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Paper Retracted After Anti-Immigrant Scientist Bans Use of His Software (sciencemag.org)
sciencehabit writes: An 11-year-old research paper describing Treefinder, a computer program used by evolutionary biologists, has been retracted after the program's developer banned its use in European countries he deemed too friendly to refugees. In September, German scientist Gangolf Jobb announced on his website that researchers in eight European countries, including Germany and the United Kingdom, were no longer allowed to use Treefinder, which builds phylogenetic trees from sequence data. The move sparked outrage among some scientists, and now, BMC Evolutionary Biology has pulled the 2004 paper describing the software because the license change 'breaches the journal's editorial policy on software availability.'
Let's do it!
There is no question. The publisher is reacting to the change in license as well they should. Regardless of the motivation the license change violates their policy. What's the point of having a policy and then not following it?
The most egregious yet prevalent error in modern news reporting, is to conflate someone being against ILLEGAL immigration with someone being against LEGAL immigration.
If you can't understand why someone who does not want people who are by definition criminals entering the country in large numbers, then heaven help you - because reality certainly will not and history just laughs at you.
"There is more worth loving than we have strength to love." - Brian Jay Stanley
The researcher has decided to act like a childish asshole.
The publisher has said "unfortunately, due to your stupid manifesto we can no longer carry this paper because it violates our policy".
This guy is perfectly allowed to go all crazy and issue his manifesto of "you can't use my stuff". That doesn't mean that other entities are required to keep hosting his stuff.
The publisher is following a policy, and the people who wrote the paper agree.
So, really, the only one acting immature is the childish idiot who has decided he's taking his ball and going home, and making up random rules about who can use his software.
But he can own that decision and the consequences.
This isn't two wrongs making a right, this is an idiot living with the real world consequences of being an idiot.
Lost at C:>. Found at C.
Treefinder has been dead for about a decade. If youre still using im surprised you have enough data from it to continue a grant proposal, but i hope you'll consider other more functional applications like PHYLIP PAUP MEGA Phylo_win ARB or DAMBE
hybridization or recombination events got you down? concaterpillar to the rescue. http://rogerlab.biochemistryan...
distance matrix analyses on nucleotide or protein sequences? seriously, get a copy of ODIN. while i couldnt get funding for a beefier desktop, i DID get compute time on our university supercomputer and ODIN absolutely screams on linux.
Good people go to bed earlier.
It sort of surprised me but then I thought about it and it pretty much paralleled how many people in the US act towards Mexican immigrants.
Legal or illegal Mexican immigrants? I live in San Antonio and we are extremely tolerant toward legal Mexican immigrants. The Mexican Americans are not please with the illegal ones due to the jobs and resources they lose/share. For the most part, they really look down on them.
Besides organizations like LaRaza, most of the support for illegal Mexicans comes from white people - usually either due to reasons of "white guilt" or cheap labor.
Thing is, in the EU (as in, throughout the EU), the antipathy is a lot higher, and for good reason: As a general guideline, unemployment is usually a touch higher than in the US, and job growth is a touch lower (though in some countries this difference is rather dramatic), leading to a lot of antagonism.
Recently, it's grown primarily because of the actions and crimes committed by a number of these migrants, as well as the increased strain on the far-more-generous social welfare systems of these countries (which as a corollary, appears to be leading to even higher taxation).
If you think the Germans are vicious about it, you should take a gander at Nebelspalter (a Swiss parody magazine) and look up the opinions there on the subject...
Quo usque tandem abutere, Nimbus, patientia nostra?
The only interesting question here is whether this would be a controversy if it were happening in reverse - if the author was denying it to countries who are not taking in refugees.
I've seen plenty of them working. They harvest crops, work construction, pave roads or anything where they need cheap labor. If it weren't for the flood of people from South of the border I don't know how all this stuff would get done. We'd probably have to make all the people on welfare go back to work.
I agree with most of that, but I think you missed the most important point: why is key academic software not open source? I'm all for this guy's right to publish software under any license he chooses, but why would you embrace such software in the academic community? IMO, that's the lesson here.
Socialism: a lie told by totalitarians and believed by fools.
You clearly have never been to a Home Depot in the morning on a work day.
This is why I will never say anything bad about Mexican immigrants. You see dozens of them out at Home Depot waiting patiently for hard work. I have NEVER seen a unemployed white guy out there. I only ever see white people standing on street corners with cardboard signs, begging for handouts. I welcome immigrants (documented or otherwise) willing to come to our country and work hard to get ahead. Good for them. The only welfare leeches I see are the native citizens with a sense of entitlement that aren't willing to try to do some real work when they are unemployed.
HA! I just wasted some of your bandwidth with a frivolous sig!
why is key academic software not open source?
Because people do the minimum required to get publications (and/or money), and cleaning up source code (so it can be exposed to the world) is a lot of work. This is especially the case if the code depends on other libraries with various different software licenses.
One of the ways to help fix this problem is to place restrictions on publication, so that open source licences are required for software. F1000 Research has just changed their policy to do this:
http://blog.f1000research.com/...
We recently strengthened our stance on software availability to better align with our Open Science principles. Now, the source code underlying any newly presented software must be made publicly available and assigned an open license. We strongly encourage the use of an OSS approved licence, but will accept other open licenses including Creative Commons. Software papers describing non-open software, code and/or web tools will be rejected.
The current situation demonstrates that forcing these licenses is required in order to get people to use them. BMC Evolutionary Biology already had a recommendation for open source licenses in its policy:
BMC Evolutionary Biology recommends , but does not require, that the source code of the software should be made available under a suitable open-source license that will entitle other researchers to further develop and extend the software if they wish to do so. Typically, an archive of the source code of the current version of the software should be included with the submitted manuscript as a supplementary file. Since it is likely that the software will continue to be developed following publication, the manuscript should also include a link to the home page for the software project. For open source projects, we recommend that authors host their project with a recognized open-source repository such as bioinformatics.org or sourceforge.net
Ask me about repetitive DNA
I've heard the exact same things said about Mexican immigrants in the US, yet I had no specific problems with my neighbours, my classmates when I was in school, or classmates of my kids. I've also heard the same thing said about Panamanians when I was in Costa Rica for a while. And for people from Botswana when I was in South Africa.
All too often people are vague when referencing problems like this because they don't have more specific things to say. Or they do have specifics, but aren't comfortable with saying what the actual problem is because some part of them doesn't think it is wrong to be upset over that. Just saying things of the lines of, "spend some time with people X and you would know why they are a problem," backfires when some people have spent time and still don't have a problem.
So. Who decides who enters the country? The citizens or everyone else? And what do you do with immigrants that do not want to conform to the norms of the parent country?
It's not simply a matter of calling someone a neo-na%i f**ta7d
If you're scared of your govt then you need to further restrict its powers
Vote 3rd Party in 2016 and beyond
There's no point in having an editorial policy if you don't enforce it. The policy says the journal only allows papers on freely available software; the author submitted the article under those conditions then reneged, so he loses.
Post may contain irony: discontinue use if experiencing mood swings, nausea or elevated blood pressure.
There was this old guy who was a friend of my wife's family who was smart, and funny, and an all around reasonable guy -- unless the topic of hispanics came up. And then it was like he was a totally different person. He became a ranter, and everyone around him would try to change the subject.
It wouldn't be an exaggeration to say that he hated Hispanics. As far as he was concerned if you were born hispanic that automatically made you useless, human trash. For the life of me I couldn't figure out where he got that hatred. As it turns out I grew up in the same neighborhood he did, albeit forty years later, and only when I was a kid were there many hispanics moving in. He'd moved up in the world after WW2; he left the neighborhood and lived in a series of lily-white suburbs. So as far as I could tell he'd never even *known* any hispanics personally.
And in the end I came to the conclusion that was the whole point. He didn't hate backs, or Poles, or Jews, or Catholics or Italians -- because he grew up in a neighborhood with all of those kinds of people, or served with them during the war. His opinions on hispanics was formed in a kind of vacuum. After that forty years of confirmation bias, unchecked by any actual firsthand experience turned what had been commonplace casual bigotry into full-blown batshit craziness.
Post may contain irony: discontinue use if experiencing mood swings, nausea or elevated blood pressure.