Richard B. Hoppe posted Entry 62 on March 28, 2004 03:09 PM.
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As I noted in an earlier posting, research using computational models of evolution are a thorn in the side of Intelligent Design proponents. That thorn is becoming sharper and more penetrating as computer models of evolution become powerful and versatile enough to begin addressing biologically interesting questions. An example from last year is Lenski, et al.’s The evolutionary origin of complex features, published in Nature.

Brief (!) Intro to the AVIDA artificial life platform

Lenski, et al., used avida to study “the evolution of complex organismal features.” Avida is an artificial life platform in which digital organisms reproduce, mutate and diversify, and compete on reproductive success in a space-limited context, and therefore evolve in a virtual world. The genomes of the digital critters are assembly language programs that can (if the necessary instruction sequences evolve) perform logic functions, mapping inputs to outputs in a manner corresponding to the performance of logic functions like AND, OR, XOR, and so on. (Avida is available free on the Web for Linux, Windows, and Mac platforms.)

An avida evolutionary run starts with a single Ancestral digital critter that can do nothing but replicate itself. The Ancestor may or may not have some “junk” instructions appended to its (human-written) replication code. As the run proceeds, that Ancestor begins to reproduce, with an occasional mutation occurring during the process. Various kinds of mutations are possible - point mutations (alterations of a single instruction), insertions, and deletions. Replication errors induced by one or another of those kinds of mutations can produce what roughly corresponds to gene duplication. It is also possible to enable a process that resembles horizontal gene transfer.

The digital critters compete on reproductive fitness: better replicators have a relative advantage in the (fixed size) population. If the experimenter has not chosen to provide an extrinsic fitness function, the critters compete solely on reproductive efficiency, and one can watch lineages within the population getting better and better at reproducing, often evolving replication code that is tighter and more efficient than even the best human-written code. A more complete introduction to avida is Biology of Digital Organisms and the technical manual (for version 1.0) is also available. The former has several examples of the use of avida to address interesting questions in evolutionary biology.

More interesting is the situation where an extrinsic fitness function is imposed on the avida world so the avida environment is selectively non-neutral. With an extrinsic fitness function, digital organisms can acquire reproductive resources - computer cycles - by performing various logic functions on 32-bit binary strings. The more (different) logic functions a critter performs, and the more complicated the functions, the more reproductive resources it acquires.

Under circumstances where digital organisms can acquire reproductive resources by performing logic operations on inputs, mapping them to appropriate outputs, one sees lineages evolving that perform first one, then two, then a number of different logic functions. After some hundreds of generations (tens of thousands of updates), some lineages of digital organisms may be performing half a dozen or more logic functions, ranging from very simple (AND) to quite complicated (XOR, EQU).

Lenski, et al., studied the evolution of lineages of digital critters in a selective environment that differentially rewarded performance of logic functions, with more complicated logic functions garnering more reproductive resources. Under those circumstances, many lineages evolved to first perform simple logic operations, then the most complicated logic functions in the avida environment, XOR and EQU. The results of analyses of the evolutionary histories of individual lineages demonstrated (given their control conditions) that plain old evolutionary processes can build complex structures on the basis of prior evolution of simpler structures, where any particular simpler structures are not required. One advantage of the avida platform is that one can dump the full evolutionary history of lineages to disk for later analysis.

Why Intelligent Design Creationists don’t like it

What gets IDCs edgy about the Lenski, et al., paper is that the assembly language programs - the genomes of the digital critters - that evolved to perform those complicated logic functions are “irreducibly complex” in exactly the definition of Michael Behe. In Darwin’s Black Box Behe defined an irreducibly complex structure or process as

A single system composed of several well-matched, interacting parts that contribute to the basic function of the system, wherein the removal of any one of the parts causes the system to effectively cease functioning.

Behe (and Dembski, following him) contends that "irreducibly complex" structures and processes are not accessible to evolutionary processes: they cannot have evolved by "Darwinian" mechanisms. (Later, both Behe and Dembski engaged in some tap-dancing about "direct" Darwinian pathways, and argued that things like cooption are too rare.) But Lenski, et al., showed that the assembly language programs evolved in avida satisfy Behe's operational (knockout) definition. If replacing an instruction with a null instruction (a knockout procedure) in a digital critter's program results in the loss of a logic function, the program is "irreducibly complex" by Behe's definition (or is part of the "irreducible core" of the critter's program, to use Dembski's term). So the Lenski, et al., analysis shows that "irreducibly complex" structures can evolve by plain old "Darwinian" mechanisms.

What was Behe’s response to the Lenski, et al. paper? He was quoted in the Chronicle of Higher Education as scoffing at it.

But Michael J. Behe, a professor of biological sciences at Lehigh University who is one of the most vocal proponents of intelligent design, says that the simulation proves nothing. “If I were a Darwinist, I would be embarrassed for this paper to be published in Nature,” he said.

“There’s precious little real biology in this project,” Mr. Behe said. For example, he said, the results might be more persuasive if the simulations had operated on genetic sequences rather than fictitious computer programs.

This from a man whose iconic example of "irreducible complexity" is a mousetrap! (Elsewhere I wondered whether Behe was fondling his mousetrap as he made that comment.)

William Dembski must tenaciously defend irreducible complexity against work like that of Lenski, et al., because his notion of “specified complexity,” the core of his ‘design detection methodology,’ depends upon irreducible complexity. (See here for Dembski’s discussion of the connection.) Dembski addressed the Lenski, et al. paper in a manner similar to Behe in the introduction to Uncommon Dissent: Intellectuals Who Find Darwinism Unconvincing:

This paper describes a computer simulation and thus contains no actual biology.

As I said in my earlier posting, physicists (and anyone else who uses computer modeling, for that matter) in the crowd had better watch out. All that fooling around with computer models is going to lead you astray.

Dembski goes on to complain that the Lenski, et al. simulation builds the results into the initial conditions:

Go to the discussion section, and you’ll read: “Some readers might suggest that we ‘stacked the deck’ by studying the evolution of a complex feature that could be built on simpler functions that were also useful. However, that is precisely what evolutionary theory requires….” In other words, the computer programmers built into the simulation what they thought evolution needed to make it work. The validity of this study therefore depends on whether the simulation faithfully models biological reality.

Um. That's what one does when one performs an experiment to test a hypothesis. One sets up the conditions that the hypothesis requires and then looks to see if the observations predicted by the hypothesis are actually observed, as compared with appropriate control conditions (which Lenski, et al. ran).

But for Dembski (who, let us recall, is a mathematician, theologian, and philosopher, not a scientist) this is a fault:

Unfortunately, the simulation presupposes the very point at issue. It therefore begs the question and doesn’t prove a thing about real-life biological evolution. The Lenski simulation requires that complex systems exhibiting complex functions can always be built up from (or decomposed into) simpler systems exhibiting simpler functions. This is a much stronger assumption than merely allowing that complex systems may include functioning subsystems. Just because a complex system can include functioning subsystems doesn’t mean that it decomposes into a collection of subsystems each of which is presently functional or vestigial of past function and thus amenable to shaping by natural selection.

Contrary to Dembski's claim, the Lenski, et al. simulation did not "... require that complex systems ... can always be built up from (or decomposed into) simpler systems ...". It asked whether complex systems can be built up out of simpler systems using only evolutionary mechanisms. Dembski cannot accept the fact that the answer is "Yes." Intelligent Design Creationists are big on the "limitations" of evolution. The Lenski, et al., study was aimed specifically at testing whether a particular limitation claimed by the IDCs is in fact a limit. It isn't, and Dembski clearly doesn't like learning that.

Finally, Dembski says

The simulation by Lenski et al. assumes that all functioning biological systems are evolutionary kludges of subsystems that presently have function or previously had function. But there’s no evidence that real-life irreducibly complex biochemical machines, for instance, can be decomposed in this way. If there were, the Lenski et al. computer simulation would be unnecessary. And without it, their demonstration is an exercise in irrelevance.

Yes, evolutionary biology does indeed suggest that complex biological systems are "evolutionary kludges" built from other, often simpler, components, and Lenski, et al., clearly showed that evolutionary processes are sufficient for that to occur. But in his "there's no evidence" remark, Dembski displays once again (see my previous posting referenced above) pervasive ignorance of the biological and biochemical literature. See critiques of Behe's claims of irreducible complexity for various biological systems, including the blood clotting cascade (and here), immune system, and the bacterial flagellum.

Further, in that paragraph Dembski made an interesting equation. He equated the evolution of complex systems with their decomposition. He appears to believe that one must be able to recover an evolutionary history (or in the case of so-called irreducibly complex systems, infer the lack thereof) by decomposing the system as it presently exists into all the subsystems that participated in its evolutionary history. It’s entirely true that evolutionary theory holds that complex systems are built from simpler systems (though not necessarily from only the most primitive parts - cooption of existing parts and divergent evolution of gene-duplicated subsystems are common), but that’s not the only source of the code, genetic or digital, that is aggregated by evolution to perform complex functions. For example, there are indications from both biological and digital evolution that so-called “junk” DNA/instructions can occasionally be pressed into service. Exclusive reliance on decomposition is also vitiated by evolutionary histories that include scaffolding. Finally, subsystems that were recognizable in an evolutionarily early form may be lost as the system evolves new ways of performing those subsystems’ functions, and thus that part of the evolutionary history can’t be recovered by decomposition of the current structure. So decomposition of a system as it exists now is not the sole means of inferring evolutionary histories, though it can be a valuable source of hypotheses.

Finally, Dembski’s remarks about decomposition are a non sequitur, a diversion. While looking for simpler homologs of the subsystems of a ‘decomposed’ complex system is helpful in analyzing the potential evolutionary history of a particular structure (see, for example, Nick Matzke’s recent analysis of the bacterial flagellum), that was simply not the question at issue in the Lenski, et al. paper. What they showed was that mechanical evolutionary processes operating on strings of primitive assembly language instructions in an appropriate selective environment can generate complex systems that meet both Behe’s definition of “irreducible complexity” and Dembski’s modification of Behe’s definition. None of Dembski’s complaints touch that conclusion.

Because the complete evolutionary histories of all the lineages that evolve in avida are available for analyses, the processes inferred from comparative biology and biochemistry to account for the evolution of complex structures can be studied in detail now. So far the analyses strengthen those inferences.

Additional reading

Andrea Bottaro has some remarks on Dembski’s critique of the Lenski, et al. paper in DR. DEMBSKI’S COMPASS or, How to lose one’s way while looking for misdirection.

There are also two threads on ISCID, one very long one originating shortly after the Lenski, et al., paper came out, and one more recent when Royal Truman posted a critique of it on ISCID. My remarks in the latter cover Truman’s error-ridden critique; those who wish to wade through the 19 or so pages of the former thread will find some strange critiques of the Lenski, et al., paper that don’t bear mentioning.

Richard B. Hoppe

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Comment #415

Posted by Ed Darrell on March 29, 2004 12:59 PM (e)

If irony were money, we’d all be rich.

First, I observe that all of Dembski’s work is abiological. For Dembski to claim that a computer model is not close enough to biology to qualify is the height of chutzpah (especially if chutzpah is defined as asking for mercy from the court upon being convicted of murdering one’s parents – on the grounds that one is an orphan).

Second, I would observe that Dembski and those who follow him in the ID movement play very fast and loose with definitions that are borrowed from other places. While Dembski’s work is not peer-reviewed in biology, neither is it peer reviewed in electronics, nor data transmission, nor any other venue where Shannon’s information theory is actually used. Dembski’s fundamental definitions of what information is assume endorsement of the idea that DNA is simply information like a flash of light, and nothing more. I would liken DNA more to the information in the newspaper, the reporter, the editor, the printing press and the delivery boy, myself.

And third, why is it that no one ever questions the claim that “oomplexity” equals “design?” I find it odd that Dembski never talks to designers in any medium, and I find it frustrating that no one takes him to task for it.

In design, intelligence of the designer is most often demonstrated by designs that are more simple, not more complex. We didn’t laugh at Rube Goldberg’s inventions because his contraptions wouldn’t work; rather, we find them funny because they are complex.

Under the usual ID definitions of complexity equalling design, one would be justified in assuming the simple, fewer-moving-parts quartz watch was the predecessor, and the multi-geared monster clocks of old European town squares the latest generation of timepiece.

It is ironic Dembski claims computer simulations that refute his arguments are not suitable for being not biological enough, when all of the claims for ID are analogies without a whit of support from any biology lab. It is ironic that ID advocates claim biologists “just don’t understand” information theory and mathematics, when ID advocates refuse to submit their work to ANY branch of science for peer review. And it is ironic that in the real world, complexity generally demonstrates an inability to design intelligently, the opposite of the foundational claim of ID.

Some years back I heard Michael Behe at the University of Texas at Arlington, speaking to biology and biochemistry students (and others). Ed Bellion, a biochemistry professor at the school pinned Behe down on just what is “design.” As the Campus Crusade for Christ organizers of the event quickly called an end to questions, Behe said, “I know it when I see it.”

No, I don’t think they do know design when they see it.

Ed Darrell

Comment #12701

Posted by Tim on January 5, 2005 12:56 AM (e)

may I point out that when people list dembski’s bizzarely long list of tertiary qualifications that forget to mention that he is also a psychologist ( he has a bachelors in psychology). I just think it’s odd that we don’t hear about it more, considering how much he seems to talk about his qualifications, and how much his skeptics make fun of his long list of qualifications.

by the way, I think that if either ID or evolution is false, the way they will be disproved is via computers. what sayeth the PH.D’s?

Comment #12702

Posted by Great White Wonder on January 5, 2005 1:21 AM (e)

he is also a psychologist (he has a bachelors in psychology

A bachelor’s degree in psychology does not make one a psychologist. You might be able to make a decent guidance counselor, though.

This Ph.D. says that neither the possibility that life was designed by all powerful alien beings or the evolution of living things will be disproven by computers.

Comment #15089

Posted by Jethro in Cali on February 6, 2005 11:17 PM (e)

I hope the authors of the Avida software realize what creationists and ID proponents will say: “Evolution seems to occur with the Avida software because it was programmed to do so. Just because there are computer programs of ‘Lord of the Rings’ doesn’t make Middle Earth real.”
The average layperson will buy an argument like that.

Comment #15090

Posted by RBH on February 6, 2005 11:32 PM (e)

Yup, that general line has been used in several responses to the Lenski, et al, paper. They seem perfectly willing to abandon all computer modeling and all computer simulations in all of science to excape the implications of the Avida work.


Comment #22578

Posted by The Balcktivist on March 30, 2005 6:10 AM (e)

i have been working hard over the past few years to make sense of the evolution/ID issue.
As a headstrong evolutionist I was hung out to dry pretty quick. But from what i learned, i had many more questions.
All i know now is that evolution evolved from a butthole which evolved from a smaller butthole and i evolved from a cigarette butt. Thats about the reality of it. Unless you don’t believe in reality or live in one of those alternate realities in which reality isnt actually reality and your hero is david hume. I have ideas on that too… they involve more cigarette butts (i have found these to be the primary ingredient in the primordial soup, as well with pubic hairs and bad attitudes).
Whatever happened to the weasel program that Dawkins cherished so much? did that go out of style? i thought it was the answer… I guess now we’re even better at tripping ourselves over using high-tech gizmozzz and wasting each others time.
That idea that avida will do what it was programmed to do is still justifiable. It doesnt imply that all simulations are rejects, simply that avida is a reject. a seed is programmed to reach the light and GRRROOOWWWWWWW, avida is programmed to get the results……. here you think it’s all SOOOOOO silly to say this, but how is it wrong? If i make a program to demonstrate key functions of a system, i wouldn’t bother releasing it, UNLESS IT WORKED to what it was designed to do. I think the cigarette butts y’all evolved from were designed to run in circles and headbutt the walls.
Consider me lay, or consider me for the next president… but i ask you this, and THIS is the point of the post, but HOW exactly is a thought/computer program/cigarette butt replication going to win the the OCTAGON against someone like Frank Shamrock? It’s not logical, or possible because Shamrock has the locks AND the striking… and a good attitude. WHICH IS MORE THEN WHAT I CAN SAY FOR ALL YOU SQUABBLERS.

Comment #22583

Posted by The Blacktivist on March 30, 2005 6:21 AM (e)

by the way ed darrell (if that IS you REAL name) using the idea, ‘fewer-moving-parts quartz watch was the predecessor, and the multi-geared monster clocks of old European town squares the latest generation of timepiece’ is pretty dull.
‘Intelligence’ involves efficiency. But then, perhaps you might well consider that at the time the multi geared monster clocks were built, the intelligence involved in constructing them could well be considered as more intelligent when taking common day technology and understanding into account.
You say so boldly that ID dudes have no definition of intelligence/design when you are shooting the same junk. You mad evoz get carried away with the now now now factor without taking into account the details surrounding the key idea.
You boys are leading with the head too much…forgetting the surroundings, but as pappa used to say, leading with your head is a good way to get KNOCKED OUT.