Mark Ludwig: Intelligent Design Theorist - Fact or Fiction?

by Mark Ludwig.
Received: 15 May 2006
Published and replies inserted by Gert Korthof: 10 June 2006.

(Please note my insertions are in red and all my page references are to page numbers as they appear on the pages in the pdf version of the book.
Additions after 10 June 2006 are only in the form of Notes).

I thank Dr. Korthof for the opportunity to respond to his critique of my book Computer Viruses, Artificial Life and Evolution. I was rather surprised that it took 13 years for a proponent of evolution to pick it up and address it. Since it has taken so long, though, you may imagine my thinking has developed somewhat in those years. As such, I will preface my remarks by saying that to the extent that anything I write here differs from what is written in my book, it is due to a development of the ideas involved in the intervening time.

  • GK[1]: You are welcome. Thank you for your detailed response. I accidentally found your book while I was preparing a presentation about similarities and dissimilarities of biological and computer viruses. In those 13 years I never found references in the evolution/creation literature to your work. Furthermore, usually biologists do not read books about computer viruses and you could have notified me of the existence of your book. You should be happy that a biologist found your work at all and found it worthwhile to give it a detailed review. By the way, Mark, did William Dembski or other ID's or creationists review your book? Furthermore, did you improve in those 13 years your AL evolutionary theory to such levels that it is now better than the abysmal mainstream theory of biological evolution?
    Regarding your remark that 'development of the ideas involved in the intervening time', I cannot do otherwise than stick to the book as it is.
Generally speaking, I think Dr. Korthof paints me as being much more hostile to evolution than I really am, perhaps because he is engaged heavily in the creation/evolution debate.
  • GK[2]: Perhaps? Perhaps you did not read your own book carefully! You Are Wrong, Mark. The facts are:
    • you wrote: "evolutionary biology is in an abysmal state" (page 45);
    • you wrote: "In fact I would be hard put to call "evolution" as we know it a scientific theory at all" (page 136)
    • you wrote: "From this vantage point, evolutionary biology today appears to be unusually vacuous." (page 136)
    • you wrote: "Darwin's hypothesis isn't really a theory of evolution. It is a mere speculation " (page 197)
    • you wrote: "It's a good book because it exposes some of the rot that lies just beneath the surface of modern Darwinism" (page 231)
    • you wrote: "the theory of evolution ... it can explain anything and predicts practically nothing" (page 295)
    • you wrote: "That is why a sensible layman like Phillip Johnson can take an honest look at the evidence and conclude that evolution is little more than a myth" (page 295);
    • you wrote: "Artificial Life holds the promise of a real theory of evolution ..." (page 296) [my emphasis]
    • you wrote: "I think it could overthrow Darwin's hypothesis ... " (page 297);
    • you wrote: "overall evaluation of evolution suggests that present day theories leave much to be desired" (page 380)
    • you included an unfriendly-to-evolution graph (page 255) but not one friendly-to-evolution
    • you uncritically copied examples from Michael Denton, a wellknown critic of evolution (p.236, 239)
    Would that be enough to paint your attitude to evolution? (2). Does that have anything to do with me ('perhaps he is ')?
The question of creation versus evolution largely devolves into philosophical issues that cannot be resolved by science, and the debate is, as a result, a stalemate until those philosophical issues are dealt with. No amount of science will resolve it. Seeing as the philosophical issues delve deeply into core religious beliefs, people are not very open to dealing with them either. Theories of origins suffer from the common fault of being able to account for just about anything with various hand waving tchniques which are rooted in religion, be it the Christian religion, atheistic materialism, or whatever.

In contrast, the beauty of Artifical Life is that the philosophical and religious issues which have been stumbling blocks for a century and a half largely disappear. There we can study ideas like creation and evolution in a philosophically neutral environment. And the subject is fascinating in that context. I believe it also leads us to the essence of science in the purest sense - a place where we can come to some kind of understanding of how the world works - in a laboratory setting - without being stymied by religious differences. It is this very neutral ground that has made several centuries of rapid technological progress possible, and it is this very neutral ground that is the only hope for us to get past religious differences in the present instance.

One of the major points of the book is also to suggest that there is an important practical reason to get over these religious differences and get on with the business of science.

  • GK:[3] I agree that we need a philosophical neutral method to study nature. However, biologists have done exactly that: developing a theoretical (Charles Darwin, August Weismann) and mathematical framework (Ronald Fisher, J.B.S. Haldane, Sewall Wright, Motoo Kimura,etc). Furthermore, don't forget that all the lab experiments in artificial evolution (Drosophyla) are "science in the purest sense". And don't forget extensive data collecting about natural selection and speciation in the field: Jerry A. Coyne and H. Allen Orr (2004) and Menno Schilthuizen (2001) (see Introduction page). Yet, you ignore all that. It is quite understandable (in view of your expertise) that you chose Artificial Life to study evolution, but it is wrong to claim that AL is the first and only method to study evolution in a philosophically unbiased way.
    "Get on with the business of science" and then you advice your readers to learn science from lawyers!

This book has plenty in it to offend everyone. (Such is the nature of trying to expand peoples' thinking and open up new territory.) It has obviously offended a defender of evolutionary origins. Yet it has offended the creationists too.

  • GK[4]: please show me the evidence that you offended creationists! Give me the quotes of creationists attacking you. I just discovered one reference to your book in the ID-literature which does the opposite. It is about the improbability of spontaneous origin of life: Robert Newman in Mere Creation (p.434-435). He was happy to use that result.
And well it might, for I go to great pains to break the philosophical commitments, and then examine a world which was not created to support life or evolution - a world where life has really been unwanted . . . the world of bits and bytes inside a desktop personal computer. And what do we learn from it? First of all, anyone who has encountered a computer virus knows that computers can support "life", like it or not. Then I go on to demonstrate that this life, if sufficiently complex, can evolve and that evolution can be a very efficient method for solving the problems of survival. That is not exactly the kind of scenario a creationist wants to see!

  • GK[5]: wait a minute: 'life', 'evolution', 'survival' are still about the computerworld? or did you silently switch to the biological world?

What I offered the reader in my book is not the well-beaten path, not the professional lecture to a room full of students, but an initial exploration of important and fascinating questions. I am not trying to defend some kind of doctrine or dogma. I am trying to find some ground from which we can understand objective scientific truth in an often muddled world that is hypercharged with philosophical bias. I admit that is not easy, and perhaps I have not always succeeded, but I hope I have at least provided a rough map of this new territory that would be useful to the next explorer.

  • GK[6]: your goal as stated here is great. However, it must fail because you chosed to despise biologists and work in isolation The only road to success is close cooperation with biologists and recognition of their expertise, not arrogantly dismissing everything what biologists have learned the last few ages. Typically, you say: "At present, it would appear that the formulation of a proper theory of evolution will be the price not of traditional biologists, but of Artifical Life researchers." (295). Does that look like cooperation???


Misrepresentation of my goals, assertions and findings

  • GK[7]: I strongly object to the word 'misrepresentation', because it means, according to the dictionary, deliberately give a wrong description of someone's opinions. I certainly never intended to do that!

There are a number of points in Dr. Korthof's article where he misrepresents my thoughts by taking statements out of context. Apparently he is doing this to support his assertion that I am an Intelligent Design Theorist - a label which did not exist when I wrote my book.

  • GK[8]: Phillip Johnson (1991,1993 Darwin on Trial) uses the concept 'Intelligent Design' several times. You use the concept 'intelligent design' and William Paley on page 217. Your discussions about spontaneous origin versus intelligently designed computer viruses and your answers are in harmony with Intelligent Design. Your statements "That is, evolution ought to be able to create information" (p.216), "We've already seen that random searches of a gene space are essentially useless" (p.217) and "We found that it was almost essential to inject intelligence into the system [of bits and bytes] in some way." (271) are typical for the way ID Dembski would later define the problem!
I assume that such misrepresentation was unintentional. I realize that when labels like "Intelligent Design Theorist' are created they tend to divide people into camps which did not exist before, and people tend to analyze what is going on in terms of those camps. This can have the effect of involuntarily putting colored glasses over our eyes. I would like to first address these points of misrepresentation in order to clarify the picture of where I stand. Only after that can we go on to look at the major issues which Dr. Korthof raises in his article.

1. Dr. Korthof is quick to point out that I discussed a fitness function that is unfriendly to evolution on page 215 of my book. He says "It is easy to construct a hypothetical Fitness Function unfriendly to evolution as Ludwig did. . . . Ludwig's figure (page 215) is just an imaginary illustration. It is not based on data. No conclusions about Darwinian selection can be based on that." Dr. Korthof does not point out that in the same breath I said "We have no reason to believe the fitness function does not look like a rising mountain range, with some populations at the peaks, and some on the slopes." (p. 215, CVALE) - the very thing needed to make Darwinian evolution work like a well-oiled machine.

  • GK[9]: However, you also wrote:
    • "For example, we have no reason to believe that the fitness function of our world does not look like a bunch of islands in the sea, with populations centered around each island (Figure 20.10). That would appear to make Darwin's hypothesis impossible." (page 214). On the same page: "We just don't know right now."
    • "It [the fossil record] would tend to suggest that the fitness function of species may look something like Figure 20.10: islands of variability surrounded by forbidden zones" on page 234
    • "All of this would tend to indicate that the fitness function for most species looks like Fig 20.10" on page 237.
    So, that is two-three times support for the unfriendly function. Psychologically, an image is far more powerful than a thousands words. The unfriendly function stays in the memory of the reader. To prevent confusion, you should have shown both the friendly and the unfriendly function.

Dr. Korthof says "to construct a realistic fitness landscape one needs a lot of data" and I agree, writing that "right now, it's hard to say what we can learn about the limitations of real-world evolution from these ideas." (p. 215)

Anyone who reads the book will see that I am not here proposing that the real world has a fitness function unfriendly to evolution. I am merely introducing the reader to the concept of a fitness function as a quantification of the Darwinian idea of "survival of the fittest". This fitness function allows one to mathematically represent fitness in some sense, which is obviously a precursor to any kind of a theory that can produce numbers.

2. Dr. Korthof is quick to point out that I cite authors like Philip Johnson who voices objections to evolution. He says "introducing and recommending Philip Johnson is introducing religious bias into his investigation. This is not the same as making his whole book worthless, but it is the opposite of what he wanted to do." He fails to note that I do not use Philip Johnson as a scientific resource. My book covers a lot of ground, from philosophy and history to science and computer programming. I clearly discuss Johnson's biases and his critics (p. 149, CVALE). His contribution, in my thinking, is primarily philosophical and clearly antagonistic. I propose not to blindly agree with him, but to use him: "This is a good way to find out how much we really know: subject your ideas to the harshest criticism and see what's left." (p. 231, CVALE). I also propose a solution to the heart of Johnson's criticism (p. 153, CVALE). For Dr. Korthof to castigate me for discussing Johnson in this context is like taking his own citation of Johnson in his review of my book as "proof that Dr. Korthof is a creationist in hiding".

  • GK[10]: ...discussing Johnson...? Mark, you did not discuss Johnson, you did recommend Johnson! You wrote: "Now Johnson is an admitted Christian with perhaps some sympathies toward the idea if divine creation" (149): this is really the understatement of the century. You wrote: "Now I don't agree with everything Johnson says" (149) and that is all your criticism! On page 231 there is no criticism of Johnson. The \B4harshest criticism\B4 is aimed at evolution. On the contrary, you wrote: "It's a good book because it exposes some of the rot that lies just beneath the surface of modern Darwinism"! (231). You just follow Johnson. What could you do otherwise, if you don't have the expertise. Is Johnson really your best scientific source?
    You say: "I do not use Philip Johnson as a scientific resource", however, you wrote on page 234 (section Major Organs) about the complexity of the eye, and this discussion is based on Johnson, pp 32-44 as you say yourself. This is supposed to be science. Furthermore, you are obviously strongly influenced and inspired by Johnson (example "Darwinism tends to turn the selection process into a tautology" (p.198) is present in Darwin on Trial chapter 2). You must have absorbed Johnson's hostility towards Darwinism (or materialsm), if you did not feel a strong affinity to it in the first place. At the same time you are apparently NOT influenced by a population-geneticist like John Maynard Smith (1988,1998) Evolutionary Genetics who gives a non-tautological definition of fitness (perhaps you did not read him?).

3. Dr. Korthof says "Ludwig's list of 'Selected References' is extremely one-sided. That is easy to establish. Nearly all his references are critical of evolution or Darwinism. Did Ludwig compensate for this bias in any way?" He fails to mention that in my list of references are such staunch defenders of evolution as Richard Dawkins and Stephen Jay Gould, Nobel Laureate Francis Crick, as well as others who are wrestling with big questions from a totally non-religious viewpoint, such as Cairns-Smith and Fred Hoyle. Neither does he note that I cite genetics textbooks, books on Artificial Life, philosophy, and the philosophy of science.

  • GK[11]: There is not any Evolution textbook in your critics-dominated list! That's why the list is extremely one-sided. In the section 'Origins' are 5 books:
    • Thaxton, Bradley, Olson The Mystery of Life's Origin (a critique of origin-of-life theories; they argue for special creation)
    • Robert Shapiro (a sceptic, a critique of origin-of-life theories)
    • Cairns-Smith (unorthodox theory; critical of standard origin of life scenarios)
    • Francis Crick (did not write about Evolution perse but about the origin of life, furthermore, he has a very unorthodox view about the origin of life (aliens send life in a rocket to the earth!)
    • Hoyle & Wickramasinghe (unorthodox views such as panspermia. Hoyle is unorthodox in his own field of expertise.)
    In the section 'Evolution' we find 6 books:
    • Philip Johnson: the father of Intelligent Design! and "a sensible layman"...
    • Michael Denton: a biologist and influential critic of evolution, certainly not a mainstream scientist
    • Stephen Jay Gould: apart from a Darwinist, he is also a well-known critic of neoDarwinism. However, his Panda's Thumb is a popular science book; not a work for professionals
    • Richard Dawkins: the only 100% orthodox neo-Darwinist in the section 'Evolution'. However, his The Blind Watchmaker is not a textbook, but 'popular literature' as you call it yourself on page 224.
    • Moorhead & Kaplan: mathematicians and engineers; critics of neo-Darwinism
    • Norman MacBeth: again a lawyer and a fierce critic! (see Tom McIver (1988) Anti-Evolution for a summary)
    Now that is a unbiased and balanced list! The reader never could imagine from your list that professional evolution textbooks existed!
    I have an explanation for the absence of professional evolution literature: Ludwig knows that "there really is no theory of evolution in the real world" (page 197), so it would make no sense looking for such a theory in the professional literature.

I also defend the fact that I cited people like Johnson and Denton because anytime anyone wants to discuss the big questions, one runs up against philosophical / religious issues. Rather than trying to pretend those issues don't exist or that they have been finally resolved one way or another (when major segments of the population, many scientists included, beg to differ) I think it is best to look at them squarely. I don't know how to do that without drawing their arguments into the discussion.

4. Dr. Korthof says I ignore important subjects such as population genetics: "Ludwig completely misses the theory of population genetics." In fact I present quite a few important observations and discuss the outcome of experiments in population genetics - experiments which the reader is invited to perform in his or her own computer. (pp. 197-223) My great fault is apparently that I present this subject in the context of Artificial Life. Since Dr. Korthof denies the essential simplification which is common to Artificial Life and biological life, this makes my population genetics irrelevant in his opinion. (More on this below.) Understand, however, that such an opinion is becoming more and more of an arcane curiosity with time. Biologists are doing more and more genetics inside of computers, and people are winning Nobel prizes for that work, while programmers are making great strides in using genetic algorithms to solve complex real-world problems.

  • GK[12]: Mark, this is your opinion about neo-Darwinism: "The neo-Darwinian definition of fitness as whatever has the most progeny does no better" (page 198). Since fitness is a basic concept in population genetics, the whole of population genetics is discarded. See for non-tautological definition of fitness: John Maynard Smith (1988 and 1998) Evolutionary Genetics. You invented your own kind of artificial population genetics as if no biological population genetics existed. However, I must admit that the experiments of mutating viruses escaping virus scanners are very interesting.

5. In a number of instances Dr. Korthof cites advertising copy for my book on the internet as if it were quotations out of my book. Needless to say, citing advertising copy as representative of an author's viewpoint is somewhat less than professional in scientific circles. To cite it in a way that could possibly confuse the reader into thinking it is a quote from the book is disingenuous. Dr. Korthof's method of quoting the ad copy and only indicating that it is ad copy with a footnote is really the limit . . . and he doesn't always do that. For example, when he says "I do think that it substantially contributed to the outrageous claim that 'evolutionary biology is in an abysmal state'" he is not quoting Computer Viruses Artificial Life and Evolution, but ad copy.

  • GK[13]:
    "Abysmal state" is in your own book on page 45 !!!
    Read your own book!
    The public pdf version of your book does not even allow full text search, but with your own private version you could have verified within 1 second that "Abysmal state" is on page 45. You really need to apologize for this unfounded attack on my person.
    - By the way, and this is of minor importance, your behaviour implies that the information on your site and in your advertising is either an exaggeration, or a distortion or a lie and furthermore, that you are not responsible for it. Nobody in the world requires you to distort your own book and subsequently deny responsibility. Furthermore, you included advertising texts in your Adobe pdf version of the book! So what's all the fuss about ad copy and internet sources?

6. Dr. Korthof states that "Ludwig's goal was an unbiased, unprejudiced assessment of the theory of biological evolution." Where he got that idea, I don't know. I stated that my goal was to explore some new territory that had never been explored before, and confessed that "I'm not writing this book because I have all the answers. Quite to the contrary, I have lots more questions than answers!" (p. 5, CVALE) Dr. Korthof should also note that I said plainly "my purpose isn't to debunk evolution here, or to argue against it" (p. 241, CVALE). More on my real purpose below....

  • GK[13A] you stated that you did not want to debunk evolution, but in practice you did. Please note that you presented subjects such as: problems with fossil record, major organs (illustration of bird's lung from Denton included without any professional or critical comment!), Breeding Experiments, Molecular Evidence, Mathematical Questions, etc. See also: GK[2].

7. Dr. Korthof says "the first half of the book is based on the idea that viruses and artificial life are nothing but instructions to be executed (by a computer). Ludwig translates this view to biological systems." Yet he contradictorily states "most of his book is based on the assumption that viruses are alive." In fact I spend a major part of the book considering the philosophical, moral and scientific ramifications of suggesting that computer programs can be alive, and hoped the reader would understand that there is no easy answer.

8. Dr. Korthof states that I espouse the idea that "when one cannot calculate the evolution of bacterium to humans, the whole theory fails." He cites a reference, number 6, here, which the casual reader might think is a citation in my book. In fact, he is citing Philip Johnson. I didn't say that and I don't believe it.

  • GK[14]: OK. Ref 6 is not about Johnson. Ref 7 is about Johnson. The idea behind my so-called Johnson quote, but is not a quote at all, is quite similar in spirit to your statement: "I am a physical scientist who is used to seeing equations that make predictions, and experiments that can test the validity of those equations. From this vantage point, evolutionary biology today appears to be unusually vacuous." (page 136).

Dr. Korthof's misrepresentations all lean in the direction of supporting his central thesis: the exposure of another Intelligent Design Creationist. In all fairness, I understand that Dr. Korthof is involved in the heat of the battle between creation and evolution, and to some extent I can excuse him for these misunderstandings. I hope they are not intentional. Yet what do those misunderstandings buy in the end? At best, it seems they short circuit people's brains so that they won't consider some of the most fascinating questions in the world any further.

  • GK[15]: My central thesis is NOT 'the exposure of Ludwig as another Intelligent Design Creationist'. Firstly, the title of my review is: Mark A. Ludwig as an early Intelligent Design Advocate, so there is no 'Creationist' in the title. Neither in the rest of the review. The title is a descriptive historical statement. As such no moral judgement is involved. 'Exposure' has a strong negative meaning. I never used the word. You did. My discovery that Ludwig is an early ID is new because Ludwig is rarely referenced in the Creation-Evolution literature (recently I found Ludwig was discussed in the chapter of Robert Newman in Mere Creation. Science, Faith & Intelligent Design edited by William Dembski). It is quite interesting that Dembski ignores you because your exploration of fitness functions (pp. 197-223) is what Dembski (2002) also tries to do in his No Free Lunch.
    Secondly, the reason I reviewed your book is because it makes strong claims about the theory of evolution and AL, and gives a perfect opportunity to discuss the nature of biological science, genetics, life and evolution. That is what I did.

Okay, let's go on now to the major issues . . . .


Are the results of AL applicable to the real world?

A major part of Dr. Korthof's critique seems to focus on emergence. He writes "How did he establish that his results are relevant for biological evolution? Surprisingly, he did not really attempt to answer that question . . . . Remarkably, Ludwig knows that biological objects are too complex and computer viruses and AL are too easy to study . . . ." This "too complex/too easy" issue seems, in Dr. Korthof's mind, to revolve around the idea of emergence. He appears to assert that biological life is fundamentally unpredictable, and thus none of the results of Artifical Life can have any bearing on biology.

  • GK[16]: You did not read very carefully. I did not say 'that life is unpredictable' but: 'complete phenotypes are fundamentally unpredictable'. That is the only occurrence of the word 'unpredictable' in my review. The context is: 'cannot predicted from genotypes'. Consequently, all the bad things about me you are quick to infer, reflect your hostile and arrogant attitude.
    Remarkably, you stated yourself that "Real world biology is too complicated" (p.295). This is my point of view: AL is potentially relevant, but not automatically valid. Secondly, a non-biologist would not even have the means to tell the valid ones from the relevant simulations.

Such an assertion seems rather surprising coming from a professional biologist, in as much as it could be understood as a virtual rejection of the whole purpose and program of science itself. It is like saying that Newtownian mechanics is irrelevant to our world because, well, the world is just too complicated to be understood.

  • GK[16a]: You are overreacting and do not read carefully. There is a difference between irrelevant and restricted applicability.
This turns back the clock to the dark ages, when men believed there were spirits in everything, controlling everything.
  • GK[16b]: people today still belief in spirits and the supernatural
If the past 400 years could teach us anything, it is that yesterday's magic is today's cutting-edge science and tomorrow's engineering. Surprising as this assertion may be, let's consider it.

The idea of "emergence" comes from the Artifical Life community's attempts to model life. At the time of my writing (1992 time frame) AL pioneers were exploring various criteria whereby one could say that something is alive, and "emergence" was one such criterion. "Emergence" can be stated as the property that "the behavior of an organism as a whole exhibits behavior which could not be deduced from the behavior of the individual parts." (p. 35, CVALE) Living organisms, it was proposed, should exhibit some form of emergent behavior.

In Computer Viruses, Artificial Life and Evolution I attempted to make a distinction by differentiating between "strong" and "weak" emergence. Weakly emergent behavior I defined as an emergence that is only apparent, due to our lack of understanding of a system under consideration. Strongly emergent behavior, I defined as a phenomenon where something really new that cannot in any way be predicted, results. (pp. 85, 86, CVALE) I believe this is an important distinction, and very relevant to our discussion. It is somewhat like the questions and issues which arise out of the irreducible uncertainty in quantum theory. One cannot pin down such uncertainties by making more accurate measurements - they are inherent in the basic physics itself.

The whole discipline of science essentially consists of studying unexplained phenomena and finding explanations for them. That study can go in two basic directions: (a) explanation in terms of existing laws, and (b) the discovery of new laws. My idea of strongly emergent behavior is simply the idea that new laws of nature must be invoked - track (b). In contrast, weakly emergent behavior implies the success of track (a), the explanation of a new phenomenon in terms of old laws.

An example of weak emergence is, for example, the emergence of Newtonian mechanics from quantum mechanics. It can be demonstrated that quantum mechanics predicts Newtonian mechanics in the appropriate limits. An area of potentially strong emergent behavior might be the emergence of mind, and the laws of psychology, from neurology.

Any assertion of strong emergence must be made cautiously. Really, the burden of proof should lie on anyone making such an assertion. Men have a way of grossly underestimating the power of science to understand things, and the history of science is littered with the remains of supposedly strongly emergent behaviors that have been thoroughly explained by the laws of their component parts.

Dr. Korthof appears to be an advocate of the idea that wet biological organisms are strongly emergent, whereas computer programs are not and cannot be. This is a surprising and unusual position for an advocate of evolution. I did not take such a strong position in my book. As I wrote, "My feeling is that emergent behavior is real, at least in nature, but I must say that timidly." (p. 71)

  • GK[17]: No, I did not claim that organisms are strongly emergent. I did claim that complete phenotypes cannot be computed from genotypes, which contradicts the computability axiom of AL.

Dr. Korthof also asserts that, because life is strongly emergent and AL cannot be, my work is irrelevant to biology:

How did he establish that his results are relevant for biological evolution? . . . Ludwig knows that biological objects are too complex and computer viruses and AL are too easy to study . . . He did not resolve this dilemma: how to gain insight into complex life if your method eliminates complexity from the start? I'm afraid there is simply no substitute for studying the messy, wet and dirty thing called "life". (From the Conclusion)

However, this "dilemma" is the very process of simplification - the elimination of irrelevant variables - that is the essence of science! If Dr. Korthof wishes to chide me for simplification just because it is simplification, then he is acting like an astrologer chiding a psychologist for failing to take planetary positions into account in his research. If he wishes to question the validity of that simplification, it is another matter. I hope the latter is the case, although his heavy reliance on trying to discredit my work merely on the basis of simplification tends to suggest the former.

  • GK[18]: I am not trying to discredit your work. Just read carefully. The next lines I say: "The secret is making the right abstractions" (Conclusion section). How do you know that you eliminated the correct irrelevant variables? The computer can't tell you. By the way: you are very good at criticising your own claims: "Real world biology is too complicated" (295).

I would say that the burden of proof in asserting that the simplification is invalid is definitely on Dr. Korthof though. The very fact of the existence of a science of genetics is strong evidence that the simplification made by AL is indeed valid. If I were mischevious I could turn Dr. Korthof's arguments a bit to assert that genetics is "no substitute for studying the messy, wet and dirty thing called 'life'", to use his own words.

  • GK[19]: ...existence of genetics...: genetics is firmly rooted in observation and experiment. The validity of both (population-)genetics and Artificial Life completely depends on the assumptions (variables) that go into it. By default they are nothing more than formal mathematics and therefore completely meaningless. Only when real-life data go into it, they mean anything. The computer can't tell you. By default AL simulations done by non-biologists are even more meaningless (due to arrogance + ignorance). Of course I do not deny that computer simulations of life and evolution can give useful results. But who is going to tell which simulations are valid in real life? 3

Let me explain this a bit, and hopefully indicate why this simplification is so possible: A computer program is only much simpler than a living organism at a certain level of analysis. If I compare a computer program at the level of the logic of the programming language to the molecules flying about in every direction in a living cell, then the program looks simple indeed. However, if I analyze the electronic states in a maze of semiconductor and ferromagnetic materials, it is questionable whether wet life would still be considered more complex.

In the case of a commercial computer, I don't have to worry about individual atoms and semiconductors because the parts of the computer have been designed to elimiate the need to consider them. This permits tremendous simplification when determining exactly what a program will do, and because this simplification is possible, computer science is possible.

  • GK[20]: Exactly: computers have been designed and we know the design specifications, unlike undesigned natural objects.

The fact that a science of genetics is possible is a direct result of a similar simplification that is possible in wet biology. Dr. Korthof does not sem to get this.

  • GK[21]: Wrong! YOU don't get my point. I pointed out that Mendelian genetics was possible because Mendel made the right abstractions despite he did not know chromosomes and genes and DNA. What happened after Mendel was not an endless series of computer simulations, but the birth of an experimental science of genetics, resulting in the discovery of the structure of DNA.
    Biologists know that genetics is based on certain aspects of living organisms, and it cannot give us the answer to all questions one ever could ask about life and evolution. Evolutionary biologists who lost sight of this, were later forced to admit that the theory of evolution was incomplete, as is shown by evo-devo.
He asserts that life is not predictable at the molecular level, quoting Jan Witkowski, who wrote that "On the basis of its structure alone, it is impossible to predict how the bases in DNA are translated into the amino acids of proteins . . . mathematics did not and could not solve the genetic code problem."
  • GK[22]: I did not say 'life is ...'. That is far too general. The quote is not from Witkowski. Read more carefully, Mark! That was a historical note of mine, to demonstrate that mathematicians did not solve the 'genetic code', but that is was solved in the lab.
Again, quoting Massimo Pigliucci, "Genes by themselves do literally nothing. Organisms do not begin with a bunch of genes that generate everything else: they need a set of environmental conditions . . ." These statements are erroneously used by Dr. Korhof as a disproof when they are exactly the essence of the simplifcation which makes AL relevant to biological life. These authors are simply making the point that DNA is like computer code. It is like bits and bytes. With it, one could code the genes for an e. coli, a beautiful brunette, a computer program that could be executed in a Pentium processor, or one of Shakespeare's plays, to be acted out on a stage. The code is inert, and fundamentally separated from whatever interprets it and processes it. Thus, one cannot tell what the meaning of that code is in isolation. Only in the context of the machinery that interprets it can we understand what it is and what it does. Only so can the code really be a code.

  • GK[23]: NO! The purpose of my quotes are to illustrate that one cannot calculate the complete phenotype from the genotype. This is a relevant point because AL is based on: 1) full genotype is known, 2) phenotype can be calculated (predicted) from the genotype. These two facts are (necessarily) known in AL, but are problematic in biology. Therefore, in biology one cannot simply calculate a phenotype from a genotype, neither bottom-up from the molecular level, nor at the whole-organism level.
    You say: "DNA is like computer code" and "that could be executed". Yes, nature seems to do something like 'executing DNA', but that is a 25 year old metaphor that does not help us anymore (1). We have moved beyond that metaphor. WE cannot duplicate that trick in the computer. Therefore, a computer simulation is not automatically justified simply because "DNA is like computer code". Maybe that is the biggest confusing factor in the whole discussion. We cannot 'execute the information content of DNA' and watch a multicellular organism develop from a genome.
    Artificial Life is NOT executing the same sort of instructions as those encoded in DNA.
    Artificial Life is executing handy artificial rules that calculate for example how many virtual organisms of certain properties are under certain conditions present in the next generation. Mainly, these properties are behaviours, not morphological or biochemical properties.
    If I would give you a complete DNA sequence of an unknown species, you cannot calculate the phenotype of the organism. Similarly, you cannot calculate the effect of an arbitrary mutation on the phenotype. And evolution means change of phenotypes on the basis of arbitrary mutations. How can we ever hope to predict evolution, if we don't understand how a phenotype is produced by a genotype? That's why AL cannot calculate what the probability is of species A (a mouse) evolving into species B (a hamster) (your example!). That's why AL cannot calculate what the probability is of apes evolving into humans.
    We have to understand almost everything, before we can produce a realistic computer simulation. However, I certainly agree that the computability of life and evolution would be a huge step forward in biology.
    The context of Pigliucci's statements is: Do genes code the organismal form? My conclusion from Pigliucci is: "Clearly, this is another reason why the phenotype cannot be computed from the genotype". The message is more subtle than you think.
    Your computer simulation of the behaviour of viruses in the presence of a virus scanner is really very interesting, but has nothing to do with 'executing DNA code'. It simulates behaviour.

Computer code works in exactly the same way. Apart from a knowledge of the hardware, the CPU and its instruction set, one cannot tell what a sequence of bits recorded in the magnetic domains of a hard disk will do. They could be a computer program for a Pentium or a Shakespeare play. Or they could be instructions for a 23rd century desktop DNA sequencing machine to code the DNA for the brunette.

Neither is this simplification a logical necessity for either biology or computers. At the frontiers of computer research, scientists try to nail down ways of making the simplification possible in a world where quantum uncertainties loom large. In biology, one might imagine a world in which the simplification is not possible. For example, those who study pre-biological chemistry often deal with such situations. Certainly we may understand that the simplification was non-trivial by the fact that men have won Nobel Prizes for figuring it out. There is something very important and fundamental here. Both the fact of our existence as a species, and the economic foundations of the modern world depend on this very simplification.

In any event, it is this simplification, this separation between code and interpreter, that makes both genetics and computer science possible, and which establishes a logical connection between the two, whereby results in one field have a bearing on results in the other. It is for this reason that computer scientists can abstract properties of life and build efficient evolutionary programs and more life-like animations. It is for this reason that geneticists can use computers to solve genetics problems that might not otherwise be tractable. There are no paradoxes or dilemmas here. Results in AL are relevant to life. The burden of proof really rests on those who would assert otherwise, and Dr. Korthof fails to make his case.

  • GK[24]: NO. My case is made in GK[23]. For those reasons no biologist ought to accept a computer simulation as relevant for biology, unless it is made clear by the person who makes the claim why it is relevant for biology.
    You wrote: "...computer scientists can abstract properties of life...", but they will make wrong or unhelpful abstractions. Especially those computer scientists who despise and look down on biologists. Years ago we were told that fractals were the secret of life. Not so. Would you accept Dawkins' "METHINKS IT IS LIKE A WEASEL" as a valid computer simulation of evolution? Exactly. You calculated that a spontaneous origin of a functional virus is impossible because of the minimum complexity required. Is that proof of the impossibility of spontaneous origin of biological life?

Of course, one must recognize that AL is perhaps best understood as a superset of real life. With the power to create worlds with their own intermediate rules inside a computer, we can not only model life, we can create worlds that have no analogy in the real world, and perhaps have no bearing on real-world biology. In my book I attempted to stand back and take a broad view of this horizon, realizing that some of the worlds I might create will support Artificial Life and some will not. Some of the worlds that support AL may support very little variety, and some may support a tremendous variety. Of those which support variety, some may support evolution and some may not.

  • GK[25]: Exactly! The crucial question is: Which artificial worlds are relevant and valid, and which are not?
    A computer simulation can explain and predict anything depending on the assumptions.

Within the superset, Dr. Korthof's assertion that biological life is more complex than AL would also seem to break down. I do not know of any professional biologists who believe that, given enough computing power and enough time to figure everything out, they will not be able to accurately model simple life forms inside a computer. At that point, we might say that at least some biological life has been brought within this superset. Dr. Korthof is strangely evasive in explaining just why he thinks this cannot happen.

  • GK[26]: I explained that in my review: 'Calculating the phenotype from the genotype', 'Calculating the 'Power of Evolution', but you have overlooked it or did not understand it. It is more subtle than you think. It is about the computability of the phenotype. See: GK[22].
Likewise, as computing power continues to grow, there is no particular reason to believe that someone might not discover forms of life that are far more complex than biological life. Perhaps they will be able to model and construct a silicon-based chemical life form, for example.

Thus Dr. Korthof's assertion that the results of AL have no value to research in wet biology is lacking in substance. Artificial Life is totally relevant to biology.

  • GK[27]: I did not say that. Relevant is not the same is valid. Secondly, valid for which real-life systems? One reason is the one you have stated yourself: see GK[24]. An additional reason is your model on page 155 (see also illustration in my review) is wrong (much too simplistic). It causes false results when used in simulations.

    GK[28]: Concluding: you ignored important topics in my review:

    1. invalid distinction creative/reactive evolution
    2. disagreement about the definition of life
    3. the status of physics (mentioned under the heading 'Calculating the Power of Evolution')
    4. whether or not Mark Ludwig is an Intelligent Design Theorist.


Where Viruses and Wet Life Really Differ

Because Dr. Korthof misunderstood the purpose of my book, he misunderstood my focus, and why I do not folow the normal path which evolutionary biologists follow. Although biology and Artificial Life have much in common, the primary questions which biologists have historically been interested in, and the questions which AL researchers are interested in, are remarkably different. Historically speaking, much of evolutionary biology's efforts have been explanatory of what exists, and backward-looking.

As a computer virus researcher, I think that one of the most significant events in history could be the invention of computer viruses. To me it is like witnessing a second creation, in which we are the gods . . . and yet we are gods that might be supplanted and spurned by our own creations. Consider the possibility that evolution really is every bit as powerful as Darwin suggested, that, from a little bit of DNA, RNA and proteins, our wonderful, complicated world really did evolve. If that is the case, then it is more than conceivable that a similar thing could happen in the world of bits and bytes. Not only could it happen, it could happen millions or billions of times faster in this digital world than it did in the real world, simply because things can work a whole lot faster inside of computers than they can in the soupy chemistry of earth.

It is easy to pooh-pooh such ideas, counting them to be mere science fiction. However, the whole idea of computer viruses was science fiction in the 1970s, quite literally. Really, it is amazing to consider that we engineered an environment which could harbor a totally alien form of life without our even realizing what we had done . . . until that life form started crawling around in our computers, much to our consternation. And not only did we create an environment that could harbor life, but (as I demonstrated in my book) this environment could harbor evolving life forms. This environment was not at all designed to harbor life. Quite to the contrary, it has not been wanted. Yet the "life" is apparently there and able to thrive.

  • GK[29]: I do not disagree with this story. You told it in your 1993 book. You did not change it since that time.

Evolutionary biologists seem to be fairly certain that life can, does and will continue to evolve in the direction of increasing complexity. Genetic programming has demonstrated that evolution can be used to speedily solve complex computing problems. If we simply take these observations and apply them naively to the world of computer viruses, we come to a rather startling conclusion: Under the right conditions computer viruses could begin to evolve in an explosive spiral of ever-increasing complexity. The pre-conditions for this possibility to materialize seem to be in place. Add to this the fact that one can mathematically prove that it is impossible to write a perfect virus scanner. That means scanners can never be used to put an end to this explosive spiral - they can only drive it and make it worse. Then place these facts in the context of the modern world, in which both governments and non-governmental organizations are spending big money to develop malevolent software, including computer viruses, for both military purposes and terrorism.

In view of these considerations, I believe the possibility now exists that one day (perhaps not too very far away) the right conditions might be fulfilled - perhaps quite by accident - to initiate an evolutionary explosion. Already sophisticated and extremely malevolent software could undergo a rapid and (at present) entirely unpredictable development in which the only goal is to survive mankind's attempts to eradicate it. It is not inconceivable that this explosion could take place in a matter of hours or days, and be far beyond the capability of all of mankind to arrest it.

As far as I can see, there is no generally accepted scientific principle by which we can conclude that such a scenario cannot happen. Quite to the contrary, the science we know today rather indicates that it is likely to happen.

Here we have the essential difference between biological life and computer viruses. The big questions which biologists have traditionally been interested in are historical. Thus, they spend time studying the fossil record, studying the genetic record for evidence of common descent, etc.

  • GK[30]: YES and NO. Mendel did not perform historical experiments! The rediscoverers and developers of Mendelian genetics performed field and laboratory experiments of a kind that included calculations and predictions. Furthermore, laboratory experiments with populations of Drosophila were done to test predictions of the theory of evolution, etc.
These questions also inevitably draw philosophical and religious ideas into the mix.
  • GK[31]: ...religious...: mainly because people blieve in certain books: the Bible, Koran, Torah...
On the other hand, the big question for the computer virus researcher is not what has happened, but what could happen in the future. In the end the question involves no real deep philosophical or religious issues, but huge practical problems. Biology has been traditionally backward-looking. What the virus researcher needs is something that is forward-looking.

All of this is not to say that biologists never look forward and computer virus researchers never look back. For example, a biologist might try to figure out how to remove a bad gene from the gene pool. A computer virus researcher might do forensics to determine where some computer virus came from.

Much of the focus of my book is on this forward-looking science. Dr. Korthof apparently did not understand this. Thus, he berates me as having "missed the argument for common descent" etc., concluding that I am "without sufficient training in biology". In reality, the argument for common descent is irrelevant to this forward-looking science. And although Dr. Korthof has to rely on advertising literature to impose on me the conclusion that I think "evolutionary biology is in an abysman state",

  • GK[32]: Wrong. I refuted that in GK[13].
I do have to admit that this science, which has flourished for the past 150 years completely fails to give me the tools to answer the big question about computer viruses. The truth is, I am left totally in the dark, without any of the tools I need to begin to answer such questions. This is a rather surprising situation for a science that has had so much human effort put into it. I must say it leaves one wondering . . . .
  • GK[33]: ... how stupid and ignorant biologists really are. You are a physicist. You are a computer scientist. You have the tools. A carefully designed and analysed AL experiment ought to be able to show up some sort of answer (225). Solve it! Prove you are smarter than any biologist!


So Will Viruses Take Over the World??

Suppose that over the course of time computer viruses and operating systems become complex enough that Darwinian evolution kicks in and begins to create new and increasingly complex viruses ad infinitum. I can learn nothing from evolutionary biologists to indicate that this can't or won't happen.

  • GK[34]: Ask Phillip Johnson: he is the evolution expert. He wrote more books. The answer must be there. Invite Bill Dembski for a free lunch and discuss your worries with him. He is an evolution expert and he seems to be good at mathematics too.
Quite to the contrary, from all that I understand, it most certainly will happen if conditions become right. The long history of the earth has been punctuated by relatively brief periods of explosive biological development from time to time. This seems to be a key feature of evolution. So suppose it were to happen. Very likely the world and the human race would be dramatically impacted by it, and - very likely - not in a very nice way.

  • GK[35]: ...the human race...: Why bother? According to J.C. Sanford (2005) our genome is degenerating and the human species is dying anyway.

Obviously, if there is a potential that computer viruses or some other kind of living program could take over the world at some point in the future, it would be good to know about it beforehand, and to have some idea of the dynamics of how that could happen. With such knowledge, we might be able to avert a potential catastrophe. Most people don't think about such things too much because they naively leave their computer security in the hands of antivirus software vendors. They fail to realize that when evolution kicks in those vendors could be overwhelmed, and unable to cope with even 0.01% of the new species of viruses that could evolve.

There are basically two ways in which we might be able to conclude that this catastrophe is not inevitable, and learn ways to deal with it. The hypothesis of this digital armageddon rests on two postulates: (1) There is no fundamental difference between computer viruses and living organisms that makes one able to evolve in a large-scale fashion and the other not, and (2) Evolution is capable of driving an ever increasing spiral of complexity within time frames that make it impossible for us to understand what it produces and overcome it.

If one of these two postulates is wrong, the hypothesis could likewise fail.

  • GK[36]: The software industry could design a new operating system that takes the existence of viruses into account right from the beginning.

Dr. Korthof appeared to take issue with postulate #1, asserting that viruses are too simple and biological life is too complex. I have dealt with this above. At bottom, computer viruses are essentially like living organisms. They are self-reproducing and they carry genetic code in their program. That is the essential point. Anything else is really irrelevant. To argue, for example, that computer viruses are really more like biological viruses, as Dr. Korthof argued is both wrong and irrelevant. (Since computer viruses do not attack self-reproducing programs, they are not like biological viruses.)

In Computer Viruses, Artificial Life and Evolution I look at both possibilities concerning postulate #1. I look at computer viruses and life and compare them. While recognizing that there could be something different about viruses and biological life, this difference is perhaps more metaphysical than scientific. Dr. Korthof catches a glimpse of this in his assertions about life being too complex and viruses too simple, but he will end up being driven to some kind of mysticism to keep life "too complex" in the face of advancing scientific knowledge.

  • GK[38]: You repeatedly claimed in CVAL that real life is too complex. That is your reason to do AL.

The other alternative is to take a second look at evolution. Most creationists take issue with postulate #2, asserting that evolution was not powerful enough to create all of the variety of life in our world, and therefore would not be powerful enough to cause viruses to evolve except in very minor ways. That is a comforting possibility, but the human race cannot really afford to entrust its future to such a blind dismissal.

Understand that 100% of the computer security specialists who deal with computer viruses are die-hard creationists in this sense. They believe that every computer virus they come across or ever will come across must have been created by some (human) intelligence. These men have the full trust and confidence of every computer user, every business, every government on the face of the earth. These specialists do not realize the incredible commitment they have made to creationism, and what they are willing to risk for that commitment. Most professional biologists are utterly blind to the existence of this community of creationists, and even take their side, as Dr. Korthof has.

In Computer Viruses, Artificial Life and Evolution, I again look at both possibilities concerning postulate #2. I consider the creationist's arguments that evolution is impotent. I consider the possibility that it isn't. In the end, I have to conclude that the good hard science - the kind that uses equations and provides solid predictions - just doesn't exist to answer this question. Given the fact that this question - Could evolution kick in in the world of computer viruses? - appears awfully important to our future economic and intellectual development, I think it is absolutely foolish to sit around and wait to find out what the answer is experimentally. Yet that is what is happening today.

The evolutionary biologists and the Artificial Life researchers are the closest of anyone to having the answers to deal with this problem. However no one will take them seriously if they just apply their general beliefs about large-scale evolution in our world to computers, because those beliefs essentially say the cataclysm is inevitable. The creationists' position is a lot more comfortable in this case, and I believe many people have adopted it for this reason (often, perhaps, encouraged by their religious biases).


Notes
  1. "In the 1940s, computer pioneer Konrad Zuse began to speculate that the universe might be nothing but a giant computer continually executing formal rules to compute its own evolution". (see here). But That Is Poetry! Not Science! [ GK ]
  2. It would clarify matters significantly, if Mark Ludwig admitted that he was rather hostile to evolution in 1993 (probably influenced by the many critics he read; probably unconsciously sympathetic to the religious critics), but changed his attitude to evolution since then. [GK 29-06-06 ]
  3. The situation would be quite different if results of computer simulations were accepted by peer-reviewed biology journals. This seems to be the case with publications of C. Adami in Genetics and Nature Reviews Genetics (see: The Digital Life Laboratory). [GK 01-07-06 ]


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Copyright ©G. Korthof/Mark Ludwig 2006 First published: 10 June 2006 Updated: -   Notes: 01 Jul 06