OpenAccess meets Donald E. Knuth

The debate around Open Access is surprisingly ignoring one important milestone: the TeX software for generating high-quality papers. Let us first take a look into the old publications by Donald E. Knuth from the 1970s in which he descibed the general idea. The early books about TeX are fresh even today, because they start not with computerprogramming itself, but a history lesson about linotype printers. From that base, Donald Knuth develops a text-language not for describing the final Postscript page, but for generating such a page out of a markup language. Everybody who is familiar with the UNIX operating system knows, that TeX is equal to troff, but with more features. Surprisingly outside of the hacker community, most scientists are not aware of TeX. :And if the know the system, because the standardtemplates of IEEE and Elsevier are based on TeX they thing the software is not very important or is outdated today.

Is TeX already relevant for publishing a paper? Yes, instead of many attempts to make TeX obsolete, the software is more important than before. Not in his original iteration, as the TeX system plus a DVI previewer, but in a improved version, called Xelatex together with the PDF format and modern Truetype fonts.

The question is, why is the TeX community obsessed by typesetting itself? Is it really important in which font a paper was written or if the linebreaking is correct? The reason why such details are discussed has to do with the aspect, that the people have time to think about it. Usually the paper itself is written in a very short time. The author enters the text, presses the run button, and the perfect formatted pdf paper is there. The pipeline is more efficient compared to MS-Word or Framemaker from Adobe. And that means, the author who has typed in the text has produced his text in half of the time, and has enough time for discussion details, for example, which font is really good. Instead, users of MS-Word have no such freetime, because they are involved in creating the manuscript itself. They are happy, if all the figures are visible and if the pdf paper is generated without crashing the computer.

Why not more people are familiar with TeX is simple: the people involved in higher educatation and the university system have simply not a background in computerscience. They see themself as historians, physicians and something between them, but not as a computer scientists or as a hacker. That results into ignorance in relation to TeX. For example, let us take a look in the last paper of Richard Price, The pdf file was created with the Acrobat Distiller in the Windows operating system and the software for entering the text is “Arbortext Advanced”. That means, Price or better his publisher at PLOS One is not familiar with TeX. Instead a proprietary MS-Word like program was used, which is compared to TeX very time-consuming.

But why is TeX not used heavily by Academic publishers? The answer has to do with copyright law. TeX and UNIX are both results of the hacker community. Their philosophy is OpenSource and free flow of information. That is not compatible with academics itself. Either physics based science nor academics are sharing these goals. Instead, the hacker community is isolated. Using a propriatary MS-Windows operating system with a 1000 US$ program for entering the text works more in a way like traditional academics. That means, the aim is not be open, but restrict the circulation of papers, create paywalls and increase the costs for reproducing the work.

The reason why TeX is not used heavily by publishers is because the software is too advanced. Their main features are: no costs and fast formatting of a paper. This is from the point of view of mainstream academics a problem. If somebody is trying to protect information, block knowledge and holding normal people out of the process TeX is something which has to be overcome. Not using TeX is the shared identity of todays publishers because it helps them to distribute copyright-protected journals.


daily OpenAccess answers

Talking about the passing percentage,

An interesting question was asked recently in the above URL. It was interesting because the normal way of talking about the situation is on a personal level. For example, a single student asks why he has failed the test and what his error was in a certain question. The OP instead asks about the percentage of all students who has failed the test. And yes, there is an answer, it has to do with costs in academics. Attending a university costs around 30000 US$ per year. The price is paid either by the student itself or by taxpayer money. Reducing the number of student who are studying on the university is an answer to reducing the costs. If a course let all students pass, not the quality of the course will decrease, but the amount of money the university gets from a higher instance.

Reducing the passing rate is possible only with new inventions in the higher education sector, for example with blended learning, Academic social networks and udacity like companies. All these new inventions are working with a different founding than traditional university sector.

Is useful?,

The same URL has another interesting question which i want to answer. In my opinion, is useful. The OP is right, if he questions, if the platform is helpful for networking with academics. Indeed, I see his critics similar. But it is also possible to use the platform alone, as some kind of backup in the cloud. After my initial signup for an account, I have learned a lot from it, only because I wrote some papers, uploaded them online and tried to improve my style. At least in my opinion, my todays papers are better than my papers 2 years ago. And it is very easy to upload many of “just-for-fun” to the website, because it costs nothing.

It’s right, that the website could be way more better, for example I miss feedback for my papers. But, this kind of feedback can the serious user get elsewhere, for example from Wikipedia. So I see as piece together with Google Scholar, Open Science and youtube lectures for free.

Another interesting question

This time the OP asks for a high-quality alternative to Arxiv. He is not alone with his mistrust against The question is, why do are researcher are fans of Arxiv but not of From a formal point of view, both websites are working equal. But there is something different. Arxiv is located inside the university system while is a for-profit company. is a kind of the cyberspace which is breathing the same air like John Perry Barlow and Richard Stallman, while Arxiv is real science which is located outside the internet. is not open to everyone and it is not devoted to Unix, but it is some kind of mirror for the serious scientists.

daily OpenAccess answers

Journal is blacklisted

At first, blacklisting in the context of academic publishing means, that the journal is on the Beall’s list of predatory journals. Somewhere in the internet is also a whitelist, which consists of all serious journals which are published by IEEE and Elsevier. If i understand the OP right, he has published a paper accidentally in such a predatory journal. Perhaps he doesn’t know the facts before submitting the paper, or because the journal was later put on the blacklist.

Usually, the author must not sending a request to the major indexing database like Google Scholar or Scopus because they are removing blacklisted journals from it’s own. It is simply not possible, that a predatory journal is searchable through Google Scholar. The second question (how will this affect the future academic career?) is a bit complicated to answer. The reason why dedicated blacklists are created is to warn scientists not to publish there. It is some kind of self-protection for the serious academics. If somebody has accidentally published there it is no problem.

Perhaps it is necessary to explain, why openaccess predatory journals like Peerj are wrong. The main idea is, that if all academics would publish there than the traditional learned societies like ACM and IEEE have no longer members who are paying the subscription fee. The university library can think perhaps, that it is not necessary to pay the subscription fee for the paywall, because the so called predatory journals are making a good job for low costs. That impression has to be prevented.

Avoid publishing costs

No, it’s not possible to avoid the publication costs. They are a fundamental criteria to separate between real science and fake science. Lowering the costs is equal to predatory publishing, which is a bad behaviour of greedy for-profit “academic social networks”. But let us investigate in detail how publishing works. On the one hand, we have well respected learned societies like IEEE which has a revenue of 480 million US$ in 2016, [] IEEE is called a non-profit organization because it is devoted to science and the money is not important. On the other hand we have predatory journals which have very little revenue per year in the area of 10k US$. This is called a greedy for-profit journal, because money is important.

daily OpenAccess answers

Cite papers behind a paywall

In contrast to the other answer i would recommend to cite never, especially in the case of doubt. The reason is, that a scientific paper is not written for the reader who is interested in additional links to other texts. Instead a manuscript is written by the author for the author. And if he feels comfortable without any citation than he is right.

I submitted a paper to a journal …

… that is the standard sentence which can read very often at Academia Stackexchange. Also in OP it can be read as the first introduction sentence. Why is using the OP such a sentence? Because he want to express of how publishing works. He makes clear, that he is an insider who knows of how the game looks like, and his question is about how to act in such an environment.

The next paragraph of the OP give some details about the peer-review process. The journal editor criticise the paper and finally rejects it. And in the end, the OP asks if he should add a note to improve the communication with the journal. The idea is perhaps that both side are agreeing to the paper. The answer which is posted so far to the topic is not very surprising. It explains what resubmitting means.

So far so good. What can we learn from the OP? At first, we can learn that all contributers have done their homework. They are playing a roleplay called “academic publishing in the 1970s” very good. The author submits a manuscript which was written on a typewriter to a journal. And he asks if he should add a additional note. And the journal is communicating with the author. All stakeholders are interested in scientific progress and and the end a compromise is found. The bad news is, that this roleplay has nothing to do with reality. The better alternative is, if the authors are learning to think as a publisher and never send a manuscript to anybody, instead an author publishes his manuscript in his journal and the only debate he must resolve is about himself.

Or to be more explicit: if an questions starts with the introduction, that an author has send his manuscript to a journal, than something is wrong. It makes no sense, to read the text until the end, because the assumption is wrong. The 1970s are over, today something better then paper-based journals were invented. But that is not a critique on the Stackexchange website. It is funny to read how to play the roleplay right. It seems very realistic.

Thinking as a journal

Here is again a typical Academia Stackexchange question which is written from the author perspective. In the OP a situation is described, in which somebody reviewed a paper for a journal and is now in a communication process with the journal. Why is this situation explained from this perspective? Because it makes it easier to explain the rules from the publisher side. Let’s take a look into the top-answer to this question, which gets currently 10 points:

“The fact that you keep getting requests shows your expertise is in demand.”

The answer is formulated in a roleplay. Somebody with a long experience in publishing explains to an author or reviewer what he has done right or wrong and give advice of how to communicate better with the journal. These social rules make sense, if such a relationship exists. But there is also a different perspective. What if the question is what a publisher should do?

I found a URL here: Here the question starts with a different perspective. This time, the OP wants to know how to start an openaccess journal. And the answer are also very interesting to read. If the OP really wants to start a journal makes no matter. It is more important that the advices are open, in a sense, that they explain of how publishing in general is working. In point #3 of the answer is explained how to select potential peer-reviewer for the new journal. The best is to search for people how have published a lot of paper in the relevant subject and request them for doing review. Potential authors have a good first impression.

Again, it makes no matter if the question is fictional or not. The difference is, that one explanation about the publishing workflow is hiding most while the other – publisher centered perspective – give details about the inner workings.

I don’t think it is general problem of the Academia stackexchange forum, because with a bit search also a thread can be found which explains how to start a new journal: Inside the thread some links a given to detailed information. So what we have learned today, is that questions about starting and running a journal are more interesting, than questions about how to behave right as an author or reviewer.

Additional i want to add a link to a OJS hosting provider: There everybody can setup his own OJS instance like a wordpress blog. Not for free, but for 900 US$ per year for institutions. To be fair it is important to know, that discount-ojs hoster are also available which costs only 60 US$ per year. Perhaps this is done on a vserver without any support. But some universities are not well equipment with money so it can be an alternative.

daily OpenAccess answers

Finding a certain paper

The thesis has an entry in worldcat:

It was published on microfilm. Also there is an entry on Researchgate

which have a button “request full-text”.

The good news is, that microfilm is one of the most reliable storage medium ever invented. If something is stored there, then it can be read for the next 400 years. Also the reading machine will be available for ever. The only problem is, that microfilm is located somewhere and it is costly to scan it.

Should i review for a predatory publisher?

The question is a bit older from the year 2015, but it is still interesting. I would answer with no. Because every peer-review request which was send from a journal is the wrong direction. It makes no matter, if the journal is predatory or not. Normally the journal doesn’t know what somebody wants to read next. The better way is to use fulltext search engine for selecting an interesting preprint and writing for that paper a peer-review. And the peer-reviewer should search for a topic on which he is right now interested, so the review can be done on a content level. The danger is lower, that formal things like the author name or the used wordprocessing tool get too much intention.

Journal submission status

At first, it means that you’re sitting on the wrong side of a table. Submitting a paper to a journal is always a bad idea, real publishers receive manuscripts in their inbox and not sending them away. The sense of the different status flags what a author can depends from the customization of OJS. OpenJournal-System is the major software for building Openaccess journals and has a template system in which the workflow is defined.

Here is a good video which shows the backend from the perspective of a journal editor. He sees the incoming submissions and runs a plagiarism plugin.

Journal workflow is agile

The answer which has 112 upvotes until now and is selected as the best explains with a nice picture a waterfall model. Waterfall means a topdown process. Normally the term is used in computer programming but it can be adapted to academic publishing. The process is started by the author who submits a paper, then a cascade of subactions are executed like the assigning of the paper to peer-reviewer. The problem with this journal workflow and also with the waterfall model in programming is, that it doesn’t work. It is an antipattern of how not to program and not to manage a journal. The better, more efficient model is bottom up driven which is called in software engineering “agile development”. Agile means, to run the process from the other side. Not the author is initiating the workflow but it is the reader. who creates a bugreport, and the other actors in the system reacts to it.

This means in reality, that an incoming manuscript is never assigned to a referee, instead they retrieve the work for their own. At the top of the pyramid is now the reader and his advocate is the publisher. The other actors like peer-reviewer, author and searchengines are subordinated.

For understanding the shift better, lets take again a short look into agile programming. In the xp-programming world the delivered software is the center of focus. That means, it is the sourcecode which the customer runs on their pc. The equivalent in academic pupblishing is the delivered paper, or more abstract the journal which can be read. That is the subject around the stakeholders are sitting. Bottom up publishing means, that the product which is under evulation is a website on which the reader has access to a paper. This can be the homepage of a journal or the homepage to a searchengine. On this place, reader and authors are meating each other. As a result some actions are started.

In a blogpost from 2012 the term “agile academic publishing” was used

daily OpenAccess answers

rejecting peer-review request

Today i found an interesting question on Academia.stackexchange. In general the OP wants to know what he should do, if he gets a peer-review request. Reading the given answers to that posts are interesting, i found one answer which is on content-base similar to what i would personally answer. But the problem is, that the Academia.stackexchange community sees it different and gave it a -3 vote. As a result the answer is greyed out and in terms of the forum the answer is wrong or invalid.

So what is so special about it? In short, the user who gets the -3 vote says, that he always rejects a peer-review request because it is a waste of time. And only if the paper is necessary for the own research right now, an exception is made and the user will review the paper. That answer goes into a direction of alchemy, where the peer-review process is realized differently. The editors are searching for their own the archive, and only if they find a paper good enough they will review it. The interesting aspect is, that i mentioned before, the Academia stackexchange community has a different opinion. The comments are giving negative feedback to the answer.

Perhaps the current, -3 votes for the answer are not the end. It is possible that this answer get -5 or more downvotes. The reason why it is not clear, but it is normal, because the answer is cheeky. It explains of how the peer-review process works.

Let us make a short recapitulation. I get myself in the past two massive downvotes in the Academia stackexchange forum. And today i found an answer which gets also downvotes but this time i didn’t write it. So perhaps the voting system in the Academia.stackexchange forum is wrong? It would be interesting to read all the negative rated answers from the side and analysing them on a content-base. Normally the voting system in the Stackexchange network has the task to bring up the best answers. That is the principle of how Stackoverflow works. If a normal people is reading the answer for a programming task, in most cases the best rated answer is indeed the best answer. I would say, that in 90% of all cases this is true for Stackoverflow. But here in the Academia stackexchange forum my apprehension goes in the opposite direction. For now, the number of examples is not high enough, but in future posting i will read the downvoted answers with more care.

getting most of Academia.stackexchange

This time i do not want answering a specific question in the forum but give a tutorial about finding the wrong answers. But before i go into the details, some remarks about the website in general. The Stackexchange notwork is a moderated forum. That means, that there are dedicated admins who can delete users and delete answers. This helps to reduce the amount of spam. Also the forum consists of a downvote upvote system, which is some kind of userfeedback which measures the quality of postings.

The question is, if the quality control is biased or not. To answering the question it is not necessary to interact with the website for testing out of how the admins will react, but instead it is possible to retrieve information which are always there. Thanks to the sophisticated search box, it is possible to retrieve in detail some information. The help explains us, that entering:


into the searchbox will result in a list which consists only of bad rated questions and answers. Currently there are 281 postings in the system. Reading them carefully give a hint of how the forum works and which answers will get downvoted. Interestingly, the downvoted posts are not equal to spam-behavior. They are normal contributions in the discussion process, but they are only be not recommended as much. The reason for downvotes are different. On OP wants to start a new science journal and gets only for this idea -5 downvotes. In the next case an answer gets downvotes because he argues against

Bug: no bias detected

If have searched into the archive of academia stackexchange, especially for answers with low and ultralow scoring. The idea was to recognize a pattern in which the posts are getting the score. But i didn’t found such a pattern. Some of the downvoted answers are really bad postings, while others not. So i think there is some kind of bias, but it is not obvious. My opinion is, that the forum is oriented in general on old-school publishing but also has some postings which are dedicated on and Researchgate ideology. The overall picture is not clear, perhaps because there are so many users with different opinions about subjects.

One thing is remarkable. The number of postings with less then -1 score is around 2000 in total, while the number of postings above +1 is around 64k. So the users are pressing mostly the upvote button. The best rated answer so far is “Why would an academic write a textbook for free?”,|1.1854#92903

daily OpenAccess answers

Let the students grade themself

The technique you asked for is called peer-review. Instead of a central authority, the students are evaluating themself. Normally this concept is not very popular among students. So I have to advices to make the process more funny. At first, let the students write a homework about a conspiracy topic. Normally, this will motivate them to invest more effort. And second, the pairing of the peer-reviewers is important. Normally the process is randomly, that student 1 reviews the work of student 10, and student 10 this one of #4 and so forth. The better approach is to scan all 30 papers into a database. Every student can the papers of every other in fulltext and must select one of them for a peer-review. The decision which one is up to the student.. So the student is choosing the paper which he likes most. The result is, that the peer-reviews become better, because the attendees are interested in the topic itself.

Paper retraction

Not only this specific paper is not very innovative, but most of mathematics which is published as Arxiv too. The problem with most of these publications is, that the authors are teaching a mathematics from the 19. century before the first computer was invented. Modern mathematics would use in every case matlab, python or something similar. This would result not in formulas but in sourcecode. This aspect is missing in the above cited paper of Yaroslav D. Sergeyev (which was retracted by the journal).

What the mathematicians at the university are doing is building up an artificial discussion room which is defined by the absence of calculators, computers and Mathematica-software. People who are publishing old-school mathematics which consists lots of formal definitions get upvotes from the community. The real enemy inside academic mathematics is the attitude of neoluddism.