Tautologies and Theatrics (part 1): adventures in Avida

Zap, I was a little annoyed since I asked you to wait till I got back to this thread. You kept right on posting before I came back. Remember, you're here at our invitation. In any case, I do apologize to you for the rough treatment. Now, let's do this in pieces, I don't want long responses where you fill up your posts with so many falsehoods and where I'll have to spend 10 pages cleaning them up. In otherwords I don't want you to do a Gish Gallop. If you do that, automatic delection. Ok? Your questions might be valuable to the readers, but if sense you going into a Chewbacca Defense of Avida or doing a Gish Gallop are argumentum ad nauseam, I'm sorry your questions and objections will just be deleted. So for starters, state your objection again about the fact that the host computer running the simulation effectively models a replication process. And then I'll respond. Keep your assertion about the length of this comment please. Finally if I pose a question to you, and you don't ignore it, I will delete any subesequent participation on this thread until you answer. Got it? Your here at my invitation, remember that. In any case, I'm sorry my treat of you was a little brusk... Salvador scordova

"Zapatero’s post deleted." Why? zapatero

Zapatero's post deleted. zapatero

Zaptero,

I don't have time to address the sophistry of your posts today, so more posts from you on this thread until I get back. Ok?

What you are doing is what is known as Chewbacca Defense

But briefly:

Zapatero wrote:

The source code is available at http://dllab.caltech.edu/avida/versions.shtml . Could you post the code that you believe is responsible for “heavily constraining” the mutations?

The reason the for the mutations being constraind is that there IS NO CODE modelling the replication process (like the RNAs and Proteins in transcription and translation).

You demand that I show in the Avida code where mutations are constrained, and I full well pointed out it doesn't exist and that's why the mutations are constrained. Avida relies on the CPU running the simulation to effect what RNAs and proteins do in real life. Hence, replication functions are totally immune to any damage from radiation induced mutation, hence the mutation is perfectly constrained because it is not even coded, much less modelled! It effectively models replication through POOF mechanisms immune from mutation.

Zapatero:

Ironically, you are the one advancing a tautology.... You object that EQU can’t really be IC since it is “trivially reachable”..... So Avida can’t reach something that it can’t reach — a perfect tautology.

I put ellipses where you made some false statements. IC cannot by definition be reached by deterministic process. It being specifed means by definition stochastic process can't reach it. This is as straight forward as the fact square circles don't exist.

"Square cirlces don't exist" is a tautology but it's one that's consistent with accepted and practiced definitions. IC is consistent with accepted and practiced conceptions of complexity and irreducibility. If one is going to try to use conceptions of deterministic and stochastic process they better be consistent with accepted conceptions of if just like we have accepted conceptions of "square" and "circle".

See:
Stochastic Processes, Deterministic Processes, and Square Circles

Avida, circumvents these problems through Orewllian double speak. Selection in Avida is anything but natural, it's a POOF! If NS needed to form complexity, the user just inputs a parameter, and NS is there. POOF! No measure of NS's complexity is calculated. It could well be thousands of bits in the real world, but Avida effectively gives it cost free. It effectively gives free lunches right there! No mention of this sleight of hand. Avida promoters are suggesting Avidain selection is "natural" or "Darwinian" when in fact it is artificial, and probably not even feasible in the natural world. Is that ethical?

The sleight of hand little removes complexity that would otherwise be in the natural world. It allows "artificial" selection to be perceived as "natural" selection. Orwellian double speak. It is unethical. In the natural world, these co-optive complexities come at cost. Is that factored in Avida? No.

Come to think of it Zaptero, why don't you address the ethics of Avidian double speak in your next post, after I get back to this thread.

Finally, the displacement theorem shows combinations of deterministic and stochastic processes will not reach IC systems, unless the boundary conditions are more information rich than the artifact itself (i.e. a computer manufacturing pipeline is more complex than a computer). The displacement theorem basically again shows looking for simple solutions for IC is looking for square circles.

Salvador

scordova

scordova wrote: "No it is not IC, and that is just computation theatrics. It violates the behe’s conception of “well-matched”. Well-mathched implies matching parts are RARE." Salvador, where does Behe give an objective definition of "well-matched", and how does the Avida EQU function fail to meet it? Second, what justifies your assertion that well-matched parts are rare? The world is full of well-matched parts. "Mutations don’t get dead organisms to reporduce in the real world. Dead organism shouldn’t even be mutating because they are dead, but they mutate in Avida, and then these critters reproduce." At the ARN page, Evan Dorn explains what is happening in these cases, concluding thus: "While yes, this process will slowly fill the grid cells, it is in no way analogous to life: nothing is replicated with fidelity, and no information is conserved.” Your complaint of "resurrection" in Avida is dependent on your own false idea of what "alive" means in the Avida world. scordova: "As I pointed out through my radiation experiments in Avida, it is apparent the mutations were being heavilty constrainted, that’s why dead creatures were still giving birth!!!!" The source code is available at http://dllab.caltech.edu/avida/versions.shtml . Could you post the code that you believe is responsible for "heavily constraining" the mutations? zapatero

Did he drop into the q-bit bucket? :=) scordova

Qbit is no longer with us. His sin was lack of originality. Fare thee well, Qbit. DaveScot

RM+NS are producing useful, non-trivial, non-designed, irreducibly complex systems for our use.

This is highly disingenuous, as the framework is anything but pure RM+NS.

RM = the mutations are intelligently constrained. As I pointed out through my radiation experiments in Avida, it is apparent the mutations were being heavilty constrainted, that's why dead creatures were still giving birth!!!!

Is this fair?

If I design a shot gun shell, I could argue the pattern with respect to the centroid of flight of the pellets is "random". Thus if I shot someone's cat with a shotgun, would I say that it's a result of randomness because of the random pattern of shotgun pellets? If the RM were not intelligently unconstrained in the simulation, Avidian creatures would not live.

NS - that is also disingenuous because the selective force in evolutionary algorithms is designed as part of a strategy to solve a problem. If the description of the selective forces were not designed, the evolutionary algorithm would go nowhere.

I will be posting on Dave Thomas's article hopefully next week. He programmed a selection strategy that would find the target. What is the probabilty that a non-programmed set of code (let's say through a random text generator) would create a selection strategy to hit the target? Practically zero.

Thomas was resorting to double speak: "oh, I didn't specify the target." Picture this, some kid with a paintball gun goes up to another and shoots his victim, and says to his vicitm, "don't be mad, I wasn't aiming at you, I was aiming at the shirt you were wearing." Thomas's double speak was hardly better.

What we have here is a case of Orwellian Double speak, where disingenous labels are affixed which are misleading. For example, let us say I created a novel and useful medicine. I could later call it "poison". I could then argue "poison" is healthy. The arguments in favor of Avida are merely double speak.

Salvador
PS
I will try to get away from cyberspace for the weekend. I'll try to get back to this thread later, or simply join the discussion in part 2.

scordova

The depth of the misunderstanding are compounded.

Avida is not a simulation of life per se, but of reproduction, mutation and selection. The program demonstrates that complex and irreducubly complex systems can arise easily once the three preconditions are fulfilled.

To complain that it is not a biological simulation is to misunderstand fundamentally that it is a simulation of very specific ideas; mutation and selection over generations.

However, you do not have to look just to Avida to see that IC system evolve from mutation, reproduction and selection, look at any of the results of genetic algorithms, from PCB designs to auditorium designs.

These may not be biological systems, but if mutation and selection are useless, victorian age concepts, it is interesting that they are used to make thoroughly modern things like cell phone networks.

It strikes me that complaining Avida is not biological is a smoke screen. RM+NS are producing useful, non-trivial, non-designed, irreducibly complex systems for our use.

To truly deal with the issue you must demonstrate that genetic algorithms do not work in general.

look at any of the results of genetic algorithms, from PCB designs Oh goody. PCB auto-routing software is something I have mucho experience with dating back decades. They work through simple trial and error, with the programmer throwing every bit of his expertise into the software so that it makes educated guesses about what might succeed. And it's *still* guided by an intelligent agent through each PCB design. Avida is a toy. It models nothing that can be independently verified. It produces nothing useful or complex. -ds qbit

qbit, I don't think your characterization is accurate. I really didn't want to have to drag in all the ugly details of this nonsense program, but you're forcing my hand. In a real cell you have the genome and then things like proteins, RNAs, a collossal network of machinery to carry out the process of duplication. In Avida, what simulates this duplication machinery? Answer: NOTHING! Genes, if they are in an appropriate semantic form just POOF another creature into existence. There is no simulation of the life process of being nourished and then carrying out all of the steps of duplication. In a high radiation environment, the duplication machinery (RNA's, proteins, etc.) would be cooked, toasted, fried....In Avida, this machinery is 100% invisible to radiation since it really doesn't exist. Life forms poof offspring without going through the steps real organisms.

scordova makes the error of thinking that all activity = life, where as it just shows a reaction occurred (this was brought up earlier but termed ‘brownian motion’).

Oh, well in that case, I'm watching dead creatures have offspring, and thus Avida proves living-dead Zombies can have kids. We can add that to Avida's list of amazing scientific discoveries. If something as irreducibly complex as life can be poofed into existence by a randomizing process like brownian motion, why should any other of its solutions to IC be trusted? scordova

es58, Hi, I'm sorry I didn't respond earlier. I don't know enough about Hillis to comment, but I doubt this was really any thing extraodinary. My computer accidentally does all sorts of intersting things all the time. Sal scordova

I think some fundamentals are missing from the debate.

The CPUs that run the Avida creatures are analogus to physical processes, molecules combining, ion flows across a space, and so on. This processing goes on whether there is a viable result or not; and if there is nothing in a cell for a cpu to process, nothing happens.

Similarly the basis of life is chemical, chemical reactions continue whether the result is life or not. Chemical reactions are deterministic, if the reagents can react (by which i mean they could and have the energy to do so and they meet) they will.

The result of chemical reaction can be 'life' or sulphuric acid, the rules governing chemistry do not care. scordova makes the error of thinking that all activity = life, where as it just shows a reaction occurred (this was brought up earlier but termed 'brownian motion').

The fact that a high rate of point mutations occurred with high radiation levels. and so caused mutations is not surprising. In this instance point mutations represent radiation entering a system. As we all know, if you add energy to reagents they react more.

I could go on....

Actually they're virtual CPUs not real ones. Even the hardware is phonied up. Hard to believe isn't it? In the real world something would come along and eat a dead cell. It wouldn't continue twitching for long. -ds qbit

However, the Avida world shares the phenomena of mutation and selection with the real world, and can therefore give us insight into how those processes operate in reality.

Objection! Mutations don't get dead organisms to reporduce in the real world. Dead organism shouldn't even be mutating because they are dead, but they mutate in Avida, and then these critters reproduce. You call that mutation, I call that misrepresentation.

When a concept is so decoupled from reality it is disingenous to try to argue it gives insight into reality.

scordova

Zapatero argues:

Ironically, you are the one advancing a tautology. Avida shows that the EQU function, which is irreducibly complex, can be produced by mutation and selection.

No it is not IC, and that is just computation theatrics. It violates the behe's conception of "well-matched".

Well-mathched implies matching parts are RARE. Avida is so lax about defining what will match it allows ressureciton of the dead. That implies the space of possible outcomes is limited, therefore well matching doesn't even exist in Avida! This is bait and switch and equivocation, and if the authors were more forthcoming they'd point out not only have their models shown co-option is solvable, but ressurection, and the origin of life to boot. Thus they would have shown "well matched" doesn't really even exist in Avida, but that would have defeated their claims wouldn't it?

Salvador

scordova

Dave,

Even though the comment in the moderation queue was not addressed directly to you, I thought it covered your questions. Let me give it another try.

Some models, like those running on the Weather Service computers, are intended to predict the future. Others are intended to model purely hypothetical events that are possible in principle but are not actually expected to occur, like a Pentagon war game simulation of an invasion of Canada. Still other models are even more abstract, like the ones you mentioned earlier which show that atoms would fly apart if the fundamental constants of nature were altered in certain ways. We're definitely not expecting that to happen, but those models are nevertheless legitimate and serve a useful purpose.

Avida is not intended to model any actual future world, and the Avida organisms are not expected to ever exist in reality. However, the Avida world shares the phenomena of mutation and selection with the real world, and can therefore give us insight into how those processes operate in reality.

What Avida "predicts" is that in the real world, irreducible complexity alone cannot tell you whether something evolved (or could have evolved). You have to look at the specific genome space and fitness function(s) to make that determination.

You often write about what you consider the unjustified extrapolation from microevolution to the emergence of new tissue types, organs, body plans, etc. What is it about the actual genomic space and fitness landscape that makes you think that microevolution hits a barrier beyond which it cannot proceed?

On the subject of model reliability, you're absolutely right that models have to be carefully checked and calibrated. A broken model will produce nonsensical results. Therefore we test models just as we would any other design: We run them through as many targeted scenarios as time, technology and motivation allow. If the results are correct, our confidence in the models increases. We also examine the models themselves for errors in construction or unwarranted assumptions built into them.

In the case of Avida, the mutations are generated pseudo-randomly, with no regard for whether they increase or decrease fitness. The selection criteria are applied fairly. And although the model sometimes generates counter-intuitive results, closer inspection shows that the model itself is working correctly, and that it is our expectations of certain behavior that are flawed.

Critics are free to inspect the Avida code and point out any flaws. Salvador has tried to do so, but I argue that he has failed.

So what you're saying is there's no way to validate Avida's model. Even a war game with Canada uses data from the real world and predicts a real world outcome. In principle the war game model can be tested. Physics models rely on precise formulas able to predict real world events down to many decimal places of precision. If the gravitational constant changed we know precisely how much our measured weight at the earth's surface would change even though there is no way even in principle to change the gravitational constant. Darwinian evolution is by definition an unpredictable, unrepeatable process because the input to it is random. There is no way even in principle to test Avida's model because 1) it is not modeling anything the real world and 2) even if it was modeling actual evolution of proteins it is attempting to model an unpredictable, unrepeatable process. Nice try and thanks for playing but the bottom line is Avida demonstrates nothing in regard to organic evolution. It's a toy playing in a world of make-believe. -ds zapatero

zapatero You have a comment in moderation but it doesn't answer my question and I asked that you not come back without an answer. For your convenience here it is again:

Models are a guide at best. Matching their results against reality is always the acid test. When weather forecasts are made a number of different models are used and their predictions are averaged. They’re often wrong and they can’t predict more than a few days into the future. Avida doesn’t even predict anything in the real world. It makes strings of artificial instructions in an artificial environment on artificial hardware. What exactly does it predict about real world outcomes that we may compare to determine if it is accurately modeling something real? Don’t come back without an answer. -ds

DaveScot

Mung asks: "If the degree of biological realism in Avida is insignificant, what of any significance does it tell us about Irreducible Complxity in biological systems?" I didn't say that the degree of biological realism in Avida is insignificant. I said that biological realism is not the point of Avida. Like any model, Avida must concentrate on some facets of the problem and leave out others in order to be useful. If I write a computer model of the bond market, I include some rules on how traders react to a drop in home sales or a hike in the federal funds rate. I leave out the fact that trader X is wearing an ugly tie and that trader Y had an argument with her husband last night, even though these may affect their trading performance to some degree. Similarly, Avida concentrates on highly abstract versions of mutation and selection, and succeeds in showing that they can produce irreducible complexity. This does not, by itself, prove that real-world biological instances of irreducible complexity evolved. But it shows that the argument "this structure is IC, therefore it couldn't have evolved" is insufficient by itself. You also have to show that there is something about the actual genomic space and fitness landscape that precludes a gradual path, via cooption, to the IC structure in question. scordova wrote: "Tuatology: 'If co-option is possible, it is possilbe'" The question actually asked in the Nature paper is not tautological at all: "Can this IC structure be produced by Avida through random mutation and selection?" The answer is not guaranteed to be yes, so this is not a tautology. salvador again: "The travesty of Avida is that violates the conception that Behe tried to put forward, namely, complexity. Avida represents simplicity as being complex. Trivially evolvable features was not what Behe was focusing on...If a system is trivially reachable, it is not by definition, complex. Avida has succeeded in selling the idea that what it’s modelling is complex when in reality it is simple!" Behe provides a precise definition of irreducible complexity which the Avida EQU function meets. How does that "violate the conception of complexity"? Ironically, you are the one advancing a tautology. Avida shows that the EQU function, which is irreducibly complex, can be produced by mutation and selection. You object that EQU can't really be IC since it is "trivially reachable". But in so doing you add a condition which is not there in Behe's definition. Under your new definition, anything Avida can reach is not really IC. So Avida can't reach something that it can't reach -- a perfect tautology. zapatero

Salvador or anyone, Dumb question about Danny Hillis evolving algorithm to sort. Evolution is undirected and has no goal in mind. Did Hillis really just let code go wild and one day discover he had a sorting program? "wow, look, this sorts stuff! - and my, it knew what kind of structure it could sort as well?" Or did he provide some kind of incentives along the way, implying that part of a sort was somehow good, even tho it didn't solve any problem? Thanks es58

Zapatero repeats the tautology:

the significance of Avida in the ID debate is not its degree of biological realism, but rather that it shows that irreducible complexity is not in principle a barrier to evolution via mutation and selection.

Tuatology: "If co-option is possible, it is possilbe"

The travesty of Avida is that violates the conception that Behe tried to put forward, namely, complexity. Avida represents simplicity as being complex. Trivially evolvable features was not what Behe was focusing on.

If a creature can be ressurected by random mutation alone, that should clue one in that Avida is dealing with trivially evolvable creatures that could only survive in make believe environments, not real ones.

If a system is trivially reachable, it is not by definition, complex. Avida has succeeded in selling the idea that what it's modelling is complex when in reality it is simple!

Is it good science to say the co-option of complex (improbable) systems was demonstrated when the system is not really complex (improbable).

Thus avida shows it can evolve simplicity, not complexity.

Salvador

scordova

Zapatero wrote:

In fairness to Evan Dorn, here are some excerpts from his post at ARN which address Salvador’s claims directly:

Evan wrote: “Instead, because such high values can cause an integer rollover, Mr. Cordova’s experiment is demonstrating the effect of turning mutations off, not increasing them by some large number.”

What is not mentioned is even when I correct the flaw of turning off the mutations, but instead turn them on, we only slow down the bizarre behavior of the simulation, we don't stop it.

Put simply, the population was dead. What Mr. Cordoba observed was slow, random activity of non- replicating random strings.

What this is showing is Avida can ressurect the dead, and this is being glossed over with techno babble. If Avida can ressurect the dead with random strings so easily, this illustrate that Avida is not very discriminating as far as what it considers Alive and functional.

If it is too lax in what it considers functional, it will of course have an easy time building IC or creating the appearance of specified complexity. But those details are not really published. Ressurecting dead organism would be a miracle or the work of design in the real world, in Avida land it happens quite easily by accident!

If I then published reports that Avida can ressurect the dead by accident, should any peer-reviewed journal find that a spectacular result. By golly, solving co-option by comparison is a lesser miracle! Yet this lesser miracle of Avida is what is reported in the journals. Why? Because saying Avida demonstrates ressurection is possible through random mutation would clearly show the program is a little more than computation theatrics.

If Avida can so easily work miracles of ressurection and healing through random mutation, then perhaps it's lesser miracle of co-option and increasing specified complexity are even more suspect.

I could have come back and gotten in Mr. Dorn's face on all of these issues, I chose not to. Adami himself would have been the better one to address these questions. I wasn't about to let Adami hide behind one of his students to avoid questions, and I really felt Mr. Dorn, a student was being sent to do some dirty work. Dorn is trying to get through school, and was probably in a delicate position working for project that was flawed from bottom up. He shouldn't have to give an account for someone else's mistakes.

Salvador

scordova

...the significance of Avida in the ID debate is not its degree of biological realism, but rather that it shows that irreducible complexity is not in principle a barrier to evolution via mutation and selection.

This argument seems self-defeating. Behe argues Irreducible Complexity as a matter of biological realism. If the degree of biological realism in Avida is insignificant, what of any significance does it tell us about Irreducible Complxity in biological systems? Mung

ds asks:
"Correct me if I’m wrong here but wasn’t Avida and all the software & hardware it runs on the result of intelligent agency?"

Something can be modeled using artificial hardware and software without being artificial itself. The National Weather Service runs lots of computer models to make its forecasts, but the hailstones bouncing off your Ford Pinto are a natural phenomenon.

Besides, the significance of Avida in the ID debate is not its degree of biological realism, but rather that it shows that irreducible complexity is not in principle a barrier to evolution via mutation and selection.

s Models are a guide at best. Matching their results against reality is always the acid test. When weather forecasts are made a number of different models are used and their predictions are averaged. They're often wrong and they can't predict more than a few days into the future. Avida doesn't even predict anything in the real world. It makes strings of artificial instructions in an artificial environment on artificial hardware. What exactly does it predict about real world outcomes that we may compare to determine if it is accurately modeling something real? Don't come back without an answer. -ds zapatero

In fairness to Evan Dorn, here are some excerpts from his post at ARN which address Salvador's claims directly:

"Mr. Cordova claims to have observed inconsistent behavior in Avida which he believes disproves its' validity as an experimental platform. Upon examination, it is clear that he is simply misunderstanding the output of his experiments, and that at high (but valid) mutation probabilities, Avida is behaving exactly as expected - all organisms are dead. In the second half of his experiment, Mr. Cordova has exposed a software bug by specifying an invalid input value. The bug effectively turns off mutations entirely, resulting in rapid and uninhibited growth of the ancestral genotype."

"Explanation: Put simply, the population was dead. What Mr. Cordoba observed was slow, random activity of non- replicating random strings.

Whether or not the strings of instructions existing in grid cells genotypes are valid, replicating organisms, Avida will dutifully execute their instructions. In this case, the ancestor organism was thoroughly randomized in the first update, as would be expected at Pmut=0.5. However, the execution of random computer instructions will occasionally include the execution the "allocate" instruction, creating new room at the end of the "genome" if other instructions happen to have put a non-zero number in the appropriate register. Also, the occasional "divide" will execute when other instructions have loaded integer values into the appropriate register ... meaning some piece of the randomized genome will get split into another grid cell. Without the actual code for organized replication, this will occur very slowly and all of these divides will contain random-length groups of random instructions. While yes, this process will slowly fill the grid cells, it is in no way analogous to life: nothing is replicated with fidelity, and no information is conserved."

"Mr. Cordova has experimentally demonstrated that there is in no mechanism protecting genomes from randomization by killing the ancestor organism with a high mutation rate and observing the "brownian motion" activity of dead, random, sequences of computer instructions."

"Mr. Cordova observed the rapid reproduction of the unmolested ancestor genotype, because all sources of mutation were effectively off. He did not "increase the mutation rate 100,000-fold", as he claims, because correctly put, mutations are applied as a probability, not a rate: 50,000 has exactly the same meaning as 1.0, if it has meaning at all. Because of that, such unusual, invalid values were never tested, and the Avida team was not aware of the potential integer rollover."

"Instead, because such high values can cause an integer rollover, Mr. Cordova's experiment is demonstrating the effect of turning mutations off, not increasing them by some large number."

Correct me if I'm wrong here but wasn't Avida and all the software & hardware it runs on the result of intelligent agency?

Avida doesn't even pass the giggle test for showing that things can evolve without intelligent agency. I really wish you'd spare us all. If I want this type of entertainment I'll go read the reports from the tobacco industry proving cigarette smoking is non-addictive and not bad for your health or the Pork Producers report that shows eating bacon prevents male pattern baldness! :roll: -ds

zapatero

It has been featured in prestigious scientific journals, was offered as evidence in Kitzmiller vs. Dover...

Are you going to go into how it was used in the Dover case and why any findings which were based upon evidence or testoimoty regarding Avida (or other simulations/GE's) are mistaken?

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.

What claims are you talking about. Please be specific. How do each of those claims conflict with information science? Please be specific. Take one at a time, if you like. Mung

Let me add this point regarding some of the crazy results like the re-acquired fertility of Avidian creatures under high radiation or that the creatures are immune to death.

This would appear to be a stupendous discovery, even beyond that of solving co-option. Why won't Lenski publish the results of such experiments. This is a far more miraculous achievement by Avida than proving co-option is true. :mrgreen:

Dang it, they should have let the trouble makers at UD file an amicus brief on behalf of the plantiff's saying, "in addition to solving the co-option problem, Avida solved the fertility problem and the problem of death".

Salvador

scordova