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Taxpayers and scientists have a deal: we provide some support for your education and research, and in return you show us how to do stuff. If you don't like tha

Taxpayers and scientists have a deal: we provide some support for your education and research, and in return you show us how to do stuff. If you don't like that deal, governments have an even better one: we give you patent rights on what you invent -- as long as you show us how it is done. These deals aren't altruism on the part of the public. Nobody thinks science is a charity. It's vital to the interests of the particular nations and the species as a whole. In my opinion, no institution of higher learning that is supported by taxpayers should be giving out credentials to people who are so insecure and unprofessional as to not be able or willing to completely describe how they reached whatever conclusions they have. And that's not even getting into the issue of taking research and making political arguments out of it. That raises the bar even higher. It's a scandal. And the only reason it's coming out is because some people -- for whatever reason -- have a bug in their shorts about climate science. It's time to set some ethical standards for all scientific research. Open data, open programming on standardized platforms, and elimination of scientist-as-activist. There's just too much dirt and conflict of interest in certain areas of science. Not all, by any means. But enough to leave a bad taste in the average citizen's mouth. I love science. We deserve better than this. Something needs fixing.

lutorm 16y ago
You do realize that the way the incentives are laid out, it's exactly the people who do what you ask who will not get permanent jobs, so you'll still be left with those who don't. You can't accomplish what you want by bitching. As someone said in the discussion about Google hiring yesterday, "incentives matter". I agree with you that more emphasis needs to be put on careful work instead of cranking out flashy publications, but until people are rewarded for that, things are not going to change much.
nickpinkston 16y ago
Very well said - I find the current state of publishing in academia appalling. Don't forget that most research is behind a pay wall just for the damn PDF! I think you nailed it with "insecure". The little PhDs need to know their work isn't designed to just get them tenure...
- RBerenguel 16y ago
  Like we choose to have our PDF's under pay walls. I don't even have printed copies of my paper, because the publisher does not want to make the expenditure. And if I were to lose my password, I would have no access to my own paper for download (and I don't have access to the rest of papers in the same issue, of course).
  - Raphael 16y ago
    Couldn't you have emailed it to yourself or copied it to a USB drive when you originally wrote it?
    - RBerenguel 16y ago
      I hope you are joking. What I mean is that access to the journal pdf is blocked. I have of course the sources, several copies and pdf's hanging around, as does my co-author.
  - nickpinkston 16y ago
    So you're saying that you can't release due to some licensing / copyright issue, or that it's just something that takes extra time? I definitely understand the former - not that I like it, but the latter is inexcusable.
    - crazee 16y ago
      it's the former. But it's lovely the way you assume the latter is even a possibility. (where by lovely, I mean fucking pathetic, passive-aggressive, and shitty of you.)
    - RBerenguel 16y ago
      It depends heavily on the journal. Most journals have a "final draft policy": What they print is only theirs to publish. But you can self-post whatever previous versions you have. In my case, I think there are one or two minor spelling mistakes in the versions I have posted in ArXiV and my homepage. It does not take extra time (at least not a lot) to self-post it or publish on ArXiV (just a little hassle with image conversion problems, YMMV)
stygianguest 16y ago
I agree that code should be made public, but I couldn't disagree more with the last paragraph. Even worse, I take offence to the sentiments expressed in it. It's time to set ethical standards?! Really? Are they so unethical? I would claim that scientists have, by and large, very high ethical standards. Considering that they themselves are being pushed more and more to market their research to get funding, the highest standard for our work remains truth, and nothing but the truth. Elimination of scientists as activists is a non-statement. Assuming that scientists believe in their own work --a very common affliction-- what does it mean to be an activist? Just that they try to convince others of the validity of their work? Isn't it unethical _not_ to warn the world of the impeding doom your research has uncovered? And to be somewhat insistent if people do not want to hear it? Don't confuse politicians, crooks and businessmen in the climate change debate with the scientists. While all pretend to use scientific arguments, very few do. The political question should be: does the risk of climate change justify the costs that might prevent it.
- webXL 16y ago
  The risk of climate change shouldn't be political. That needs to be studied, rigorously. Al Gore may have closed the debate on whether climate change is happening, but to what extent is far from settled. Are X costs worth preventing Y damage, should be the political debate. We don't know Y yet.
jonhendry 16y ago
"And the only reason it's coming out is because some people -- for whatever reason -- have a bug in their shorts about climate science" On the other hand, scientists have spent decades fully aware that they'll have to build their own labs, obtain their own equipment, get their own animals if the work requires them, and follow the described procedures. They can't use the other guy's mice or zebrafish or monkey. They probably can't use the other guy's lab. They might be able to use the same telescope for astronomy, but it's better to use a different telescope to control for some fluke of the original. So given all that, it hardly seems a huge deal to not be able to use someone else's code, as long as you know what the code was supposed to be doing.
- jerf 16y ago
  "So given all that, it hardly seems a huge deal to not be able to use someone else's code, as long as you know what the code was supposed to be doing." But that's a vacuous statement. The only description of what the code is doing is the code. The description you get in a paper is the goal of the code, but goals aren't results. (Mistaking stated goals for results is a surprisingly common systematic error, programmers make it all the time when they believe the hype a project puts out before the project actually has any results. Once you start looking for it it's hard to see a day go by without someone doing this.) I can make a simple information theoretic argument that it is blindingly obvious that any significant code base will have many more bits in it than any journal article could, so it is literally mathematically impossible for a journal article to accurately describe the code. If goals were the same as results all of our jobs would look very different. Moreover, the reason why you can't use the other guy's monkeys is purely physical. If they could use the other guy's monkeys, they would. They try as it is; the entire purpose of controlled breeding gene lines is to try to erase variations. If they could use guaranteed-atomically-identical lab hardware, they would. (The story of cold fusion would probably be very different if this were possible, for instance; instead of an effect that nobody could reliably replicate, there would be one set of results that everybody could replicate and probably rapidly explain. Note I'm not making a claim about cold fusion itself, just the way history turned out.) Don't elevate an accidental physical limitation to an essential component of science. Very few things hit the true ideal of science, and in general the closer you can get, the closer you should get.
davi 16y ago
on standardized platforms This would be horrifying. Maybe it could work in some fields, but not in mine (neuroscience). What, I'm going to use Java v.<whatever> on Ubuntu v.<whatever> because a funding agency tells me I have to? I agree with much of your post, but not this bit. edit: I think much of the professional insecurity of my field -- which feeds into the stuff you're complaining about -- is driven by the fact that way more grad student positions are funded than there are academic jobs. I wrote about this in more detail here: http://news.ycombinator.com/item?id=470181 http://news.ycombinator.com/item?id=470181
- SkyMarshal 16y ago
  I think lutthorn's point above is on the money. Publish the algorithms, data, assumptions, and any other implementation-agnostic information required to reimplement, but don't bother with the actual code. Successfully reimplementing the experiment on disparate platforms would liekly serve to support the findings even more. It might be more work up front for researchers to have to do the complete implementation in their preferred platform and then work out the kinks, but it might improve the actual science being done.
  - anamax 16y ago
    > I think lutthorn's point above is on the money. Publish the algorithms, data, assumptions, and any other implementation-agnostic information required to reimplement, but don't bother with the actual code. If you don't publish the code and I come up with a different result while supposedly using the same algorithm, data, and assumptions, how do we know where a discrepancy between my results and yours comes from? Note that if you're taking public money, the code isn't yours. It's the publics. Don't like that? Don't take public money. (If you work for Google, Facebook, etc, they own what you do on their dime - same deal here.)
deleted 16y ago
[deleted]

lutorm 16y ago

You do realize that the way the incentives are laid out, it's exactly the people who do what you ask who will not get permanent jobs, so you'll still be left with those who don't. You can't accomplish what you want by bitching. As someone said in the discussion about Google hiring yesterday, "incentives matter". I agree with you that more emphasis needs to be put on careful work instead of cranking out flashy publications, but until people are rewarded for that, things are not going to change much.

nickpinkston 16y ago

Very well said - I find the current state of publishing in academia appalling. Don't forget that most research is behind a pay wall just for the damn PDF! I think you nailed it with "insecure". The little PhDs need to know their work isn't designed to just get them tenure...

RBerenguel 16y ago
Like we choose to have our PDF's under pay walls. I don't even have printed copies of my paper, because the publisher does not want to make the expenditure. And if I were to lose my password, I would have no access to my own paper for download (and I don't have access to the rest of papers in the same issue, of course).
- Raphael 16y ago
  Couldn't you have emailed it to yourself or copied it to a USB drive when you originally wrote it?
  - RBerenguel 16y ago
    I hope you are joking. What I mean is that access to the journal pdf is blocked. I have of course the sources, several copies and pdf's hanging around, as does my co-author.
- nickpinkston 16y ago
  So you're saying that you can't release due to some licensing / copyright issue, or that it's just something that takes extra time? I definitely understand the former - not that I like it, but the latter is inexcusable.
  - crazee 16y ago
    it's the former. But it's lovely the way you assume the latter is even a possibility. (where by lovely, I mean fucking pathetic, passive-aggressive, and shitty of you.)
  - RBerenguel 16y ago
    It depends heavily on the journal. Most journals have a "final draft policy": What they print is only theirs to publish. But you can self-post whatever previous versions you have. In my case, I think there are one or two minor spelling mistakes in the versions I have posted in ArXiV and my homepage. It does not take extra time (at least not a lot) to self-post it or publish on ArXiV (just a little hassle with image conversion problems, YMMV)

stygianguest 16y ago

I agree that code should be made public, but I couldn't disagree more with the last paragraph. Even worse, I take offence to the sentiments expressed in it. It's time to set ethical standards?! Really? Are they so unethical? I would claim that scientists have, by and large, very high ethical standards. Considering that they themselves are being pushed more and more to market their research to get funding, the highest standard for our work remains truth, and nothing but the truth. Elimination of scientists as activists is a non-statement. Assuming that scientists believe in their own work --a very common affliction-- what does it mean to be an activist? Just that they try to convince others of the validity of their work? Isn't it unethical _not_ to warn the world of the impeding doom your research has uncovered? And to be somewhat insistent if people do not want to hear it? Don't confuse politicians, crooks and businessmen in the climate change debate with the scientists. While all pretend to use scientific arguments, very few do. The political question should be: does the risk of climate change justify the costs that might prevent it.

webXL 16y ago
The risk of climate change shouldn't be political. That needs to be studied, rigorously. Al Gore may have closed the debate on whether climate change is happening, but to what extent is far from settled. Are X costs worth preventing Y damage, should be the political debate. We don't know Y yet.

jonhendry 16y ago

"And the only reason it's coming out is because some people -- for whatever reason -- have a bug in their shorts about climate science" On the other hand, scientists have spent decades fully aware that they'll have to build their own labs, obtain their own equipment, get their own animals if the work requires them, and follow the described procedures. They can't use the other guy's mice or zebrafish or monkey. They probably can't use the other guy's lab. They might be able to use the same telescope for astronomy, but it's better to use a different telescope to control for some fluke of the original. So given all that, it hardly seems a huge deal to not be able to use someone else's code, as long as you know what the code was supposed to be doing.

jerf 16y ago
"So given all that, it hardly seems a huge deal to not be able to use someone else's code, as long as you know what the code was supposed to be doing." But that's a vacuous statement. The only description of what the code is doing is the code. The description you get in a paper is the goal of the code, but goals aren't results. (Mistaking stated goals for results is a surprisingly common systematic error, programmers make it all the time when they believe the hype a project puts out before the project actually has any results. Once you start looking for it it's hard to see a day go by without someone doing this.) I can make a simple information theoretic argument that it is blindingly obvious that any significant code base will have many more bits in it than any journal article could, so it is literally mathematically impossible for a journal article to accurately describe the code. If goals were the same as results all of our jobs would look very different. Moreover, the reason why you can't use the other guy's monkeys is purely physical. If they could use the other guy's monkeys, they would. They try as it is; the entire purpose of controlled breeding gene lines is to try to erase variations. If they could use guaranteed-atomically-identical lab hardware, they would. (The story of cold fusion would probably be very different if this were possible, for instance; instead of an effect that nobody could reliably replicate, there would be one set of results that everybody could replicate and probably rapidly explain. Note I'm not making a claim about cold fusion itself, just the way history turned out.) Don't elevate an accidental physical limitation to an essential component of science. Very few things hit the true ideal of science, and in general the closer you can get, the closer you should get.

davi 16y ago

on standardized platforms This would be horrifying. Maybe it could work in some fields, but not in mine (neuroscience). What, I'm going to use Java v.<whatever> on Ubuntu v.<whatever> because a funding agency tells me I have to? I agree with much of your post, but not this bit. edit: I think much of the professional insecurity of my field -- which feeds into the stuff you're complaining about -- is driven by the fact that way more grad student positions are funded than there are academic jobs. I wrote about this in more detail here: http://news.ycombinator.com/item?id=470181 http://news.ycombinator.com/item?id=470181

SkyMarshal 16y ago
I think lutthorn's point above is on the money. Publish the algorithms, data, assumptions, and any other implementation-agnostic information required to reimplement, but don't bother with the actual code. Successfully reimplementing the experiment on disparate platforms would liekly serve to support the findings even more. It might be more work up front for researchers to have to do the complete implementation in their preferred platform and then work out the kinks, but it might improve the actual science being done.
- anamax 16y ago
  > I think lutthorn's point above is on the money. Publish the algorithms, data, assumptions, and any other implementation-agnostic information required to reimplement, but don't bother with the actual code. If you don't publish the code and I come up with a different result while supposedly using the same algorithm, data, and assumptions, how do we know where a discrepancy between my results and yours comes from? Note that if you're taking public money, the code isn't yours. It's the publics. Don't like that? Don't take public money. (If you work for Google, Facebook, etc, they own what you do on their dime - same deal here.)

deleted 16y ago

[deleted]