How can an average joe publish a scientific breakthrough?
Say I am an average joe and I made a breakthrough scientific discovery. How do I publish the work so that I am taken seriously, and ensure I get proper credit for it?
Second, use a site like Google Scholar to find similar work in the area, or go to the library and do the same. This gives average joe an idea of which journals are relevant to the field.
Third, pick an appropriate journal, go to its web site, and follow its instructions to the authors when writing the paper. It's a good idea, though not required, to read some of the recent publications in that journal to get a sense of its style.
Another concern here is that some papers require a publication fee, and others don't. Some of the ones which require a fee are also disreputable, and will publish essentially anything in order to get the fee. See http://www.biosciencewriters.com/Selecting-a-Target-Journal-... for more details about how to select a journal.
Fourth, send in the paper, or as that previous link suggests, send in the abstract and ask the editor if the journal is interested in a paper of that sort. The paper (or abstract) submission might be rejected by the editor or reviewers, in which case it's a matter of picking another journal or improving the paper based on the comments. Or it might be accepted with some changes needed, or it might be accepted outright. In which the paper is published.
There are many resources on "how to write a scientific paper", such as http://www.phys.unsw.edu.au/~jw/paper.html and even a book with the title "How to Write and Publish a Scientific Paper", which you can get from your library either directly or through InterLibrary Loan.
To increase the chances of recognition, average joe could also do a good job of making the paper readable and reproducible, with details that are cognizant of the history of the field and the reasons why the new discovery should be considered "breakthrough" rather than "novel." Said joe could also attend relevant meetings and talk with others who are interested in the topic, and even present that information.
There is certainly a required style - a paper needs an abstract, it needs a body, and it needs a references section. This is because it fits into a larger system of use. People read the abstract to get a sense of if the paper is relevant to their interests. If so, then they might spend the money to get the rest of the paper, or spend the time needed to fully understand it. People use the references to get a better sense of the background required to understand the paper. Only people who fiercely believe they are exceptional (ie, not an average joe) might think they don't need to include this information.
Another part of the orthodoxy is that it needs to be written in the language of the journal. Angewandte Chemie only accepts papers in German, so if you submit a paper in Malay then it's not going to be accepted no matter how good it is. It also needs to be relevant to the interests of the journal - even if it's in German, Angewandte Chemie won't publish a paper about low-energy neutrino detection.
The "instructions to the author" describe these sorts of points. If that is too much orthodoxy for your hypothetical average joe, then joe will have a hard time doing anything, which makes joe decidedly not average.
On the other hand, editors will usually bend over backwards to get a seriously ground-breaking piece published. They just have to be able to understand that it's 1) ground-breaking, 2) relevant, and 3) likely to be true. Joe's first step is to convince the editor of that. If no editor can be convinced, then it's unlikely that other, non-editors will be convinced.
You mentioned "mis-formatting" as a possible hang-up. To start, this means you haven't read many papers, because I find mis-formattings all the time.
Remember, editors in nearly all cases are working joes who volunteer their time. As the UNSW link points out "Even sending the [manuscript] back to you, unread, with a covering note saying "Read the Instructions to authors" takes time." - time that the editor would rather spend doing research. The problem is that editors get a lot of crank submissions and a lot of poorly done research. These are disproportionately poorly formatted. Editors are human, and if they see something that looks nothing like a scientific paper, it's much more likely to trigger the "crank" flag than to be seen as a breakthrough paper.
There's a balance at work here. A novelist who just wrote the next Great American Novel, but wrote it using a leaky ball-point pen on tissue paper, making the result difficult to decipher, will find it harder to publish. Xkcd #483 points out that the probability of new words created by the author is inversely proportionally to the probability of the book being good. And so on, and so on, and so on.
I think one of the points of confusion here is that "ground-breaking" is a very broad term, almost to the point of uselessness. Every single published scientific paper is supposed to break new ground. Some find a new sandbox, others a back yard, others an island, and a very few find a new continent. Without more information about your hypothetical case, it's impossible if this is something like "discovered antigravity" or "found a new intermediate of acetylene catalysis on the Platinum(100) surface", but odds are that it's not something like the first, so the requirement for convincing people that it's actually ground-breaking is higher.
For the record, scientists are average joes in just about every measure, except that they can put some extra letters before or after their name. Don't get hung up by thinking they are special in any way. Also, editors have no clue on the background of a new author, and I've seen many papers where the author has no institutional affiliation, so it's not like they can tell if someone is/isn't a scientist. "By your words are ye known", to misquote Matthew. To directly quote George Lundberg, editor of JAMA, after publishing a paper which included Emily Rosa, a 9 year old, as co-author: "Age doesn't matter. It's good science that matters, and this is good science".
The format is the message to some degree. Lazy editors help perpetuate this as you suggest.
If you are an editor and you receive a 100 page treatise which starts out with 50 pages on the numerology of the Great Seal of the US, 25 pages on the quality of the author's boogers, and 24 pages tracking the lineage of David Hasselhoff back to Adam, then are you really "lazy" if you missed the elegant 1 page proof of Fermat's Last Theorem on page 78?
Odds are most editors would reject that paper after reading the first page or two and leafing through the rest to double-check that it was more of the same dreck. Yes, I would place the fault more on the author than the editor for this case. Wouldn't you?
1. Even experienced academics / researchers have difficulty in getting published. Especially if their discovery contradicts any widely accepted theories.
2. How do you know that yours is a breakthrough discovery? Have you read up on all the publications in the relevant field(s)?
3. As a general rule, anything you write for publication needs to cite the relevant existing knowledge and then show how your contribution builds upon that, extends it, etc.
I assume that announcing your discovery is time-critical. Then I would suggest that you setup a website, that you own and control. Publish the material on that site. Doing so establishes that time of release and the facts. Then you could push your material to http://arxiv.org - that might require some seeking out of connections, but you have protected yourself by publishing on your website. Finally, submit to Hacker News, Reddit, etc so that the "news" gets picked up.
If your discovery is a breakthrough you will generate some interest. Of course, be prepared for the trolls and all those who are protecting the status-quo.
Other than that quibble, I agree with your points.
Even for the average joe, publishing their findings in such a journal will very likely trigger the "crank" flag and thus erode any credibility.
In it he forcefully makes the case that unless you really understand all the science at hand you can't possibly expect that you've actually invented anything worthwhile. He also lays out how you can make a credible case for your breakthrough -- it's hard, but if you do it clearly you'll be able to get someone's attention.
Example: "A scientific experiment performed by a high school student, later published in The Journal of Medical Toxicology, suggested that a domestic electric iron at its hottest setting (at least 400 °F (204 °C)) used for at least 5 minutes should destroy all anthrax spores in a common postal envelope". - From wikipedia. Source contained within the article.
Now did this student probably have help with a formal publication? Most likely. But the answer to your question is yes.
Except when you submit to the journal just put "No affiliation" in the institution field.
Academic institutions are, generally, keen to be seen to be collaborating with industry. So if said joe can work that angle there might even be collaborative research grants available to the cooperating institution.
As mentioned in my reply, it might be prudent to establish priority by self-publishing on average-joe.com and a reputable internet scientific archive like ArXiv. Doing so mitigates the risk of somebody else claiming the discovery as their own.