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On the Deep Disanalogy
Between Text and Software and
Between Text and Data
Insofar as Free/Open Access is Concerned

Stevan Harnad
Moderator,
AMERICAN SCIENTIST OPEN ACCESS FORUM:
A complete Hypermail archive of the ongoing discussion of providing open access to the peer-reviewed research literature online (1998-2004) is available at:
http://www.cogsci.soton.ac.uk/~harnad/Hypermail/Am sci/index.html To join or leave the Forum or change your subscription address:
http://amsci-forum.amsci.org/archives/American-Sci entist-Open-Access-Forum.html
Post discussion to: american-scientist-open-access-forum@amsci.org

On the Deep Disanalogy
Between Text and Software and
Between Text and Data
Insofar as Free/Open Access is Concerned

Stevan Harnad
Moderator,
AMERICAN SCIENTIST OPEN ACCESS FORUM:
A complete Hypermail archive of the ongoing discussion of providing open access to the peer-reviewed research literature online (1998-2004) is available at:
http://www.cogsci.soton.ac.uk/~harnad/Hypermail/Am sci/index.html To join or leave the Forum or change your subscription address:
http://amsci-forum.amsci.org/archives/American-Sci entist-Open-Access-Forum.html
Post discussion to: american-scientist-open-access-forum@amsci.org

I've been involved in these discussions for years, and happen to work for one of the major scientific publishers. Unfortunately this meme that scientific publishing model is somehow unique with dastardly publishers standing in the middle extracting payments from all has become far too entrenched, but it's really not a unique sort of situation at all.

Simple counterexample where exactly the same model applies: the Olympics. Just as billions of dollars are spent every year by publishers on the process of selecting the best scientific articles to publish, billions of dollars are spent by the host Olympic organization every four years establishing a venue for the world's best athletes to compete. A lot of that money goes into things that might seem unimportant to an outsider, like buildings and computers and IT and security staff etc. None of the money spent on the olympics goes to the athletes who bring their talents - other than the small amount that goes into paying for the medals themselves. Athletes in fact have to pay their own transportation expenses (or usually their home country takes care of it) - and then all those spectators pay again for the privilege of watching them compete. And you who watch on TV are paying via the advertising you have to endure, who have paid the TV network that has paid the Olympic organizers for the rights to broadcast.

Obviously, it would be much simpler and more efficient for athletes to just record their best performances in whatever stadium is available, and post it up on a website - then every four years somebody just picks the best performances and awards medals. Simple, right?

So why do we still spend all that money on the spectacle? Hmmm.

Anyway, I wish Brown all the best success, but as others have mentioned, it's a somewhat harder problem than it first seems (at least he's asking for $20 million, which is somewhat realistic for handling real peer review for a substantial number of articles - 10's of thousands at least).

What's behind this nebulous "peer review" concept, at least for us, is a complex and historically based system of checks and balances involving communications between authors, editors, and (anonymous and non-anonymous) reviewers; we're essentially a legal/court system for scientific articles. There's a lot of information-related issues in there, and information technology helps a lot (that's the part I'm involved in). But fundamentally, at least the way we do it, there needs to be a paid, responsible human being reading most communications and monitoring the process, and as far as we've been able to work out, you can't get the cost under about $500 or so per article.

Now, just distributing the papers can be done essentially for free (to as many people as would want to read for about $1-5 per article, for hardware, software, disk, network, etc.) which is what the famous physics e-print archive does so well. Of course it doesn't cost publishers any more than that to distribute articles online either - the costs are in the review part (and whatever copyediting they do), not in distribution.

You'll hear about journals now that are essentially free - this is almost always for one of two reasons:

1. The journal is very small, and some institution is picking up all the salary and incidental costs - $500/article works out to just $50,000/year for a 100 article/year journal.
   
2. The journal is heavily skimping on the "peer review" side of things - publishing conference proceedings papers for example with no review beyond the acceptance of the paper at the conference. Nothing wrong with that, but it's not what we normally mean by peer review.
   

Given the $500/article cost, the other question is does science really need this level of peer review, or can it get by with less? Well, we've already seen a couple of instances of scientific fraud that slipped by in physics in the last few months even with the current level of review - is skimping really a good idea? And is the $500 minimal cost or even $1000-$2000 typical cost per article now all that bad, compared to the typical $50,000-$100,000 research grant that generally funded such research?

Yet another proposed solution has been to publish fewer papers in those journals that receive the full peer-review treatment. Unless authors miraculously constrain themselves somehow, the only way that would save us money would be to reject a lot of things without review (because the costs are in the review process itself) - but then you've thrown out the whole "peer" process you're using to determine what's published!

So, maybe Brown has found a way through this morass - but the scientific system has a complex, little studied dynamic in which peer review as it currently stands plays an important role... if we really can't afford it (the old way) any more, we're headed into some uncharted waters...

Darwin's Black Box Review

The book basis its premace on six fallacies:

Fallacy one: There is a boundary between the molecular world and other levels of biological organization.

Fallacy two: The current utility of a given feature (molecular or otherwise) explains "why" the feature originally evolved.

Fallacy three: Unless we can identify advantages for each imaginary gradual step leading to a contemporary bit of biochemistry, we cannot invoke a Darwinian explanation.

Fallacy four: Molecular evolution: "a lot of sequences, some math, and no answers."

Fallacy five: There is a conspiracy of silence among scientists concerning the failure of Darwinian explanation.

Fallacy six: The evolution of complexity is unaddressed and unexplained.

More: Darwin's Black Box Review

Behe's empty box
"Behe's colossal mistake is that, in rejecting these possibilities, he concludes that no Darwinian solution remains. But one does. It is this: An irreducibly complex system can be built gradually by adding parts that, while initially just advantageous, become-because of later changes-essential. The logic is very simple. Some part (A) initially does some job (and not very well, perhaps). Another part (B) later gets added because it helps A. This new part isn't essential, it merely improves things. But later on, A (or something else) may change in such a way that B now becomes indispensable. This process continues as further parts get folded into the system. And at the end of the day, many parts may all be required."

"The point is there's no guarantee that improvements will remain mere improvements. Indeed because later changes build on previous ones, there's every reason to think that earlier refinements might become necessary. The transformation of air bladders into lungs that allowed animals to breathe atmospheric oxygen was initially just advantageous: such beasts could explore open niches-like dry land-that were unavailable to their lung-less peers. But as evolution built on this adaptation (modifying limbs for walking, for instance), we grew thoroughly terrestrial and lungs, consequently, are no longer luxuries-they are essential. The punch-line is, I think, obvious: although this process is thoroughly Darwinian, we are often left with a system that is irreducibly complex. I'm afraid there's no room for compromise here: Behe's key claim that all the components of an irreducibly complex system 'have to be there from the beginning' is dead wrong."

[b]The Fallacy of Conclusion by Analogy[/b]

When it comes to explaining science to the public, analogies and metaphors are essential tools of the trade. We all can better understand something new and unusual, when it is compared to something we already know: a cell is like a factory, the eye is like a camera, an atom is like a billiard ball, a biochemical system is like a mouse trap. An A is like a B, means A shares some conceptual properties with B. It does not mean A has all the properties of B. It does not follow that what is true for B is therefore true for A. Analogies can be used to explain science, but analogies cannot be used to draw conclusions or falsify scientific theories. Yet Behe commits this fallacy throughout his book.

For example:

[ol][li]A mousetrap is "irreducibly complex" - it requires all of its parts to work properly.
[li]A mousetrap is a product of design.
[li]The bacterial flagellum is "irreducibly complex" - it requires all of its parts to work properly.
[li]Therefore the flagellum is like a mouse trap.
[li]Therefore the flagellum is a product of design.

More: Features: Behe's empty box

Publish or Perish

On page 179 of Darwin's Black Box Michael Behe claims:

"There has never been a meeting, or a book, or a paper on details of the evolution of complex biochemical systems."
He closes the chapter with this ludicrous statement:

"In effect, the theory of Darwinian molecular evolution has not published, and so it should perish"

(Did someone say publish or perish?: The Elusive Scientific Basis of Intelligent Design Theory)

To be honest, I suspect that the extent of detail Behe is demanding would require a combination cutting-edge biochemistry lab and a time machine. How else can science fully recover, for example, every single step in the evolution of the bacterial flagellum that took place billions of years ago?

More: Publish or Perish

Review of Michael Behe, Darwin's Black Box (1998)
For those who have not already encountered this book or one of its numerous reviews, let me simply say that the author sets out to argue that the organic world is so complex, particularly at the level of molecular biology and biochemistry, that Darwinian evolution cannot possibly have led to it. As evolution cannot produce irreducibly complex systems (the blood-clotting process, for instance, the biochemist's analogue of the eye), they must be the outcome of the activities of an Intelligent Designer. In other words, the book is a tiresome reworking at the molecular level of the timeworn "design" argument.

So much has already been written by reviewers of this book that it seems unnecessary to add anything more (go to ahref=http://www.talkorigins.org/faqs/behe/publish .htmlhttp://www.talkorigins.org/faqs/behe/publish. html>). Specialists far more competent than me have analyzed the numerous and gross deficiencies in Dr. Behe's flatulent arguments in considerable technical detail (see especially ahref=http://www.cbs.dtu.dk/dave/Behe.htmlhttp://w ww.cbs.dtu.dk/dave/Behe.html>), so there would be an emptiness in my remarks if I were to try to emulate them. If I am to add anything to the discussion, I am forced to choose to look at the book from a different perspective. The perspective I shall adopt is that of misrepresentation, for that quality pervades this book at every level.

More: Review of Michael Behe, Darwin's Black Box (1998)

See this article in Scientific American (from 1996). Yes, there is such a thing as Ice-9 (actually Ice-IX), but it doesn't have the properties of the substance in the Vonnegut book.

had an interesting article on the structure of the galactic center. An abstract of the article is here.

Most people don't know, but the official name of the magazine was changed to Popular Scientific American a number of years ago. The same time that they started printing profiles of scientists with their photos. (I understand next year they'll be requiring them to pose in swimming suits). For something much like the old Scientific American, I suggest you check out American Scientist . I've heard they got some of the SA staff, but can't verify that myself.

I've been writing SF stories set at Oort-cloud planets and brown dwarfs for a couple of years now. (You can find one, "Halo", in the Tor Books anthology Northern Suns; I am just completing a novel set among these objects). This planet, if it exists, is probably not unique. The astronomer J. Davy Kirkpatrick said in a press release last year that brown dwarfs appear to be so abundant that we'll probably find one closer than the nearest star.

So what? Well, let me put it this way: while the stars remain as far away as ever, the distance between planetary systems has been halved by the recent calculations of the abundance of brown dwarfs and the possible existence of this planet.

Consider Jupiter. It's got a couple of Mars-sized moons orbiting it; one of them might even have a subsurface ocean (Europa). This theoretical new planet could easily have similar moons. Might as well call 'em planets at that size.

The resources of the Jupiter system are huge, and the same could be true of this distant world. It's not likely to be a frozen ball; Jupiter radiates more heat than it receives from the sun, and it heats its own moons with tidal force. Even half a light-year into the Oort cloud, we might find a Europan-style oceanic world orbiting Nemesis (or whatever you want to call this 10th planet).

While the radiation environment around Nemesis is likely to be nasty, if its magnetic field is anything like Jupiter's it will be trivially easy to draw power from it; easier, in fact, than it is to generate power from solar cells. A simple wire orbiting a jovian planet produces electricity in colossal amounts through interaction with the magnetic field. A nascent colony at Nemesis would have as much power as it needed for light and heat.

If this planet does exist it should be our target for settlement after Mars and Jupiter. It will be the place where we'll learn if and how we'll travel to and survive at other stars.