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It's too bad the article didn't touch on the adverse effect science journalists are having on science journalism. Every day we see another "breakthrough" that isn't a breakthrough, a correlation reported as a cause-effect relationship, or a premature conclusion based on one unreplicated study.
Well said - so much of science journalism and even academic publications are attempts at career-advancement more than scientific advancement.
In many countries, the amount of government money spent on scientific research is rather low. Therefore a lot of researchers have to attract interest from companies willing to fund them, otherwise they can't afford to do any research at all. Unfortunately, even if the researcher is a good scientist and the data is valid, they won't be able to continue in their field unless they dress it up as the latest great breakthrough and hint that it will enable lots of profitable new technology.
I would say it's the "everyday" part that is the main cause of that problem - if it weren't for the 24 hour news cycle model, journalists wouldn't be trying to grab attention with hyperbole as much.

This is one of the reasons why I prefer magazines like Scientific American and New Scientist - because they come out once per month/week this is less of an issue, and the main articles are not so much about breaking news.

I wonder what their definition of "troll" is. It appears they're conflating matter-of-fact criticism with true blue trolling. Perhaps by their definition, I too am a troll and I've just helped cement your preexisting biases!
From the quotes in the article it looks like they're focussing on "uncivil online comments", "rudeness", "name-calling" and "pushing people’s emotional buttons, through derogatory comments". That gives a reasonable picture of their definition of troll, doesn't it? And I don't think it's an unreasonable one. I don't think there's much danger of conflating the above with civil, rational debate. Not sure what you're getting at.
They also say that "trolls take pleasure in bashing a story from every possible angle" and indicate that trolling involves leaving "negative comments", both of which could include pointing out an article's flaws, for example. Only later do they move on to these other definitions you mentioned.

Their definition of trolling appears to be a moving target throughout the article and this is why I feel they're conflating actual trolling with benign criticism.

In my experience, many people perceive all criticism to be rude and harsh. My definition of rude might be different to yours and what I consider to be straightforward criticism, someone else might consider to be a harsh rebuke!

As I interpreted the article, it boils down to having emotional buttons pushed and that blocking reasonable discourse - the intent is less important.

I don't think my German friends are trolling me when they freak out at the word "nuclear" before I can even begin to describe the potential of Thorium, but it's still a problem.

That's an even looser definition of trolling though! A comment that might push my emotional buttons might wash over someone else, and vice versa. Many things, including cultural and subcultural norms, will dictate what's emotionally charged.

Why do your German friends freak out at the word "nuclear"?

We've interpreted the article differently. I think it's mainly talking about negative commenter vs. commenter interactions, not commenter vs. article criticism.
It would be interesting to follow these people and their beliefs over time. I know that in the face of hostility, my first instinct is to defend my point of view. But later, after I've cooled down, I am able to consider both sides of the argument more rationally. It's at this time--later--that my beliefs will evolve.
Calling someone Troll on a science related subjects is tricky business. Science is often based on some form of consensus that is evolving over time. On many subjects, especial in social science, it is possible to show studies coming to opposing results. Critic boils ultimately down to opinions on if the sample size, method, research questions were the right choices.

I have my doubts that today Galileo Galilei wouldn't have been classified as a troll as well as those back a while ago who made the wild accusation that smoking causes cancer.

I used to do a lot of science-blogging (not in English) and in our circles, a troll wasn't something you'd get from 4chan who'd try to post offending pictures etc., but a "lone crusader on a mission" -

someone with apparently unlimited time, someone with his or her own absolutely crazy pet-theory [1], someone who would come to personally attack the author on some past issue on every single post. These people ruin the entire blog, you have to be fast to ban them (very useful with dynamic IPs..) and constantly monitor the comments. I've personally been attacked in "open letters" to government officials [2], calling me a "dangerous lying scientist" because I had the audacity to shred apart a terrible paper on the "apparent dangers" of WLANs.

I wouldn't see these people anywhere near Galilei.

[1] Examples: evolution is a lie, or global warming is a hoax, or the theory of general relativity is wrong, or the blogger is a fraud

[2] - that no-one reads -

The most useful take-away from the article:

"In other words, it appeared that pushing people’s emotional buttons, through derogatory comments, made them double down on their preexisting beliefs."

Sounds like politics, doesn't it?

It doesn't just sounds like politics, it is politics. If something is about more than just the truth and the 'answer' has consequences for you or your tribal affiliates you are certainly going to fight against any conclusion that seems to hurt you. Derogatory comments just raise the stakes for you.

The great thing about science is sooner or later the truth just bashes down all resistance and makes holding contrary opinion impossible.

Although science is that which explains and predicts, there is a wide range of impact in the jump from journal to journalism.

A paradigm shift in the wake of a minor but widely experienceable portion of a representative sample is simply more prone to recent advances in the speed and dissemination of journalism. The all too observable phenomena of seeing becoming believing.

Contrast this with any meta commentary upon a journal by the same body of journalism. Indeed, it is much more difficult to see the wider reading audience take an interest if said audience is less exposed to something happening in their own back yards. Far more likely than paradigm shift is the placement of a collective reading audience's heads in the sand.

It's funny that a study from Wisconsin tries to speak about this as it's similar if not exactly the same as this case:

http://www.law.cornell.edu/supct/html/98-1189.ZS.html

Without re-reading the case(from memory) the idea is that students didn't want to pay fees that ALL student groups would be able to make use of. ie. Students of Color paying for NeoNazi groups, etc..

The court ruled that the idea of higher education is bolstered by more extreme specificity in as many areas as possible.

Drawing a parallel to this case, I for one, could argue that having strong counterpoints helps me choose faster what side of a debate I am on. Thus, the polarization is actually a quickened education of the subject matter resulting in decision.

...and hacker news.