definitely wrong; that's why, for example, licenses exist, i.e. to define what you're permitted to do with published material and what you're prohibited from doing. Let's hope your advice ("free to do as you wish") doesn't cause anyone trouble!

If you use the figure directly, you'd best get the permissions in line.  If you modify the figure, you most likely don't need to, but properly attribute (i.e., "Modified from...."
My own preference for stuff like this is to use a tool like datathief to grab the data from the figure, and remake my own figure, formatted optimally to make my point.  Attribute the original.

Thanks for your answer. Of course I meant to attribute any re-used data. I understand that your feeling is that data doesn't always need to be made available and can sometimes be reverse-engineered from figures (if authors report a distribution, you may only get the mean and some percentiles, though). But then, to what extent would you re-analyse their data, that is, plot it with different axes than what they have?

There are zero restrictions.  I would do whatever I felt I could scientifically defend.

all_licenses: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/


text:
Is there added value in having your own presentation layout and using it consistently?
From the perspective of a Ph.D. student, how much of an added value is it to have your own presentation slides layout, that is used consistently throughout your Ph.D. conference presentations and other talks (and possibly throughout your academic career afterwards)?
Here is one such example from the Computer Science community.
This as as opposed to using existing Beamer templates with LaTeX, or built-in PowerPoint templates, or simply preparing each presentation on its own (without a specific layout).
A couple of axes I can think along:

Creating a signature layout that distinguishes one in their community
Ease of preparation of presentations (especially over time), maybe overcoming constraints with existing templates.

Note that I am not concerned with the question of content, but just design and layout.

Is the reason for using your own layout that there is something you don't like about the existing templates? Or just to have a distinctive look?

@ff524: your questions are exactly the kind of questions I'm hoping to get answers for. I'll edit the post to clarify this

I have certainly noticed when someone's presentation has been particularly well laid out, and they will probably have gone through several iterations to reach that level. Using the same design over and over again can certainly help you perfect a design, but I don't think anyone will know that you are being consistent (this is what you were asking). Furthermore, nobody is using transparencies anymore: Perfecting your LaTeX/Beamer skills might quickly become obsolete with HTML5 based, more interactive, presentation methods. This said, in industry, though, having consistent presentations is key.

I'd say there's value in creating a template and style to stick to, but I wouldn't focus on making it distinctive. Instead, focus on making it good, clean, and clear. There are lots of easy mistakes to make when you're preparing a presentation, and having a good, well-designed style in advance can avoid them if you stick to it rigorously.

Also note that some departments or universities require you to use their own template. In Sweden, you can immediately spot KI (the medical university) for their plum coloured banners in posters and presentations.

I disagree with some of the responses saying that if people notice your design, then your science must be weak or it must be a bad design. When I see a nicely formatted table (e.g. clear fonts, legible footnote, lighter table grids, etc.,) I would appreciate the speaker's effort. Instead of it being a "signature" or not, I'd focus on just one question: does the format/design enhance the expression or understanding the contents? If yes, then go ahead and add that into your repertoire. Science and design do not have to be in a constant tug-a-war.

I don't think there's any inherent value in having your own "signature" presentation layout.
Generally, you want to keep the focus on the content of your talk.  If people are noticing your layout, they are paying less attention to your science.  Would you rather stick in their minds as "the speaker with the cool result" or "the speaker with all those weird colors on their slides"?
If you really dislike the usual templates, or you can make your own workflow more efficient by creating your own, then go ahead and do it.  But I would suggest keeping your (visible) changes conservative; if your layout is radically different from what people are used to seeing, it may become distracting.

If people are noticing your layout (to the extent that it’s distracting them from the talk), it’s simply a bad layout.

Why would having your own "signature" layout result in people thing they have "all those weird colours"? Is it not possible to have a signature layout that is appealing to the eyes? What if people said "Look at that speaker with the cool results and they have these great slides they use all the time".

If you are presenting in a classroom it is an advantage to have same templates because students do not prefer to see a new template each session. But in the conferences the audience is not aware you are always using the same template. The only thing he sees is the content you are presenting. Moreover, some conferences have their own template and all the speakers have to use the conference template not their own.
P.S. If you have the best designed slides and you have nothing to talk about, your audience will get bored soon.

Using the conference template, if there is one, is important. However, if people at conferences are interested enough in your work to look up your past publications and conferences, they may very well be exposed a number of presentations, and consistency might be beneficial.  Now that so many venues have wireless, people might look at your past presentations while you're presenting.

Even at the conferences, people are looking for his past publications and contents, not comparing his template styles. But you are right, if audience compare his slides, they may say that how neat his slides are, nothing more. I can not find what extra is delivered to the audience by these unique presentation slides.

The content is the important part, but, , if the formatting for critical assumptions in one presentation is the same as important result in another, it more easily leads to confusion.  Consistent formatting might, e.g., have "key assumptions" on a pale yellow background, "research methods" on a pale blue, and "important results" on pale green.  People might not be consciously aware of the formatting styles, but it still helps for a consistent experience.  We see that in textbooks, where authors use margin icons to highlight certain points, and don't switch icon sets between chapters.

I have seen presentations from famous professors that were only white background with a black colored font; Nothing more. Those persistent presentation slide layouts seems to be efficient while presenting in a classrooms where the lecturer wants to teach something to the students and wants his slides to be efficient. In a conference presentation where the paper itself is more alluring to the audience, "persistent layout" worth nothing to the clever audience who doesn't care about the fonts and colors of a 15 minute talk.

Sitting in a seminar, the audience goes directly to the title of each slide page and they may not bother themselves to remember which color was for which topic.

Definitely.  As I said, for any single presentation, the content is the important part, and not the formatting (unless the formatting makes it harder to process the content).  The OP's question only makes sense in the context of multiple presentations, though.  This isn't about a single presentation, but rather about the presenter's personal library of presentations related to a topic.  Those might later be used in a lecture series, or incorporated into something else.  Consistent formatting, whether minimalist or not, will make reuse easier.

First of all, I do not think that having a signature layout is any good for its own sake. In most fields, few people (apart from your workgroup) will attend more than one of your talks and even those who will, will likely not notice the consistency of your layout¹ – unless it’s particularly memorable, which is almost certainly not a good thing². And even if somebody notices, they will likely (and hopefully) value the quality of your design more, let alone the quality of your content.
Considering the required work, there are two aspects: (1) Creating (or choosing) a layout and (2) Using the layout throughout your presentations.
Aspect 1 takes a few hours, if you are sufficiently apt with your presentation program (and it does not suck) and know some basics of graphic design (which I suppose you do, if you are asking such a question).
Mostly it’s selecting a colour scheme, one or two fonts and a default arrangement of your slides as well as realising them in your presentation program and in the programs you use to generate your figures.
Regarding the constraints of existing templates, remember that (unless your problems are very individual) if no templates are the way you want them, it is very likely that you should be careful what you are wishing for.
Also beware that the fact that you have to rely on (usually unknown) projectors imposes some constraints on your font and colour selections.
Aspect 2 will usually save you some time, whether you are using a prebuilt design or your own: For example, you are very likely to reuse some material – in particular figures. And if you care about your slides being consistent (which I suppose you do), you avoid spending some time in adapting colour schemes, for example. In particular, there is usually no benefit in switching designs.
From personal experience, I have spent some time in working out a design and have not regretted it yet.
¹ Just think about, how few people give horribly designed presentations and thus can be assumed not even to notice the flaws in their own presentations, let alone the qualities of yours.
² As you should not notice good design that much.

I see pros and cons; which ends up winning out depends on your skill mix.
First - designing a good layout takes effort and expertise. Graphics designers study many years to get good at it. Just because tools are provided to make it easy doesn't mean everyone is suddenly a graphical designer. The right blend of colors, fonts, space etc is not an easy thing to achieve. 99% of "I can do better" layouts look horrid.
Having said that, I have at times come across layouts that made me go "wow". This is where the layout really supported the flow of the presentation, and while I was not getting distracted by the details, I came away more impressed. This was mostly because the presentation itself was very good - the contents were impressive, the speaker was very clear, and the layout of the presentation supported the spoken words.
In those cases, the personal layout was the icing on the cake - not a substitute for good work. There is a lot you can do to improve your presentation without spending any time on the layout. Fiddling with layouts (like fiddling with LaTex) can become an easy distraction from the real issues with your presentation. I urge you to consider whether your interest in the "look" is coming at the right time: in other words, is every other aspect of your presentation skills (content, pacing, connecting with the audience) so good that layout is the only thing left to play with?
If the answer is "yes", then my answer to your question is "yes". Otherwise, I think it's a bit early to work on creating your brand through a custom layout. Many people in the scientific community - especially at the PhD level - could do with honing their presentation skills. They could learn not to confuse slides with notes. They could learn to connect with their audience. They could learn to speak at an appropriate pace, and project their voice. They could learn to focus on the essentials and not bombard the audience with details. They could learn to use slides as visual aids - not "the main course" of the presentation.
While I don't know you or your skills, I would say that I have statistics (based on 25+ years of empirical evidence) on my side when I answer "probably not" to your original title question.

Yes. If you're like me you'll never like everything about a standard layout, and you want your tools to disappear as quickly as possible when creating content.
Noticing something in your slides that you want to change (bullet type, or title colour, or whatever) is the easiest way to get distracted from doing so.
Having a standard layout for your own work means you have to spend the least amount of time worrying about the formatting.

Standardising layouts have three advantages:

You can reuse slides across presentation without changing the styling.
When you create presentations, you don't need to think about styling; the templates are already set up for you.
Creating templates and styling can be delegated to someone with design skills, and everyone else gets to use them.

The first two points are applicable whether you have your own signature style, or you follow a team or corporate style.
The last point is different. In theory, having a corporate style is a really good idea because everyone gets the benefit of using templates created by the design genius in the marketing department.  In practice, corporate templates are almost universally awful.
So, if a corporate template exists, and you are lucky enough to like it, then use that.  There's no point in reinventing the wheel.
If there is no template, or it is dreadful, then create one for yourself and stick to that.
Either way, you don't want to have to keep deciding on new fonts to use for every presentation that you make.

If you use e.g. Beamer with LaTeX, changing style is literally changing two or three lines. Not worth getting all tied up for.

I always appreciate when someone cares about their presentation. There are some things that are just inexcusable (e.g., tables that are left aligned on one slide and centered on another), and make you look lazy, so to the extent a consistent template would mitigate those then it can't hurt.
My presentations tend to look the same and stand out against my peers. I do all of my writing in Markdown, analyses in R, and create dynamic presentations with some available R packages. Therefore, all of my graphs tend to have a style (ggplot2), tables look the same in HTML, fonts (and related consistencies between headings and body text) work together nicely. It's not just about the style of the presentation, as I know a few people who give presentations and have a very distinctive voice in their text, and a welcomed minimalism in slide content.
I never thought too much about it, but I do have a "style" or "brand" in my presentations that most people who have met me and seen me present a few times recognize as clearly a presentation I crafted. However, this "brand" is really just me using a specific set of tools that most people don't use. What's the standard for most fields? Unfortunately Powerpoint, and some use the Mac Office Suite, while a few others use Prezi (and most use that tool poorly).
There's a range of tools out there that you can utilize that might help develop a consistent "style" for you, but also will help to vastly improve your workflow, and also make your scholarship better (i.e., tools with an emphasis on reproducibility).
Whatever you do just do it well and make sure it works for you and our audiences.

What you're describing in your question is called good branding.
Branding is a major part of marketing, as it allows companies to craft a particular image for consumers. It's important for brands to be distinguished from one another, and focus on a target audience, which is why you've probably heard of brands such as "Arm & Hammer" and "Oxi Clean", but probably don't know "Church & Dwight" which owns both of those brands.
Establishing a brand takes a lot of time and effort, and is difficult to measure. How can you objectively tell whether a sponsor chose to give you money because they liked your science or because they trusted your brand? It's always a mix, but it's important to remember that good branding will help open doors that otherwise would have been closed to you.
If you approach your presentations as part of your brand (which they are) then any marketer will tell you how important it is to have a clear consistent message. Simply using a consistent theme for presentation material, business cards, and any and all academic communication is one way to develop your brand. That way, when someone watches your presentation it might remind them of the friendly email that you sent.
The contents of your presentations is certainly important, and I think the other answers speak to that a great deal, so I'm going to explicitly ignore the contents of your presentation beyond a reminder that if your presentation is good, it will help your brand, and if your presentation is bad, it will harm your brand.
I highly recommend discussing your brand with a marketer or designer and investing in yourself.


text:
How to properly cite a comment from reddit
I know this is somewhat strange, however I'm trying to properly cite a quotation from a comment on Reddit.
I'm quoting Edward Snowden from an AMA that he did about 9 months ago. The specific quote for those interested is “Arguing that you don’t care about the right to privacy because you have nothing to hide is no different than saying you don’t care about free speech because you have nothing to say.”
In the references list (APA format), how would I cite this?
This is a direct link to the comment that the quote was taken from: https://www.reddit.com/r/IAmA/comments/36ru89/just_days_left_to_kill_mass_surveillance_under/crglgh2
This is my best guess at how to cite this:
Reddit. (2015). Just days left to kill mass surveillance under Section 215 of the Patriot Act. We are Edward Snowden and the ACLU's Jameel Jafer. AUA. Retrieved February 20, 2016 from https://www.reddit.com/r/IAmA/comments/36ru89/just_days_left_to_kill_mass_surveillance_under/crglgh2

Proper citation fully depends on the desired/required publication style.

This should be APA format, sorry I left that out.

I believe that your best guess is pretty close to the right answer. According to the APA Style (6th ed.), you should list as much information as possible for non-periodical publications, which you have done well. I think that your resource falls under category "Nonperiodical Web Document or Report", as described on this page of the Purdue OWL's APA Formatting and Style Guide.
However, on the second thought, it seems that a more correct option to use would be APA's electronic sources guidelines for "Online Forum or Discussion Board Posting". Not only Reddit better fits this category, but it also allows you to specify the author of the quote you are citing. Therefore, the optimal citation in question, in my opinion, should be as follows (note that I took liberty to remove date of retrieval as the link you provide is a permalink and, thus, pretty stable):

Snowden, E. (2015). Just days left to kill mass surveillance under
  Section 215 of the Patriot Act. We are Edward Snowden and the ACLU's
  Jameel Jafer. AUA. Retrieved from
  https://www.reddit.com/r/IAmA/comments/36ru89/just_days_left_to_kill_mass_surveillance_under/crglgh2

+1 for explicitly mentioning the author in the first place. I would also suggest adding a link to an archive.org copy of the page in case this exact AMA will become unavailable in the future.

@svavil: Thanks. Good suggestion about archive.org, even though, as far as I know, APA is silent about possibility of using multiple URLs.

I really appreciate the help with this. I think because comments are able to be edited or deleted on Reddit, even months or years later (and happens somewhat regularly, that including the date of retrieval would make sense.

@UnSined: It's my pleasure. Glad I could help. I agree with your point on potentially temporary status of comments on Reddit.

Citing quotes is not always necessary, particularly when Snowden has said this many times in TV/Magazine interviews. As official as that Reddit AMA was, I would either just quote without referencing where he said it, or reference the quote in something that gets archived in a library like one of his Time Magazine interviews, or a BBC interview, etc.
This is all under the assumption that the quote itself is whats most important, not that it was said on Reddit.

I had a hard time finding this particular quote outside of the Reddit AMA, which is why I opted to use it. I would have preferred to reference it from a more reliable source.


text:
Hiring an academic researcher to implement an algorithm in a paper they wrote
I recently joined a technology startup company where a key business value-proposition depends on solving certain various problems that no current business competitor solves. There is one particular sub-problem we're looking to offer a commercial solution to - and it has been already solved by an academic team who published a paper describing an algorithmic solution about 15 years ago. To our knowledge, no commercial operation employs their approach. We would like to capitalize on this.
The team-members are still working at the original university and fully contactable.
The problem is the solution as described in the paper is beyond the current academic-ability of the startup's employees - and given time constraints I'm considering the possibility of contacting the team to ask them to implement it for us - as paid professionals, of course.
Is this appropriate? Is there a good way to frame this? Would paying them for their work introduce any kind of conflict-of-interest or other consequences?

Your proposal is a bit like saying that you want to hire somebody who designs electric guitars to play in your band. Many academic computer scientists aren't particularly good coders, so hiring one to code for you might not be a good move. I would suggest instead that you get the academics to explain the algorithm to your coders so that they can implement it themselves.

+1 for "Many academic computer scientists aren't particularly good coders." My employer has contacts with and sponsors research projects at many universities, and I've never seen a software implementation of something developed by a PhD or Postdoc which we didn't have to recode completely to make it into a useful product - and if the recoded version runs 100 or 1000 times faster than the original, that's about par for the course. In any case, you will end up responsible for the bug-fixes etc in your commercial product, so you need to know how it works!

@alephzero Yep, I think the paper in question had an implementation written in Matlab or something. I guess what I really want is to ask the researcher "plz email me the codez" - just in a polite and respectful way. It can be argued that any published academic research paper must be easily reproducible, and that includes bundling their source-code in their submission to the journal or conference.

If you don't fully understand the solution, how certain are you that it solves your problem? Maybe the proposed solution only works under very special cirucumstances that hardly occur in practice.

I see no problem with any of the other answers, but also, after thirty years in software engineering, I would think that if an algorithm can be described, it shouldn't be hard to find a programmer who can code it. In many shops, the people writing the code are implementing algorithms described by others. Sometimes these others don't know how to code. Sometimes the coders can't design algorithms. Most can do both.

To expand on @Akavall's answer - if you pay the academics to implement it, how are you ever going to maintain it? I suggest getting your developers up to speed math-wise so they can understand it, or hiring someone who understands it, can implement it, and can explain it to your developers. Otherwise you're building your business on quick-sand...

To add to what @alephzero has said... We have a couple of researchers who work with us as part of a University partnership. They're smart people but absolutely clueless in a business environment. Things that would take a professional developer a month to implement can take 9-12 times as long. Also, expect to get the "perfect" solution, not an acceptable compromise. None of that is inherently bad, but it can hugely impact product development, especially at a startup.

"Many academic computer scientists aren't particularly good coders". Whether that is true or not, you should judge the researcher on his individual skills - not on some shallow prejudgment.

I'd be curious to hear which algorithm it is.

It is definitely appropriate to ask.  University policies on outside work for employees vary.  But typically it is allowed.  There are at least three possible approaches to this.

You hire the academic directly, and it is a side job for them.
You provide the university with research funding, which is then used to pay to make the implementation.  This might have tax benefits, it will make the academic look good, and will allow the university to take a cut of the money.
You partner with the university to obtain funding from a third party (probably a government program).  Your company pays for the commercial part of the project and the third party provides pure research funds the academics want.  This makes everyone look good but can be slow.

The key thing here is that you need to convince the academics that there is a benefit for them to participating.  This is a matter of their personal preferences.

Excellent response with good view of the options. Note that, albeit the academic themselves may be reluctant to do this type of job, perhaps they have students completing which may like utilising their expertise. So, that's an option #4.

In the US, that 3rd option is (usually) an STTR and is designed explicitly for grants to transition academic resources to commercial technologies usable by government agencies through small businesses.

It may be necessary to go through the University, depending on the policy concerning intellectual property. Here in Australia, my university has priority on any IP created as part of or incidental to my research position. I'm guaranteed fair compensation for any commercialisation of the IP, but the uni is also guaranteed their cut, so this type of work would definitely have to be negotiated via the uni.

We do #3 in the UK. We got smart people doing research and coming up with very accurate solutions. Unfortunately, that's nothing like shipping a product where acceptable compromises are the norm. We're glad we did it, but it turned an estimated 3-month internal implementation into a 2-year project by the academics that had the be recoded from scratch at the end. We got something a lot better than if we hadn't had their help - so we're happy - but we're fortunate that we could sell on other features in the meantime.

This is definitely something you can ask the researchers, and something that's quite common in many fields. Paying them for their work can create some minor conflicts - there are often guidelines about how much outside work a faculty member can do, rules about hiring grad students, etc. There's also likely some IP concerns surrounding the work. But most universities have offices to set up these kinds of things, and a simple email to the team is probably a good way to get going. There are a couple ways this can happen (there are more, but these are the ones I'm most familiar with):

Consulting. You hire the researcher (or a student, etc.) at a negotiated rate as a consultant. Usually this means they can't access university resources while they do their work, but this is often the fastest and most direct way to get something done. The limits here are that it's hard to make a tenure case (for example) out of consulting work, and if the problem needs specialized equipment, it needs to be your specialized equipment (or you need to buy it for them). It's possible, as @AnonymousPhysicist notes, that equipment from the university may be available for a fee. In my experience however, once you start hiring both researchers and their "stuff", the university starts asking why this is a consulting gig.
Some sort of work-for-hire contract with the university. This will likely be slightly more expensive and complex, but may be necessary, and is the best way for the faculty member to get "credit" for their work within the university. This is often distinct from giving the researcher a "grant" - at my institution at least, the university is much pickier about IP, publication rights and overhead rates for grants than they are "Here's a problem, we need you to solve it."
As mentioned in a comment, there are both funding mechanisms and often resources within the university to facilitate tech-transfer, licensing and spinoffs. This may help if they already have an implementation, and you just need to license it.

The easiest framing is just "Hey Dr. So-and-so, I work for XYZ Incorporated. We're really interested in your work, and think it might have some commercial applications we'd like to talk to you about..."
Just be direct, open and honest. Many researchers like consulting - it's a good way to supplement their income, work on some small but fun projects, etc. Work-for-hire contracts, similarly, are a decent way to get unallocated funds into a lab, or keep a graduate student or lab tech employed.

"if the problem needs specialized equipment, it needs to be your specialized equipment (or you need to buy it for them)."  Not true, some university facilities are open to private sector users, for a fee.

@AnonymousPhysicist Fair. I'll put that in - with a caveat about my experience going down that route.

Previous answers were about how to structure the formal relationship. I'll focus on how to make it be productive, given the "academics can't code" concern from the comments on the question.
The academics in question clearly implemented enough of their method to produce the results shown in their publications. Hopefully, they even still have that code somewhere. It may not be a complete implementation of the theoretical material their papers describe, though - if the experiments they ran didn't need that, it's quite possibly absent or much more likely to be buggy.
So, here's some things you could consider asking for in this partnership:

The original code, appropriately licensed from whoever holds rights to it (maybe the individuals, maybe the university, maybe some other funding source)
Test data (ditto on licensing)
Their knowledge of omissions in the code or test data
Knowledge of limitations of generality, performance, applicability to your problem, etc
Ideas on how to make their method more applicable to your problem, and research effort to test those ideas
References to related work done by them or others that's applicable to your specific problem, or other problems you may have a business interest in
Full participation or technical assistance of various people involved in productizing the necessary code
Cooperation in seeking funding for the work from various sources - e.g. SBIR/STTR grants from government agencies

For all you know, some of them may actually be excellent developers, and happy to have funding to put their ideas into practice. Ask a lot of questions, keep an open mind about what each side can get from the relationship with the other.
The biggest take away from my answer is that the code in question may not be the most important thing in achieving your desired results, if it's even important at all.

article quality code is usually not production quality, which is what the comment addressed

@ThorbjørnRavnAndersen is spot on.  I say that as someone who writes scientist-code.  Even something as simple as testing the inputs is often neglected when you're in control of the only source of data.

license: Creative Commons - Attribution Share-Alike - https://creativecommons.org/licenses/by-sa/4.0/

authors: Bob Jarvis - Слава Україні


text:
What does assigning the copyright of a paper mean?
I have been reading that a publisher called WIT Press has the following copyright agreement:
http://www.icsis.org/WITcopyright.pdf
It has one part that says:

We will not withhold permission for any reasonable request from  you
  to publish parts of this paper in connection   with any other work by
  you, provided the  usual acknowledgements are given regarding
  copyright notice and reference to the original  publication.

What does it really mean? It means that if a paper submitted to that publisher gets accepted I cannot put it on my personal webpage or in the repository of the university that I am?

The title of this question doesn't quite tie up with the body of it - perhaps some clarification would be in order?

I believe this means you are OK to publish your paper on your site and submit to uni repository. Typically, respected publishers have policies that de facto allow a scholar to publish an "offprint" or a "preprint" copy of their paper on their webpage, along with citation to the published version. My understanding is, the preprint version can be identical in content to the published version, but be formatted as a paper for a class (font 12, double-spaced with 1'' margins on 8x11 pages), whereas an "offprint" of the published article is a 100% exact copy as it appears in journal.

Again, in this case the language seems fairly standard for decent publishers. You should be able to just assume 'fair use' permission for the type of dissemination you mention, and not have to specifically request it, either.

How did you end up understanding the exact opposite of what the text pretty clearly says?

I have read the agreement and do not see any direct contradiction between the text and my understanding, or the common sense approach I recommend...correct me if I am wrong? Perhaps we differ in our perception of the agreement itself: one might treat it as a set of hard rules; someone else as a set of prescriptive guidelines. I tend to lean toward the latter...

Publishers have to resort to relatively strict-sounding agreements as a way to rope in whatever control they ostensibly hope to exercise over content in the information age. Academics, either as a consequence of naivete or a slight nonconformist bend, plaster their preprints and offprints all over the Web these days. Both sides pretend things are OK: the former due to inability or lack of strong incentive to actually control the situation (any exposure = free marketing for the journal); the latter because why not ;)

By default, you hold the copyright for everything you write (note that some things such as contracts of employment may change this default).
When you "assign" the copyright, as often one must to an academic publisher, you give them control over your work. At that point you are correct that you would not be able to put it on your personal webpage without permission from the copyright holder - although in practice many publishers have policies that grant you permission to do this.
The part of the article that you quote appears to be promising that the publisher in question will grant you permission to use parts of your own work in other work, under certain conditions.

You should ask the publisher.  It is simply obvious they will give permission "under certain conditions."   The concern is to know what those conditions are.  I find the wording about "any reasonable request" vague and much less author-friendly that what I usually see.  But their actual intent might be just fine.  Ask specifically about your personal webpage or in the repository of the university.  Most publishers in my experience talk about those things in their copyright transfer form in the first place.
Do not approach this by trying to guess what is "reasonable."

This copyright statement does not say whether you can put it on the repository or your personal website. Unfortunately, it doesn't look like WIT Press actually have a clear policy on this. The "publish parts of this paper in connection with any other work by you" wording is usually used to refer to, as Simon says, reusing parts in later publications.
SHERPA/Romeo list WIT's journal policies as "unknown" (see eg the International Journal of Safety and Security Engineering entry, which suggests they do not have a repository (etc) policy at all. If they don't have one, you can't assume you're allowed to do it - they may let you if you ask, but you'd have to ask, and they can say no.
If you're required to deposit material in an institutional/funder repository, talk to your institution or funder before publishing in this journal. (WIT do have a very limited paid "open access" system, but this is unusually restrictive, and would not comply with many funder OA policies in any case)