With the aid of smoke and mirrors and beautiful women, David Copperfield can make the impossible seemingly happen before the very eyes of live audiences. He is an illusionist by profession, and is so adept at what he does, he has become one of the highest paid celebrities in the world (57 million a year).
It is one thing for cleverly crafted theatrical illusions to be consumed for entertainment. It is another when theatrical illusions in computer simulations are used as evidence in a landmark federal case like Kitzmiller versus Dover.
This will be the first installment of a 3 part series where I will explore the work on evolutionary algorithms by Chris Adami, Dave Thomas, Wesley Elsberry, and Jeff Shallit. (In no way am I claiming the theatrics of their evolutionary algorithms were deliberate or meant to mislead or deceive. I simply use the phrase to hammer the point that these simulations are little better than theatrical illusions.)
Avida is the premier computer simulation in the anti-IDist arsenal. It supposedly illustrates Darwinian evolution, creates an instance of artificial life, provides a refutation of Behe’s irreducible complexity, and disproves Dembski’s assertions of information conservation and specified complexity. It has been featured in prestigious scientific journals, was offered as evidence in Kitzmiller vs. Dover, brought a measure of fame to its promoters, and possibly paid a few mortgages.
Chris Adami is the principal scientist on the Avida project . (Earlier I ripped into Adami’s book review of Yockey here.) Avida probably has roots as far back as the early 1990’s. The official website is at: Avida
Rather than going into the painful details of Avida, I’ll give a few anecdotes, and then provide links to more information. Readers with serious interest in the topics are invited to visit the links as it is not possible that I can even touch on the major issues in the short space of this thread.
Avida is a computer simulation where artificial life forms evolve in artificial environments. An Avidian creature is made of very tiny amounts of software, a mere 20 bytes or more (a suspiciously low amount for a living creature!). The evolution of these make-believe organisms in make-believe environments has been the subject of various scientific studies and have been used to various ends.
If one thinks I’m being overly dismissive of the Avida project, I think I have something of a right to be because a microscopic part of the default Avida configuration files arguably bear my authorship. Yes that’s right, part of Avida 1.6 files are traceable to me, an IDer. How did an ID trouble maker like me get involved in making part of Avida’s files?
In a classic, grueling internet debate from June 30, 2004 to August 28, 2004, Dr. Richard B. Hoppe (RBH of PT) and I argued at ARN over Adami’s work. I had never touched Avida in my life prior to this debate. The only reason I knew I would win the debate was the assurance that Avida’s fantastic claims could not possibly be right based on information science alone.
In contrast, Hoppe was an Avida expert of several years, and a master rhetorician. He nearly delivered a knockout in the early weeks of the debate before I was able to recover and eventually gain the upper hand. (Hoppe has truly been one of my most worthy counterparts in the ongoing jousts between the UDers and Pandas. He and PvM will be happy to know they had a lot to do with getting me involved in ID. 
)
The debate took a decisive turn when I discovered a documentation bug in Avida’s configuration files. I was doing some studies on these make-believe Avidian organisms by pouring unbelievable amounts of radiation on them. Imagine taking a pair of creatures and putting them in a microwave for 3 days at high power and then asking them to make offspring. Well that’s exactly what I was simulating on these critters, and they were still reproducing like rabbits.
It turned out a comment in the Avida “genesis file” was misleading to experimenters (including Hoppe and myself). Hoppe confirmed my experimental findings and wrote the Avida group. To make a long story short, the final disposition of the bug was described by one of Adami’s PhD students to me here at ARN, Avida: Response to S. Cordova
There is an erroneous note in the default “genesis” file distributed with Avida 1.x. The line specifying point mutation rate has a comment (x10^-6), implying that the user value is multiplied by this quantity before application. This is in error; the specified point mutation is used as-is as a probability. This erroneous comment has been removed in Avida 2.x releases.
We will shortly be releasing a bug-fix of Avida 1.6 (the stable, current version of the Avida 1.x codebase) which corrects this error in the documentation.
As far as the documentation error is concerned, the (x10^-6) comment in the genesis file is unquestionably in error upon examination of the code. I do not believe that it affects the interpretation of any currently published results.
The documentation error is unfortunate and must be corrected. I personally am glad to have it cleared up.
However, it was of much greater concern to myself and others on the Avida team that an apparent result showed faster growth when point mutations were increased, since I think all would agree that should not be the case. In particular, the resulting conclusion that an artificial mechanism protected key instructions from mutation.
If it existed, such a mechanism would obviously render the entire system unscientific and all results invalid. Those of us who have worked with Avida’s code know that no such protection mechanism exists, but that of course made it important to us to understand what was happening when one set Pmut = 50,000, in order to explain the apparently aberrant result.
I really did not want to quarrel with Even Dorn, but felt it better to leave the channels of communication open, even though I was a fierce critic of the Avida project, and even though I knew some of his other comments contesting my position were wrong. I simply cut my discussion with him short.
The fix really still did not correct a far more underlying problem, namely, Avidian creatures have some features which seriously decouple them from reality. The proof was right there, because even after this bug was fixed, the make-believe creatures could still be made to breed in high radiation environments (not quite like rabbits, but still enough to draw notice). The bug fix only slowed down reproduction in high radiation environments, it didn’t stop it. In fact the creatures (being immortal) would oscillate between sterility and fertility as long as one kept bombarding them with radiation! Doesn’t that strike you all as a bit odd?
Would we expect Steve Studly, wearing intensely radioactive underwear, having massive amounts of gamma rays pumped into his private plumbing – would we expect him to reproduce viable offspring? Further in Avida, if a creature becomes sterile, one merely needs to pump more radiation into it, and with enough time (a minute or so) and radiation, voila, the critter can make immortal babies again. One could almost argue that radiation bombardment didn’t just result in the creation of fertility but practically worked a miracle of resurrection. Isn’t Avida wonderful!
Why are such miracles possible? Fundamentally because Avida is not reality. Just look at one of the Avidian genomes. Does it resemble anything like the …GATACC… of DNA?
search-f
nop-A
nop-A
add
inc
allocate
push
nop-B
pop
nop-C
sub
nop-B
copy
inc
if-n-equ
jump-b
nop-A
divide
nop-B
nop-B
Artificial life. Yeah right.
Finally, one of the more serious claims of Avida is that it counters Behe concept of Irreducible Complexity. The Avida promoters claim they have successfully created IC systems through co-option. Well, that claim is about as valid as the fact that Avidian creatures can re-gain fertility by bombardment of their private parts with radiation.
What Avida allows a programmer to do is assert the following tautology with computational theatrics:
if co-option is possible, co-option is possible
This is not a remarkable statement at all. In fact it is a zero knowledge statement. With Avida one can create selective pressures for various traits or combination of traits of the creature on an absolute whim. There is a parameter file where one can effectively say: “if these three pieces come together, that will result in selective advantage…and if these other three come together that will result in selective advantage…†and so on.
The programmer creates selective feedback loops on a whim. No provision is made whatsoever as to how close to reality the programmer’s whims might be. One can pretend partial biological systems can serve some selectively advantaged function in a computer simulation, with no justification whatsoever except perhaps it might affirm the thing one wishes to prove.
By allowing programmer whims rather than empirical reality to dictate the likelihood of outcomes, Avida merely shows that
something is possible, if something is possible,
and
co-option is possible if co-option is possible
Profound indeed, but it never actually proves what is possible. The only thing it proves is that those who wished to be duped can find a way to be duped.
Let me end on a positive note. Avida may not have much scientific value, but it does have entertainment value. However, if one really wants serious entertainment, one should check out Pandamonium!
Salvador
PS
The links I provide below will go into grueling detail of the software with less of the linguistic liberties I took in this essay.
Refutation of Irreducible Complexity? ?Get a Vida! by Casey Luskin
Darwinists Prove Computers Work by Jonathan Wells
Bit’s Bytes and Biology by Eric Anderson
PCID: Evaluation of neo-Darwinian Theory with Avida Simulations (part 1) by Royal Truman
PCID: Evaluation of neo-Darwinian Theory with Avida Simulations (part 2) by Royal Truman
Truman, Cordova, RBH, and others on Avida
Spiegelman’s Experiment : Natural Selection Goes the Wrong Way (debate between Richard B. Hoppe of PT and Salvador Cordova of UD)
ARN, Avida: Response to S. Cordova (Evan Dorn of the Avida group responding to technical queries from RBH and Salvador )