How to do ID: (1) Find a shark. (2) Jump it.

| 100 Comments

Denyse O’Leary, she of the multiple blogs and little reliable knowledge of evolution, is offering a prize for the original code for Dawkins’ cumulative selection demonstration program (‘METHINKS …”), described in The Blind Watchmaker, originally published in 1986. The winner actually gets to choose between two prizes, a copy of Stephen Meyer’s new elaboration of the standard ID argument from ignorance, Signature in the Cell, or a copy of Dawkins’ forthcoming The Greatest Show on Earth. (Actually, for the latter prize, O’Leary says she will ask Dawkins’ publicist to provide the prize. Strange to offer a prize she can’t herself deliver.)

The comment thread is strangely reminiscent of the recent “birther” rhetoric in the U.S. A commenter called “kibitzer” replicates the birther script almost flawlessly. For example

It is simply unconscionable that over 20 years after the program has been out and used to argue for Darwinism, Dawkins still has not made this code publicly available.

and

But the program has been much discussed on the Internet in the last decade. So where is the code?

and

Then provide the original code. Repeat after me: WE WANT TO SEE THE ORIGINAL CODE, WE WANT TO SEE THE ORIGINAL CODE, WE WANT TO SEE THE ORIGINAL CODE …

and

Of course, as programs go, Dawkins’ WEASEL is trivial and it’s easy enough to reconstruct something that’s close to it. But given the controversy surrounding it, let’s see the original program. Why is that so difficult?

and

We’re all beating our gums. Please, let’s see the original code. Why is that so much to ask? To paraphrase Ben Stein, Does anyone have it? Anyone?

Controversy? Only in the fevered imagination of Bill Dembski, who has now infected Robert Marks.

Hat tip to Glenn Branch.

100 Comments

1986? If the source still exists, it’s probably sitting on some floppy or tape that can’t be read by any computer currently in production (not that there aren’t geeks who save the old technology just for fun, and could read just about anything if offered enough beer for their trouble).

But about your headline: since when was D’Oh!Leary ever on the right side of the shark to begin with?

May I ask a polite question? WHO CARES!

It was just a demonstration of a concept, but for some reason they think that if they can find a flaw in the program eevolluuion wil fall apart.

Do you have to have been dropped on your head to be a creationist, or is it just very helpul?

Eamon Knight said:

1986? If the source still exists, it’s probably sitting on some floppy or tape that can’t be read by any computer currently in production (not that there aren’t geeks who save the old technology just for fun, and could read just about anything if offered enough beer for their trouble).

But about your headline: since when was D’Oh!Leary ever on the right side of the shark to begin with?

Or, they could just pull ou their twenty year old programming guides and re-create it to see for themselves how it runs.

They have every intention of adulterating the code to suit their own ends, i.e., make genetic changes to it, evolve it, then claim it was theirs to begin with. I suspect they would end up with something like “creintelligent designationism.”

I should have noted that Dawkins’ birth certificate shows that he was born in Kenya. That settles it. Right?

Lots of the UD comments appear to get it - i.e. its the algorithm, not the code, thats important; the algorithm is available; you can produce a code that makes the same point any time you want; etc.

Of course I fully expect that in a day or two all those comments will be gone.…victims of intelligent design…

And how’s he going to verify the code?? Anyway…

So why not hold a proper contest and do some science? The challenge would be to code up at least the two different versions of the thing and try and compare and contrast them w/ one another and with what (if anything) is in the book (I haven’t read it). Top prize goes to the best comparison and (snarky) writeup??

The only rules I can think of are (1) to use a freely available language so that any and all can replicate your analysis, and (2) address the original quibbling honestly, and discuss it’s (ir)relevance to the theory of evolution by natural selection.

Just a thought ;)

Special invitation for Denyse O’Leary – but any civil ID/creationist is entitled to enter.

Write an essay demonstrating that you have a complete understanding of evolution and the role of natural selection without having to mischaracterize any of it

Mike Elzinga said:

Special invitation for Denyse O’Leary – but any civil ID/creationist is entitled to enter.

Write an essay demonstrating that you have a complete understanding of evolution and the role of natural selection without having to mischaracterize any of it

Do you realize that you’ve just doubly disqualified all of the members of the Discovery Institute, as well as all of the Intelligent Design proponents on the Internet?

I mean, I’ve never encountered a civil or even polite Intelligent Design proponent before, and malicious mischaracterization of evolution (and the rest of science) is the life-manna of Intelligent Design and Creationism.

Mike Elzinga said:

Special invitation for Denyse O’Leary – but any civil ID/creationist is entitled to enter.

Write an essay demonstrating that you have a complete understanding of evolution and the role of natural selection without having to mischaracterize any of it

I have for some time tried buttonholing Ray Martinez to tell us in his own words, of course without having to believe any of it, his interpretation of the term “natural selection”. His only response so far is something like “Concept of Natural Selection is not seen in nature.”

I could post one comment on O’Leary’s thread:

Dawkins describes his algorithm in the following way:

It again begins by choosing a random sequence of 28 letters, just as before:

WDLTMNLT DTJBKWIRZREZLMQCO P

It now ‘breeds from’ this random phrase. It duplicates it repeatedly, but with a certain chance of random error - ‘mutation’ - in the copying. The computer examines the mutant nonsense phrases, the ‘progeny’ of the original phrase, and chooses the one which, however slightly, most resembles the target phrase, METHINKS IT IS LIKE A WEASEL. […] the procedure is repeated.

This is enough to replicate his program: 1. chose random string 2. copy string n times with mutation. NOTE: at this step you don’t know which letters are correct in place, so no letter is safe from being mutated! 3. chose best fitting string. NOTE: best fitting seems to be generally understood to be the string with the most correct letters, the fitting is expressed by a number between 1 and 28 4. Stop, if the number of correct letters is 28, otherwise 5. goto 2

The parameters which you can chose is the number of copies n, and the probability that a letter in a string is mutated, p. You may even chose another procedure of mutation - but keep in mind the NOTE of step 2.

It’s really basic to realize steps 1 - 5 in the programming language of your choice…

But now I seem to be blocked, so my follow-up didn’t come through:

Just to elaborate: The interesting part is what Atom describes as oracle, i.e., the application of the fitness function. In Dawkins description we read

The computer examines the mutant nonsense phrases, the ‘progeny’ of the original phrase, and chooses the one which, however slightly, most resembles the target phrase

An oracle - a black box - which accomplishes this just hints to one string when presented with a population of strings. No further information has to be exchanged. It is not necessary to know how the oracle defines the best string: It could just give hint you to the one with the greatest number of correct letters - or perhaps the one which shares the longest substring with the target phrase.

Dembski - who emphasizes the importance of information - strangely (?) doesn’t see that his - and Dawkins’s - algorithm get different amounts of information from the oracle

Mike Elzinga -

Write an essay demonstrating that you have a complete understanding of evolution and the role of natural selection without having to mischaracterize any of it

During the years between 1999 and Dover, when open creationists still showed their faces on science blogs and used AIG style arguments, and when some borderline intelligent lay people had vague ideas that “intelligent design” was something that might be worthwhile (*although then as now, only because they confuse it to imply theistic evolution, as the duplicitous types who made up the name “ID” intended), this was always the first thing I said to creationists.

None of them ever managed to do it. Most just ran away, and a few of the bloated, pompous, elderly lawyer “big word creationist” types would bloviate on and on without answering.

However, I now prefer the Stevaroni approach - “Pretend that you never heard of evolution; how do you explain the pattern of life’s diversity? Never mind what’s wrong with the theory of evolution, what is your explanation for what we see?”. At least as an initial question.

I was going to comment on how asinine this Denise O’Leary thing is - the Dawkins program has nothing to do with the real evidence for evolution (I’m not sure if he ever even published it in an actual journal), and it’s obvious that a program could be written to do exactly the same thing, using either contemporary or 1986 technology.

DiEB -

It’s so ridiculous it’s unreal. You offered a rational solution to the “dilemma”, so your subsequent comments were blocked.

Speaking of ID, here’s a new paper in today’s PNAS with a nice ID baiting title:

Clements, A. et al. (2009) The reducible complexity of a mitochondrial molecular machine. PNAS, advance online.

http://www.pnas.org/content/early/2[…]106.abstract

and the authors appear to be taking IDists on pretty directly:

Molecular machines drive essential biological processes,from protein synthesis transport to genome maintenance, expression and inheritance (1, 2). Good examples include bacterial flagella (3, 4), the RNA polymerase holo-complex (5), and various protein transport machines that selectively transfer protein molecules across biological membranes (6). Proponents of Intelligent Design have argued that these sophisticated machines are ‘‘irreducibly complex,’’ with this standing as the proof that, at the molecular level, Darwin’s principles of evolution cannot explain the complexity of living systems (7, 8). Our current investigation of the function and evolution of the protein transport machines in mitochondria provides an excellent, and perhaps unique, system to provide evidence that a sophisticated molecular machine can evolve from simpler components, in a process strictly adhering to Darwinian principles of evolution.

DiEb said:

I could post one comment on O’Leary’s thread:

Your post was embarrassing to them for a number of reasons:

1) They are incapable of generating code from a detailed verbal layout of a workable algorithm.

2) The educations of most ID/creationists seldom, if ever, involve having to synthesize knowledge to accomplish something unique.

3) They are almost always are asked to regurgitate specific information on multiple-choice tests with double and triple negatives thrown in to make the test “difficult”.

4) They would have no way of knowing if they got something that was correct. What would they use for comparison?

5) They have presented no criteria by which they would judge the code to do what it was designed to do.

6) They would be required to have specific and correct understandings of scientific concepts and terms in order to understand an algorithm that mimics the natural world.

There are many more such reasons, but I think this gives the general idea of the problem.

Show me the “X” is a lot like the creationist argument based on “were you there?”

I wrote a program in 1982 that was used successfully and re-written and modified up to around 1996.

Today, the computers it ran on, all of the backup tapes, source code documentation and even the building that housed it are gone.

Who gives a weasel’s ass?

I could recreate the program to run on the iPhone, but 20 years from now with the xFon Implant we’d be back to square one and DOL would still be jumping sharks, albeit in her walker.

Denyse yammers…

It is simply unconscionable that over 20 years after the program has been out and used to argue for Darwinism, Dawkins still has not made this code publicly available.

Notice the ID mode of thought.

The program. As if anybody who’s actually capable of forensically examining the code couldn’t simply write their own testbed in an hour.

To the ID crowd, “Weasel” is not a concept. Instead, it has to be anthromorphosed into a single, pagan, object that everybody somehow worships.

The program.

It’s just like all the ID tripe about calling evolution Darwinism. You have to personify (or at least objectify) the thing you attack, because a mere object is assailable, whereas attacking an easily demonstrated concept is a real problem.

It’s especially if you’re scientifically illiterate.

The ironic thing, readily apparent to anybody who actually cares, is that “Weasel” is such a strong demonstration precisely because there are so many versions - the vast majority developed in true “black box” environments, where the programmer knew something about the algorithm in general terms, but hadn’t actually seen the underlying code at all.

He didn’t need to see the code, it’s so damned easy to write these things.

Consequently, there must be thousands of “fitness functions” out there.

And yet all these disparate versions of “Weasel”, all these variants that have nothing in common, still work.

Just like all the experiments that measure gravity in all the “physics 101” labs all over the world still measure the same value.

That should tell you something.

stevaroni said:

Denyse yammers…

It is simply unconscionable that over 20 years after the program has been out and used to argue for Darwinism, Dawkins still has not made this code publicly available.

Notice the ID mode of thought.

The program. As if anybody who’s actually capable of forensically examining the code couldn’t simply write their own testbed in an hour.

Well, what you gotta unnerstand is that scripture is inerrant only in its original ‘autographs.’ If you don’t have that original program, no other program embodying the same algorithm can demonstrate the same point – they’re not the original autographs.

Once again, IDists miss another important point about science, which is that experiments which can be replicated are better than those which can’t. The nice thing about Dawkins’s experiment is that anybody posessing a modicum of coding skills and some curiosity can replicate the purported results. So what if the original experiment is lost, it’s real strength is the number of times its results were replicated.

And honestly, who cares? Even if Dawkins is shown to have made the whole thing up in ‘86 after having too much coffee, which seems to be the O’Leary’s insinuation, why does O’Leary, or anyone, care?

GuyeFaux said:

Once again, IDists miss another important point about science, which is that experiments which can be replicated are better than those which can’t.

This is similar to those AiG idiots in Ken Ham’s cult who argue that they are looking at the same data from a different perspective.

First of all, we always observe them filtering out most evidence and data, and then playing gestalt games with the little that remains.

But simply making such a claim is blatant admission that they are not practicing science and don’t know what science is.

If we just look at technological spin-offs alone, scientific evidence and consequences are independent of “philosophical perspective”. Even plants and non-human animals can benefit from what has been learned from science.

stevaroni said:

Denyse yammers…

It is simply unconscionable that over 20 years after the program has been out and used to argue for Darwinism, Dawkins still has not made this code publicly available.

Notice the ID mode of thought.

The program. As if anybody who’s actually capable of forensically examining the code couldn’t simply write their own testbed in an hour.

Agreed. It reveals a lot about creationist thinking.

You start with the Bible – the perfect word of God. It gets miscopied, mistranslated, misinterpreted, so that what we have today is but a shadow of the magnificent original. The old is better than the current, information is always lost, things always get worse.

Tell a creationist that we know more this month than we knew last month … that new information is has come to light … that in any given month 1000 pages of new information are available through Physical Review Letters alone (to pick a single small scientific journal) … and the idea is so far outside of his ken that he doesn’t even reject it – the idea bounces off his mind before it even enters.

To the creationist, it’s not the ideas in the Bible that are important, it’s the Bible itself, the perfect word of God.

They are so trapped in this mode of thinking that they can’t even recognize that the ideas in Dawkin’s book are important, but the exact word choice is irrelevant. That the idea of the Weasel program is significant, but its implementation in BASIC is not. That the program itself is not even intended to simulate evolution, but to demonstrate a facet of evolution.

Scientists are accused of worshiping Darwin, and of venerating Origin of Species, not because of any evidence (there is none), but because creationists cannot conceive of operating except through a venerated “font of wisdom”.

RBH said:

Well, what you gotta unnerstand is that scripture is inerrant only in its original ‘autographs.’ If you don’t have that original program, no other program embodying the same algorithm can demonstrate the same point – they’re not the original autographs.

And yet they keep making up new translations of the “original” when they don’t like the other translations. I guess that’s ok even though this process leases to constant splintering of “proper understanding”.

Yet hundreds of computer platforms and computer languages implementing from scratch and by different individuals the same algorithm involving the natural world all get the same results that all can agree upon.

Go figure.

DOL wrote:

“It is simply unconscionable that over 20 years after the program has been out and used to argue for Darwinism, Dawkins still has not made this code publicly available.”

Right. And it is simply unconscionable that after more than ten years, Dembski has yet to calculate the amount of complex specified information in a single thing, living or not. You first Sir Issac.

DiEb said:

I could post one comment on O’Leary’s thread:
[snip]
But now I seem to be blocked, so my follow-up didn’t come through:
[also snip]
Dembski - who emphasizes the importance of information - strangely (?) doesn’t see that his - and Dawkins’s - algorithm get different amounts of information from the oracle

I read that earlier. At least you got to post something; I’ve tried to register twice and never got confirmation e-mails.

Remember the PT thread where contributors had WEASEL-like programs coming out of the woodworks in nearly every significant language? You’d think those would be evidence enough that the basic premise is examinable. But even back then, Dembski and UD didn’t seem inclined to actually follow up on anything.
Reminds me of the time Andrew Schlafly demanded the “original data” from Richard Lenski’s long term E. coli evolution experiment: they wouldn’t know what to do with anything even if they could have it.

GuyeFaux said:

And honestly, who cares? Even if Dawkins is shown to have made the whole thing up in ‘86 after having too much coffee, which seems to be the O’Leary’s insinuation, why does O’Leary, or anyone, care?

So let me summarize

1. Opponents of evolution go around saying “Darwinism” is a theory of random evolutionary change, that it assumes that adaptations just happen as a result of purely random processes.

2. Dawkins gets mad at this deliberate misrepresentation and makes his Weasel program as a simple teaching program to show that change by mutation and natural selection can achieve a cumulative, very nonrandom result.

3. It can get to the Weasel sentence in hundreds (or a few thousands) of tries instead of the 1040 which would be needed for a purely random search such as a monkey with a typewriter.

4. Opponents say “but it has latching”! Supporters say “no it doesn’t”. Opponents say “let’s see the program!” Supporters say “it doesn’t matter!” Opponents say “but if it has latching then [dramatically horrified indrawn breath] it is doing partitioned search!”

5. The implication they try to give is that the latching is the only reason is succeeds in much less than 1040 tries.

6. Everyone is hung up over this (non)issue. Nonissue because even if it did have latching it would not be all that much faster. Latching isn’t why it does a lot better than purely random search.

People like O’Leary who make a Big Deal about whether the program has latching are not explaining in detail why that matters all that much. Can they explain why it is the critical feature of the program? Can they show that latching is the only reason why the program takes less than 1040 trials? (No, they can’t).

What is really funny about all this is O’Leary’s offer to Dawkins that, if he will provide the program, she will reward him by (as one possible prize) asking Dawkins’ publicist to send Dawkins a copy of his own book. That takes real imagination. And chutzpah.

What is really funny about all this is O’Leary’s offer to Dawkins that, if he will provide the program, she will reward him by (as one possible prize) asking Dawkins’ publicist to send Dawkins a copy of his own book. That takes real imagination. And chutzpah.

Has anyone told Dawkins? I would, but I’m a nobody, so he won’t even notice.

I think I’ll write a Weasel in BrainFuck and submit it. Or perhaps Malbolge.

Well, thanks. That lead me to LOLCODE, and I’m still snickering, getting frowns from coworkers.

And I almost forgot; look at what the ID/creationists are doing with their constant word games, distortions of meaning and their introduction of jargon and memes into their propaganda.

They don’t like evolution, yet it is the larger part of their shtick.

stevaroni said:

So where is the code

I’ve been thinking about the red herring of front-loading for a while and one of the ironies that struck me is that you don’t even need a computer to run the weasel algorithm.

You could “easily” do it with a bingo hall full of 50 undergrads, each one of which had a bucket of balls with the letters A through Z and the numbers 1 through 23.

(And if I remember my college days correctly, a hall full of students comes much closer to the idealized “monkeys with typewriters” model than any computer simulation ever could.)

In the beginning, each student would randomly pluck letter balls out of the bucket 23 times to produce a random starting string. He’s then tot up the string’s score.

A “bingo caller” in the front of the room would then call out “OK, anybody got a 1?, How about a 2? a 3?”

Once the high score was identified, the string would be called out, and everybody would write down that “child”. Then they’d reach into the bucket, pull out a random number and letter and “mutate” that position with that letter, repeating the process.

Once people got good at it, you could probably do a cycle per minute, or 60 cycles an hour.

The irony is that humans would be much worse than machines at adding up the scores and transferring the winning strings, thereby making errors and adding an entirely new level of randomness to the process.

Given the extant computer simulations, even with that small sample, the odds are very good that you could get “Methinksitislikeaweasel” in one moderately long day.

Although the method would be clunky (hey-evolution is clunky), the beauty is it would have the advantage of being in a very understandable medium.

Most people can wrap their heads around the idea of reaching into a bucket and pulling out a ball.

I’ve got a version of the algorithm you describe running on a 1960’s mainframe. With a possibly more “aggressive” fitness function and 100 32-character strings per generation, I get a cycle time similar to your 1 minute, and a run time of around 40 minutes.

Of course, this is probably not precisely Dawkins’ algorithm, since precisely one position is mutated in each candidate string. What you need to do is discard the bucket of numbers and replace it with one containing a very large number of red and black balls, with the number of red balls wrt the total number being proportional to the mutation rate. Each student works along their string, pulling a ball out of the bag for each position. If they pull out a red ball they replace the letter at that position with a random letter drawn from the bucket.

The problem is, of course, that the students will know what the correct letter for each position is, and so it is possible that latching (or as it should properly be called, “cheating”) may occur due to this inherent imperfection.

Kevin B said:

I’ve got a version of the algorithm you describe running on a 1960’s mainframe.

I’m sure the algorithm is quite nice, but I’m actually more fascinated by the idea that you have a 1960’s mainframe out in the garage…

stevaroni said:

I’m sure the algorithm is quite nice, but I’m actually more fascinated by the idea that you have a 1960’s mainframe out in the garage…

I’m still trying to get it running on my Babbage Engine. Machining the gears is taking some time …

Hey, if we’re going to dream, let’s dream Steampunk.

Anyone know a good soroban lubricant? Mine is starting to smoke.

I have the one shown in the upper picture.

Try sesame oil. It might not work but at least it’ll smell good.

Anyone know a good soroban lubricant?

No, but not long ago, I had to find some steam locomotive oil.

My father was a retired machinist, and apparently, at some point in every machinist’s life, they start dabbling with steam engines. Some of them even band together to dabble in really big steam engines.

Impressive hobby, but dramatically inconvienent, at least from a garage-space point of view.

Steam locomotives have very particular lubrication needs for their cylinders. Cylinders are (were) typically cast iron, with the resultant tendency to corrode unless protected, and the oil has to form clingy, films in an environment that’s very hot, subject to mechanical scraping, and bathed in steam that’s changing phase between dry and saturated five times a second.

The odd part is that there were companies that still make the stuff, although you had to buy a 55 gallon drum of it at a time. On the other hand, if you have a locomotive around, you know you’re going to use 55 gallons of locomotive oil, eventually, so you might as well keep it handy.

sswitaj said:

Anyone know a good soroban lubricant?

Steam locomotives have very particular lubrication needs for their cylinders. Cylinders are (were) typically cast iron, with the resultant tendency to corrode unless protected, and the oil has to form clingy, films in an environment that’s very hot, subject to mechanical scraping, and bathed in steam that’s changing phase between dry and saturated five times a second.

:-)

This is a particularly good context in which to bring up these properties of steam engine lubricants.

The ID/creationists’ criticisms of the Dawkins Weasel program revolve around “smuggling the answer into the program”.

But we in the science community know something they don’t. All systems in nature interact; not only with the surrounding environment, but the constituents of these systems interact with each other.

So the IDiot perceptions of Dawkins program are dead wrong.

The properties you describe for steam engine lubricants are a nice description of the gooey world of organic chemistry and biological systems.

Kevin B said:

I’ve got a version of the algorithm you describe running on a 1960’s mainframe.

While I was flying recently on a trip, I started outlining a version for the HP48/49/50 series of calculators. Then I’ll also try to replicate it for the TI-89 and the TI-83/84 series. I’ll be using vectors or lists instead of strings; it’s faster on these machines.

I think I may have to trim down the sizes of the target, parent, and offspring in order to keep from running the batteries down during the program execution. We’ll see.

It might also be useful to allow different probabilities for the mutations of each element; i.e., a different probability for going from “incorrect” to “correct” than for vice-versa. That would allow for latching as well as for investigating more realistic conditions that would suggest it more probable for mutations in the “correct” direction than in the “incorrect” direction as the offspring approach greater fitness.

stevaroni said:

Kevin B said:

I’ve got a version of the algorithm you describe running on a 1960’s mainframe.

I’m sure the algorithm is quite nice, but I’m actually more fascinated by the idea that you have a 1960’s mainframe out in the garage…

I don’t, but I know a computer museum that does.…

(Although “garage” is not a very good description of a building that was probably the first erected specifically to house an electronic computer.)

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This page contains a single entry by Richard B. Hoppe published on August 26, 2009 2:18 PM.

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