Dave Thomas posted Entry 2531 on August 21, 2006 10:45 AM.
Trackback URL: http://www.pandasthumb.org/cgi-bin/mt/mt-tb.fcgi/2526

They came for a contest that might someday be viewed as a pivotal moment in the eternal conflict between Darwin and Design.

On one side were the Intelligent Designers. They came from California and Alabama, New Mexico and England, Finland and the Netherlands, and from all around the world. They came from academia, and from industry, and from the armed services. They came armed with computer spreadsheets, home-made programs, graph paper and calculators. They applied trigonometry and calculus, intuition and insight, knowledge of minimal soap films and surface tension, database optimizing algorithms and random searches, and other techniques available only to Intelligent Designers. And they strived to answer the tricky question “What is the Steiner Tree (smallest possible network of straight line segments connecting six given points) for the network shown in “Take the Design Challenge!”

smalGrid.gif

On the other side were Evolutionary (or Genetic) Algorithms, in which herds of digital organisms were bred over many generations. Each organism was a string of numbers and letters, which were “transcribed” by fixed rules as representing some of the billions upon billions of possible candidate networks for the given problem. Those organisms whose lengths were smaller gained a slightly better chance at being a parent of one of the organisms of the next generation, and mutations of the strings were allowed to happen occasionally. In this process, no trigonometry or calculus was required. No information about characteristics of Steiner Trees was necessary. But, as the strings competed with each other, marvelous and unexpected designs began to appear.

critters.gif

Although most of the Intelligent Designers were not members of the “Intelligent Design” movement, which had been officially invited to respond, the ID community did indeed weigh in, via the efforts of Salvador Cordova, one of the IDers running the show at William Dembski’s blog Uncommon Descent.

So, what is the Answer? Did Salvador do better than Darwin? Did our team of Intelligent Designers find the True Steiner, or did they, like the evolutionary algorithm, find “MacGyver” (not-quite-perfect-but-extremely-functional) solutions also?

Readers, let’s enter the Design Room and meet our Winners!

Let’s waste no time in meeting some of the entries that were closest to the actual Steiner Tree for the given six points.

One of these was generated by an assistant professor of mathematics and computer science at a major state university, and the other was generated by the Genetic Algorithm I discussed back in July.

design1.gif

design2.gif

The interesting question now is, how can the Intelligently Designed answer be distinguished from the Evolved answer? Neither design is the exact Steiner solution, because one of our Designers might have rounded off too soon in his calculation, or perhaps mis-typed something somewhere along the line. If someone had access to the exact solution, they might be tempted to rule anything else out as “not designed.” But that’s not fair, according to Jonathan Wells’s new book, The Pig Ignorant Guide Politically Incorrect Guide to Darwinism and Intelligent Design, where on page 87 (Chapter 8), Wells writes

Nor does intelligence imply perfection. Some Darwinists criticize intelligent design on the grounds that some features of the natural world could have been made better. In other words, they argue that if something is not optimal, it is not designed. But things can be designed without being optimally designed. An automobile that is constructed in such a way that its fuel tank explodes whenever another vehicle bumps it from behind is badly designed, but it is designed nevertheless.

Before moving on to our other Winners, I’m issuing a Second Challenge, again open to all: using whatever ID theory you need (Explanatory Filter, Design Inference, whatever), show how this theory can be applied to the above two solutions to determine which was actually designed (e.g. “real” Complex Specified Information (CSI)), and which was evolved (and thus in possession of only the “appearance” of CSI).

Anyone can enter, but unlike the previous challenge, all contestants are asked to show their work. Again, e-mail your responses me at nmsrdaveATswcp.com (please replace the AT with an @), and do not post them as comments on this or other blogs. This new contest will be open for as long as needed (i.e. until the ID community makes a formal response), as it might take a couple of years for the top ID theorists to crack the case.

Let’s move on to the the Hall of Fame, and see what our industrious, hard-working Intelligent Designers came up with. It turns out that there are actually two perfect Steiner Trees possible: in one, the hexagonal grid is twisted counter-clockwise, and in the other, clockwise. Both Steiner Solutions are rotationally symmetric: like the Queen of Spades, they look the same if you spin them by 180 degrees. In addition to finding both of these solutions, the Genetic Algorithm (GA) production run I completed before issuing the challenge (300 simulations of populations of 1000 competing for 2000 generations each) found numerous other shapes, ten of which I’ve collected as official “MacGyver” solutions. I’ve tried to pick the MacGyvers to represent the various topologies (shapes) possible, but may have missed some. Many of our Intelligent Designers independently derived MacGyver solutions. Almost all of these were also found in the evolutionary simulation (the only ones not so appearing involved the overall shape above, but with flat horizontal segments instead of tilted ones). Interestingly, the Genetic Algorithm managed to find some interesting designs overlooked by all of the human contestants.

And the Winners Are…
Please - if I’ve made any mistakes in the following, do let me know and I’ll make corrections. There were so many entries, it became hard to keep track of them all!

The Exact Steiner Tree

steiner.gif

Kudos to George Atkinson, Bram de Beer, Paul Flocken, Virgil Keys, Alex Labram, Mike McCants, Ray Spurlin and Kim Van der Linde for nailing it, and showing us that the answer to this tricky problem can indeed be obtained via Intelligent Design!

All of these contestants came up with answers at or very close to the actual minimum length, 1586.53 units.

Congrats also to Kari Tikkanen for getting very close with the basic network, but with horizontal lines for the two long sideways-going segments; this length is also excellent (about 1591 units). Paul Flocken also designed this answer, but also kept after it until he acheived the true Steiner above.

Congrats also to those who simply visualized what the solution should be, qualitatively. That’s actually the hardest part of the problem, and kudos go to Bryan, Wes Elsberry, Dave Havlicek, Myron Souris, and Roy Thearle.

Additionally, Julian Onions also found the true Steiner, but did so with his own home-brewed Genetic Algorithm, thus providing independent confirmation that evolutionary processes can produce Designs.

While several Intelligent Designers found one or the other Steiner, it’s of interest to note the Genetic Algorithm found both.
GAsteiner1.gif
GAsteiner2.gif

First MacGyver

GA_Mac1.gif
My first calculations for this curious shape led me to think it was the Second MacGyver, when in fact it was the First. My apologies to those contestants whom I confused with this error.

Kudos for finding this solution go to Roy Thearle, Ray Spurlin, Duncan Buell, Kevin Vicklund, Matthew Vonk, and Salvador Cordova (our official IDM respondent). At a length of 1596.3 units, this shape is only 0.6% longer than the formal Steiner solution!

It is of interest to note that Salvador’s first response was simply a drive-by URL drop on August 15, 2006 at 08:59 AM. Then, Salvador derived the “double bowtie” (Tenth MacGyver) over at
UD on August 15, 2006 at 6:31 pm.

Cordova found a qualitative version of the above solution (First MacGyver), at UD on
August 15, 2006 at 11:12 pm
. After four more days of effort, Sal finally achieved the First MacGyver (and all four versions, too) at UD on August 19, 2006 at 5:04 pm.

While I appreciate his participation, this of course leads to some interesting new questions for Mr. Cordova. The first is, why did Salvador go the conventional route, finding web pages that discussed Steiner Trees or Fermat Points, and using trigonometry and algebra, like our other Designers? Why didn’t Salvador instead simply go get the answer from the Fortran listing of my genetic algorithm, as he said he could do in his Panda Food post:

Here is one of the many places where Dave sneaks the answer in:
Dave Thomas’s Code Bluff

This is especially ironic because Cordova claims that my Steiner GA is just “theatrics,” and equivalent to his so-called “Genetic Algorithm” for summing integers. Although Salvador insisted that “The solution was never explicitly stored anywhere” in his summing algorithm, I was able to show exactly how Cordova “front-loaded” his algorithm with the specific solution desired. I did not simply go out and look up the formula N(N+1)/2 in a book - I reverse engineered Cordova’s Code to see how his answer was sneaked in. So, if I’m sneaking in the answer(s) with the Steiner GA, exactly where is that front-loading being performed?

Another question. Salvador, if we gave you a tee shirt with a bullseye on it, and told you to wear it so that you could find and shoot yourself in a game of paintball, would you be still be able to hit the Target?

My last question for Mr. Cordova is: what is it going to be like having to go to Bill Dembksi and admit that you’ve learned the hard way of the true meaning of what Daniel Dennett terms Leslie Orgel’s Second Law: “Evolution is smarter than you are“? Even after a week’s worth of effort, you still couldn’t find the correct Answer. You were close, but it’s Charlie Darwin (along with some very Intelligent Designers) who got the cigar. I predict there’ll be some ‘splainin’ to do backstage at Uncommon Descent.

Second MacGyver
GA_Mac2.gif

Unlike the First MacGyver, the Second MacGyver has eye-pleasing symmetry, and was engineered by several of our industrious Intelligent Designers. At a length of 1619.7 units, it is but 2.1% longer than the optimal Tree. Kudos to Ron Bear, Matt Brauer, Duncan Buell, Reed Cartwright, Otto Froehlich, I.R. Pen, John Shipman, Lance Stewart, and Kevin Vicklund..

Third MacGyver
GA_Mac3.gif
Only Darwinian processes found this optimal form of curious shape, weighing in at around 2.3% longer than the formal Steiner. However, Andrew McClure ran a Random Search algorithm for 24 hours, and found a topologically-correct (but severely distorted) version of the Third MacGyver on the 3,191,313th iteration.

Fourth MacGyver
GA_Mac4.gif
Again, only the Genetic Algorithm found this odd shape, coming in at 3.4% longer than the best solution.

Fiifth MacGyver
GA_Mac5.gif
This pretty bilaterally-symmetric design was found by the GA, and also by Kevin Vicklund, and is 4.2% longer than the ideal tree.

Sixth MacGyver
GA_Mac6.gif
Only the GA found this artistic rotationally-symmetric shape, at 5.3% longer than the official solution.

Seventh MacGyver
GA_Mac7.gif
Again, only the GA found this odd shape, at 5.7% longer than the optimum.

Eighth MacGyver
GA_Mac8.gif
This solution was derived by Reed Cartwright and Kevin Vicklund, and is 7.2% longer than the formal answer. There are several equivalent networks, forming an M or W instead of an S, and all with length 1700. A horizontal line through three verticals would also yield the same length (kudos Kim Johnson. Many of these fit the “Traveling Salesman Problem” class of solutions (i.e. having no internal “Steiner Points” for making connections).

Ninth MacGyver
GA_Mac9.gif

Again, only the GA found this curious tree, at 13.5% longer than the Steiner.

Tenth MacGyver
GA_Mac10.gif

This elegant design was found by Kevin Vicklund, who, while not getting the Steiner itself, is commended for finding five different MacGyvers. Evolution may be smarter than Kevin, but Kevin is doing a great job catching up, and is hereby named the Master of MacGyvers for this contest! Credit also to Salvador Cordova for finding this shape as his first serious attempt, as was mentioned previously.

I got into the six-point problem by trying to find the network that could produce the Double Bowtie as its Steiner Solution. Without giving the matter a great deal of thought, I started a simulation to look at the six-point problem, figuring that I might get lucky and snag a Double Bowtie or two from the run. But, when I sat down to review the solutions, the Double Bowtie was nowhere in sight. In fact, to get the image of the Double Bowtie shown above, I had to deduce its DNA pattern and feed it directly into my plotter routine. I had to chuckle at myself when I realized that at 1839.2 units in length (almost 16% longer than the optimal solution), the Double Bowtie would always be out-competed by shorter, tougher MacGyvers.

However, looking over the simulation results, I noticed that the best answers indeed came from a mutated version of the Double Bowtie, in which the four segments connecting the middle two points (2 and 5) could be replaced by only three segments in the shape of a dog-leg, and that this could be realized by tilting both Bowties at a slight angle, either clockwise or counter-clockwise. And so I learned that Evolution is smarter than me, too. Once I stopped chuckling, I realized that this was an excellent example of a problem with no obvious answer, and a good candidate for the Design Challenge, which followed shortly thereafter.

Honorable Mention

Kim Johnson derived “The Asterisk,” in which two long diagonals and one vertical all meet in the center of the figure, forming an asterisk shape. This has length 2009 units.

And Rupert Morrish sent in this whimsical answer:
ID6nodeGrid.gif

CONCLUSION

In The Pig Ignorant Guide Politically Incorrect Guide to Darwinism and Intelligent Design, Wells writes

Ferry passengers entering Victoria Harbor in Canada are greeted by a bank covered with flowers that spell out “WELCOME TO VICTORIA” in large letters. Everyone who sees the greeting knows immediately that it was intelligently designed.

Likewise, anyone who comes across one of the Steiner or MacGyver designs shown in the Design Room would probably infer design, especially if they knew of the effort required to derive such designs. But, given that these “designs” can also be found simply by breeding herds of alphanumeric strings, it becomes clear that evolutionary processes can also produce the appearance of design.

To those Designers who found “MacGyvers” instead of the official Solution - pat yourself on the back. You have helped to show that the McGyver solutions are Complex Specified Information in their own right.

Expect to see more of the typical ID/creationist reactions to these results. We will hear (again) that the GA won’t run if program lines are switched or mangled randomly, as if this means anything. I mean, really - if all the oxygen atoms in the world were suddenly replaced with sulphur atoms, wouldn’t Life cease immediately? And the point is…?

When I showed this algorithm to William Dembski in 2001, he dismissed it as mere “frontloading” of the answer via the GA’s fitness function. But what such “frontloading” really entails is the erroneous belief that simply Asking a Question is sufficient to produce the Answer. We all know from personal experience that not all Questions have obvious Answers.

And, we’ve learned this past week that answers to the question “What is the Steiner Tree for a given network?” are anything but obvious. Thanks to all of the many contest participants who sent in their designs. You have participated in a unique experiment that puts Darwin and Design to the test under precisely controlled conditions. I appreciate and applaud your earnest efforts!

P.S. Contestants, if you are feeling a need for some new puzzles to engage the ol’ brainpan, check out the Pirate Chest Challenge over at NMSR.

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Comment #121277

Posted by Kim on August 21, 2006 11:14 AM (e)

Yeah, an evolutionary biologist working in intelligent design…. This problem was quite easily to do with an excel spread sheet, and realizing that the problem can be reduced to half a problem as the starting point is symmetric. It would become rapidly impossible to solve it in such a way when the symmetry is broken, or when the number of line elements is increasing.

Comment #121281

Posted by hooligans on August 21, 2006 11:26 AM (e)

Mr. Thomas!

Kudos to you! This series of posts, for me, was spellbinding. I’ll admit that I await, with baited breath, the response by Salvador. I hereby predict that Salvador will attempt to dismantle your code and show it doesn’t work when a particular part is removed. This, of course, will be his evidence that you frontloaded an answer. This avoids him actually having to prove (show) where the answer is and demonstrating that you have frontloaded the code.

He has already stated that the code wouldn’t exist without you, therefore the natural process that it is designed to demonstrate must be intelligently designed. Even to a rookie like me, this argument is ridiculous. Your code attempts to copy an observed natural phenomena (RM +NS). According to his logic any program that simulates a observed natural phenomena, like the law of gravity, demonstrates the law of gravity is intelligently designed.

Well done!

Comment #121282

Posted by ofro on August 21, 2006 11:27 AM (e)

Kim said:

This problem was quite easily to do with an excel spread sheet, and realizing that the problem can be reduced to half a problem as the starting point is symmetric.

I am not following. Isn’t the exact Steiner solution asymmetric?

Comment #121289

Posted by juju-quisp on August 21, 2006 11:38 AM (e)

NNNEEERRRDDDSSS!!!!!!!

Comment #121295

Posted by Kim on August 21, 2006 11:51 AM (e)

ofro wrote:

I am not following. Isn’t the exact Steiner solution asymmetric?

Well, I came to the exact value using symmetry, so no, not in this case. Which is of course logical as the starting point is symmetric.

Comment #121297

Posted by João on August 21, 2006 11:52 AM (e)

ofro wrote:

Isn’t the exact Steiner solution asymmetric?

It is symmetric under a 180 rotation around (400,150), the “center” of the six points given.

If you assume (prove?) that then the problem reduces to a four-point one. (3 original, e.g. the two left and the top-middle, plus the “center”.)

Comment #121299

Posted by Ian Menzies on August 21, 2006 12:13 PM (e)

Well, I don’t know if the true Steiner Tree is symmetric (though it’s probably a safe assumption), but the symmetry (or lack thereof) of a given solution is (I think) a big clue as to whether or not that solution was designed by a person, as opposed to a GA.

Comment #121301

Posted by PvM on August 21, 2006 12:15 PM (e)

Excellent posting. Sal is often quick to make assertions but often very slow to support them in any manner, exhibiting the typical scientifical vacuity of Intelligent Design.
As for Wells… Sigh, it seems his latest book is not much better than his ill fated Icons…

Comment #121304

Posted by Dave Thomas on August 21, 2006 12:30 PM (e)

Ian Menzies wrote

Well, I don’t know if the true Steiner Tree is symmetric (though it’s probably a safe assumption), but the symmetry (or lack thereof) of a given solution is (I think) a big clue as to whether or not that solution was designed by a person, as opposed to a GA.

The True Steiner is rotationally symmetric, like a playing card, as noted above.

Symmetry is nice, but is found in many MacGyvers, as well as the actual Steiner itself (see the Second, Fifth, Sixth, Eighth and Tenth MacGyvers for examples).

Dave

Comment #121305

Posted by W. Kevin Vicklund on August 21, 2006 12:35 PM (e)

ofro wrote:

I am not following. Isn’t the exact Steiner solution asymmetric?

No, as near as I can tell with the Mark I Eyeball, the exact Steiner solution exhibits odd symmetry. That is, you can rotate it 180 degrees and it will look the same. Most people think only of even symmetry (also known as mirror symmetry) when symmetry is discussed.

I admit, I did not formally submit all of the solution families I considered, mainly because I already knew that a shorter solution existed.

The ones I considered but did not formally submit were the 3rd, 7th, and 9th (or variations thereof). One thing of note is that the 5th solution family actually consists of 4 unique solutions and a total of 12 solutions, IIRC.

I also visualized the Steiner Solution (by twisting the 2nd), but couldn’t figure out a way to calculate the actual points using graph paper, pencil, and simple geometry and trigonometry (note, I didn’t even use a straightedge!). My problem? Too many variables. My solution would have been to create some 120 degree Y’s and arrange them on the page until they all lined up - a rather Darwinian process.

Anyway, I’m going to pop in the first season of MacGyver this week to celebrate.

Comment #121308

Posted by Andrew McClure on August 21, 2006 12:39 PM (e)

Thanks, Dave, for having provided such an amusing way for wasting part of my weekend! :)

If anyone is curious, the random search program I wrote is at:

http://vote.grumpybumpers.com/tornado.txt

And a second script for turning its results into animated GIFs is at:

http://vote.grumpybumpers.com/gif-tornado.txt

I figured that as long as we were having a contest between evolution and design, it would be fun to submit a solution on behalf of the proverbial “Tornado in a Junkyard” which serves as a straw man of evolution in so many creationist arguments. So I wrote a program which was as close as I could figure to the “random search” algorithm which, in Dembski’s writings about the “no free lunch” theorems, we are given the impression that evolution is incapable of performing better than at solving problems. The program repeatedly generates entirely random attempts at a Steiner solution using a method of construction and “fitness function” similar to Thomas’ FORTRAN evolution program, keeping a running record of the best solution it has found so far as it goes. The program is also written in Perl, which itself tends to resemble a tornado in a junkyard.

You can see the progress of the program in this animated GIF, which has one frame for every time the random search found a new minimal proposed solution:

http://vote.grumpybumpers.com/tgif2.gif

The final frame shows the best proposed steiner solution the tornado program ever found. (I’ve still got it running, actually, but it never did find a solution better than that one.) This “solution” is 1674.3 units long, which incidentally is poorer performance than Thomas’ evolutionary algorithm achieved either overall or for the specific graph topology that the tornado solution represents– even though Thomas’ genetic program only ran for about 200 generations to find that solution, and the tornado search has been running for over a full day. This should of course be no surprise to anyone with the slightest amount of familiarity with algorithms. Whether it would be a surprise to a reader of Dembski’s “no free lunch” is another question :)

Comment #121309

Posted by W. Kevin Vicklund on August 21, 2006 12:43 PM (e)

Dave, are you going to release the new code?

Also, do we get a chance to see soap film solutions?

It should be noted that I submitted both symmetric and asymmetric solutions. Symmetry is not a reliable indicator of intelligence in this case.

Comment #121310

Posted by Ray Spurlin on August 21, 2006 12:53 PM (e)

Dave, thanks for an intriguing and illuminating puzzle.

I found the tenth MacGyver early on when attempting to solve the problem by reduction - two four node trees. As a designer, I realized quickly that removing just one of the connections to either center point would result in a significant reduction in line length. I would expect evolution to find this solution earlier on, as it has no built in bias towards symmetry, as many of us humans do. Of course with pressure to reduce total line length, it would also be discarded soon after in favor of better answers. It did in fact lead me to the first MacGyver solution and ultimately to the actual answer.

Comment #121311

Posted by Ray Spurlin on August 21, 2006 1:02 PM (e)

Regarding symmetry, the actual Steiner solution can be flipped vertically about the horizontal centerline with no change in total line length. The diagram above seems to indicate differently. Likewise, the first MacGyver can be flipped about either the horizontal centerline or the vertical centerline yielding 4 equivalent solutions. I wonder if in Dave’s genetic code they could interbreed or would they be an example of speciation?

Comment #121317

Posted by Kim on August 21, 2006 1:40 PM (e)

It is point symmetry, also resultng in rotational symmetry. What is important, is that if you know that single point (in the middle between the mid points), you only have to calculate the distances of one halve to get to the answer.

Comment #121336

Posted by Dave Thomas on August 21, 2006 3:13 PM (e)

Kevin Vicklund wrote

Dave, are you going to release the new code?

Sure, why not! I’ve placed the code on PT, here, putting the date as way back in July so as not to clutter up the PT main page. (But it might confuse time-travellers!)

Also, do we get a chance to see soap film solutions?

I haven’t made any for the 6-point problem. None of the contestants reported trying that either. My guess is that Salvador doesn’t like going to the Lab - it sure would have been an easy way to derive the Solution.

It should be noted that I submitted both symmetric and asymmetric solutions. Symmetry is not a reliable indicator of intelligence in this case.

Agreed!

Dave

Comment #121349

Posted by Marshall on August 21, 2006 4:10 PM (e)

Dave,

Congratulations! An absolutely superb and challenging experiment. And funny too. ;-)

Marshall

Comment #121351

Posted by David B. Benson on August 21, 2006 4:14 PM (e)

Dave Thomas: This was well done, indeed! I encourage making comparisons between GA and RA(Random Algorithm) by the number of generations multiplied by the number of individuals versus the number of random attempts for a solution. Not only does this seem ‘fair’, but it is enough to demonstration how quickly GA develops a ‘good enough’ solution in comparison to RA’s stumbling in the dark…

Comment #121364

Posted by Weka on August 21, 2006 6:00 PM (e)

Dave, would you please provide a very careful, concise and clear list of exactly which point or points in the evolution/creation debate this demonstration was created to address?

I was browsing the UD weblog and from comments I saw there you run the very real danger that your GA will run into the same misinterpretation/ misrepresentation problems as Dawkins’ “Methinks it is Like a Weasel” algorithm: namely, that people will attempt to claim that it is supposed to prove points, or simulate situations, that you never intended.

The problem with this is:

1) It is easy for opponents to obscure the points you are making by bringing in irrelevant scenarios.
2) If an opponent can show that your GA is simplistic or unrealistic for their artificial scenario, then they can dismiss all of your demonstration without addressing the specific points you make (essentially using your demonstration as their straw man).

Comment #121368

Posted by Frank Sullivan on August 21, 2006 6:22 PM (e)

I am not sure I understand why it is fallacious to build the “Answer” into the fitness function. If you’re level of “fitness” is defined as the extant at which you match the phrase “WILLIAM DEMBSKI IS A BOOB”, then isn’t it appropriate to save that phrase as a constant somewhere and compare strings at each generation in order to judge your level of fitness?

Comment #121371

Posted by secondclass on August 21, 2006 6:44 PM (e)

Frank, the idea is to show that a dumb algorithm can come up with a specific, hard-to-find solution. IDers say that Dawkins’s WEASEL program is cheating because the answer is built into the program, which of course it is. Dave’s program addresses that complaint.

Comment #121372

Posted by Dave Thomas on August 21, 2006 7:00 PM (e)

Weka, Frank, this post is a continuation of a thread started earlier this summer, Target? TARGET? We don’t need no stinkin’ Target!

The purpose of the “Target” post was simply to show that Genetic Algorithms can produce elaborate designs without anything like the actual form of those designs being fed into the fitness test.

As explained there, IDers and creationists alike have all latched onto Dawkins’ “Weasel” algorithm as evidence that all genetic algorithms need to have the final answer snuck into the fitness test. You’ll find several references of exactly that happening in July’s “Target” post. It’s not just creationists, but ID stalwarts like Meyer and Dembski too.

So the “strawman” I’m going after is the undeserved “guilt by association” linkage of any and all GA’s with target-specific simulations like “Weasel.”

The second major aim of this work is to directly address the ID claims that any novelty produced in a Genetic Algorithm is “frontloaded” in the algorithm itself. If such “frontloading” was being done in my Steiner GA, then anyone looking at the source code should be able to determine where the algorithm will go. Not one person from the ID community stepped up to demonstrate this.

And the third aim was to provide a Test for the detection of “real” versus “apparent” CSI. If Intelligent Design Theorists can indeed identify when something has or has not been “designed,” as they claim they can, then they should get cracking to decide which of the two networks shown above (just below the fold) was produced by a human Intelligent Designer (a college computer sci prof, by the way), and which was produced by simulated mutation and natural selection on a population of strings over many generations.

I hope that helps.

Dave

Comment #121376

Posted by Lurker on August 21, 2006 7:37 PM (e)

Well done, Dave.

But I think the IDer’s complaint that the Steiner solution is prebuilt is to some extent valid. There exists a unique global minimum (but not necessarily a unique configuration of the tree) for the problem. Thus, the GA will always tend towards that solution.

May I propose a defeater to the “front-loading” argument? Allow your metric to vary subtly per generation of your GA. One simple way to extend it is to vary the exponent of your distance metric according to, say, a Gaussian distribution, centered about 2. In other words |x-y| = sum (xi-yi)^p, where p is a random variable with mean of 2. You can further complicate the problem by introducing uncertainty in the locations of the terminal points.

Now, there is no fixed landscape for which a unique fitness value describes all global minima. Would the GA still tend towards the exact SMT? I suspect it would… or perhaps additional behaviors might manifest, such as the GA alternating between configurations that tend to be robust for extremal cases.

Comment #121381

Posted by Patrick on August 21, 2006 7:50 PM (e)

Whoo! I found the first MacGyver, but I never sent it in because I wasn’t able to figure out the length exactly.

Comment #121408

Posted by Tulle on August 21, 2006 8:29 PM (e)

Dave, I am a software engineer and am very interested in playing with the code. You posted SteinerGAdlg.cpp code, but without the header files and resources it is not easy to recreate, and being the lazy guy that I am, I am not willing to spend the few days it would take to reverse engineer the code. Is there any way for me to get the complete code? Either way, thanks for listening.

Comment #121421

Posted by Dave Thomas on August 21, 2006 9:09 PM (e)

Tulle wrote

Dave, I am a software engineer and am very interested in playing with the code. You posted SteinerGAdlg.cpp code, but without the header files and resources it is not easy to recreate, and being the lazy guy that I am, I am not willing to spend the few days it would take to reverse engineer the code. Is there any way for me to get the complete code? Either way, thanks for listening.

Not out of the question, but I would be reluctant to release the entire code in its present form. It’s got some non-standard stuff, such as writing the best of every nth generation off to a text file in folder C:\dt\text for subsequent review of the results of an all-night run in just a few minutes. But, if you don’t have that folder on your box, it Bombs. When I get it more user-friendly (for example, a File button to let you choose an output file name if desired), I might be willing to let it out the door. It does currently have all sorts of nice GUI features, like reading/writing problem geometries, editing and/or mouse-digitizing same, etc., but there are still too many undocumented features for me to let it out the door. Empty nest syndrome? Maybe. But the C++ listing covers everything needed for the GA itself, so you could certainly try to implement some of that in your own testbed, as Julian Onions did with his.

Give me a week or two to ponder/clean up/etc.

Dave

Comment #121423

Posted by Frank Sullivan on August 21, 2006 9:29 PM (e)

Please forgive me. I just finished reading the “Target? TARGET? We don’t need no stinkin’ target!” post, including the explanations you quoted from John Bracht, and while I appreciate that you are going through all the trouble to jump through the hoops that the ID’ists are throwing at you (I’m truly impressed by all of this), I still cannot understand what their complaint is.

It seems to me like they want to remove anything resembling a fitness function from the program. But if you do that, then all you have is randomness, without anything simulating natural selection. Am I erecting a straw man here, or are they that stupid? Of course, in order to simulate Evolution, you MUST have some function that is capable of SELECTING those organisms which are the “fittest.” Complaining about the 5-point Steiner program because it, “[selects] for networks that (1) connect all five points, and (2) have shortest path-length” seems, to me, like complaining about Alaska because it selects for organisms that (1) are white, and (2) have fur and layers of fat to keep them warm.

I don’t even fully understand why targeted GA’s are a problem, even after Dawkin’s explanation of it. I’m not saying they’re NOT a problem; just that I can’t grasp why.

Comment #121430

Posted by CJ O'Brien on August 21, 2006 10:08 PM (e)

Hmmm.
No trackback, no triumphalist crowing?

Where’s the brilliant engineering squad at UD?

Anything to say, Sal? Anything at all? Or are your thoughts no more profound than the sound I hear, which is the proverbial crickets chirping?

Comment #121438

Posted by juju-quisp on August 21, 2006 10:56 PM (e)

I’ll bet your pocket protectors are overstuffed. Goddamned nerds.

Comment #121475

Posted by caligula on August 22, 2006 2:52 AM (e)

Lurker wrote:

But I think the IDer’s complaint that the Steiner solution is prebuilt is to some extent valid. There exists a unique global minimum (but not necessarily a unique configuration of the tree) for the problem. Thus, the GA will always tend towards that solution.

It is trivial that the GA will *functionally* tend towards the formal solution. But in this case, the “function” is simply to be short, i.e. to save energy. Could you show that the GA will also *structurally* tend towards the formal solution? I don’t think so. Instead, the MacGyvers show great diversity both in the detailed structure of the solution (“phenotype”) *and* in the respective “DNA”. Even when static, the fitness landscape in this demonstration is hardly one giant hill.

Comment #121485

Posted by Inoculated Mind on August 22, 2006 3:45 AM (e)

Dave, this was a thoroughly brilliant investigation, and I learned a lot about a subject altogether foreign to me. My sister is a mathematician, and she’s told me a bit about soap films, but I think this whole exercise was very beneficial. Also, I’m surprised that William Dembski didn’t participate, maybe he anticipated being beaten by evolution??

Anyhow, there is one flaw I think in how this was carried out - and that is, what to think of the results. Correct me if I’m wrong, but did Salvador Cordova in any way state an opinion about the fairness of the project? When James Randi debunks charlatans, he gets them to say on record how fair they thought the test was. Most of the time, they are fully confident that it was fair, and then when Randi reveals that they did no better than chance, they are caught. They grumble and make up excuses afterwards, but they have been caught on tape saying that they were 100% sure that it was fair, and sure that they were successful.

So now that the project is over, Salvador Cordova will be spinning like a flagellum, making excuses and denying the meaningfulness of the contest. Did Sal make any admission or statement that could show that he was confident about it, and sure that design would beat out evolution?

Seriously, we need to treat these people like psychics… they will spin and spin until they barf - but they will never admit that any test was fair after they hear the results.

Comment #121486

Posted by Anonymous_Coward on August 22, 2006 3:46 AM (e)

And let’s not forget that back in the real world, “solutions” may not need to be optimal. I don’t think 2% makes too much of a difference to survival. Afterall, we’re all MacGuyvered solutions ourselves.

Comment #121507

Posted by Sparx on August 22, 2006 5:26 AM (e)

I posted this series of panda posts on metafilter. Looking back I could have described the post sequence better in the front page description - though the format demands brevity and interestingness so I played upp the challenge, possibly to its detriment. But within the thread I flatter myself that I described the essential basics of the results in four shortparagraphs.

I like the writing thing, and I was following this experiment in all its aspects with interest from it’s start - as I said within, it’s a very visually descriptive example of how a raft of concepts work, so I can only applaud Mr Thomas for its design and execution. But I am interested in improvement, so if I got any nuances or facts wrong I would like to apologise and be instructed. Suggestions welcome.

Comment #121509

Posted by Lurker on August 22, 2006 5:53 AM (e)

“Could you show that the GA will also *structurally* tend towards the formal solution? “

Well, actually you could. You can think of Dave’s GA as a local optimization routine coupled with a metaheuristic global optimizer, such as simulated annealing. There are proofs for SA that as the number of trials approaches infinity the probability of achieving the global minimum is 1. All Dave had to do was wait long enough for the space to be sufficiently well sampled.

As for the local optimizer, consider Dave’s Transcribe() function was designed with a structure that would permit fairly smooth transitions from parent to child. From my initial scan of the code, each coordinate was integer, given a max of 999, and so the GA was merely crawling along a reduced search space of finite grid points. Now, look at the Mutate() function, and you can see that he jury-rigged the mutation rates on his organism’s DNA to minimize mutations in # of steiner points. Further, it is restricted to a preset m_varbnodes variable. How would a GA know a priori to limit m_varbnodes to m_fixdnodes - 2? This is strictly a mathematical result – a MacGyver heuristic, if you will.

The net effect was that the complexity of the problem was severly restricted from its initial presentation. This design is, I suspect, so that Dave could get an answer within his lifetime, and punish Sal in a timely manner. But it doesn’t escape the fact that the GA had a helping hand in a number of ways.

Having said all of that (I feel like I am doing all of Sal’s work for him), let me say that I personally do not buy into the jury-rigging/ front-loading argument about Darwinian evolution. Existence proofs of a solution does nothing to demonstrate the actual construction of the solution itself. Design is about the latter, and the fact that Sal failed to construct something a GA could is for me quite telling. To generalize, it may well be that our Universe permits the existence of many mechanical solutions to dilemmas facing organisms on the planet Earth. But the fact that some of these solutions do exist, despite an absence of a handbook that describes the construction of these solutions, requires a person to take a theory like Darwinian evolution seriously.

Comment #121515

Posted by Sam on August 22, 2006 6:53 AM (e)

“Could you show that the GA will also *structurally* tend towards the formal solution? “

Well, actually you could. You can think of Dave’s GA as a local optimization routine coupled with a metaheuristic global optimizer, such as simulated annealing. There are proofs for SA that as the number of trials approaches infinity the probability of achieving the global minimum is 1. All Dave had to do was wait long enough for the space to be sufficiently well sampled.

Wouldn’t the fact that the formal solution is in a significant minority of achieved results disprove that? I mean, you could think of it like that, but you’d be wrong.

Comment #121517

Posted by Lurker on August 22, 2006 7:02 AM (e)

“Wouldn’t the fact that the formal solution is in a significant minority of achieved results disprove that? I mean, you could think of it like that, but you’d be wrong.”

How would being a minority prove that the exact SMT would not necessarily be found later?

Comment #121522

Posted by Popper's ghost on August 22, 2006 7:13 AM (e)

But I think the IDer’s complaint that the Steiner solution is prebuilt is to some extent valid. There exists a unique global minimum (but not necessarily a unique configuration of the tree) for the problem. Thus, the GA will always tend towards that solution.

This is incorrect, as was demonstrated by Michael Suttkus, II’s comment about his poker hand GA in the “Calling ID’s Bluff, Calling ID’s Bluff…” thread:
http://www.pandasthumb.org/archives/2006/08/call…

I repeat here what I wrote there about it …

Michael Suttkus, II wrote:

The highest possible poker hand, a royal straight, never appeared. If “the solution” was hard coded into the selection routine, this should have been it, but it never appeared in all the times I ran the simulation. This makes sense, of course. Building pairs allows step by step improvement, but in poker a four-card straight isn’t particularly better than a three-card straight. You either have a full five-card straight or you don’t.

This is the most significant comment here, as it completely puts the lie to Sal’s BS. This point about the unevolvability of straights is the true version of creationist canard “what good is half an eye?” — an argument that Sal conveniently ignores in this case. Simply stating the optimization criterion — shortest network, highest hand, or accurate image formation — isn’t sufficient to reach it, there has to be an evolutionary path, as there is for Steiner networks and eyes but not for poker hands. If the optimal Steiner network is implicit in Dave Thomas’s GA, then the eye is implicit in biological evolution. If Dave Thomas’s GA is a case of “smoke and mirrors”, then so is biological evolution. But in any case, biological evolution is capable of producing the biological systems we observe, and the IDist arguments against it are thoroughly refuted.

Comment #121523

Posted by Sam on August 22, 2006 7:16 AM (e)

I’d think it was because the pathways found would preclude other solutions. Once the shorter fitness function has done its work you are left with a subset of naturally selectable alternatives. With “naturally selectable” being equivalent to the fitness function for the purposes of the model. MacGyvers won’t mutate into “better”/shorter Macgyvers.

I feel this very strongly - though admittedly I am not able to say categorically until the code is released.

Comment #121524

Posted by Popper's ghost on August 22, 2006 7:32 AM (e)

until the code is released

It has been – see http://www.pandasthumb.org/archives/2006/08/desi…

Comment #121528

Posted by caligula on August 22, 2006 7:49 AM (e)

Lurker wrote:

You can think of Dave’s GA as a local optimization routine coupled with a metaheuristic global optimizer, such as simulated annealing.

An interesting claim, and IMO extremely relevant if true. Browsing through the code, I failed to spot where it is using metaheuristics to prevent getting stuck in local optima. As in “cooling down” mutations when making nice progress and “heating up” mutations when stuck. Could you be more specific here, please? I still believe Thomas’ GA can and does get stuck at local optima…

Now, look at the Mutate() function, and you can see that he jury-rigged the mutation rates on his organism’s DNA to minimize mutations in # of steiner points.

Hmm. Yes, point mutations in the DNA apparently don’t have uniform probability regardless of “locus”. Seems unnecessary to bias the mutations in this way. Not sure how fatal this is, but I’d like to see Dave’s explanation. (Your previous point in my opinion is fatal if shown true, however.)

Further, it is restricted to a preset m_varbnodes variable.

Limiting the number of extra nodes to four was clearly advertised by Dave Thomas well beforehand. I don’t think anyone disagreed. Yes, more extra nodes would mean a much wider space of possible end results, and much more diverse starting points. But I think even the current practice ensures that the vast group of MacGyvers is still vastly outnumbered by other kind of results. I consider this to be practical in a rather harmless way.

Comment #121529

Posted by Lurker on August 22, 2006 7:49 AM (e)

“Simply stating the optimization criterion — shortest network, highest hand, or accurate image formation — isn’t sufficient to reach it, there has to be an evolutionary path, as there is for Steiner networks and eyes but not for poker hands.”

I agree. But, the existence of an evolutionary path depends on the designed landscape used in the GA. Consider if in searching for the royal flush, you constrain the problem such that all hands initially start with K,Q,J of the same suit. The search problem is considerably simpler than if it started with some random set of hands. Also, note what Suttkus wrote,

“but it never appeared in all the times I ran the simulation.”

This is also something else I pointed out. A solution exists. Dave had to constrain the problem so that he could achieve the SMT within his lifetime. Combinatorial optimization problems are typically finite (perhaps inpractically so, but that is a different problem altogether).

“If the optimal Steiner network is implicit in Dave Thomas’s GA, then the eye is implicit in biological evolution.”

This is most definitely false. DA’s GA is explicitly teleological. It aimed to solve a problem, quite well posed by the metric and the search mechanism. The notion of biological organisms solving “problems” is on the other hand quite problematic, for the simple reason that there is no single specified problem an organism has to solve. Problems change all the time in biological evolution. This is why I proposed a stochastic modification to DA’s GA as a defeater to the “front-loading” argument.

Comment #121530

Posted by Popper's ghost on August 22, 2006 7:51 AM (e)

Dennett’s notion of cranes and skyhooks can be applied here. There are all sorts of systems that would be more effective in terms of the “produce viable offspring” global optimization function (top-down skyhook), but never occur because they can’t be reached via bottom-up cranes. A global optimization function does not guarantee that an optimal solution will be reached, and there is no meaningful sense in which the solution is implicit in the function, any more than the solution to the three-body problem is implicit in its statement, or the proof of Fermat’s Last Theorem is implicit in its statement. One can say that the Steiner network solution is implicit in the program as a whole, but only if one can say that extant biological systems are implicit in the mechanisms of biological evolution.

Comment #121531

Posted by Lurker on August 22, 2006 7:56 AM (e)

Let me suggest something to think about: Everyone here is so focused on the _instance_ of a solution to the SMT problem. Try focusing instead on the emergence of higher order strategies developed by GAs, instead. For instance, can a GA evolve the heuristic of minimizing trees by parts? Could a GA evolve robustness?

Comment #121534

Posted by Lurker on August 22, 2006 8:02 AM (e)

“A global optimization function does not guarantee that an optimal solution will be reached, and there is no meaningful sense in which the solution is implicit in the function, any more than the solution to the three-body problem is implicit in its statement, or the proof of Fermat’s Last Theorem is implicit in its statement.”

A global optimization strategy can be demonstrated to locate a global minimum, provided it exists. A simple naive search is a global optimization strategy. What you are talking about is the notion of tractability. I have never argued that SMT problems need be solvable in a given amount of time. In fact, I believe the problem is known to be NP-complete.

But I agree with you it is meaningless to suggest that by asking the question, the answer is already implicitly there. That is in the domain of existence proofs. As I said, constructions (i.e. designs) are much more difficult problems. And it is telling that trial-and-error approaches beat out a lot of supposedly “intelligent” designers.

Comment #121535

Posted by Popper's ghost on August 22, 2006 8:06 AM (e)

A solution exists.

Sure, but I have no idea why you think that is relevant.

“If the optimal Steiner network is implicit in Dave Thomas’s GA, then the eye is implicit in biological evolution.”

This is most definitely false. DA’s GA is explicitly teleological. It aimed to solve a problem quite well posed by the metric and the search mechanism.

It’s most definitely true, and it’s incoherent to call the GA “teleological”. The program no more aimed to solve a problem then evolution aims to solve a problem; both are algorithms that operate mechanically, and the outcome is a consequence of their operation. That the metric and search mechanism will have a certain outcome is a deduction that we make by analyzing the algorithm. The only teleological factor is Dave’s intent of finding a solution by running the algorithm; the GA algorithm itself is not the sort of thing to have intentions.

Comment #121538

Posted by Lurker on August 22, 2006 8:11 AM (e)

“The only teleological factor is Dave’s intent of finding a solution by running the algorithm; the GA algorithm itself is not the sort of thing to have intentions.”

Strawman. I explicitly said “DA’s GA” is teleological.

Popper’s Ghost, if you don’t mind, I’m going to cut this short. I’d rather not have any discussions with you, as you are from my experience as abrasive as the Christian fundamentalists we have to deal with routinely. You don’t think. You merely react.

Comment #121540

Posted by sam on August 22, 2006 8:12 AM (e)

It has been — see http://www.pandasthumb.org/archives/2006/08/desi…

Yes, but http://www.pandasthumb.org/archives/2006/08/desi…

that’ll take some time.

That said - my first inclination when Dave posted his original code was to take it and run it through as many generations as my CPU could stand to see if it did end up in a final Steiner solution regardless. It doesn’t. The pathways, once traversed, seem somewhat unique - backtracking doesn’t occur both because of the limitations imposed on mutable qualities and the fitness function (I’ve been wrong before so it was good to test it). Such was my guess, but it’s appropriate - a penguin will not evolve into a polar bear as a result of mutation, even though their fitness functions are all about survival in the cold (to simplify it horrendously).

It’s getting late and I can already see ways I have not been clear. And on preview heavier math theory guns than I are loading up (I have a potato gun). See you in the morning - but I would like to thank Mr Thomas for his fascinating experiment and the excellent commentary it has engendered.

Comment #121543

Posted by Popper's ghost on August 22, 2006 8:14 AM (e)

Note that there are simple mechanical theorem provers than can prove any true statement in first order propositional logic. It would be bizarre to say that all these proofs are implicit in such a theorem prover, or that such a theorem solver is “teleological”.

Comment #121546

Posted by Popper's ghost on August 22, 2006 8:17 AM (e)

“The only teleological factor is Dave’s intent of finding a solution by running the algorithm; the GA algorithm itself is not the sort of thing to have intentions.”

Strawman. I explicitly said “DA’s GA” is teleological.

I can’t see where the strawman is; “DA’s GA” refers to exactly the same thing as “the GA algorithm itself”.

Popper’s Ghost, if you don’t mind, I’m going to cut this short. I’d rather not have any discussions with you, as you are from my experience as abrasive as the Christian fundamentalists we have to deal with routinely. You don’t think. You merely react.

If I don’t mind? Of course I mind your blatant and offensive ad hominem.

Comment #121547

Posted by Popper's ghost on August 22, 2006 8:20 AM (e)

Yes, but http://www.pandasthumb.org/archives/2006/08/desi…

that’ll take some time.

Right, of course … sorry.

Comment #121553

Posted by Popper's ghost on August 22, 2006 8:31 AM (e)

Such was my guess, but it’s appropriate - a penguin will not evolve into a polar bear as a result of mutation, even though their fitness functions are all about survival in the cold (to simplify it horrendously).

This is another example of cranes vs. skyhooks; there is no “survive the cold” magic wand that can transform one thing into another; everything must be achieved through the meticulous operation of bottom-up cranes.

Comment #121556

Posted by Josh S on August 22, 2006 8:39 AM (e)

The answer is that both were designed.

In both the GA and…uh…”classical geometry” approaches, you had an intelligent designer with some kind of goal in mind. The designer then developed a method that would reach this goal.

Further the “classical math” method is just as “evolutionary” as the GA method. Analytical geometry and calculus did not simply fall out of the sky. They are the product of centuries upon centuries of development of mathematics that goes back to Euclid and before. Without Euclid, Pythagoras, Arabic work in algebra and numerals, and the Cartesian plane, you don’t have calculus.

Hence, all you’ve really done is compared methods of design. Is it better to design a recursive algorithm to solve a problem, or take some direct approach?

If you had designed a bad algorithm, you never would have had your tree emerge. As anyone with experience in this field knows, stopping your “for” loop one iteration short, screwing up an array index, or accidentally overwriting the data a pointer is addressing will destroy the results of an algorithm. You need a non-designed algorithm with no particular goal to really make this the challenge you want it to be. So in this particular case, you have failed to demonstrate anything other than that there is more than one way to design something.

Comment #121558

Posted by mike1962 on August 22, 2006 8:44 AM (e)

“And the third aim was to provide a Test for the detection of “real” versus “apparent” CSI. If Intelligent Design Theorists can indeed identify when something has or has not been “designed,” as they claim they can, then they should get cracking to decide which of the two networks shown above (just below the fold) was produced by a human Intelligent Designer (a college computer sci prof, by the way), and which was produced by simulated mutation and natural selection on a population of strings over many generations.”

This is a good challenge test of design detection. I think the design detection angle of ID is lacking, so far. But guys like me, who are agnostic about a designer, are open to ID for a different reason: MET/NDE along with OOL hypotheses have not sufficiently demonstrated the ability to generate the entities that actually exist. Your tests have been no help. I would like to see a test where the fitness algorithms themselves are randomly generated, and capable of generating interesting virtual “entities”.

Comment #121559

Posted by Flint on August 22, 2006 8:45 AM (e)

You need a non-designed algorithm with no particular goal to really make this the challenge you want it to be.

So what do you recommend? Should we sit around waiting for such an algorithm to emerge from somewhere somehow, or should we design it?

Comment #121561

Posted by Lurker on August 22, 2006 8:50 AM (e)

“The answer is that both were designed.”
“there is more than one way to design something.”

Bingo. Design need not be the philosophically-laden term that it is. In other words, there is no need to follow the IDists into making the illogical leap from design to some amorphous, immaterial mind.

If anything, Dave set himself up for failure with the second challenge. It was already a poignant demonstration that “intelligence” operates no more efficiently than trial-and-error (and indeed, one may even say that intelligence _operates_ on trial-and-error strategies). To go further is to sink into the philosophical quagmire where IDists want to live.

Comment #121564

Posted by Popper's ghost on August 22, 2006 8:55 AM (e)

So in this particular case, you have failed to demonstrate anything other than that there is more than one way to design something.

He demonstrated that an evolutionary algorithm without a fixed target can “design” a solution, which is all he set out to do.

Comment #121566

Posted by mike1962 on August 22, 2006 8:58 AM (e)

Having though about this a bit, your challenge shows that an “entity” could be designed or not, and that the detection of design would be impossible. This should be pretty obvious, and requires no computer to demonstrate. I could chuck a piece of wood into a chipper and have it produce small wood chunks. Then I could whittle a wood chunk to look similar to one of the randomly carved, chipper ‘generated’ ones, in such a way that nobody could tell which one was designed and which one wasn’t.

How does your challenge relate to the bacteria flagellum, for example, with regards to the question of design? Nothing, as far as I can tell, since nobody knows if the flagellum was designed or not. (Duh.) In other words, your challenge doesn’t help to answer whether a particular entity IS designed or not. If you set up a test where the fitness algorithms were randomly generated as well as the mutations, and could generate something on the order of a flagellum, that would be impressive.

Comment #121568

Posted by Popper's ghost on August 22, 2006 8:59 AM (e)

If anything, Dave set himself up for failure with the second challenge.

He only set himself up for failure if someone can meet it. Rather than play Cordovan games, perhaps you can either meet the challenge or admit that it can’t be met.

Comment #121572

Posted by Popper's ghost on August 22, 2006 9:04 AM (e)

How does your challenge relate to the bacteria flagellum, for example, with regards to the question of design? Nothing, as far as I can tell, since nobody knows if the flagellum was designed or not. (Duh.) In other words, your challenge doesn’t help to answer whether a particular entity IS designed or not.

The burden is on the IDists to prove that it was (intelligently) designed, since they make they claim that it must be (intelligently) designed. The only burden on evolutionists is to show that it need not have been (intelligently) designed.

Comment #121576

Posted by Lurker on August 22, 2006 9:07 AM (e)

“If you set up a test where the fitness algorithms were randomly generated as well as the mutations, and could generate something on the order of a flagellum, that would be impressive.”

And if we made the demand on IDers to produce God, would you similarly comply?

Comment #121577

Posted by PaulC on August 22, 2006 9:10 AM (e)

Well, I don’t know if the true Steiner Tree is symmetric (though it’s probably a safe assumption), but the symmetry (or lack thereof) of a given solution is (I think) a big clue as to whether or not that solution was designed by a person, as opposed to a GA.

I just want to correct an apparent misconception about optimization. Just because the constraints of an optimization problem are symmetric does not mean that the optimal solution is symmetric. It’s tempting to look for a symmetric solution, since it reduces the search space, but this additional constraint may result in a suboptimal solution.

Note that if the constraints are symmetric and some optimal solution is asymmetric, the implication is that there are additional optimal solutions that are identical up to the symmetries of the original constraint.

Actually, this is similar to the Buridan’s ass “paradox.” The donkey that cannot choose which food to go to is looking for a single symmetric solution to a symmetricaly posed problem. But in fact there are two distinct asymmetric solutions–pick one and go to it–that are identical up to symmetry.

Comment #121579

Posted by Braxton on August 22, 2006 9:19 AM (e)

mike1962 wrote:

How does your challenge relate to the bacteria flagellum, for example, with regards to the question of design? Nothing, as far as I can tell, since nobody knows if the flagellum was designed or not. (Duh.) In other words, your challenge doesn’t help to answer whether a particular entity IS designed or not. If you set up a test where the fitness algorithms were randomly generated as well as the mutations, and could generate something on the order of a flagellum, that would be impressive.

Except that the relevant factor here is that the IDiots claim they can detect design. No, this example does not help determine whether any one thing is designed, only refute creationists’ idiotic claim that they alone can detect design with the EF/CSI/whatever.

Comment #121583

Posted by RBH on August 22, 2006 9:22 AM (e)

Frank Sullivan asked

It seems to me like they want to remove anything resembling a fitness function from the program. But if you do that, then all you have is randomness, without anything simulating natural selection. Am I erecting a straw man here, or are they that stupid? Of course, in order to simulate Evolution, you MUST have some function that is capable of SELECTING those organisms which are the “fittest.” Complaining about the 5-point Steiner program because it, “[selects] for networks that (1) connect all five points, and (2) have shortest path-length” seems, to me, like complaining about Alaska because it selects for organisms that (1) are white, and (2) have fur and layers of fat to keep them warm.

In three years or so of arguing about GAs and evolutionary algorithms in general with ID creationists in several venues, including ARN and ISCID’s Brainstorms, that’s the core of their objection, yes. In one membrable thread on ARN, Salvador argued that because replicators in an environment that selected solely on replicational speed got shorter, evolution went the wrong way because they didn’t get longer and more complex. (And yes, that deserves the furrowed brow you undoubtedly have now.)

Lurker asked

For instance, can a GA evolve the heuristic of minimizing trees by parts? Could a GA evolve robustness?

Evolution of robustness to high mutation rates in Avida.

sam wrote

The pathways, once traversed, seem somewhat unique - backtracking doesn’t occur both because of the limitations imposed on mutable qualities and the fitness function (I’ve been wrong before so it was good to test it). Such was my guess, but it’s appropriate - a penguin will not evolve into a polar bear as a result of mutation, even though their fitness functions are all about survival in the cold (to simplify it horrendously).

Evolution, be it in Dave’s GA, Avida, or biology, is a historically contingent process: Where you can go depends on where you are, and that depends on where you came from.

mike1962 wrote

I would like to see a test where the fitness algorithms themselves are randomly generated, and capable of generating interesting virtual “entities”.

And again

If you set up a test where the fitness algorithms were randomly generated as well as the mutations, and could generate something on the order of a flagellum, that would be impressive.

Since “fitness algorithms” is an ambiguous term – e.g., it’s not used anywhere in this thread except in mike1962’s post – that’s a hard request to interpret. Just what does Mike1962 think needs to be “randomly generated” in order to satisfy him?

RBH

Comment #121584

Posted by mike1962 on August 22, 2006 9:26 AM (e)

“And if we made the demand on IDers to produce God, would you similarly comply?”

I’m not an IDer.

Comment #121586

Posted by mike1962 on August 22, 2006 9:30 AM (e)

RBH: I was referring to Avida fitness functions, not the Challenge. Sorry I didn’t make that clear.

Comment #121588

Posted by Lurker on August 22, 2006 9:31 AM (e)

Nevertheless, do you think an IDer should produce God at the demand of their critics?

Comment #121589

Posted by mike1962 on August 22, 2006 9:34 AM (e)

“The burden is on the IDists to prove that it was (intelligently) designed, since they make they claim that it must be (intelligently) designed.”

I agree.

“The only burden on evolutionists is to show that it need not have been (intelligently) designed.”

If by “evolutionist” you mean a pure non-designed evolution (MET/NDE), then I also agree. However, this hasn’t been done. It is encumbent on anyone making positive claims to justify those claims. Neither side has done so, IMO. And maybe nobody cares what I think, but I sure care what I think.

Comment #121591

Posted by demallien on August 22, 2006 9:43 AM (e)

Dave, you can’t really use this example to attack CSI - the problem is that there is a single correct mathematically-defined solution. That both a human and a GA come up with pretty much the correct solution is hardly surprising.

Comment #121592

Posted by Anonymous_Coward on August 22, 2006 9:44 AM (e)

Nevertheless, do you think an IDer should produce God at the demand of their critics?

They’ve done that already.

To them, God is basically just any form of a God-of-the-gaps.

They’ve been producing gaps (note the word producing, instead of finding) since time immemorial.

Comment #121595

Posted by Anonymous_Coward on August 22, 2006 9:50 AM (e)

Nevertheless, do you think an IDer should produce God at the demand of their critics?

They’ve done that already.

To them, God is basically just any form of a God-of-the-gaps.

They’ve been producing gaps (note the word producing, instead of finding) since time immemorial.

Comment #121596

Posted by mike1962 on August 22, 2006 9:52 AM (e)

“Of course, in order to simulate Evolution, you MUST have some function that is capable of SELECTING those organisms which are the “fittest.” Complaining about the 5-point Steiner program because it, “[selects] for networks that (1) connect all five points, and (2) have shortest path-length” seems, to me, like complaining about Alaska because it selects for organisms that (1) are white, and (2) have fur and layers of fat to keep them warm.”

Which is kind of the point, for guys like me: what is the origin of fitness/selection criteria that let to the bio-entities we actually see on this planet? Designed or not? Particularly with regards to the origin of life.

I don’t think Dave’s Challenge demonstrates anything useful in determining that, nor does it help us understand how things like the vaunted flagellum arose, etc. Didn’t everyone already know that GAs can find goals theyre intended to find? I’ve been using GAs for 20 years to do that.

When somebody can find some randomly produced fitness algorithms that use random inputs to generate some complex virtual machines like the flagellum, please let me know. The war will be over.

Comment #121597

Posted by Popper's ghost on August 22, 2006 9:58 AM (e)

“The only burden on evolutionists is to show that it need not have been (intelligently) designed.”

If by “evolutionist” you mean a pure non-designed evolution (MET/NDE), then I also agree. However, this hasn’t been done.

Of course it has been shown that it need not have been designed – Dave Thomas did it here in a small domain, and the theory of evolution does it for biological diversity – “a pure non-designed evolution” is a possible explanation of biological diversity.

Comment #121599

Posted by mike1962 on August 22, 2006 10:06 AM (e)

“Of course it has been shown that it need not have been designed — Dave Thomas did it here in a small domain, and the theory of evolution does it for biological diversity — “a pure non-designed evolution” is a possible explanation of biological diversity.”

I disagree. Nobody has ever demonstrated that it’s even possible for a flagellum to have been assembled the way MET asserts. For that to be true, at least one precise (down the molecule) developmental pathway would have to be demonstrated. For all we know, the laws of nature might actually *forbid* any putative pathway that could be devised due to various chemical interactions. It’s an open question.

Comment #121601

Posted by Dizzy on August 22, 2006 10:09 AM (e)

mike1962 wrote:

what is the origin of fitness/selection criteria that let to the bio-entities we actually see on this planet? Designed or not?

I think it’s not entirely appropriate to draw too many parallels between a very targeted GA and all of life on earth.

That said, the overarching criterion of natural selection’s “fitness” is simply the ability to survive and produce progeny that will survive. You could consider that criterion “originating” from the fact that multiple organisms compete for scarce resources.

If you need food, and food is limited, and something else is much better at getting food than you are, you’ll run out of food and die. That “something else” will have children, and you won’t. There’s no need for intelligence or design in defining those fitness criteria.

Particularly with regards to the origin of life.

It’s been said, over and over again: evolution as a scientific theory does not address abiogenesis (although there are several abiogenesis hypotheses that make use of evolutionary theory).

Comment #121602

Posted by Popper's ghost on August 22, 2006 10:10 AM (e)

Which is kind of the point, for guys like me: what is the origin of fitness/selection criteria that let to the bio-entities we actually see on this planet? Designed or not?

The question is incoherent; the fitness/selection criterion is reproductive success, which is not the sort of thing that can be designed or not designed.

Didn’t everyone already know that GAs can find goals theyre intended to find?

Not all GAs can find goals that they are intended to find.

When somebody can find some randomly produced fitness algorithms that use random inputs to generate some complex virtual machines like the flagellum, please let me know. The war will be over.

The war will be over when everyone stops making factual and conceptual mistakes and irrelevant demands.

Comment #121603

Posted by demallien on August 22, 2006 10:13 AM (e)

“When somebody can find some randomly produced fitness algorithms that use random inputs to generate some complex virtual machines like the flagellum, please let me know. The war will be over.”

Mike, the problem is that the type of system you are talking about is a system that reproduces successfully depending on it’s ability to reproduce (as opposed to systems like the challenge, which reproduce successfully based on their ability to solve a problem).

Such systems can (and have) been created. We see virtual life that develop a whole host of reproductive strategies such as viral infection of hosts, producing multiple offsping in one go, etc. The problem is that they are virtual life. They do nothing except exist in a computer world. To win the war, we would have to show something a bit more concrete, ie things that are useful in the real-world, where we can actually touch them. That’s why solutions such as the Challenge are used to illustrate the point.

Comment #121604

Posted by mike1962 on August 22, 2006 10:16 AM (e)

“The question is incoherent; the fitness/selection criterion is reproductive success”

That’s part of it. There is also environmental pressures.

And of course, reproductive succuss certainly did not generate the initial reproductive machine in the first place.

“which is not the sort of thing that can be designed or not designed.”

How so?

Anyway, my challenge stands. Mine is a lot most difficult than Dave Thomas’s. Let’s see if anyone can pull it off. It would be wonderful if someone could.

Comment #121605

Posted by Popper's ghost on August 22, 2006 10:16 AM (e)

Nobody has ever demonstrated that it’s even possible for a flagellum to have been assembled the way MET asserts. For that to be true, at least one precise (down the molecule) developmental pathway would have to be demonstrated.

No it would not; no such requirement is imposed on any other scientific theory.

For all we know, the laws of nature might actually *forbid* any putative pathway that could be devised due to various chemical interactions. It’s an open question.

Look up “Occam’s Razor” and “inference to the best explanation”. “For all we know”, there are “laws of nature” that forbid the migration of continents, but there’s no evidence of of such laws.

Really, learn something about science.

Comment #121608

Posted by mike1962 on August 22, 2006 10:20 AM (e)

Mike1962: “When somebody can find some randomly produced fitness algorithms that use random inputs to generate some complex virtual machines like the flagellum, please let me know. The war will be over.”

Demallien: “Mike, the problem is that the type of system you are talking about…is a system that reproduces successfully depending on it’s ability to reproduce (as opposed to systems like the challenge, which reproduce successfully based on their ability to solve a problem). Such systems can (and have) been created.”

I explicitly specified “virtual machines like the flagellum.” Are you saying that something like that has been generated by randomly produced fitness algorithms acting on random inputs? If so, I’d like to see them.

Comment #121611

Posted by stevaroni on August 22, 2006 10:23 AM (e)

mike1962 wrote

Which is kind of the point, for guys like me: what is the origin of fitness/selection criteria that let to the bio-entities we actually see on this planet? Designed or not? Particularly with regards to the origin of life.

Mike;

Frankly, I’m baffled. You’re telling me that you don’t see selection all around us?

The slow antelopes don’t get eaten first, the tall, skinny arctic animals don’t freeze first, the less-resistant strep doesn’t die from the penicillin first?

You don’t watch much National Geographic channel, do you?

The selection criteria is painfully simple, and has been since the beginning of time. The thing that can make a successful copy of itself goes on.

It’s easy, it’s simple. It does not require any intervention.

It works for wombats, it works for bacteria. It even works for single molecules (your much-debated origin of life - No, I can’t prove how it happened, but that’s besides the point, I can show that if it happened, yes, we could get here from there).

GA simulations with selection criteria no more complicated than “survive better” regularly produce complicated structures.

I can’t make an argument that’s any better than “Here is is. on the table right in front of you. Pick it up, examine it. Play with it yourself.” A step that the ID proponents never, ever even get close to

If you want to look up at the sky and say “Blue! waddya talking about!? It’s clearly purple polka dots and there’s nothing more you can say to change my mind”, well, there’s nothing more I can say to change your mind.

Comment #121612

Posted by Popper's ghost on August 22, 2006 10:24 AM (e)

There is also environmental pressures.

Uh, no, those are not “fitness/selection criteria”. And do you really want to debate whether environmental pressures are designed? Of course some are – by humans. Anything beyond that is an irrelevant metaphysical question.

And of course, reproductive succuss certainly did not generate the initial reproductive machine in the first place.

But that has nothing to do with the theory of evolution, and so questions about “fitness/selection criteria” don’t apply.

“which is not the sort of thing that can be designed or not designed.”

How so?

It’s self-evident that “reproductive success” as a fitness/selection criterion is not the sort of thing that can be designed. If you think not, please explain what it could mean to design it.

Anyway, my challenge stands.

All that stands are your conceptual confusions.

Comment #121614

Posted by Popper's ghost on August 22, 2006 10:29 AM (e)

It’s self-evident that “reproductive success” as a fitness/selection criterion is not the sort of thing that can be designed. If you think not, please explain what it could mean to design it.

And please don’t respond with a discussion of biological mechanisms that result in reproductive success – that’s a totally different matter; mechanisms are not criteria.

Comment #121617

Posted by mike1962 on August 22, 2006 10:39 AM (e)

Stevaroni: “Frankly, I’m baffled. You’re telling me that you don’t see selection all around us?”

Of course I do. Did I seem to imply that I don’t? Variation and selection can certainly account for much, if not all, of what we see on the scale of wombats and gazelles. And we can artificially select for our own ends. However, when it gets down to the small scale specific protein machines such as the flagellum, nobody has proffered any precise, definite specified chemical pathways for it’s development, that is demonstrably possible simply given *chemical* considerations, forgetting the irreducibility business. Just assuming that it’s possible certainly doesn’t convince me. It’s an open question.

Comment #121618

Posted by mike1962 on August 22, 2006 10:41 AM (e)

Mike1962: “There is also environmental pressures.”

Popper: “Uh, no, those are not “fitness/selection criteria”. And do you really want to debate whether environmental pressures are designed? Of course some are — by humans. Anything beyond that is an irrelevant metaphysical question.”

Hmm. I’ll have to digest this puzzling statement and get back to you.

Comment #121620

Posted by mike1962 on August 22, 2006 10:44 AM (e)

“It works for wombats, it works for bacteria. It even works for single molecules (your much-debated origin of life - No, I can’t prove how it happened, but that’s besides the point, I can show that if it happened, yes, we could get here from there).”

OK, then, are you going to be the one to provide a precise chemical pathway to the flagellum? Not necessarily the real one, but one that would work, given what we know about chemical processes? That would be great! :)

Comment #121622

Posted by Popper's ghost on August 22, 2006 10:50 AM (e)

Just assuming that it’s possible certainly doesn’t convince me.

This charge of “assuming” is common from people utterly ignorant of the actual science.

Comment #121624

Posted by Popper's ghost on August 22, 2006 10:53 AM (e)

However, when it gets down to the small scale specific protein machines such as the flagellum, nobody has proffered any precise, definite specified chemical pathways for it’s development, that is demonstrably possible simply given *chemical* considerations, forgetting the irreducibility business. Just assuming that it’s possible certainly doesn’t convince me. It’s an open question.

It’s not an open question that there’s some causal explanation for the existence of flagella – not in science.

Comment #121625

Posted by mike1962 on August 22, 2006 11:01 AM (e)

Popper: “It’s not an open question that there’s some causal explanation for the existence of flagella — not in science.”

Where can I find a blow by blow evolutionary sequence of the flagellum, with no gaps whatsoever?

Comment #121626

Posted by demallien on August 22, 2006 11:02 AM (e)

mike1962 wrote:

I explicitly specified “virtual machines like the flagellum.” Are you saying that something like that has been generated by randomly produced fitness algorithms acting on random inputs? If so, I’d like to see them.

Mike, you won’t see anything like the flagellum. Virtual organisms live in an environment of register, processes and memory, not an environment of physics and molecules. Their equivalent of a flegellum would be a program script that does something clever to help it reproduce/compete against other organisms. As I mentioned previously, such organisms managed to discover how to infect other virtual organisms. That’s pretty clever if you ask me.

But if you REALLY want to hold out for seeing something evolve like a flagellum, look no further than bacteria. We see them evolving clever physical attacks and defences all of the time.

Comment #121627

Posted by Popper's ghost on August 22, 2006 11:06 AM (e)

Popper: “It’s not an open question that there’s some causal explanation for the existence of flagella — not in science.”

Where can I find a blow by blow evolutionary sequence of the flagellum, with no gaps whatsoever?

You didn’t understand my statement. Try harder.

And I already responded to this. Where can I find an exact chemical breakdown of the migration of continents? Demands for such sequences are intellectually dishonest, and your persistence in asking this question is trollery.

Comment #121628

Posted by mike1962 on August 22, 2006 11:09 AM (e)

Popper: Look up “Occam’s Razor” and “inference to the best explanation”. “For all we know”, there are “laws of nature” that forbid the migration of continents, but there’s no evidence of of such laws. Really, learn something about science.”

Occam’s Razor is a good guiding principle, indeed. And I accept your explanation as the best possible explanations thus far if we disallow a priori any intelligent cause. There are still gaps in our knowledge with respect to the precise chemical pathways of things like the flagellum. I’m interested in someone filling these gaps. I would be willing to consider an intelligent source as the *only* way, if it could be determined that there is no chemical pathway *possible* without intelligent tweaking. Nevertheless, MET has not “explained” the flagellum to MY satisfcation. Forgive me if my standard of “explanation” is tougher than yours.

Comment #121632

Posted by Popper's ghost on August 22, 2006 11:19 AM (e)

Nevertheless, MET has not “explained” the flagellum to MY satisfcation. Forgive me if my standard of “explanation” is tougher than yours.

Your standard is intellectually dishonest. I’ll view it otherwise when you either provide a molecule-by-molecule explanation of the movement of the continents or assert that there could be laws of nature that prevent such movement, that there may be no causal explanation of how the continents got where they are, and that without without such a “blow by blow” explanation, tectonics does not explain how they got where they are to your satisfaction, etc. Of course, if you say that, I will consider you to be a loon.

Comment #121634

Posted by Dizzy on August 22, 2006 11:23 AM (e)

Your standard is intellectually dishonest. I’ll view it otherwise when you either provide a molecule-by-molecule explanation of the movement of the continents or assert that there could be laws of nature that prevent such movement, that there may be no causal explanation of how the continents got where they are, and that without without such a “blow by blow” explanation, tectonics does not explain how they got where they are to your satisfaction, etc. Of course, if you say that, I will consider you to be a loon.

Try applying that standard to the hypothesis that flagella are designed by an unnamed, intelligent force.

Comment #121636

Posted by mike1962 on August 22, 2006 11:23 AM (e)

popper: “Where can I find an exact chemical breakdown of the migration of continents? Demands for such sequences are intellectually dishonest, and your persistence in asking this question is trollery.”

If you can’t do it, fine.

As far continents go, we can detect processes right now that are *demonstrably* capable of producing what exists today. You, me, and the milkman can reproduce these sorts of productions on a small scale which can be extrapolated, without hopping any gaps in chemistry or physics. Can the same be done for the flagellum? I haven’t seen it. If it exists I would seriously love to read about it. Selection pressures working on variations within a population cannot be scaled down to chemical and atomic levels without the induction of developmental gaps which are not analogous to the macro scale selection.

Insisting on a precise, detailed, and (most importantly, gap free) developmental pathway, is scientific question. I suppose it would be trollish for me to continue asking for something that obviously isn’t going to be forthcoming. I got my answer, which is you can’t provide an answer. And that’s fine with me. If and when somebody can, please let me know. I would much appreciate it.

Comment #121637

Posted by Popper's ghost on August 22, 2006 11:26 AM (e)

And I accept your explanation as the best possible explanations thus far if we disallow a priori any intelligent cause.

BTW, we started out with the possibility of non-designed explanations, not the necessity of non-designed explanations; thus talk of “disallowing” any intelligent cause is irrelevant. But as so often happens in these debates with IDers or crypto-IDers, they keep shifting the goalposts until they come full circle. I’ve already answered all your arguments at least once, so it would be a waste of time to pursue this further.

Comment #121639

Posted by Popper's ghost on August 22, 2006 11:28 AM (e)

As far continents go, we can detect processes right now that are *demonstrably* capable of producing what exists today.

You posited “laws of nature” that might make development of the flagellum impossible. Prove that there are no such laws of nature in re tectonics. Oh wait, I already asked for that and you didn’t respond. Around and around we go on the troll-go-round.

Comment #121640

Posted by Braxton on August 22, 2006 11:30 AM (e)

mike1962 wrote:

When somebody can find some randomly produced fitness algorithms that use random inputs to generate some complex virtual machines like the flagellum, please let me know. The war will be over.

Excuse me, but what the hell does that mean and what would it prove?

Comment #121641

Posted by Popper's ghost on August 22, 2006 11:33 AM (e)

You, me, and the milkman can reproduce these sorts of productions on a small scale which can be extrapolated, without hopping any gaps in chemistry or physics.

I haven’t seen it.

Can the same be done for the flagellum?

At least as well as for continental movement, which is much harder because there’s a great deal that we don’t know about the dynamics of crustal movement.

I haven’t seen it.

Bully.

Comment #121642

Posted by Dizzy on August 22, 2006 11:34 AM (e)

the milkman can reproduce these sorts of productions on a small scale which can be extrapolated

I don’t see the connection here.

Can you provide a step-by-step, atom-by-atom traceback from the current position of continents to their position 3 billion years ago, please?

If not, there’s no proof. At least, not by my standards.

Comment #121646

Posted by Popper's ghost on August 22, 2006 11:38 AM (e)

I don’t see the connection here.

It isn’t even true; the movement of the continents results from processes that are currently far more opaque to us than the processes of the cell.

Comment #121649

Posted by DistendedPendulusFrenulum on August 22, 2006 11:54 AM (e)

Just a note from a lowly English teacher here–I’ve been reading the dialog between you all and Cordova, specifically the part where he disavows the Irreducible Complexity argument that begins with a completely constructed, functional entity and instead maintains that IDers “don’t think that way.” This is after declaring that the end result of your AI experiment is specified beforehand, therefore invalidating the experiment.

You’ll notice that he also never specifies the way in which he wants us to think that IDers *do* think.

Incidentally, in Kitzmiller v Dover, you’ll find that Michael Behe admits that the IC argument “doesn’t address the central task of natural selection,” so it’s kind of amazing they’re still using this argument.

It occurs to me that if you are reduced to saying the tautological “look, there is no empirical data that shows evolution to work any other way than has been empirically observed,” then, although you have not lost the argument, the usefulness of continuing the debate is somewhat questionable.

It’s pretty clear you are dealing with ideologs here. I can’t say it better than seventypercent did yesterday in a Fark.com thread:

“The lessons of the Cold War taught us that a real commitment to science and technology can produce a generation that would end up winning that war for us. And now that we face a threat that many would consider more grave than the Soviet Union, that lesson has been forgotten by many Americans, who are now descending into a frenzied pit of religious fanaticism, not unlike their fundamentalist brethren on the other side of the globe – the same people they claim we’re at war with.”

Yours,
DistendedPendulusFrenulum

Comment #121652

Posted by Stevaroni on August 22, 2006 12:04 PM (e)

We’re back to the flagellum again.

Somehow I seem to recall that back around tehre were some references to a very recent paper tracking down the little spinner protein and showing it was a single mutation version of a cell wall protein (or something along those lines). Which is the kind of information that should have laid this moronic argument to rest.

I though it was posted here, but I can’t find the key search term.

Anybody remember the link?

Comment #121653

Posted by mike1962 on August 22, 2006 12:07 PM (e)

“I don’t see the connection here. It isn’t even true; the movement of the continents results from processes that are currently far more opaque to us than the processes of the cell.”

Point taken. I’m not qualified to comment on geological topics such as that. My apologies.

Comment #121654

Posted by Popper's ghost on August 22, 2006 12:12 PM (e)

Which is the kind of information that should have laid this moronic argument to rest.

Not so, because he wants “a precise, detailed, and (most importantly, gap free) developmental pathway“. Calling this moronic is being kind.

Comment #121656

Posted by Stevaroni on August 22, 2006 12:13 PM (e)

I babbled…

Somehow I seem to recall that back around tehre were some references

Woah - english please Steve-O!

Slip of the send key. I meant to babble…

Somehow I seem to recall that back around the end of the Dover trial therre were some references to a very recent paper tracking down the little spinner protein and showing it was a single mutation version of a cell wall protein (or something along those lines). Which is the kind of information that should have laid this moronic argument to rest.

I though it was posted here, but I can’t find the key search term.

Anybody remember the link?

Comment #121657

Posted by Popper's ghost on August 22, 2006 12:14 PM (e)

I’m not qualified to comment on geological topics such as that.

Then renounce plate tectonics as a satisfactory explanation of the locations of the continents and demonstrate that you are a loon, or admit that you’re intellectually dishonest in not applying the same standards in both cases.

Comment #121660

Posted by secondclass on August 22, 2006 12:16 PM (e)

mike1962 wrote:

When somebody can find some randomly produced fitness algorithms that use random inputs to generate some complex virtual machines like the flagellum, please let me know. The war will be over.

I don’t know whether by “fitness algorithms” you mean “fitness function” or “search algorithms”. I’ll assume “fitness function”.

By “randomly produced”, I assume you mean that the fitness function is selected from a uniform distribution of all functions over omega. Such a fitness function would indeed be useless, since its gradients would be completely random.

But what if our selection process included a low-pass filter, which would guarantee a smooth function? In that case, the function would likely be useful. Given that low-pass filters are ubiquitous in nature, and that they are not intelligent (they remove rather than add information), it seems that a randomly selected fitness function could easily lend itself to evolutionary algorithms.

Comment #121665

Posted by Popper's ghost on August 22, 2006 12:30 PM (e)

I don’t know about steveroni’s cell wall mutation, but here’s Nick Matzke’s paper on “a model for the origin of the bacterial flagellum”:

http://www.talkdesign.org/faqs/flagellum.html

Comment #121668

Posted by mike1962 on August 22, 2006 12:31 PM (e)

Popper: “Then renounce plate tectonics as a satisfactory explanation of the locations of the continents and demonstrate that you are a loon, or admit that you’re intellectually dishonest in not applying the same standards in both cases.”

I have no reason to renounce plate tectonics. I don’t know enough about the subject to make a judgement. Nor do I renounce evolution, per se. What I stand unconvinced of is MET to explain many things, like the flagellum. You’ve provided me with no information I can use, so it seems to be a waste of time chatting with you (singular.)

Comment #121676

Posted by stevaroni on August 22, 2006 12:41 PM (e)

but here’s Nick Matzke’s paper on “a model for the origin of the bacterial flagellum

OK, that’s pretty freakin’ thorough.

Mike?

Comment #121679

Posted by Popper's ghost on August 22, 2006 12:43 PM (e)

I have no reason to renounce plate tectonics.

I wrote “as a satisfactory explanation of the locations of the continents”. Previously you argued that we could extrapolate a molecule by molecule story of continental movement; now that you admit we can’t, you pretend that it’s not relevant. But all your objections apply either to both plate tectonics/continental locations and the theory of evolution/development of the flagellum or to neither.

You’ve provided me with no information I can use, so it seems to be a waste of time chatting with you (singular.)

It’s a waste of time for anyone to chat with dishonest trolls.

Comment #121683

Posted by Ric on August 22, 2006 12:51 PM (e)

Well, Cordova’s response is up over at UD, and predictably its simply “this isn’t evidence of evolution, because the computer program was created by human intelligence.” Since I’ve already shown the error in this thinking, I won’t do so again, but I will repeat that Sal’s response is a joke.

Comment #121688

Posted by Popper's ghost on August 22, 2006 12:58 PM (e)

Here’s an indication of where mike1962 is coming from:

http://www.uncommondescent.com/index.php/archive…

I would like to add that NDE explains everything in general, because it explains nothing in particular. Impossible to falsify such a concept because it does not deal with particulars. Rather it is an ideological axiom. Axioms are not subject to falsification by definition. And this particular axiom is simply the mirror corollary of an a priori bias against design, supernatural OR natural.

It’s amazing to me how bad philosophy can pass as a “scientific” paradigm.

Comment #121690

Posted by CJ O'Brien on August 22, 2006 1:07 PM (e)

“…at least one precise (down the molecule) developmental pathway would have to be demonstrated…”

I think Judge Jones said it best:

the ID argument is dependent upon setting a scientifically unreasonable burden of proof for the theory of evolution.

Kitzmiller, p. 78

Comment #121694

Posted by mike1962 on August 22, 2006 1:14 PM (e)

Popper: “Here’s an indication of where mike1962 is coming from: … It’s amazing to me how bad philosophy can pass as a “scientific” paradigm.”

Indeed. See my most recent post at UD.

The CSI camp and the MET both operate under a particular philosophy. Nothing wrong with that, and it’s impossible to the avoid. The only thing is, one should not pretent to be merely methologically naturalistic when one is actually philsophical materialistic.

At any rate, I see your view regarding the flagellum comments above, as one that’s ideologically based. Imagine chastisting someone for damanding evidence to fill in the gaps, and telling him he’s being an unscientific, ignorant troll. That seems to me like ideology talking. Whatever it is, it doesn’t help anyone learn or understand. Nothing has been gain in the trasactions, except that I’m even more confident that my challenges will go unanswered. Enough for this “troll” for now.

Comment #121695

Posted by mike1962 on August 22, 2006 1:16 PM (e)

Scordova: “I would like to address your concerns regarding CSI.”

Mike1962: No, I have not read No Free Lunch, or any of his books, except for excerpts, and also discussions related to it. But I do believe I understand the gist of it, however, from an information theory angle.

The problem with the CSI angle as I see it is that you still cannot detect design vs accident by mathematics alone if one’s philosophy is wrongheaded. The concept of information originator and information receiver is irrelevant when one accepts the idea that an *infinite* variety of combinations are possible within the universe, or multiverse. The problem with the MET-only crowd is not their science, even though it is limited, and doesn’t explain what they think it does. The problem with them is their philosophy, which is ridiculous. They embrace a methodological meterialism a priori (which usually turns out to be a philosophical materialism in disguise), and then skip along with the notion that matter *can* combine in just the right way to get the self-replicating process going, and then *can* reproduce and develop along the lines MET suggests. Talk about calling the blue sky a different color. They deny the sky is even possible, let alone blue. There’s no use trying to convince someone that the sky is blue if they don’t believe a sky is possible.

I am agnostic on design. I’m likewise agnostic about MET in many respects. MET fails to explain many aspects of the cellular world. And by explain, I mean explain in detail, of how something like the flagellum *could* (not *did) come together by unguided processes. I’m not saying it can’t. But they can’t show that it can. I’m the agnostic here. MET adherents are the ones making the positive claim about their theory. If it’s true, fine. I’d love to see real proof.

Anyway, CSI doesn’t seem to help a guy like me, since it’s *conceivable* (if particulars are of no importance) that ANYTIHNG can happen given enough universes and enough time. And the anti-ID MET adherents are simply not on the same playing field philosophically with the pro-ID guys.

Comment #121696

Posted by Popper's ghost on August 22, 2006 1:18 PM (e)

I see your view regarding the flagellum comments above, as one that’s ideologically based.

I don’t really care what you “see” because you are ignorant, conceptually confused, and intellectually dishonest.

Comment #121697

Posted by Popper's ghost on August 22, 2006 1:20 PM (e)

Imagine chastisting someone for damanding evidence to fill in the gaps, and telling him he’s being an unscientific, ignorant troll

Imagine some jackass making ridiculous demands and then pretending that I didn’t even post a link to a paper giving a detailed model of the evolutionary development of the flagellum.

Comment #121698

Posted by Henry J on August 22, 2006 1:20 PM (e)

Re “I’ll bet your pocket protectors are overstuffed.”

I resemble that remark!

Comment #121704

Posted by Popper's ghost on August 22, 2006 1:30 PM (e)

I’m not saying it can’t. But they can’t show that it can.

This is deeply dishonest. You can’t show that the continents can move into their places, but that isn’t your burden; the burden is on anyone who claims that they can’t to show that they can’t, since there is no reason to believe otherwise. And there is no reason to believe that the flagellum cannot evolve. Imagining that there could be “laws of nature” that prevent it is quite stupid and anyone who indulges in such absurdities is in no position to claim that the entire scientific community subscribes to a “ridiculous” philosophy.

Comment #121705

Posted by Dizzy on August 22, 2006 1:31 PM (e)

I see your view regarding the flagellum comments above, as one that’s ideologically based.

And yours regarding continental drift is…scientific?

And again, what does applying your “standard of evidence” against ID’s view yield?

Comment #121707

Posted by Dave Thomas on August 22, 2006 1:33 PM (e)

Some summary observations:

mike1962 : who or what is “MET”?

Lurker wrote

Now, look at the Mutate() function, and you can see that he jury-rigged the mutation rates on his organism’s DNA to minimize mutations in # of steiner points. Further, it is restricted to a preset m_varbnodes variable. How would a GA know a priori to limit m_varbnodes to m_fixdnodes - 2?

The GA doesn’t set the numbers of fixed or variable nodes, the program’s user does. For the 6-point problem, I used 6 fixed and 8 variable nodes. I could have required only 4 nodes (=6-2, the known maximum of points needed for a Steiner problem with 6 fixed points), but have found that the GA does better at solving Steiner’s problem in a node-rich environment. Similarly, that’s why mutations to the active number of variable nodes is made a rare occurrence.

If I didn’t include a requirement that fitness include a measure of whether or not all fixed nodes are connected, the algorithm simply sheds all active segments until the length of the candidate solutions is zero, which is indeed a “minimum.” Requiring connectivity is simply a method for preventing the GA from going the easy route to a trivial zero-length solution, which is like throwing the baby out with the bath water.

Similarly, if it’s too easy to reduce the numbers of variable nodes, the GA tends to quickly find that the shortest solutions have no internal Steiner (variable) points at all, leading to Traveling-Salesman-Problem types of networks as shown for the Eighth MacGyver above. Thus, I’ve taken steps to keep the organisms steeped in a node-rich environment, as this helps the algorithm find lots of interesting solutions for any given Steiner problem, be it 6 points or 16, and not just the trivial ones. I consider this to be part of setting up the environment for the evolutionary simulation, much as one might specify a temperature or pressure gradient in a different simulation.

Salvador Cordova has responded at UD with this:

Computers can compute certain things faster than us, that is why they exist to help us. For Thomas to argue that evolution is smarter than humans because computers can compute faster than humans is a non-sequitur…. No backstage explaining to do. The little puzzle Thomas offered was amusing. It only shows that computers can compute faster than humans and that some at Pandas thumb can connect dots with lines better than others. What he didn’t prove was mindless undesigned agents can create Genetic Algorithms from scratch.

Talk about your Moving Goalposts! As I’ve stated, a primary goal of developing this algorithm was simply to address the main ID objection to GA’s, which is that they aren’t really creating any new answers, because the final Answer (the “Target”) has to be an explicit part of the Fitness Function, as it is in Dawkins’s Weasel algorithm. I thus demonstrated a Genetic Algorithm that does not require a given fixed “Target” for solving a class of math problems.

Rather than deal with ID’s continuing misrepresentation that all genetic algorithms suffer the same limitations as “Weasel,” Cordova changes the subject to the fact that I employed a computer to perform the evolutionary simulation.

Here’s the deal: I posed a difficult math problem, and asked readers to design answers for it. The problem’s solution was not obvious, as was demonstrated by the variety of proposed answers. Furthermore, Cordova himself failed to derive the correct answer, although he did find a sub-optimal solution.

My program was not intended to reproduce the history of the flagellum, as some commenters seem to be requesting.

The purpose of the exercise was simply this:

To show that the processes of selection and mutation, in a reproducing population of organisms with variations in their genotypes (DNA) and corresponding phenotypes (e.g. networks), can lead to striking results featuring both Irreducible Complexity and Complex Specified Information (CSI), and all without front-loading the algorithm with any specifics regarding the actual problem solutions.

That’s why Cordova can’t pinpoint where his alleged “front-loading” is being done in my program. The only “front-loading” is that the program actually simulates evolutionary processes. When Cordova complains that the GA’s ability to solve complex math problems is simply because “computers can compute faster than humans,” he is missing the entire point of the discussion. I used computers simply to show that simulating evolutionary processes (reproduction, mutation, selection) over time can indeed produce precise solutions to difficult math problems, with no a priori knowledge of the correct answer(s).

Sal’s attempt to change the subject to “but you used a computer, and computers do math faster than humans, so there!” is pretty pathetic in my book.

Dave

Comment #121713

Posted by Glen Davidson on August 22, 2006 1:40 PM (e)

I have no reason to renounce plate tectonics. I don’t know enough about the subject to make a judgement.

Then why aren’t you on a geology forum, asking for a step-by-step process of hot plume formation, the appearance and operation of the dynamo in the earth (whose effects are crucial to a number of observations re continental drift), and the mechanisms of plate transport?

See, we know how you trolls operate, you simply read some idiotic criticism of evolution, adopt it as your own, while ignoring the difficulties and evidence that support the various theories in the so-called “soft sciences”. There is a great deal not understood about plate tectonics, and your fobbing off of the difficulties only demonstrates that your knowledge of scientific criticism is faulty.

Nor do I renounce evolution, per se. What I stand unconvinced of is MET to explain many things, like the flagellum. You’ve provided me with no information I can use, so it seems to be a waste of time chatting with you (singular.)

Deal with the homologies (type III export apparatus, most notably) within the flagellum, and tell us how and why any other mechanism would predict such homologies. Also, tell us how supposedly designed elements within organisms differ fundamentally from evolved elements, and from the predictions of evolutionary theory.

See, you have no concept of science, only aping the pseudoscience of those who deny the propriety of science standards. We infer mechanism through the evidence, then we use those supported inferences to study the intricacies of the evident mechanism. Plate tectonics was adopted well before we knew what made the plates move (the reasonable hypotheses were known, but which was/were correct was not) because of the evidence that plates moved under, over, and against each other. We know that the flagellum evolved because it is not discontinuous with other evolved systems and taxonomic categories, its genes evolved through time (after it appeared in essentially the present form, is what mean here), and it has homologies with other structures (granted, the secretory apparatus is not definitely known to be the source rather than the derivation, but it is highly reasonable that the more complex flagellum would have to evolve from less complex precursors).

That is what is essential to recognizing plate tectonics and evolutionary theory, the evidences that would be expected from them. If we didn’t recognize those evidences and make the appropriate inferences, we could not then proceed to fleshing out the step-by-step processes, so far as these may be discernable. Not that you care, since you want to deny the inferences in order to prevent what you demand from being researched, as far as possible. What is more, we may never know exactly how the flagellum evolved, nor how plate tectonics was operating 4 billion years ago. It is understood by competent scientists that some things in the past will never be known, or at least not known very surely, and it is the mark of the pseudoscientist to demand what is beyond the possibilities of the evidence that is in hand.

Deal with the evidence, or just admit that you have absolutely no reason to believe that the flagellum was designed, while we have ample evidence that it evolved, regardless of the many losses of information to time.

Btw, we wouldn’t have to have genetic homologies to reasonably infer that flagella evolved, either. It is not expected that all related genes and “machines” will continue to exhibit evident homologies throughout all time. That’s sort of implied by the term “evolutionary theory”. We’re just fortunate that the example with which IDists wish to make unreasonable demands for demonstration (while they explain nothing with their “hypothesis”) happens to have significant evidence of evolution via homologies.

The fact is that, without evidence against evolution by RM + NS +, we would have sufficient reason to believe that the flagellum evolved, because it has no evident differences from the masses of evolved organelles, machines, and information, found in the various organisms. That’s Occam’s Razor, for we need evolutionary theory to explain the derivation of the related genomes, and it is sufficient (as far as we know) to explain the flagellum, even without homological evidence that it does. Bringing in a “designer” with unknown capabilities and goals is completely superfluous and meaningless, and would continue to be superfluous and meaningless even without the substantial evidence that life has only evolved through time.

We do, though, have homologies to indicate that the flagellum evolved. Explain that meaningfully using something other than evolution, or admit that you’re an ignorant troll who brings up unreasonable demands because he has no explanation for what we know about the flagellum.

Glen D
http://tinyurl.com/b8ykm

Comment #121719

Posted by Popper's ghost on August 22, 2006 1:54 PM (e)

who or what is “MET”?

I believe this is ID/DI/UD speak for “materialistic evolutionary theory”.

Comment #121722

Posted by mike1962 on August 22, 2006 1:55 PM (e)

Popper,

I’ve seen the Matzke treatment before, and read much of the stuff on his website. Sorry. Not impressive. May too many gaps left unexplained. I’ll will be glad to hash through it, if you like.

Comment #121731

Posted by mike1962 on August 22, 2006 2:05 PM (e)

“I believe this is ID/DI/UD speak for “materialistic evolutionary theory”.”

No, rather Modern Evolutionary Theory

Comment #121735

Posted by caligula on August 22, 2006 2:13 PM (e)

Dave:
Could you address all of Lurker’s post #121509, please? I think he’s making some rather relevant claims. Such as:

Why is the probability of a mutation different for each type of locus? Indeed, why not just use a “packed” sequence of bits (instead of a char sequence) and just invert one random bit? (You could use a 1024x1024 grid to avoid redundancy in coordinates.) Even if relatively frequent mutations in the “number of nodes” gene would cause a lot of excess garbage (hopeless candidates), you seem to be inviting criticism by biasing mutation frequencies.

Most importantly, what is your response to Lurker’s claim that your code makes use of a global optimizer which kicks lineages off local optima?

Comment #121737

Posted by Popper's ghost on August 22, 2006 2:15 PM (e)

Not impressive. May too many gaps left unexplained.

Yeah, all of science isn’t impressive because it leaves so many gaps unexplained.

Silly troll.

Comment #121756

Posted by Dave Thomas on August 22, 2006 3:25 PM (e)

caligula wrote

Dave:
Could you address all of Lurker’s post #121509, please? I think he’s making some rather relevant claims. Such as:

Why is the probability of a mutation different for each type of locus? Indeed, why not just use a “packed” sequence of bits (instead of a char sequence) and just invert one random bit? (You could use a 1024x1024 grid to avoid redundancy in coordinates.) Even if relatively frequent mutations in the “number of nodes” gene would cause a lot of excess garbage (hopeless candidates), you seem to be inviting criticism by biasing mutation frequencies.

Most importantly, what is your response to Lurker’s claim that your code makes use of a global optimizer which kicks lineages off local optima?

As I explained, I was trying to set up a node-rich environment, so mutations to the actual number of active variable nodes are rare. The other two types of loci (numerical digits for positions, and T/F characters for connections) are split 50/50 as regards mutation frequency. Do see comment #121707 in this regard.

As regards “global” versus “local,” I don’t have the foggiest notion of what you’re referring to. In the GA, an organism is represented by a DNA string, period. The DNA is transcribed to determine the “phenotype” of the organism - its shape and connectivity. The lengths of active segments are then summed, and connectivity checked, to deliver a single number that describes the organism’s “fitness.” These numbers are used to help decide which organisms survive to be parents for the next generation. Where’s the “local”? Where’s the “global”?

There’s another reason that the number of active nodes is restricted. When the program runs, it creates and allocates arrays to store positions. For the 6 fixed plus 8 variable node set-up, the dimension of the scratch arrays for processing variable node locations is 8. If that number was changed to 93, say, then the program would attempt to address memory where none had been allocated, followed shortly by the computer’s announcement that the application has crashed, and asking if the user wants to tell MicroSoft about it.

Of course, I could make the number of nodes more variable, or even make the length of DNA variable. In Julian Onion’s GA, he did just that. Note that his GA can solve Steiner problems too.

We can argue all day about how this or that might have been implemented. Indeed, perhaps some of these suggestions should be experimented with. Why don’t you give it a try?

Dave

Comment #121758

Posted by Inoculated Mind on August 22, 2006 3:34 PM (e)

Yeah, Salvador is busy denying that it means anything, and he is relying on a dull tautology to do it. Basically, if you simulate evolution, then you cannot conclude that X evolved because you designed the experiment, thus, you can only conclude that it was designed. This is as dumb as saying that if you simulate lightning on a lab, then all lightning was caused by humans.

Like I said, these people need to be treated as psychics, deviners, dowsers, etc, and made to admit the fairness of a particular test BEFORE it was tested. Then afterward, we can call them on their dodging when they change their tune. Like when Behe said that a two-part IC system would be unlikely to evolve, and then dover hits, he admits that a 2-part system can be IC, under OATH. Then afterward, the evolution of a two-part system is elucidated, and Behe claims that THREE (!) parts are required for an IC system. Slam-dunk, clear move of the goalpost that everyone should be made aware of.

So that Salvador Cordova is dodging all of this at UD is no surprise, and he has taken the lame excuse that it is due to a computer’s superior calculating skills. The computer is the environment, and he has a computer too, but the tools being tested were a genetic evolution algorhythm and his brain. His brain lost, and he’ll be spinning for a while.

The point is, he will never change his position based upon evidence, just as a psychic wouldn’t, but there are many people out there who would change their positions based upon a clear demonstration that he and other IDers admit to beforehand, and then you show them fleeing after the test is completed.

Comment #121769

Posted by Coin on August 22, 2006 3:58 PM (e)

I see a couple of people here saying things along the lines of that because this GA test had a specific goal, and evolution does not have a specific goal, the GAs make a poor test of evolution. The problem is, how can we perform ANY test of evolution– using GAs or anything else– that has no specific goal? We can certainly set up tests involving simulations that have no specific goal, but without such a goal overall how exactly would we know whether or not the test is a success?

I’m not sure some of these objections have been very clearly thought out.

mike numbers wrote:

I would like to see a test where the fitness algorithms themselves are randomly generated, and capable of generating interesting virtual “entities”.

http://dllab.caltech.edu/avida/ ?

http://www.genetic-programming.com/humancompetit… ?

In other words, your challenge doesn’t help to answer whether a particular entity IS designed or not.

That is fine, since after all it is literally impossible to determine whether a particular entity is designed or not.

How does your challenge relate to the bacteria flagellum, for example, with regards to the question of design?

Why would it?

Anyway, my challenge stands. Mine is a lot most difficult than Dave Thomas’s. Let’s see if anyone can pull it off. It would be wonderful if someone could.

Your “challenge” is, frankly, so incredibly vague as to be impossible to even attempt, much less meet.

What sort of “entities” would be acceptable? Is a graph, such as Dave’s operates on, an “entity”? The nice thing about a simple kind of entity like Dave’s graph is there’s no room for sleight-of-hand– the entities being generated and operated on are so simple there are relatively few opportunites for fine-tuning, and if someone says “you just snuck in the ingenuity through your algorithm”, Dave can point at his code and say “okay, show me where”. Is a circuit, such as the genetic programming outputs above, an “entity”? Must a thing be in some way self-replicating to be an “entity”?

What does “on the order of a bacterial flagellum” mean? This is quite crucial. No one is going to want to take any kind of challenge if there is real risk of the challenger afterward just brushing it off with “nah, I still think bacterial flagella are more ‘impressive’”. We can’t, of course, reasonably come up with the bacterial flagellum itself in a computer simulation; first off the idea of simulating real, molecular-level physical systems is a project enormously beyond the scope of anything we could wind up doing here, and second off the actual flagellum in real life evolved by chance over many, many years over a space probably the size of the entire ocean, whereas we’d want our GA program to run within the RAM of a consumer PC and terminate within our lifetimes. What exactly is it that makes the bacterial flagellum so “impressive”, and what would be the flagellum’s analogue within the digital environment where these “entities” would exist?

And what’s this about “random” fitness functions? Within what parameters is it acceptable for the fitness function to change? From what space of possible fitness functions should these “random” functions be selected? Should or must these fitness functions be linked to changes in some sort of simulated environment?

Could any version of this “challenge” be reasonably adapted from the Avida software, and if no, why not?

If you present a specific challenge, perhaps someone can meet it (so long, of course, as you don’t inadvertantly wind up offering as a challenge “simulate the universe” or something else that would require a massive budget and programming team). But so long as you go on with this thing where you can’t explain exactly what it is you want, except that it hasn’t been met yet, I will consider you to have not issued any “challenge” at all and say that said “challenge” does not stand.

Comment #121772

Posted by Corkscrew on August 22, 2006 4:04 PM (e)

Woot, /me feels 1337 now.

For the record: the easiest way to figure out what the correct topology should be is to think soap bubbles. Note that if two soap films meet at an angle of less than 120 degrees, the system is not stable. The result is that the two films form a node that zips them together until the required angle is achieved.

In the above case, for example, the tenth MacGuyver is the obvious starting point. The two films will then start to zip in towards the middle, producing a rather odd MacGuyver - a version of the second MacGuyver with a diamond instead of a point in the middle. This diamond will naturally contract to a point, at which time the only way to proceed is by breaking symmetry. Which generates the correct solution.

The question I find really interesting is: can you ever have more than one stable solution for a given network? I’d imagine you can, but have yet to find an example.

Comment #121776

Posted by Sir_Toejam on August 22, 2006 4:18 PM (e)

earlier, Stevaroni was wondering about the thread discussing flagella that appeared on PT recently.

I think this is what you were thinking of Steve:

http://www.pandasthumb.org/archives/2006/08/frid…

Comment #121850

Posted by Ichneumon on August 22, 2006 5:15 PM (e)

[Dave Thomas:] I used computers simply to show that simulating evolutionary processes (reproduction, mutation, selection) over time can indeed produce precise solutions to difficult math problems, with no a priori knowledge of the correct answer(s).

If I may exercise a pet peeve of mine, genetic algorithms do not “simulate” evolutionary processes, they *are* evolutionary processes.

Similarly, a computer does not “simulate” addition and other numeric operations, it actually performs actual addition, etc.

Information processes, like evolution and addition, are transformations that information undergoes. When information in a computer (or anywhere else) is subjected to some form of selection, variation, and replication, the transformations that occur in the information is real honest-to-goodness evolution, not a simulation thereof.

Now whether the particular kind of evolution taking place in a particular instance is a good analog of the kind of evolution taking place in a different instance (e.g., Dave’s GA versus biological evolution) is a valid topic for discussion, because the exact behaviors and characteristics of a given instance of evolution will depend upon the nature of the selection, replication, variation, and information in that instance, and may or may not result in the same behavior/characteristics of a different instance of evolution which results from selection/replication/variation/information of a different nature.

But getting back to my point, using a GA as a test case of the behavior of an evolutionary environment simple enough to fully examine and analyze doesn’t make the GA a “simulation” of evolution, any more than rolling a ball down a measured incline in a laboratory is a “simulation” of gravitation or the physics of rolling balls. Whether the conditions in the simplified test case sufficiently encapsulate the conditions in the more complex situation out in nature is a different question, but not one of “simulation” versus reality.

What GA’s do is real evolution. The information in them actually evolves, and it does so via the interplay of the three key processes that, when they occur together, inevitably produce evolutionary change: Replication, variation, and selection.

Calling them “simulations” can confuse the honest reader, and give the dishonest critic a dishonest line of argument to use to attack the analysis: “It’s only a simulation…” The (false) implication is that like many simulations, it’s only as valid as the amount of understanding of the real world that went into crafting a scale model of the reality and the toy versions of the real-world processes affecting it. But using GA’s to study evolution is not subject to these limitations, because the experimenter is not “simulating” evolution based on how he thinks evolution acts, he’s simply setting up the conditions necessary for real evolutionary processes to kick into gear, and then sitting back to watch and learn how these real processes actually unfold for real.

Comment #121866

Posted by Dave Thomas on August 22, 2006 5:48 PM (e)

corkscrew wrote:

The question I find really interesting is: can you ever have more than one stable solution for a given network? I’d imagine you can, but have yet to find an example.

Not sure I get this, but here goes. For the 6-node problem discussed here, there are indeed two unique Steiner solutions. Each is rotationally symmetric (like a playing card), but each has different handedness. The only way to get the right-handed one from the left-handed one is, not by spinning it around an axis perpendicular to your puter screen, but rather picking it up, twisting it around in our three dimensions, and placing it back down so as to be reversed. (A neat sci-fi story exists where a 3D person is plucked into the 4th dimension, turned around, and placed back into the 3D world to find himself to be his mirror image).

So, yes, there are two stable (but different) solutions for the 6-node problem.

For the 5-node system described in my July essay on We don’t need no stinkin’ Target, there is but one proper Steiner solution, but any number of stable soap-film MacGyver solutions. There are photographs of such stable networks (as physical soap films) there.

Ichneumon wrote:

What GA’s do is real evolution. The information in them actually evolves, and it does so via the interplay of the three key processes that, when they occur together, inevitably produce evolutionary change: Replication, variation, and selection.

An excellent point!

Cheers, Dave
Dave

Comment #121870

Posted by trrll on August 22, 2006 5:56 PM (e)

The notion of biological organisms solving “problems” is on the other hand quite problematic, for the simple reason that there is no single specified problem an organism has to solve. Problems change all the time in biological evolution.

This depends upon what is meant by “specified.” All higher organisms require networks of some sort—vascular networks, neural networks—that have to connect particular targets within the body. And thermodynamics dictates that there is some energy cost per unit length for these pathways. Thus, a creature with pathways that are unnecessarily long will require more energy than an otherwise identical creature with more efficient network design, and will be less likely to survive when food is scarce. So this particular problem is pretty much constant, and it is “specified” by the fundamental laws of physics.

Comment #121893

Posted by trrll on August 22, 2006 6:35 PM (e)

Regarding the flagellum: It would certainly be nice to have a detailed history of the evolution of the flagellum. On the other hand, given the number of degrees of freedom of protein folding and interaction, resulting in an extremely high dimensionality of the “search space” traversed by evolution, I believe that we can with confidence make the following prediction from evolutionary theory:

The detailed, mutation-by-mutation pathway of evolution of the flagellum (and indeed, or most biological structures) will never be known

(Of course, that doesn’t mean that we won’t be able to come up with models, but they will always contain a substantial degree of speculation)

So does this meant that we must reject evolutionary theory because it refuses to provide us with an answer that we would like to have? If so, it will be in good company, because we will also have to discard such things as quantum physics, which perversely refuses to provide us with the exact trajectory of a photon through a slit. And Newtonian physics, which perversely refuses to provide us with an exact solution of the n-body problem, enabling us to accurately extrapolate planetary positions for any time.

But the scientific criterion for rejection of a theory is not whether it fails to answer a question that we would like it to answer—it is whether its predictions are contradicted by the results of experiment and observation. Of course, for a theory to even be in the running, it has to make such testable predictions. Here, of course, evolutionary theory has no problem, because it serves up a wealth of predictions, testable by methods ranging from computer simulations of genetic algorithms to genomic sequence comparisons (and so far has accumulated a remarkable track record of success).

ID on the other hand has a big problem. Predictions, after all, arise from the limitations of a model: the things that it cannot do. And since the ID crowd, apparently for political reasons, is unable to get specific about the nature—and particularly the limitations—of their hypothetical designer, they have been unable to make any testable predictions. The closest they can get to a prediction is “No pathway for evolution of the flagellum exists.” Unfortunately, this kind of prediction is next to worthless, because to test it, they would have to show that they have examined every possible sequence of mutations from every possible set of protein precursors, and determined whether all of them are blocked by low-fitness “chasms” in the fitness landscape. Of course, they have no desire to take on this impossible task themselves. So instead, they turn to biologists, and say—“You must carry out the impossible studies to test our theory; if you can’t disprove it, then our theory must be right.”

But of course, biologists have no interest in trying to carry out this impossible study, because they have a rich theory that makes lots of testable predictions, and are busy testing those predictions and making discoveries. And all the ID guys can do is yell, “Hey, what about the flagellum?”

Comment #121981

Posted by mempko on August 22, 2006 10:08 PM (e)

I wrote a program where digital creatures shaped like circles had evolving nueral network brains. The brains output was a force vector. The circles had a energy level that increased whe they touched food and decreased when they touched each other. A circle cloned its self when it reached a high energy level and died when it reached 0. The clone had a sightly mutated brain. There is no fitness function, only a digital world. No goal. Eventually, in about a half hour, there were circles that can track down food and avoid other circles. They actually could avoid other circles at high speed nd find food.It was very clear that their movemets were not at all random. The input to the neural net was x,y position of its’ self, nearest food, and nearest circle. What, if any are the problems with this aproach (mike?)? What was amazng is how fast smary circles evolved. I typed this on a nintendo ds lite…sorry for bad and short setences

Comment #122013

Posted by Andrew McClure on August 23, 2006 1:11 AM (e)

David B. Benson wrote:

I encourage making comparisons between GA and RA(Random Algorithm) by the number of generations multiplied by the number of individuals versus the number of random attempts for a solution. Not only does this seem ‘fair’, but it is enough to demonstration how quickly GA develops a ‘good enough’ solution in comparison to RA’s stumbling in the dark…

If you make this comparison against the RA run I did, make sure to keep in mind that 3,191,313 is only the iteration number of the best guess it ever came up with– I don’t know how many iterations the program wound up running total, but it would have been several times that, as it kept churning through even more unsuccessful attempts…

Also be sure to keep in mind that the GA has several other advantages. For example, while not every generational line will hit the global minimum, the GA finds at least a local minimum essentially every time it stabilizes. The RA is only barely any more likely to ever find a local minimum than it is the global minimum.

mempko wrote:

I typed this on a nintendo ds lite

Really, is this homebrew or did you import Opera? If the latter, is it any good?

Comment #122024

Posted by Marek 14 on August 23, 2006 2:41 AM (e)

DaveThomas wrote:
A neat sci-fi story exists where a 3D person is plucked into the 4th dimension, turned around, and placed back into the 3D world to find himself to be his mirror image.

I remember reading this story :) The only problem with it is that such a person wouldn’t be unable to survive for long, for a very trivial reason (can you find it)?

Comment #122031

Posted by Popper's ghost on August 23, 2006 3:24 AM (e)

I remember reading this story :) The only problem with it is that such a person wouldn’t be unable to survive for long, for a very trivial reason (can you find it)?

Presumably the person would starve to death.

Comment #122036

Posted by Paul Flocken on August 23, 2006 3:33 AM (e)

Marek 14,
Presumably because his amino acids would all be the wrong handedness. He would starve, being unable to digest and process food.

Paul

Comment #122037

Posted by Paul Flocken on August 23, 2006 3:34 AM (e)

Damn server time outs.

Comment #122093

Posted by Michael Suttkus, II on August 23, 2006 8:49 AM (e)

If I may, a few people have read Mike####’s demands for *a* point by point evolution of the flagella for *the* point by point evolution that actually produced it. This isn’t actually fair. Mike’s demand is possible, while the other is something we will probably never achieve without time travel.

Doesn’t change the fact that Mike’s demand is unreasonable. The weight of evidence that life did evolve is astounding; demanding that one particularly bit of it be demonstrated to that degree is just be persnickety.

For several years, I had a screensaver that evolved organisms out of colored lines I found online. It was fun to watch. Green lines produced energy. Red and blue lines consumed energy to maintain. Red lines stole energy if they touched a green line in another organism, but not if they touched a blue. (I don’t remember how red/red interacted.) You could vary the amounts of energy each line type used or produced to create different selection environments.

It was fun to watch organisms evolve. You could see ecosystems try to develop with primarily green producers, trying to protect themselves with a minimal shell of blue, etc. Good fun. And no selection function to sneak in design! (Not that they really ended up “designed”.)

Comment #122103

Posted by mempko on August 23, 2006 9:15 AM (e)

I imported the opera browser. Its good enough to surf and post comments, access gmail, etc. I enjoy it very much

Comment #122118

Posted by Anonymous_Coward on August 23, 2006 10:42 AM (e)

If I may, a few people have read Mike####’s demands for *a* point by point evolution of the flagella for *the* point by point evolution that actually produced it. This isn’t actually fair. Mike’s demand is possible, while the other is something we will probably never achieve without time travel.

What the hell is a “point” anyway?

I would have thought that the existence of simpler versions and more complicated versions of flagella than the one Behe utilises would have clinched it.

Furthermore, why doesn’t Mike#### consider the readily information available about the evolution of eyes to be pivotal? I thought the evidence for is a good “point by point” description of the fact. Didn’t Darwin also propose a (what turned out to be mostly correct) sequence of developments for eyes?

Comment #122175

Posted by Henry J on August 23, 2006 2:52 PM (e)

Marek 14 wrote:

“DaveThomas wrote:
A neat sci-fi story exists where a 3D person is plucked into the 4th dimension, turned around, and placed back into the 3D world to find himself to be his mirror image.
—-
I remember reading this story :) The only problem with it is that such a person wouldn’t be unable to survive for long, for a very trivial reason (can you find it)?

A question here - would this mirror image thing also reverse the electric and magnetic properties of the subatomic particles? ;)
(i.e., he might not have time to starve, or even breath… )

Henry

Comment #122176

Posted by Torbjörn Larsson on August 23, 2006 2:53 PM (e)

“If I may exercise a pet peeve of mine, genetic algorithms do not “simulate” evolutionary processes, they *are* evolutionary processes.

Similarly, a computer does not “simulate” addition and other numeric operations, it actually performs actual addition, etc.

Information processes, like evolution and addition, are transformations that information undergoes. When information in a computer (or anywhere else) is subjected to some form of selection, variation, and replication, the transformations that occur in the information is real honest-to-goodness evolution, not a simulation thereof.”

I think such a view, especially abstracted with the concept of information, invites all sorts of problems. Information isn’t sufficient to describe addition or evolution. And it is problematic to discuss even the numeric operations in a computer.

Granted, you can set up natural addition and subtraction with the help of bitoperations on the positions on vectors or similar algorithms, simulating moving beans between containers. But when you look at computer numerics you find that they are essentially binary 1’s (unsigned) or 2’s (signed) complement addition. It barely captures integer addition/subtraction on low numbers.

When you get into numeric on reals (or decimal approximations thereof) it doesn’t capture for example superposition of field strengths when adding charges, due to roundoff errors. So you have to argue about a limited “ghost in the machine here”, soemwhat removed from idealised mathematical addition operations or most real additive processes.

But considering this I think that if anything could be said to really happen inside a computer instead of being modelled by its algorithms, evolution of the GA type is probably the *best* example. The objects mapped inside are actually operated on by a selective process.

Comment #122186

Posted by Popper's ghost on August 23, 2006 3:28 PM (e)

If I may, a few people have read Mike####’s demands for *a* point by point evolution of the flagella for *the* point by point evolution that actually produced it.

I don’t know who you have in mind; I certainly didn’t. I addressed his demand for a demonstration that it’s possible (which is even weaker than a demand for a demonstration of an actual pathway).

Comment #122191

Posted by Popper's ghost on August 23, 2006 3:32 PM (e)

A question here - would this mirror image thing also reverse the electric and magnetic properties of the subatomic particles? ;)

Electrons don’t left and right sides, so mirror-imaging them wouldn’t change anything … certainly not their charge.

Comment #122195

Posted by Popper's ghost on August 23, 2006 3:41 PM (e)

P.S. The “spin” of subatomic particles is a fundamental physical attribute, distinct from the fundamental physical attribute of charge. Electrons and positrons both have spin of 1/2.

Comment #122198

Posted by Corkscrew on August 23, 2006 3:57 PM (e)

For the 6-node problem discussed here, there are indeed two unique Steiner solutions. Each is rotationally symmetric (like a playing card), but each has different handedness.

OK, fair point, I didn’t think that one through properly. Would be interesting to figure out some way to characterise the Steiner points of an arbitrary network - I have a sneaking suspicion that there’s some sort of number-theoretic way of handling this.

Comment #122278

Posted by Henry J on August 23, 2006 9:12 PM (e)

Re “Electrons don’t left and right sides, so mirror-imaging them wouldn’t change anything … certainly not their charge.”

Not right/left, true. But I don’t know if they might have geometric distinctions (from positrons) in some other dimension (not one of the four we can detect directly). I don’t know enough physics to judge that offhand.

Henry

Comment #122289

Posted by Torbjörn Larsson on August 23, 2006 10:55 PM (e)

Henry:

“But I don’t know if they might have geometric distinctions (from positrons) in some other dimension (not one of the four we can detect directly).”

According to string theory they have, and some of them may be large (brane worlds). But I doubt a rotation affects this.

Spin is basically a topological effect with no left/right problem, if I understand correctly. (See Popper’s comment.) But there are P (and CP) violations, so parity has a small effect from geometry. A parity transformation is flipping all coordinates and that is AFAIK possible by rotations in a higher dimension. But it wasn’t done here.

Comment #122321

Posted by Marek 14 on August 24, 2006 3:07 AM (e)

Actually, I wonder if he would starve. Are proteins from right-handed aminoacids just undigestable or are they downright toxic? If so, even touching a biological material (like an apple) could have some unpleasant effects…

Of course, the story was written by H.G. Wells, who could know nothing about the assymetry of living world - I think.

Comment #122352

Posted by Michael Suttkus, II on August 24, 2006 7:36 AM (e)

They are certainly indigestible. They may also be anything else. A stereoisomer can have any chemical properties any other molecule can, relatively unrelated (biologically, their general properties will be similar).

Thalidomide, for instance, is a powerful, safe anti-nausea drug, but it’s stereoisomer causes nasty birth defects.

Comment #122387

Posted by Dizzy on August 24, 2006 10:43 AM (e)

Maybe slightly off-topic here, but since we’re talking about genetic algorithms (apologies if posted before):

http://www.demo.cs.brandeis.edu/golem/press/UsNe…

…[Brandeis University computer scientist Jordan Pollack] and mechanical engineer Hod Lipson run the Golem Project, a colony of machines that evolve and give birth to other machines without human guidance.”

Wonder what a cool name for their next generation project would be…hmm…oh, how about “SkyNet”? Hey, that’s a cool name!

Comment #122506

Posted by Jeff on August 24, 2006 5:56 PM (e)

I’m not real familiar with Steiner trees, so my question is how was the exact solution determined? Is there some type of general way to do it? How can you be sure that your best solution actually was the best solution, and that with a little more playing you couldn’t get something with an even shorter length than your 1586.53?

Comment #122541

Posted by Dave Thomas on August 24, 2006 7:15 PM (e)

Jeff wrote:

How can you be sure that your best solution actually was the best solution, and that with a little more playing you couldn’t get something with an even shorter length than your 1586.53?

Being the one in charge of herding the thousands of genetic solutions, and also keeping track of dozens of intelligently designed submissions, I confess I haven’t actually worked out a closed-form analytical solution for the problem.

I am confident that 1586.53 is indeed the best network, however, because when I assigned this math problem to the World, there were eight clever people who found that precise answer, using a variety of methods.

In other words, consilience works for me.

If you think you can do better than 1586.3 - hey, by all means, do it, and send it in! All the respondents used their own noggins, and no one tried canned software like the package Salvador tossed out, so that option may be something to consider.

Cheers, Dave

Comment #122643

Posted by Dizzy on August 25, 2006 8:49 AM (e)

Hi Dave,

Do you know of any place to find sample mutation algorithms for GAs?

It looks like your code hardcodes probabilities for certain mutations, then mutates one(?) locus at a time.

I’m trying to put together a simple GA-based program that takes a set of input bits and manipulates them into a set of (user-defined target) output bits using only NAND operators.

Not sure exactly how the “DNA” is going to look yet, but if a mutation can only replace one locus at a time, it’s going to be impossible for the GA to co-opt “groups” of operations that might serve a generally useful purpose [e.g., (a NAND a) NAND (b NAND b), equivalent to (a OR b)]. Unless I allow the reproduction mechanism to mutate, which is a bit more work than I want to do right now…

Anyway…any resources you can think of that would help me with this?

Comment #122726

Posted by GuyeFaux on August 25, 2006 2:57 PM (e)

I’m trying to put together a simple GA-based program that takes a set of input bits and manipulates them into a set of (user-defined target) output bits using only NAND operators.

So basically you’re gonna apply a bunch of these transformations:

00 -> 1
01 -> 1
10 -> 1
11 -> 0,

And to go from a string of size n to a target of size t would require n-t applications of NAND. So I guess a “creature” is a list of places to apply the transformation, represented such as:
{T_1, T_2,…,T_(n-t)}
where 1 = T_i = n-t-i
which makes it easy to cross two creatures, at say a point x:
{T_1,T_2,…,T_x,T_(x+1),…,T_(n-t)} x
{S_1,S_2,…,S_x,S_(x_1),…,S_(n-t)}
should be
{T_1,T_2,…,T_x,S_(x+1),…,S_(n-t)}
and
{S_1,S_2,…,S_x,T_(x+1),…,T_(n-t)}

Comment #122776

Posted by Jeff on August 25, 2006 5:31 PM (e)

Dave Thomas wrote:

In other words, consilience works for me.

Good enough for me, too. Just to clarify - my original e-mail wasn’t meant to be hostile at all, it’s just that the couple Steiner series posts I’ve read of yours are extremely interesting, and piqued my curiosity.

Comment #124081

Posted by Patrick May on August 29, 2006 2:59 PM (e)

Dave,

You inspired me to develop a genetic algorithm engine to solve the Steiner Problem you described. I went through your three articles, making copious notes, then spent an afternoon building the core functionality. I tried it out on the six node challenge problem and consistently got solutions with a segment length more than 400 longer than the Steiner solution.

Over the course of the past week I’ve spent an hour or two every day adding to my engine, implementing more sophisticated crossover, trying alternative selection techniques, changing the encoding of variable node positions from standard binary to Gray code, and running test after test. Still, my evolved solutions remained stubbornly 30% longer than yours.

I was getting concerned. Had you, no doubt unknowingly, introduced information about the solution in your encoding of the problem? Was this a potential source of embarrassment for The Panda’s Thumb? Did I have an ethical obligation to publish my results?

Before contacting you with these questions, I went back once more to the original articles. It turns out that I’d written down the wrong value in one section of my notes. I have been hacking furiously in an attempt to get the fitness of my solution to the six node challenge problem down to that of the five node example you’d provided. In fact, my engine had been generating Steiner solutions and MacGyvers all along, even in its most naive implementation.

The code is available if anyone is interested in having a look. I used a simple binary string rather than your more complex encoding. My first version allowed the number of variable nodes to mutate, but as you also reported, this leads to local optima with no variable nodes.

Thanks for the interesting puzzle.

Regards,

Patrick

Comment #124156

Posted by Dave Thomas on August 29, 2006 7:41 PM (e)

Dave Thomas wrote:

As regards “global” versus “local,” I don’t have the foggiest notion of what you’re referring to. In the GA, an organism is represented by a DNA string, period.

OK, I get it now. The Steiner Solution itself is the Global Minimum (for length), while the numerous MacGyvers represent Local Minima. Indeed, there can be large gulfs between the DNA of organisms parked at local minima. The double bowtie (MacGyver #10) is genetically much different from the actual Steiner solutions, wherein two bowties are twisted and mutated to form the central dog-leg junction-of-bowties. That’s a “macromutation,” I guess.

Dizzy, the program allows both a number of organisms to mutate per generation (typically 50 of 1000), and also a number of mutations per organism (usually three per creature). Thus, it’s not just single-locus mutations; each creature that is to be mutated is hit three times, not just once.

Jeff, no hostility was detected. I was just trying to make the point that we’ve collectively gotten the real solution to the given problem.

Patrick, excellent work! That’s a third independent confirmation.

I’m closing comments on this post, but stay tuned for a follow-up post, “Genetic Algorithms for Uncommonly Dense Software Engineers.”

Thanks for a great discussion!
Dave