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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writes: An 11-year-old research paper describing Treefinder, a computer program used by evolutionary biologists, has been retracted after the program's developer banned its use in European countries he deemed too friendly to refugees.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
Is it even possible to retroactively change the terms of a software license like that?
Or did the new license only apply to new versions of the software?
"First they came for the slanderers and i said nothing."
I spent 3 years in Germany while in the US air force. While I found the German people to be very friendly for the most part I did notice a decided antipathy towards foreign immigrants from Turkey. 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.
https://www.youtube.com/watch?...
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.
License change and re-release in February 2015:
Starting from 1st February 2015, I do no longer permit the usage of my TREEFINDER software in the USA. For all other countries, the old license agreement remains valid.
http://www.treefinder.de/
One of the main reasons there are issues with migrants in Europe right now is the very fact that Germany declared itself a free for all with no way for those migrants to make it to Germany without forcing the countries in the migrants paths to break their own laws.
I think the thing that is really going to bite Europe in the butt with this is the fact that if even 0.1% of those migrants are radicalized then Europe is going to end up with large numbers of terrorists in their midst. I would also bet its more then 0.1%
Corporations apparently can, and do it all the time.
Many of us disagree you should be able to change the terms of a license retroactively or at all.
But since corporations have apparently bought the right to do it, why not crazy idiots?
Lost at C:>. Found at C.
Some people recognize immigrant has become synonymous with "slave" or "underclass", depending on the culture.
When the US Republicans talk about needing to compete in the global economy and how the US is strangling business, they aren't talking about the EU powerhouses which have higher business and social taxes. They are talking about the industrializing asian nations with penny wages and how the US needs to compete with them (ostensibly via the immigrant workforce). Many western nations have a similar problem and solution, where cheap labor/immigrants are available. Morality aside, at least he's bringing up the topic.
If he's retroactively changed the license, it's not as if they have any choice in the matter.
You are not alone. This is not normal. None of this is normal.
Europe is facing that already. Look at what happened in Paris with Charlie Hebdo, then the wave of violence and terror related arrests throughout many countries in the region following those attacks. There's debate as to whether or not Germany is even obeying its laws, because a lot of these "refugees" don't really seem to meet the definition of the term. They're migrating for economic reasons, not necessarily because they fear for their lives. Germany is rejecting a significant number of them, but that just adds to the chaos.
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.
http://www.treefinder.de/
Original License
License change and re-release in February 2015:
Updated Oct 2105:
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.
Refugees should probably not just mean people who are migrating to a wealthier place to get on the dole.
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.
You clearly have never been to a Home Depot in the morning on a work day.
APK likes to ask for responses to the same things over and over. Maybe he just likes the responses?
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.
Yep, not just Germany. Check out the violent crime and rape stats in Sweden: http://www.gatestoneinstitute....
It's not so much that the statistics went up, it's that the courts are sympathizing with the rapists! Mind-boggling.
P.S. to mods: This is not a troll. This is data.
or you can pay a decent wage?
I don't think there is yet a clear legal precedent about what conditions in EULAs are and aren't legally binding. I want some German person to actually use this software, get sued and take this to Strasbourg, or maybe some higher court. I'm very confident that any sane court would rule that the researcher broke no law in using the software while German, and this is what we need to invalidate many other stupid conditions stipulated in software EULAs.
And the paper is theirs to pull.
Everybody wins.
You are welcome on my lawn.
So extremely tolerant that it is now a major rhetorical issue even though illegal immigration is 1/4 of what it was a decade ago and illegal Mexican immigration has fallen by 1/2.
It's been a problem for a long time, not just now. It was a big enough problem that Reagan gave mass amnesty in exchange for stronger borders and the understanding that mass amnesty would never need to be offered again.
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!
You are creating a false dichotomy and clearing forgetting about how this country came to be. The Irish came to this country in much the same fashion and numbers as Mexicans. They were fleeing starvation and lack of opportunity for a land that could provide them with opportunity as well as sustenance. It amazes me how similar the rhetoric is. The Chinese immigrants went through much the same which is why they ended up building large portions of our rail system that we use even today.
We closed our borders and created this problem because we no longer wanted open immigration in an attempt to limit our population growth. In addition to closing our borders we created rigid rules which say we can only allow so many people to immigrate from any single country. So we eliminated a majority of legal avenues for Mexicans to immigrate and then we're surprised when they walk on over because they want more opportunity than they can get in their home country.
That is also the problem with trying to punish them. If they are already here what are you accomplishing by spending billions of tax payer funds to relocate them back to Mexico or Honduras, or any number of other countries who's people are often confused with Mexicans? You have to change your immigration policy if you're going to even attempt to repair the problem. You have to let more Mexican immigrants in, you have to give the people here a chance to become citizens, then the pressure is released and populations will begin to stabilize. Once that is done then you can absolutely send them home but since those numbers won't be on the order of 10s of millions of people you can actually accomplish your goal.
America is obsessed with making sure criminals are punished hard instead of actually rehabilitated into a person that is actually useful to society instead of just being a drain that costs tax payers again more money than someone who makes minimum wage would make in a year.
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
Isn't that usually how religion passes from one generation to another?
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.
Most of these people are economic migrants, not refugees. In the case of Syrians now flooding into Europe, for example, most did not come directly from Syria — they came from migrant camps in Turkey. Turkey is a stable and safe country, but doesn't provide quite the level of social services and economic opportunities that a Western European country does. Of course, as has been pointed out in various places, the German government is worried about an aging population and needs young workers, so they opened the gates under the pretense of humanitarian reasons — preservation of culture, values, and social cohesion be damned.
"Politicians and diapers must be changed often, and for the same reason."
I'm sure that's true, due to your extensive knowledge. Also, most black people agree with you that black teens need to pull their pants up and stop blaming society for there problems, and most gays agree with you that homosexuals should have some legal protection but not be given full rights of marriage, which are historically understood to be between a man and a woman.
The liberals are making up these platforms all themselves! All people discriminated against, in any way, know that right wing Texans speak the truth.
Slashdot: providing anti-social weirdos a soapbox, since 1997.
Good thing you have no ancestors in you phylogenetic tree that were immigrants.
or you can pay a decent wage?
That's not very "business friendly."
Did OkCupid act like an asshole when they blocked Firefox to demonstrate their disdain for Mozilla's CEO?
Yeah, pretty much. They were both dicks. Restricting access to software to those whose political beliefs you share is going down a pretty dark path.
Open source doesn't mean free.
But Brawndo's got what plants crave. It's got electrolytes.
love is just extroverted narcissism
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.
Maybe that's just a San Antonio thing. In the rest of the country, Mexican Americans are trying every rhetorical and legal trick they can to make illegal immigrants welcomed. That includes:
*) Lobbying for "sanctuary city" status, where the local government is prohibited from working with state/feds unless the subject is suspected of non-immigration-related crimes.
*) Opposition to the phrase "illegal immigrants," because they say a person can't be illegal. Even though their very presence is a continued, illegal action, that there's pretty much nothing they can do short of returning across the border without it being illegal.
*) Using "immigrant" as much as possible to describe both legal and illegal immigrants. They want to blur that line as much as possible so they can attack politicians and other groups for being "anti-immigrant," when they only oppose illegal immigrants.
*) The usual cries about pulling apart families, etcetc.
*) Not bring up the issue of legal immigrants going through the legal process and waiting to become US citizens. They don't want to talk about that at all.
I disagree with the assertion that most of the support comes from white people. Just listen to Latino USA on NPR, watch Univision, or other Hispanic or Mexican American channels. It's stated by both sides without controversy that the reason Republicans have so little support with Hispanic/Mexican-American is their illegal immigration stance, and their attempts to court those ethnicities is a big reason why Republicans have blocked action on illegal immigration matters.
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
The fun bit is that there's no need for cheap foreigners to drive down wages in Germany. The unemployment benefits system is designed to take care of it.
If you have worked enough in the last 3 years, you can get up to 12 months of full unemployment benefits depending on your age (60% of your previous salary without kids, 67% with kids). If you refuse a "reasonable job offer", you don't get the benefits for up to 12 weeks. Reasonable is defined as "up to 3 hours daily commute" and paying 80% of your previous salary if it's in the first quarter, then it goes down to 70%, then 60%. Refuse several "reasonable job offers" and you lose the benefits. At the end of the benefits period, you get switched to subsistence allowance: maximum of 399 per month if I am not too mistaken.
I'm a non-German living in Germany for 9 years, crossing the border every day for better wages.
It's amazing how once you make something legal, it's no longer illegal. Those tricky Mexicans!!
It's the cultural differences that matter.
In the EU the cultures don't vary much, even when comparing most western to most eastern countries. Turks, Syrians, Kurds are very very different than, say, Romanians, Greeks or Bulgarians.
This matters a lot because while you change the country, changing yourself is hard and many of them bring that culture with them, finding it easier to compromise a little and continue as they did back home instead of adopting everything from their new country.
This is what angers people when it comes to immigrants. They don't see them as fellow citizens born in another country, but foreigners with the same rights and benefits, but with additional perks. Recognition from the state for their special status, help to integrate in various ways, belonging to a minority, political or social group. I don't know any social psychology but it's all there.
To get back to your issue, Mexico is USAs neighbor and both cultures interconnect a lot. There are very few cultural barriers and most of them are either understood by both sides or simply accepted as normal.
Personally, I was curious about moving to another country early in life, but it was just wanderlust. If you can't make a home where you are now, changing the geographical location won't help much. Of course, living in a country with any kind of war going is different matter.
Yes you do- or can. It's all about efficiency and productivity though. Paying someone who produces 1000 units an hour an extra 10 dollars per hour comes out to just 1 cent difference on the per unit costs.Of course taxes add to it and it wouldn't be that simple because there would be an additional employment tax as well as social security and so on on top of that 10 dollars but you can get the point easily.
It is a lot harder however when you are providing services of some sort or when the production is lower. At 100 units per hour, the cost difference would be roughly 10 cents per unit (not considering taxes and all). So if someone could pick your tomatoes at a rate of 100 packs an hour (lets say 2 tomatoes to a pack), paying them $20 an hour would have a cost associated with 20 cents on each pack of tomatoes purchased. Paying them a minimum wage of $7.25 per hour would be 13 some cents cheaper so it isn't a huge cost increase to pay them a little more.
Where it hurts is when you can only service or produce 10 units per hour. An extra $10 dollar per hour would be $1 per unit. A typical waitress at one of these full service chain restaurants can likely handle 4 to 6 tables an hour depending on the number of people at each table. If every table leave $2 for a tip, they are earning $8 to $12 more per hour than their base salary. But as restaurants usually have it, they are not packed enough at all times of the day to enable this type of turnover so there will be several hours which the waitress/waiter would only service 1 or 2 units per hour and you would need a tip increased quite a bit to make up the difference.
This has been a problem since before humans were humans, humans and most other primates are highly territorial, they naturally form tribes with a hierarchical social structure. It's possible our invention of civilization will eventually change that but it hasn't happened yet, however it has dramatically changed the size of our tribes from a few hundred to hundreds of millions and those who attempt to swap tribes are likely to survive the ordeal, the behaviour of our species is moving away from the standard primate model, it now behaves like a cross between human tribalism and a technologically advanced termite mound.
At the end of the day the fighting is always about resources but we justify and rationalise it with our natural xenophobia. This is the way "nature intended", it is in the wetware toolbox we were given at birth. Peaceful co-existence in a land of plenty is what we all want, ironically our xenophobic tendencies mean we are more than willing to wipe out other tribes to get it.
And did you exchange a walk on part in the war for a lead role in a cage? - Pink Floyd.
Yes you do- or can. It's all about efficiency and productivity though. Paying someone who produces 1000 units an hour an extra 10 dollars per hour comes out to just 1 cent difference on the per unit costs.Of course taxes add to it and it wouldn't be that simple because there would be an additional employment tax as well as social security and so on on top of that 10 dollars but you can get the point easily.
It is a lot harder however when you are providing services of some sort or when the production is lower. At 100 units per hour, the cost difference would be roughly 10 cents per unit (not considering taxes and all). So if someone could pick your tomatoes at a rate of 100 packs an hour (lets say 2 tomatoes to a pack), paying them $20 an hour would have a cost associated with 20 cents on each pack of tomatoes purchased. Paying them a minimum wage of $7.25 per hour would be 13 some cents cheaper so it isn't a huge cost increase to pay them a little more.
Where it hurts is when you can only service or produce 10 units per hour. An extra $10 dollar per hour would be $1 per unit. A typical waitress at one of these full service chain restaurants can likely handle 4 to 6 tables an hour depending on the number of people at each table. If every table leave $2 for a tip, they are earning $8 to $12 more per hour than their base salary. But as restaurants usually have it, they are not packed enough at all times of the day to enable this type of turnover so there will be several hours which the waitress/waiter would only service 1 or 2 units per hour and you would need a tip increased quite a bit to make up the difference.
For a single tomato, 20 cents a tomato vs. 8 cents doesn't seem like a lot but to someone like a Sam's Club who buys millions of tomatoes it's a huge difference. And you have to remember that picking the tomato is just one step in the process of getting it to the produce counter. If you paid everyone along with way $20 an hour, the cost of a single tomato would be much larger than it is today. The other thing about tomatoes (and produce in general) is that there's a huge amount of loss between the time they are picked and the time they are bought. I used to work in a produce department while in college. We'd sometimes throw away entire cases as soon as they came off the truck. For the remaining cases, a certain percentage wasn't fit to sell, so they would get tossed in the process of filling the display. Then a couple of times a day at least, the ones on display would be gone through and the ones started to look bad would get pulled.
It wouldn't surprise me at all that for every tomato sold, at least one is tossed and that money has to be recouped in the price of the tomatoes that actually get sold.
I'll give you a hint: science has nothing to do with politics, and restricting access to science based on lack of support for Nazi policies makes him a neo-Nazi fucktard. And you a neo-Nazi sympathizer.
It's a BMC journal, born in the Web age - it didn't exist in the 70s. But there may well be other software that's no longer available even in the lifetime of the journal just through link rot (which is why they encourage authors include a copy of the software and ideally the source as supplementary material).
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.
I agree. So everybody of European descent in North America... if you would kindly board the boats in an orderly line...
Unicode killed the ASCII-art *
In this particular case. It doesn't matter because tree finder is out of date and shit. But it should be noted that he did this work while doing a PhD (which he refused to finish). Also not solo. I am not sure he is the sole legal copyright holder.
br Yea i sort of am personally know the guy. Sort of. in a round about way. He has been a certified nut job for the ten years I was on his batshit insane mailing list.
If information wants to be free, why does my internet connection cost so much?