Welcome to European Tribune. It's gone a bit quiet around here these days, but it's still going.
You've no idea in sort of trouble you can get with advocacy like that?

YOU, not me. But the privatization of science will lead to the destruction of science, or, at the very least, cause new discovery to greatly slow down. This is especially problematic for those working for governmental agencies and public universities.

How can a paper based on a model be critiqued if the model and the data are not available to reviewers chosen by the journal? If the participants in the endeavor cannot understand that, perhaps they should switch their fields of endeavor to theology.  I would suggest they consider pondering Paul's dictum: "Faith is the evidence of things unseen." They should be able to get jobs with faith based institutions.

"It is not necessary to have hope in order to persevere."

by ARGeezer (ARGeezer a in a circle eurotrib daught com) on Sat Nov 21st, 2009 at 01:52:12 PM EST
[ Parent ]
Some people are already trying to have climate change legally defined as a belief...

Climate change believer takes firm to tribunal | Environment | The Guardian

At an employment appeal tribunal in central London today, Dinah Rose QC, for Nicholson, said: "The philosophical belief in this case is that mankind is headed towards catastrophic climate change and that, as a result, we are under a duty to do all that we can to live our lives so as to mitigate or avoid that catastrophe for future generations.

"We say that that involves a philosophical and ethical position. It addresses the question, what are the duties that we own to the environment and why?"

She told Mr Justice Michael Burton - who ruled last year that Al Gore's environmental documentary An Inconvenient Truth was political and partisan - that beliefs about "anthropogenic climate change" could be considered a philosophy under the Employment Equality (Religion and Belief) Regulations 2003.

But really this:

ARGeezer:

How can a paper based on a model be critiqued if the model and the data are not available to reviewers chosen by the journal?

has been the crux of this highly charged trench war, and it has been for years on end.

by Nomad on Sat Nov 21st, 2009 at 02:26:13 PM EST
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Three months ago there was an internet round of a scandal when CRU revealed that they do not keep the original raw data of weather measurements; they keep only adjusted or "reliable" homogeneous data. This is absolutely inexcusable. Was it hard to keep the original data (whatever quality) while storage capacity of hard disk technology grew exponentially?
by das monde on Tue Nov 24th, 2009 at 03:17:01 AM EST
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The "privatization" of science is already leading to the "destruction" of science.

The vast amounts of money made in various technological implementations of science: computers, bio-pharmaceuticals, etc., has given rise to a predatory capitalist group-think among scientists and technologists.  Partially due to the normal course of human competition - see the foo-foo over Who Invented The Calculus - and partially due to the current course of Science -> Technology -> Product -> "Money makes the world go around."  

I've been a part of, and observer of, this in computers.  Back in the 70s people would freely talk about their work and even explain ... in excruciating detail ;-) ... how it was done and why it was done.  Now I'm so NDA'ed I can't talk about anything remotely related to my work, as Mig can attest.  

She believed in nothing; only her skepticism kept her from being an atheist. -- Jean-Paul Sartre

by ATinNM on Sat Nov 21st, 2009 at 03:39:43 PM EST
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Yup.

Also, as Science and Nature and the other print publications continue to move to online-only access, it gets harder and harder to read the refereed literature. Used to be you could walk into a public university library here in the U.S. and browse through piles of journals, but budget cuts combined with higher prices for the print versions has led to the shelves being empty. As a university student or staff member, you have an account and can get the articles, but otherwise it's pretty hard.

And the patent and copyright situation is completely ridiculous. The idea was to allow individual inventors to protect their ideas, but the effect of the current system is to make the barrier to entry into any technical industry extremely expensive. The first thing you have to do is buy reciprocal patent rights with the big players, since nobody can make anything these days without running into a patent.

Frankly, I hope this hacking leads to a bunch of lawsuits, because at this point the legal system is probably the best place to argue it. The scientific community has lost their position as an unquestionable elite, but the lawyers at least still have a grip on the legal system.

by asdf on Sat Nov 21st, 2009 at 03:45:43 PM EST
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And the patent and copyright situation is completely ridiculous.

Nailed that one.

In the SO's field - genetics - the US Patent Office issued patents, back in the 70s, for basic molecular biology laboratory techniques.  

 

She believed in nothing; only her skepticism kept her from being an atheist. -- Jean-Paul Sartre

by ATinNM on Sat Nov 21st, 2009 at 03:50:35 PM EST
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What I find amusing is the Ruling Class utterly depends on exponential growth to keep things moving along, in their view, while they steal the economic value of the production of the producing class lowering their purchasing power to nothing and they require a constant stream of new products from the R&D staffs which they prevent from blocking free and open information exchange.

We're getting to the point where we can't move because we're standing on our own hands.

It's nuts.  

She believed in nothing; only her skepticism kept her from being an atheist. -- Jean-Paul Sartre

by ATinNM on Sat Nov 21st, 2009 at 03:59:47 PM EST
[ Parent ]
Luckily, the lower classes will recognize this problem and vote for representatives who will fix it. Right?
by asdf on Sat Nov 21st, 2009 at 04:02:52 PM EST
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Wrong, because information remains controlled, and without info, no one does nothing except lineup for Palin signatures.

But you were being sarcastic, so i agree.

"Life shrinks or expands in proportion to one's courage." - Anaïs Nin

by Crazy Horse on Sat Nov 21st, 2009 at 04:16:57 PM EST
[ Parent ]
Yeah.  Change.  That's what's up!

Not.


She believed in nothing; only her skepticism kept her from being an atheist. -- Jean-Paul Sartre

by ATinNM on Sat Nov 21st, 2009 at 04:19:23 PM EST
[ Parent ]
While women are certainly affected by this, I cannot help but believe this whole cultural FUBAR situation is primarily the result of male domination and testosterone run amok. Amusingly, it is not our hands that we are standing on, but another member. Perhaps by so doing from an early age, natural selection will come to the rescue of the species!  (A vain hope I know!)

The stupidity of trying to lock away everything for private profit of course originates in the ethos of our capitalist ideology. Everything must have a price and an owner and the value of everything must be discounted so as to be capable of finance and of an estimate of the present value of the resulting future income and all decisions must be made on the basis of optimizing the sacred "Return on Investment".  The stultifying effect this has on all aspects of our lives is the second greatest of all of the "internal contradictions" of which Marx did or could have spoken. The greatest, at present, IMHO, is the embedded need for exponential growth in a finite world.

While the problem of finite resources is, in theory, capable of at least partial resolution via a switch to renewable resources, resolving the problems inherent in having a mono-valent culture seems to me more problematic. The attraction of Chris Cook's ideas regarding unit trusts for me, beside the effect of undermining the need for exponential growth, is that, intuitively, it seems that this approach would free up some cultural energy that could be applied to quality of life issues.

Were we to put the economy on a "fail-safe" auto-pilot mode in which booms and busts due to the effects of money created based on debt are obviated, the scope for world domination through monetary manipulation could be confined to areas on which our lives and the lives of our children do not depend. Perhaps the energies of those with hyper-competitive tendencies and the need to manipulate and dominate others could be channeled, before they reproduce, into lethal blood sports. A few centuries of such a regime might result in a species that would actually be deserving of being called a "social species."

[Jonathan Swift has just ceased channeling through ARGeezer.]  

"It is not necessary to have hope in order to persevere."

by ARGeezer (ARGeezer a in a circle eurotrib daught com) on Sat Nov 21st, 2009 at 10:35:19 PM EST
[ Parent ]
How can a paper based on a model be critiqued if the model and the data are not available to reviewers chosen by the journal?

Peer review is a joke most of the time, data or no data. It is rare that a reviewer will actually check a paper's calculations for errors.

En un viejo país ineficiente, algo así como España entre dos guerras civiles, poseer una casa y poca hacienda y memoria ninguna. -- Gil de Biedma

by Migeru (migeru at eurotrib dot com) on Sun Nov 22nd, 2009 at 07:35:59 AM EST
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Peer review is not about checking people's arithmetic. In fact, in order to do that, one would need their raw data, their tabulated data, and an exact copy of all the software. We reviewers have to assume that when someone sez: we colleced X data and applied Y analysis to test Hypotesis Z using stats package R, that they did so correctly.

Peer review assesses the appropriateness of the data collected and the method of collection as reported, the validity of the statistical analysis as a test of the hypothesis, and checks that the discussion and conclusions actually follow logically from the results reported. Some reviewers will do some mental assessments of the tabular or summar statistics reported and may flag apparent anomolies for revisions or further explanation.

But the suggestion that we "check their calculations" is absurd beyond any possible practice in any discipline except perhaps in mathematics.

by PIGL (stevec@boreal.gmail@com) on Sun Nov 22nd, 2009 at 10:23:04 AM EST
[ Parent ]
Well, in most theoretical physics papers, everything before the section on simulations should be amenable to checking by reviewers - it's mostly just calculus.

If it's not amenable to checking, then it needs to be re-written, because then it won't be readable for the target audience either.

The simulations are a different kettle of fish, of course.

- Jake

Friends come and go. Enemies accumulate.

by JakeS (JangoSierra 'at' gmail 'dot' com) on Sun Nov 22nd, 2009 at 11:07:05 AM EST
[ Parent ]
I was told (I will have to put this in a Glen Beck style of discourse) that in some areas calculation errors were detected in near 100% of papers assessed.

Note that I agree: reviewing complex papers by repeating the calculations is asking too much. When software is made available I tend to download it and evaluate it. But with mathematical formulae even reading is a big pain.

I know of a top scientist in population genetics that says that when he sees lots of maths in papers is because authors are trying to make something difficult to detect. ;)

But this only exposes how the current process is flawed: peer-review can only go so far. And that "far" is not enough to detect even gross mistakes.

Science is also riddled with Dunning-Kruger effect. For instance I work in biology/medicine with a CS background. Most people developing software in bio/med think that because they are so good bio/med people they immediately become fantastic programmers. And then you see people devising results done with software which has the quality coming from a high school student. Don't even try to suggest that they are completely ignorant in the subject of programming.

I once had a discussion with a top scientist which does only theoretical modeling on the advantages of indenting code. This person doesn't even indent code. And why? "Well, with 8/9 levels of code, indenting makes it unprintable. And it is impossible to break the code in less levels of indentation"

Another suggested that an optimization algorithm always finds the maximum if the algorithm is stochastic (whereas if it is deterministic only local maximum can be found). Code was made, published and used like this.

by t-------------- on Sun Nov 22nd, 2009 at 12:34:17 PM EST
[ Parent ]
I too am a former CS type (up to MSc) turned ecologist, so I appreciate your remarks.

Probably, any major collaborations in simulation and data analysis should have a statistician and an algorithms guy and a programmer on board. Just try funding that in my world.

It's not that I object in principle to making code and data available. I rely on other peoples' code and data all the time. It just there is no mechanism for funding the systematic provision of what you are asking for, or or rewarding the scientists who take the time to do it. Fixing this is no simple matter. You must know well the time and effort required to produce, for example, a reliable distribution of even a minor piece of code.

by PIGL (stevec@boreal.gmail@com) on Sun Nov 22nd, 2009 at 02:02:01 PM EST
[ Parent ]
The rewarding system is very simple: if you don't make the software available then it is rejected for publication. Some journals do this partially or totally (depends from case to case).

If everybody is on the same level (ie everybody has to make the software available) then competition is fair.

Your new field, ecology is fairly bad field in terms of secrecy and closeness (but not bad in terms of predicting BS, me thinks). I have a completely ridiculous paper on an ecology journal (but at least the source code is available ;) ).

Half of my PhD is conservation genetics and people are really secretive. We should have a paper submitted very soon to Molecular Ecology and it is predicative (fall of expected heterosigosity over 200 years). It will probably be used to change policy. I actually intended to make a diary about it (after it is published).

I mainly work with population genetics simulations (effective population size and selection) and spread of drug resistance (selection, pharmacology). I have some "part/time" with phylogenetics also.

In some sense I became proud of being a CS guy at the origin. The problems in CS are less bad. I plan to return to CS (if I stay in science - which I probably wont).

by t-------------- on Sun Nov 22nd, 2009 at 02:14:06 PM EST
[ Parent ]
And to just add a personal note: during the last 2 years I gained 40 pounds and more or less became an alcoholic because of the things I describe here and how the affected me at a profound level.

I recently "got out of the hole" through becoming a cynicist: I don't really want to give a nice contribution to society anymore, at least through science I think it is impossible.

I just want to live the quiet life and "do no harm" is now enough for me.

I need a beer.

by t-------------- on Sun Nov 22nd, 2009 at 02:23:42 PM EST
[ Parent ]

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