Intelligent Design-ers Strike Back

At the end of this post about the Avida experiment -- a computer simulation of evolution that is claimed to demonstrate that random mutation and natural selection could generate great complexity -- I rhetorically asked Intelligent Design advocates what they had to say about it. I decided to e-mail that question directly to mathematician, philosopher, and ID maven William Dembski, author of The Design Revolution and other books on Intelligent Design, with whom I've had the pleasure of corresponding briefly. I asked him if there was a convincing rejoinder to the Avida experiment, and he responded with this link to an essay [in PDF] by Royal Truman (now there's a name!) of Mannheim, Germany.

It's arcane and densely mathematical and not for the fainthearted [UPDATE: a less substantive, but funnier, riposte is here], but the essence of it is that Avida produces the desired results because it has an intelligent designer(s), who has predisposed it to do so by what was selected to put in and by the characteristics of complex living organisms that were left out. A few key quotes: [by the way, if anyone could tell me how to highlight, copy and paste from PDF documents, I'd be most beholden.]

Neglect of key factors or unrealistic parameter settings permit conclusions to be claimed which merely reflect what the decision maker intended . . . We conclude that the simulations "work" because of several judicious assumptions and parameter settings which insure this outcome a priori . . .

Specific examples follow. The one that was easiest for me to understand was that the code for the "metabolic" functions that enable Avida's "digital organisms" to replicate was not made vulnerable to mutation, the way it would be in a living organism, where most random mutations would be deleterious or lethal -- "a fact subtle enough to escape the attention of many specialists":

The only thing mutating are short strings of symbols . . . and not any computer programs. The software shell actually or figuratively performing critical functions ("replicate your genome from here to there"; "generate metabolic energy"; etc.) are written in C++ and are neither coded for by the genome (unlike real organisms) nor subject to mutation. The rest of the infrastructure is provided for free in the form of computer technology (stacks, registers, electricity, cables, chips, etc.), unlike real cells in which physical ribosomes, cell walls, ATP and so on must be genetically coded, and thus in the Avida program cannot be damaged by mutations. . . . Over 99.9% of the indispensable coding material needed for a minimally sized real organism to survive has been shielded from the possibility of any kind of mutation.

Also, the "digitorgs" have been outfitted with smaller genomes and higher mutation rates than even the smallest, simplest real-world bacterium. And "[n]ovel functions are easy to attain, compared to living organisms, and these offer immediate, dramatic selection advantages." Truman's conclusion:

By generously rewarding instruction patterns which produce logic functions, the net effect of Avida type mutations over many runs is virtually guaranteed to ensure increased functional complexity over time . . . This is not some kind of law of nature, but an inevitable result of how the Avida system and runs are designed.

This is deeper into the guts of the Intelligent Design debate than most people care to go, deep beneath the emotions in the realm of science where the question, with all its moral and metaphysical repercussions, will ultimately have to be decided. Many thanks to Bill Dembski for keeping this blog on the front lines of the debate.

- amba

Comments

[Michael]

A response to you posting.

(and I tell you how to copy text from acrobat at the bottom!)

First, a major point. It is not up to 'evolutionists' to disprove ID (yet), it is up to IDer's to demostrate that their -beliefs- (word chosen with malice aforthought) are based on solid science - something they haven't done yet. When I see testable hypothoses, and a definition of ID that is truly falsifiable, then I'll start examining whether ID might be valid science.

The scientific theory of evolution is falsifiable (despite Demski's claims to the contrary). A demonstration that the genetic make-up of organism could not change over time would do it. Even fossils of modern organisms found in rock dated to a pre-cambrian period would raise significant issues.

The problem I have with many critics of evolutionary theory relates to things like their pointing out (quite accurately) that evolutionary theory did not, for example, predict the discovery of fossils of that species of small humanoids recently found in Indonesia. We don't know every species that every existed on this planet, evolutionary science by itself won't predict every species that ever existed. Evolutionary theory, at its base, deals with the change in the genetic makeup of species over time. The evidence supporting this theory crosses many scientific disciplines, from Paleontology to Genetics to Moleculary Biology.

If Dembski wants to invalidate all of that evidence, he will need more than his math, he will need testable hypothesis, observation, retesting, and the like.

As for the essay he points to to refute Avida - a couple of points.

First, the fundamental arguement for ID is that some biological structures are complex, and have a functionality that cannot exist without all parts being in place. In other words, a part of a structure, per their argument, would not evolve because it would provide no evolutionary advantage, so the whole structure could not evolve. Avida, athough it does not simulate the full complexity of living organisms, does demostrate that in models, it's quite possible to have complex structures evolve incrementally.

As for other points:

Let's look at this statement from the PDF

"Suppose the original state was optimal at some point in time and all subsequent variation degrading. Differential fitness would select the less damaged on average, but the long-term outcome will still be an inferior population. Dennett’s criteria do not ensure neo-Darwinian processes result in the complex biological structures we observe."

The statement "But the long-term outcome will still be an inferior population." is an assumption, and one that seems to underly much of his refutation. The assumption seems to be based on the idea that -all- mutations are damaging. While I don't question that 99+% are, even if a very small percentage are not, the assumption breaks down.

And let's look at this statement:

"- The ratio of indispensible / total genetic material is initially 15 / 50
- Increasing the genome size with worthless genetic material is compensated with extra
metabolic energy<15> instead of penalized, as should be the case in nature."

I would recommend you review this article that touches on the amount of 'junk' DNA discovered in genome studies:

http://en.wikipedia.org/wiki/Junk_DNA

Finally, this statement which you extracted..

"By generously rewarding instruction patterns which produce logic functions, the net effect of Avida type mutations over many runs is virtually guaranteed to ensure increased functional complexity over time . . . This is not some kind of law of nature, but an inevitable result of how the Avida system and runs are designed."

The implication of this statement is that the way natural world works does not allow for 'increased functional complexity over time".

Now, the article itself does provide some excellent pointers for where the Avida developers can enhance their simulation, and make it more accurately reflect observed biological processes. As designed, the software is -optimised- for certain types of 'evolution'. I certainly hope the developers of the software pay attention to that sort of criticism.

But, even as is, the Avida software provides a solid challenge to the idea of irreducible complexity.

Now, you made the statement:

"deep beneath the emotions in the realm of science where the question, with all its moral and metaphysical repercussions, will ultimately have to be decided. "

The problem I have here is your implications of 'moral repercussions' - which is fundamentally an -emotional- issue. Science is based on certain assumptions about how the world works. It seems to me that much of the opposition to acceptance of evolutionary theory is -emotional- and includes the idea that the theory has -moral- implications. Science deals with undestanding 'how' things work. It is we human beings who add the moral dimension, that dimension is not inherent in the science involved.

I would suggest these links - by christians who accept the theory of evolution.

http://www.anevolvingcreation.net/evolution.htm
(and I had another one but I can't find the link - damn but I hate it when I do that!)

Oh, to cut and paste from Acrobat Reader, select the icon that looks like a 'T' with a little dashed line box - hilight the test you want to copy, then click on the fairly standart 'copy' icon in the toolbar.

(And if I keep writing replies this long, I'll have to start my own blog!)

[amba]

Start your own blog! Not a bad idea at all. I've been getting my whole family to do just that.

I expressed myself poorly in one regard. When I said "the question with all its moral and metaphysical repercussions," I did not mean that those repercussions were within the scientific realm. I meant that whatever is demonstrated and sufficiently proven in the scientific realm will inevitably have such repercussions outside the scientific realm.

Despite what scientists say, science IS based on a belief system, which says at root that a) phenomena like consciousness are epiphenomena of matter and b) the interactions of matter are at bottom blind and random. As a demarcation of the realm that science can profitably study, that's fine. As a definition of the nature of the universe, it is a BELIEF.

[Michael]

In your last comment, you delineate the difference between Scientific Naturalism and Philisophical Naturalism.

Now, science is -not- rooted in a belief system that says

"a) phenomena like consciousness are epiphenomena of matter and

b) the interactions of matter are at bottom blind and random"

Scientific method defines as within its scope that which is a result of natural processes, and can be measured.

The idea that what is not within the scope of science does not exist is -not- inherent in scientific method.

Philisophical Naturalism, on the other hand, does encompass the idea that consciousness is an epiphenomena of matter. It does not necessarily encompass the idea that "the interactions of matter are at bottom blind and random" but that the interactions of matter are determined by natural, not magical forces (and, in this case, I would include 'God' or a 'Designer' as a magical force). Natural does -not- mean random.

And - much of the objection I see to evolution seems to me to be at its core an objection -not to the theory of evolution per-se- but an objection to the concept of philosophical naturalism.

I also think human discomfort with the idea of philisophical naturalism does not invalidate the concept - instead it illustrates an aspect of our humanity.

Now - my default view of the universe is weak athesim - which amounts to philisophical naturalism. I would claim that, for me, this is not a belief, but a position based on lack of evidence for anything else.

IE: I lack belief in magic (God or other), I -do not- believe magic (God or other) does not exist. The distinction is subtle, but it's the difference between sketicism and the positive assertion of a negative truth (a leap of faith).

[amba]

I think that's also called "agnosticism."

And, I think the problem is not so much going "outside nature" to find consciouness or intent or magic as possibly expanding the boundaries of what we recognize as "natural." The hot action there is probably in quantum physics (Google Henry Stapp).

[Michael]

I choose to call it atheism because, in the end, it is. a-theism (without god).

Now I wouild also call myself a strong agnostic, in the sense that I think certain -objective- knowledge of metaphysical truth is not possible for human beings (vs. weak agnosticism - 'I don't know if God exists, but I think it's possible to know).

One is a statement of my lack of belief in god, the other a statement of my ideas on the limits of human knowledge.

I have friends who are fundamentalist evangelical Christians who are comfortable calling themselves strong agnostics per my definition - and who acknowledge that their belief in God comes through a leap of faith.

[outadatheswamp]

In response to Michael's posting. I disagree with your point that it is not up to 'evolutionists' to disprove Intelligent Design. In fact that was why the theory of evolution was, in theory, accepted over design in the first place. Darwin postulated that natural selection was the "primary mechanism" of change over time. The variety of organisms and life forms could be explained apart from a designer. When it was shown that natural selection does not give rise to novel information the theory was changed to incorporate random mutations. Now that that theory is coming into question, is it surprizing that the design argument is once again challenging the whole origins debate?

In the same string we have this statement regarding science:
Despite what scientists say, science IS based on a belief system, which says at root that a) phenomena like consciousness are epiphenomena of matter and b) the interactions of matter are at bottom blind and random. As a demarcation of the realm that science can profitably study, that's fine. As a definition of the nature of the universe, it is a BELIEF.

I trust that the majority of scientists would agree that this statement is gravely flawed. To say that the interactions of matter are "blind and random" contradicts the very basis of science itself. We may disagree with the workings of matter and the origns of life but we agree that our senses can be trusted and that however these laws came to be they are neither blind nor random. "Natural Law" may not be "designed" but common sense tells us that if it isn't, the burden of proof lies with those who claim it is an accident.To quote Richard Dawkins and Charles Darwin life "appears to be designed".

Furthermore these two "beliefs" or "laws" that you mention are in fact the fatal flaw in the materialistic position. If, as you claim, the basis of science is that "at the bottom matter is both blind and random" Design is rejected from the beginning. It's rejection is NOT due to a lack of evidence but because it falls outside the scope of your belief. So the possibility that something that appears complex, specific and designed, like human consciousness cannot be accepted because it contradicts your underlying presuposition that there is no designer or purpose "at the bottom".

I must finally disagree with your point that to use these statements "As a demarcation of the realm that science can profitably study, that's fine." With these large presupositions Intelligent Design theory could never be proven. So as not to conflict with your beliefs and presupositions you might even go as far as to say the enormously complex systems of life itself came about by accident in some primordial stew.