Computer Simulations and Darwinism

Petrushka: I haven't had the patience to follow Chardin's at best turgid and at worst pompous writing, but I will take your word for what he says. Denton's writing, on the other hand, is lucid and accessible, and I highly recommend him to all. Your final statement is true, so far as it goes, but it is important to add that, while Denton does not see anything but natural causes operating in the world, he is very clear that, without the prior "setup" of nature, we wouldn't have the results that we do. Darwinism denies that there was any such "setup". For Denton, all the outcomes were, in broad terms at least, necessary; for Darwin, they were all contingent. Thus, anyone who accepts the naturalistic premise (and hence rules out supernatural intervention) has to decide between these two views by calculating how likely it is that a truly contingent process of the Darwinian kind would produce what we see. And I agree with the ID people that the probability is exceedingly low. Thus, even within a purely naturalistic way of viewing events, the "best explanation" is that nature was set up for us -- as Hoyle said long ago. T. Timaeus

GinoB:

The issue is the ID proponents’ claim that all extant biological life was intelligently designed.

Strawman. IDists claim that the ORIGIN of living organisms was designed and that extant organisms have evolved from that starting point(s). Joseph

William J Murray

Unless you are going to deny that humans intelligently design things, ID is not only a valid theory (as in: arson, murder, cryptography, forensics), it is an indisputable fact.

Sorry if I wasn't clear: The issue is not whether any object can be intelligently designed. The issue is the ID proponents' claim that all extant biological life was intelligently designed. That is the claim which currently is an unsupported hypothesis. It's not anywhere even close to being a scientific theory. GinoB

That’s the problem right there. ID proponents started with the religiously motivated conclusion that ID is the correct explanation, and have been working backwards, twisting and ignoring facts, trying to justify the conclusion. That’s not science.

Whether or not that is what ID proponents do, and whether or not that is their motivation, is entirely irrelevant to the fact that one cannot pursue investigation into the nature of any designer until one establishes that a designer likely had a hand in the cause in question. If we agree that some things require an intelligent designer as part of their necessary and sufficient explantion (computers, battleships), and we agree that some things require scientific investigation before one can tell if they require ID as part of the causal explanation (arson, murder, archaeology), then we agree that there must be some acceptable means by which to make such distinctions. Is anthropic intuition/recognition of design ("it looks like design to me") acceptable? From your discourse so far, I'd say "no" is the answer. What, then, do you propose one use in making the distinction between "natural causes" and "artificial causes" (ID)?

There is no such thing as ID theory. Right now there is only a completely unsupported ID hypothesis. Not to say the ID hypothesis can’t be researched, but to date no one has provided any sort of positive evidence that indicates ID to the exclusion of natural non-intelligent processes.

Unless you are going to deny that humans intelligently design things, ID is not only a valid theory (as in: arson, murder, cryptography, forensics), it is an indisputable fact. The only question about ID is whether a particular<cite? phenomena / artifact requires ID as part of its causal explanation or not. William J Murray

kelly holmes:

But you can’t actually tell me any specific empirical evidence that tells me a single thing about the designer, how the design was implemented, when it was implemented or anything at all.

Which proves ID is not a scientific dead-end as it is obvious there are questions to be answered by reaching a design inference. Ya see kelly, reality dictates that in the absence of direct observation or designer input, the only possible way to make any scientific determination about the designer(s) or specific process(es) used, is by studying the design in question. And THAT is what ID is about- the detection and study of the design. That said your position has had the man-power and the resources and hasn't produced anything. Perhaps you should focus on your position... Joseph

Can your position even muster a testable hypothesis? Could you produce it here? Joseph

GinoB:

ID proponents started with the religiously motivated conclusion that ID is the correct explanation, and have been working backwards, twisting and ignoring facts, trying to justify the conclusion.

That is just plain ole ignorant- 1) The design inference has nothing to do with religion and 2) the design inference is only achieved after your position has been considered and found incapable and some specification is met. Also IDists have provided plenty of positive evidence for the design inference. Strange that you cannot produce anything to falsify the design inference- for example by actually stepping up and producing positive evidence for your position. Joseph

William J Murray

Before any investigation into the nature of a putative designer can begin (by whatever investigatory methodology that might call for), one must first reach the conclusion that the best explanation for a phenomena is ID.

That's the problem right there. ID proponents started with the religiously motivated conclusion that ID is the correct explanation, and have been working backwards, twisting and ignoring facts, trying to justify the conclusion. That's not science.

What ID theory is about, is identifying (as best provisional explantion) cases of ID. From that point there may be many investigatory paths to pursue.

There is no such thing as ID theory. Right now there is only a completely unsupported ID hypothesis. Not to say the ID hypothesis can't be researched, but to date no one has provided any sort of positive evidence that indicates ID to the exclusion of natural non-intelligent processes. GinoB

In Denton, however, the whole evolutionary process is end-directed, and the production of man is the end. The universe is, as it were, an extended computer program for the production of man.

Teilhard de Chardin took that a step further in "The Phenomenon of Man." What Denton and Chardin have in common is the understanding that the history of life is the same whether viewed from the point of view of a theist or of a methodological materialist. Petrushka

Before any investigation into the nature of a putative designer can begin (by whatever investigatory methodology that might call for), one must first reach the conclusion that the best explanation for a phenomena is ID. What ID theory is about, is identifying (as best provisional explantion) cases of ID. From that point there may be many investigatory paths to pursue. Earlier, you issued this challenge:

So, tell me KF, what advantage does allowing the divine foot in the door bring? Give me a *single* example of that advancing the cause of human knowledge? Just a *single* example. Go on, dare you.

The examples are too numerous to mention, because virtually all modern science (up until relatively recently) was conducted from the premise of a "divine foot"; that the universe was lawfully and rationally ordered by god, and that humans had the bestowed and correlational capacity to investigate and comprehend this rationally ordered cosmos - something that materialist atheism doesn't have any grounds for as an a priori. The "divine foot" provides a reason for the ensuing categorical methodology, which was unavailabe in other kinds of cultures, which accounts for explosion of progress in science and technology under rational Christianity. Biological features were "backwards engineered" to understand the design theory and purpose of the phenomena, and still are today even if scientists attempt to avoid design language and inferences. The idea that something is designed provides an entirely different investigatory heuristic that the idea that things are just happening haphazardly, chaotically or by the intentions of billions of willful, invisible entities; even the concept of a "physical law" comes from the heuristic that a prescriptive, invisible, universal force operates "at a distance" and guides predictable behavior throught the cosmos. As another example, if we find an object on a planet we discover, how would one know if it was a natural object, or a designed one, without some sort of metric that made a scientific distinction? Would we appeal to instinct, anthropic recognition by comparison to our own artificial artifacts? Think of the different kinds of investigations that would ensue depending on the finding of "natural" or "artificial"; from the former, we spend decades attempting to explain the artifact in terms of natural causes,and from the latter we might attempt to understand the design theory, reverse engineer the object, and even attempt to find clues to the location or nature of those who created it. More broadly than that, the understanding that such an object is natural, compared to the understanding that it is a designed, artificial object, have radically different effects on our understanding of ourselves and aspects of our existence. If we find intelligent design to be necessary causal factors both for life and the structure of the cosmos, then that has a tremendous impact in and of itself on every aspect of human existence, including scientific investigation, even if we never find the identity of the designer. William J Murray

Onlookers (and KH): I have a moment to respond on points to several key remarks by KH in this thread, for record and reference. In steps on snippets -- please refer above for context: 1: KH, 24.1: if you want to redefine science to allow the divine foot in the door you are free to do so. All you have to do is give *a single example* of that explaining something that materialistic science cannot. Then scientists around the world, seeing the fruitfulness of your methodology will copy you and you’ll get the worldwide revolution that you want. This is, right from get-go, a strawman caricature of the real issue. As I have discussed and repeatedly linked here, science historically -- cf. Newton's discussion of scientific methods in Opticks Query 31 (and its explicitly Biblical context of design thought under the Creator of the cosmos!) -- is a progressive pursuit of the empirical observation anchored warranted credible truth of our world, based on making observations, inferring best -- and unfettered -- current explanations, deducing and testing further consequences and resulting in a progressive cycle of theories across time. But, in our time Lewontinian a priori materialism, usually disguised under the theme that "science can only explain by NATURAL[istic!] causes" has censored that search for the unfettered truth, leading to institutionalising materialism under the false colours of science. In addition, KH is insistently ignoring the premise that the issue of science is that it investigates on EMPIRICAL observations, on signs that point to patterns and causal factors. Ever since Plato, and beyond, it has been notorious that material/natural causal factors [chance and necessity] and intelligent/artificial factors exist and leave characteristic signs. So the rhetorical contrast natural vs supernatural is suppressing discussion of the real one to be examined: nature vs art, on empirical traces that point reliably to the presence of chance, necessity and intelligence. The proper approach, KH, is not to try to bar the door against a Divine Foot by imposing materialistic censorship on scientific findings, but to freely study signs that point to chance, necessity and art, aspect by aspect for an object, phenomenon, process etc. And this is routinely done in all sorts of scientific fields of endeavour, pure and applied. So, the problem is to remove a recently imposed censorship, not to set up and knock over strawmen the materialist censors in lab coats want us to focus on. And when it comes to explanations, observe the utter breakdown of materialistic attempts to explain the origin of life, and the strong signs that our material cosmos is the product of design. 2: It seems to me that when I ask “well, how does ID explain the origin of bodyplans” you say “It was designed, all the signs point to it”. So if you allow that divine foot in the door you can then add the detail “It was designed by god”. As has been repeatedly pointed out to you -- and plainly willfully ignored -- modern design theory, from its outset in Thaxton et al, TMLO, 1984, has explicitly accepted that we can detect on empirically reliable sign that cell based life as we observe it was ceredibly designed, but that does not by itself warrant the conclusion that the relevant designer[s] is/are within or beyond the cosmos. A molecular nanotech lab a few generations beyond Venter would be sufficient. That you and ilk have to keep trying to set up a godddit strawman is telling on the real agenda, the selfsame that insists on imposing a priori materialism and dressing it in a lab coat to demand our genuflection. 3: So, tell me KF, what advantage does allowing the divine foot in the door bring? Give me a *single* example of that advancing the cause of human knowledge? Just a *single* example. Go on, dare you. Strawman again. If you refuse to accept that the removal of a worldview level question-begging a priori imposition of materialism that censors science from freely pursuing the truth about our world in light of empirical evidence is not an improvement, there is little hope that we can help you. We can only expose and hold up the consequences as an illustration of why this a priori materialism is so destructive to the process of science. 4: 25: s the reason why you are so reluctant, going off into multiple diversions, to talk about the actual “design” in “Intelligent design” and how it was done? As you really think it was god but know that saying such makes a mockery of the idea that the designer is not the Christian God? Onlookers, of course, I have long since pointed to a whole theory of design and invention out there that KH and ilk studiously ignore. Namely, TRIZ. When it comes to the designer of life on earth, the direct evidence in the cell points to design, but not the identity of a designer. That is why a scientific investigation of that narrow problem will stop with that conclusion. Just as, an initial forensic study can conclude arson, without knowing the arsonist. The fixation on debating goddit on the part of KH and co is of course a wedge rhetorical issue, since there is in our day a large body of people who have been polarised against God. Appeal to prejudice is effective rhetoric but it is poor science and worse science education. What is being conveniently neglected is that there are two major origins foci for design theory, cell based life and the cosmos. When we raise our eyes to look at the latter, we see that there is strong reason to infer that our cosmos had a beginning, so is contingent and even through a multiverse requires a necessary being as root cause, per logic of cause. In addition, it turns out that the observed cosmos is at a credibly highly fine-tuned operating point that would become radically inhospitable to C-chemistry, aqueous medium cell based life with relatively minor fractional changes. That points to design of the cosmos by a powerful, intelligent, skilled necessary being, powerful enough and intelligent enough to be the architect and maker of the known cosmos. One that from the steps taken, would be intent on creating a cosmos habitable for cell based life. In that context, it is reasonable to infer that the best explanation for the design we see in the cell, directly or indirectly is the same, responsible for design of the cosmos. Beyond this, we have really crossed over the borders into a worldviews level discussion, one in which it is fair comment to say that Judaeo-Christian theism can hold its own. But that is not the focus for this blog. 5: Perhaps you could show me where in the work of sending Apollo to the moon [by Wernher von Braun] divine causes were referenced? If you can’t what possible relevance does his beliefs have? A capital example of setting up an out of context strawman to knock over, distracting attention from a serious ad hominem attack that creates a climate of contempt and bigotry. The context is that in the infamous 1997 NYRB article, Lewontin snidely dismisses fundamentalists by making reference to a woman who said that since she could not get even Dallas on her TV, she doubted that there was real TV broadcast of the moon landings. in reply, I pointed out how this is a misrepresentation: von Braun, the man who sent the rocket to the Moon, was a Christian and a Creationist; a direct proof that such are not all ignorant or stupid or insane etc. Instead of acknowledging the point and calling for fair-mindedness, KH tries to pivot the issue into a talking point on a priori materialism in science. That speaks volumes on his attitude and none of it good. I have already pointed out the pernicious effects of a priori materialism imposed on science so I need not go over that again. 6: and I don’t expect a short answer to this nor an answer actually relevant to the question asked but here goes anyway: What changes once “materalist science” allows “a divine foot in the door”? What will we investigate and say “oh, we can’t invesitgate that any more as that’s divine”? The issue is that science must not be censored, or it sacrifices its integrity. And, the second issue is that the proper contrast in empirically based investigations is natural vs artificial, instead of the rhetorically polarised and loaded natural vs supernatural. So, the question is scientific integrity, vs its sacrifice on the altar of materialism. 7: Is the designer not study-able because of sciences refusal to allow the divine into science? If so then you’ve obviously already decided the “designer” is in fact god. When it could well be aliens, remember? Pathetic. Again, and again, we see snide repetition of the same already adequately answered points. This utter unresponsiveness joined to scornful superciliousness is the mark of indoctrination speaking, not a serious discussion on the part of KH. Just to sum up one more time: the issue is that science must not censor its investigations on a priori materialism or any other censoring a priori. Instead it must be free to examine the empirical facts and seek explanations for the traces of the deep past in particular based on the reliable signs of natural and artificial causes, which are equally empirical. _____________ We could go on and on, but this is already repetitious, showing that the basic problem is already cogently addressed. KH needs to see the pernicious effects of imposing a priori materialism on scientific investigations, thus dressing the self-referentially incoherent, self refuting and necessarily false worldview of materialism in the holy lab coat and demanding genuflection. GEM of TKI kairosfocus

Elizabeth: Some footnotes to your "last word" above (on the previous page; there was no reply tab to nest this reply). 1. Yes, I know that in one part of your reply you appeared to grant my point that ID might be possible without tinkering, but in another part of your reply, you said in apparently unequivocal terms: "If ID is true, something tinkered." It was that I was objecting to. 2. Re Margulis, if we are trying to understand her thought, and not yours, the issue is not what you consider to be the essence of neo-Darwinian theory, but what Margulis considers to be the essence of it. She sets forth that essence and then repudiates it. There isn't any doubt on this point. Read the sources that I gave you. I don't think you should defend your statement any further until you have done so. In any case, it is not the label, but the substance of the thought that is important. I have read a number of posts now of yours on evolutionary theory. I have a pretty good idea of how you think evolution works. Margulis is saying that evolution does not work in the way that you think it does. She is saying that the causes that you think are sufficient to generate substantial evolutionary novelty are nowhere near sufficient to do so. Again, read the sources I pointed you to. 3. The history of teleological thought goes back to the ancient Greeks. I am well versed in this history, from ancient times to modern, and I have translated some of the key Greek passages on the subject. (This is one of my areas of academic expertise, as neurology is one of yours.) Teleology pertains to ends or purposes. A teleological evolutionary theory would be an evolutionary theory in which nature drives towards ends. "Ends" does not mean mere outcomes, however stable or functional; it contains within it the idea of, at a maximum, purpose or plan (as in Paley), and at a minimum, of a natural resting point where potentiality has reached its fitting actuality (as in Aristotle/Aquinas). There is thus inherent in teleology the notion the fixedness of a goal which processes eventually reach. That is not what Gaylord Simpson (who had certainly read Monod) means by the term "teleonomy" -- he does not believe there are purposes, plans or fixed goals directing the evolutionary process. I know because I have just finished reading his book. You accuse me of simply defining Darwinian as non-teleological. This is a false accusation. I am a well-trained scholar, and I don't argue by such means. I have read Darwin very closely. His theory is inherently anti-teleological, when the word "teleological" is being used properly, and not in the loose and sloppy way that you are employing it. This is an empirical result of my reading of Darwin, not some a priori definition I imposed on Darwin. I have also read enough of Gaylord Simpson, Dawkins and other Darwinians to know that their view of evolution is also non-teleological. Again, that does not come from any definition that I imposed on them; it comes from reading their works. I can't take the time here to go over all the literature in the history and philosophy of biology. If you aren't inclined to take my word for it that the overwhelming consensus of the historians and philosophers of biology is that Darwinian theory is non-teleological, you will have to do things the slow way and read the thousands of pages that I have read on this subject over my lifetime. In Denton, however, the whole evolutionary process is end-directed, and the production of man is the end. The universe is, as it were, an extended computer program for the production of man. The unfolding all takes place through natural causes, but the end is inevitable -- man or something very close to man. Denton's account is a teleological account, in the strict and proper sense of the word. It's not up to me to discuss or elaborate the meaning of the term "teleonomic." Whether or not Darwinian evolution is "teleonomic" is not an issue I raised. What I said was that Darwinian evolution was non-teleological, and that is correct. T. Timaeus

Thank, Timaeus. Just a few comments, not intended to be "the last word" but not expecting a response either! "That there is evolution, that there is differential reproduction, that there is selection — they accept. " And that is what I mean by "Darwinian". I agree that the "way of handling" these concepts has changed radically, but I do not see that the basic Darwinian (as I call it) principle, namely that self-replication with heritable variation in reproductive success is violated by anything proposed by Shapiro or Margulis, whatever terms they may use. I do not insist that ID must involve "tinkering" - in fact I specifically laid out testable ID models, tinkering and non-tinkering, and questioned why they are not tested. I still do not think you have adequately distinguished between the concept of teleonomy and "inbuilt teleology", or indeed explained what you mean by "inbuilt teleology". It seems to me that you are defining "Dawinian" evolution as "non teleological" and then therefore calling any evolutionary theory that seems "teleological" as "non-Darwinian". My view is that this is fallacious. The essence of Darwin's theory (or what I am referring to as the essence - he got much wrong in his "handling" of it) is, as I've said, that if an entity self-replicates with heritable variance in reproductive success to its environent , it will adapt to that environment. This is self-evidently true, and as true when the entity is a population as when it is a population of populations in an environment of environments. Moreover, this process has what I would call "inbuilt teleology" in that it leads to the evolution of "functions" that serve the intrinsic "purposes" of survival and fecundity. At the population level those "functions" may include mechanisms for optimising reproductive fidelity (including repair mechanism) and, indeed mechanisms like recombination that lead to optimal kinds of novel variants. Only if we refuse to grant this "inbuilt teleology" to Darwinian theory on some exogenous principle can we call this "non-Darwinian". And there are, in my view, no grounds to do so. That is why Monod uses the word "teleonomy". Unless you can clearly distinguish between "inbuilt teleology" and "teleonomy", and show that the evolution of life exhibits the former rather than the latter, I must beg to differ :) Cheers Lizzie Elizabeth Liddle

Elizabeth: Thank you for your latest reply. I won't tax you with another extremely long answer, and I won't reply to you point by point, but I want to make a few last points before I exit, and then you can have the last word if you wish. You wrote: "In other words there is nothing non-Darwinian about Shapiro or Margulis..." NOTHING non-Darwinian? This is false. There is much that is non-Darwinian in each of them. There is an extensive interview with Margulis in Chapter 18 of *The Altenberg 16*. She there offers a scathing criticism of the neo-Darwinian (Modern Synthesis) explanation of evolutionary novelty and of other positions that have been taken by Darwinians over the years. You can find similar views expressed in her interview in *Discover Magazine*: http://discover.coverleaf.com/discovermagazine/201104?pg=68#pg70 (Note in passing Margulis's statement that ID is correct in its criticism of neo-Darwinism. This is significant as she totally rejects ID conclusions. It indicates that in her view ID understands what neo-Darwinism is about.) I think that Lynn Margulis, who has been a major contributor to evolutionary theory, understands what terms like "Darwinian" and "neo-Darwinian" mean quite well. It is with full consciousness of what they mean that she criticizes them, and quite radically. Shapiro also clearly has some significant differences with neo-Darwinism, as is clear from his new book, as you will see if you read it. One doesn't speak of a "new paradigm" of evolution if one is merely putting finishing touches on neo-Darwinism. One doesn't speak of the "ad hoc assumption" of random mutation if one is deeply committed to the Modern Synthesis. And his book explores new possibilities of evolutionary mechanism that go in directions unimagined by the neo-Darwinians, and in key ways attacks the gene-centered model of evolution. To say that there is "nothing" non-Darwinian in Shapiro is to say something that is simply false. It is possible that you are using the terms "Darwinian" and "neo-Darwinian" differently from the way that I (and all ID supporters) use them. I take my usage from the leading figures -- Gaylord Simpson, Dawkins, Margulis, Shapiro, etc. And in that usage, Dawkins is a classic neo-Darwinian, and Margulis is implacably opposed to that classic neo-Darwinian view, and Shapiro wants to go well beyond it. If you want to use the term "Darwinian" more loosely, to mean something like "modern evolutionary theory" (and thus to include things like evo-devo, etc.), you can do as you please; but everything I have said is true within my usage of the term. Of course I am not arguing anything as stupid as that Margulis and Shapiro reject every single proposition accepted by Darwinian evolutionary theory. I am saying that they reject enough of it that their respective evolutionary theories can no longer be called Darwinian, without seriously misrepresenting their character. That there is evolution, that there is differential reproduction, that there is selection -- they accept. But the characteristic neo-Darwinian way of handling those facts to explain evolutionary novelty and evolutionary change -- the way of Mayr, Dobzhansky, etc., -- they see as seriously defective, to the point where it must be either mostly abandoned (Margulis), or significantly demoted in importance in relationship to other approaches (as in Shapiro). The main point where I would continue to correct you is your continued insistence that ID requires "tinkering". It does not. I'll tell you one more time: read Michael Denton, *Nature's Destiny*. He offers a version of intelligent design which requires no tinkering. And Behe wrote a glowing endorsement of the book. Behe has also denied that tinkering is required. He has said that "design" is required, but he has never argued that design requires tinkering. It *might* involve tinkering. It can *allow* for tinkering. It does not *require* tinkering. I do not know why you continue to repeat this point, when the ID people are telling you in their writings that you have misunderstood what they are claiming. But I don't have time to argue with you about it any further. You ask me for clarification about "inbuilt teleology." No, I do not mean teleonomy. I have just finished reading Gaylord Simpson's final book on evolution, and there he has a lengthy discussion of teleonomy, and it is not what I am talking about. Again, read Michael Denton. Another version of inbuilt teleology in evolution (though less deterministic than in Denton's scheme) can be found in Mike Gene's notion of an evolutionary "nudge." It is also possible that some of the theories of self-organization which are now floating around (e.g., in some of the Altenberg group) will eventually be formulated in teleological language. None of these views are Darwinian. Again, as someone who has read Darwin extremely closely, I repeat: Darwin is intensely and inherently anti-teleological in his outlook. Similarly, all the classic neo-Darwinists -- Mayr, Dobzhansky, and Gaylord Simpson, and later doctrinaire Darwinians such as Dawkins, and maverick Darwinians such as Gould, are all anti-teleological. The hostility between any Darwinian or quasi-Darwinian view of evolution and teleology is inescapable. ID is compatible with teleological evolution. It is not compatible with Darwinian evolution. (Or, put more carefully, ID is not compatible with Darwinian evolution as the main driver of macroevolutionary change; it can of course allow Darwinian mechanisms an ancillary role -- as does Behe.) T. Timaeus

Regarding your first point, you have to distinguish between ID as a coherent theoretical position and a whole host of things which ID enthusiasts might say about ID. If you want to see ID as a coherent theoretical position, I would recommend that you focus mainly on the writings of Behe, on Dembski’s No Free Lunch, on Dembski and Wells’s Design of Life, on Denton’s Nature’s Destiny, and on some of the articles on the Discovery web site where a short, pithy definition of ID is articulated. Remember that on an open-for-comments website such as UD, you get comments from scores of people, some of who know the ID literature extremely well, and others who know it less well, and you get comments from scores of people whose interest is more in religious apologetics than in theories of design detection. So in some of the comments here you are bound to get a blurring between design theory proper and religious applications of design theory, just as on some other websites you will get a blurring between arguments for evolution and anti-religious polemics allegedly based on evolution. You have to take the time to sort out the core assertions of ID from the peripheral material.

I understand this, Timaeus, but thank you for the reminder.

That said, there are many commenters here who understand the core assertions of ID very well, including Vincent Torley, Gil Dodgen, scordova, nullasalus, Cudworth, and StephenB, to name just a few. So if you follow the posts and comments of people such as that, along with the core readings suggested above, you and I should end up on the same page regarding what ID is.

OK.

It is possible to assert ID without raising battle-cries against atheism and without launching into Christian apologetics. Those of us who have studied the history of philosophy and the history of science in some depth know that the modern debate between ID and Darwinian theory has ancient pre-Christian parallels. We have in the debates between the Epicureans, on one hand, and the Platonists, Aristotelians, and Stoics, on the other hand, many passages which (adjusting for the archaic scientific vocabulary) look as if they could have been pulled out of ID-Darwinist debates. The Epicureans argued that it was perfectly plausible that complex order, including the order of living things, could have come about through the unguided interaction and combination of blind, non-foresighted particles, and the others argued that this was nonsense, that order on the highest level cannot come from disorder, that a designing mind must have been involved, etc. And none of the participants in these debates had read Genesis or were concerned to attack or defend the Bible. So if you want to understand the theoretical core of ID, think of those pre-Christian debates. What ID does is to update the anti-Epicurean side, and what The Modern Synthesis does is to update the Epicurean side. The Bible and Christian theology ought to be kept out of it, as far as the basic theoretical debate goes.

Yes indeed. I completely agree. I have actually never argued that ID is fallacious because it isn’t science, or because it is religion in disguise. I have, however, argued, and continue to argue, that it is bad science and arises from fallacious reasoning! In many cases it also attacks a straw man version of evolution. More formally: it misstates the null hypothesis.

And in ID at its theoretically most pure, this is exactly what we find: the Bible and Christian theology are kept out of it. You don’t find arguments from the Bible or theology in Behe’s books, for example, or in No Free Lunch by Dembski. And when Darwin is criticized by Behe or Denton, he is not criticized for being an atheist (which he probably wasn’t, anyway), or for being responsible for Hitler or eugenics or the moral depravity of modern America, etc.; he is criticized for proposing a flawed evolutionary mechanism. (Of course, by that mechanism they have in mind not simply Darwin’s ideas, but Darwin’s ideas as updated and polished by the Modern Synthesis.) So you have to keep your eye on the ball, and ignore the extraneous religious flak. If you want to disagree with Behe or Dembski about this or that biological claim, that’s fine. But don’t try to characterize ID as a doctrine of divine tinkering, when its core theoretical writings do not argue for or discuss divine tinkering.

But here is the problem as I see it, Timaeus, and why your admirable efforts to distinguish ID qua science and ID qua religious argument won’t do. What ID conspicuously lacks is a testable hypothesis. There is one (“frontloading”) but I don’t see much enthusiasm for testing it, which is odd, because it makes clear differential predictions from evolutionary theory, and a positive finding would require major adjustments to, if not abandonment of, evolutionary theory. But even then, ID would lack a mechanism by which any designer (even if we allow for the possibility of a disembodied mind) actually implemented his/her/its design. That’s where the “divine tinkering” part comes in. If ID is true, something tinkered. If you don’t want to call it “divine” fine, but if we postulate that it was not divine that raises two obvious follow up questions: where are the traces of the tinkering mechanisms, and what designed the tinkerer? Those questions vanish if the tinkerer is postulated to be non-divine, but in that case, where is the research? And if the tinkerer is postulated to be divine (as, in fact, Dembski postulates), then we are back to where we started.

Second, regarding your statement that you are entitled to express any theological opinion that you want, I agree. So if you object to “God as tinkerer” — though it is unclear to me why such a view would bother you, since, if I understand previous statements you have made elsewhere, you don’t believe in God in the first place — you can of course protest this notion.

Well, given a coherent theology, I might reconsider! But the theology I used to have was pretty coherent, I think. But I found a flaw.

But it is pointless to bring up the inadequacies of God as tinkerer as a criticism of ID when ID as such does not affirm God as tinkerer. Denton has explicitly denied that God tinkers, and Behe, when the question has been put to him directly, has denied that tinkering is a necessary implication of ID.

But if ID is to make progress at science, then tinkering and non-tinkering hypotheses should, and can, be tested. Behe is inconsistent on that as far as I can tell. He seems to accept common descent, but maintains that some variants needed designer help. So he seems to belong to the Tinkerer school. Meyer, I’m not sure, but he seems prepared to accept that Darwinian mechanisms work, as long as you have Darwinian-capable starting population (with which I would agree) but maintains that the simplest Darwinian-capable starting population must be as complex as a modern cell, and couldn’t have arisen by chance. I agree with the last part, but the first part of his argument is not clearly demonstrated to me, and progress in OOL research would suggest he is wrong. More to the point, it puts him in the: Designer as Seed Planter school. Again, unless we postulate a divine designer, that hypothesis leads directly to questions about both implementation of the Seeding process, and the designer of the designer.

If an individual ID proponent, speaking for himself as a religious believer, affirms that God is a tinkerer, then you can of course sensibly raise your objection then. But such an objection is irrelevant if you are pretending to characterize ID as a pure theoretical position.

Any “pure theoretical position” taken by a scientist remains completely speculative unless it makes testable predictions that are then tested and found to be supported. That’s been the big criticism launched at String Theory, for instance. Theoretical Science is sometimes useful, and Theoretical Physicists are awesome, but they aren’t ultimately any use to anyone unless you can derive a testable hypothesis from the theory. And that’s where ID sticks (well, there are some other stickinesses IMO, but I’ll leave those for now): if allows for a non-divine designer then testable hypotheses can be readily derived, but ID proponents refuse to produce them, claiming that ID is only about design detection, not about “the identity of the designer”; but the only reasonable justification for not going further is if you think your designer is undetectable i.e. divine

The correct formulation is in fact that ID does not exclude the possibility of divine tinkering, but does not require it. A designer could achieve his end either by constantly modifying a pre-existing design, but could also set things up so that the design would unfold by an automatic process. So the designer could be something like a tinkerer, but could also be something like a computer programmer. Denton’s designer is a sort of cosmic computer programmer, with the set of evolutionary outcomes being the output of the program.

OK, but in that case, why not test those alternate hypotheses? They make different predictions after all.

You wrote: “Yes, you do have “one possible interpretation of evolution from an ID perspective”. It’s the very one I suggested myself in my post you quoted. However, that interpretation does not emerge from, for example, Dembski’s argument, and does, interestingly, emerge from Darwin’s, who famously said: “‘There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.’ “The ID case, as I understand it, is that Darwinian evolutionary processes cannot account for the evolution of “endless forms most beautiful and most wonderful” from “so simple a beginning”. I think that case is fundamentally flawed.” There is confusion here. The form of evolution that I was indicating was Dentonian. You here identify what I was talking about with Darwin’s form of evolution. But the two are quite different, even though in both cases only natural causes are involved. The Dentonian form is driven by an inbuilt teleology, whereas the Darwinian form is resolutely anti-teleological, both in its original Darwinian form and in its later version in the Modern Synthesis. Keep in mind that ID in its pure form is not anti-evolutionary but only anti-Darwinian. The debate between ID and Darwinism is not over evolution but over teleology. (And yes, I know, there are many ID proponents who are not just anti-Darwin but also anti-evolution. But anti-evolutionism is merely compatible with ID, not essential to ID. Again, one must keep one’s eye on the pure theoretical position.)

Please explain exactly what you mean by “driven by an inbuilt teleology”. Because “inbuilt teleology” sounds remarkably like Monod’s “teleonomy” which is of course what Darwinian evolution is all about.

So yes, ID proponents do deny the capacity of Darwinian processes to accomplish the results claimed for them; but this is not an inherently anti-evolutionary position, since non-ID evolutionary biologists like Margulis and Shapiro also deny the same thing. That’s all I have to say about the mischaracterization of ID. I now turn to your response to my final point, about the nature of modern science.

I think there is a straw man lurking here. Margulis and Shapiro have serious and valid criticism of the application of Darwin’s theory solely to the level of the organism. What they do is apply it also to the level of the population. Rightly so, in my view, and this expands the original Darwinian notion to a nested Darwinian system where “replication with heritable variance in reproductive success in a given environment” at the organism level is mirrored at the population level by “persistence with heritable variance in successful adaptation to new environments”, so that it is not merely organism-survival-enhancing functions that are “selected” but also population-survival-enhancing functions. In other words there is nothing non-Darwinian about Shapiro or Margulis, but both do have highly pertinent challenges to traditional applications of it. Which are, at least at a theoretical level, largely accepted as valid.

You wrote: “Science is all about finding regularities in the universe, not about accounting for every single individual phenomenon. We know why meteor craters form. We cannot trace the trajectory of a single meteor.” Two points. First, your first sentence is true of experimental or “operational” science; it is not true for historical sciences such as cosmology, geology and evolutionary biology. The latter necessarily affirm the occurrence of particular contingent events, and cannot dispense with detailed accounts of how those events might have happened. Second, even in the case of experimental or operational sciences, while it is not necessary to trace particular causal paths in all cases, it certainly is necessary to do so in some cases. For example, when scientists concern themselves with predicting whether a certain rogue asteroid is going to hit the earth X years from now, and contemplate how a nuclear device might be sent up to intercept it, they must indeed be able to trace the trajectory of the of the rogue asteroid, and they can in principle do this using their knowledge of celestial mechanics. (For that matter, the same knowledge enables them to land craft safely on Mars within a few dozen feet of the projected target.)

Yes indeed, though I think it is misleading to draw too sharp a line between “historical” and “operational” science. All science is operational, and we can even make testable hypotheses about historical events (just as we can use operational forensic science techniques to establish what happened at a murder scene). But there is certainly a difference between research that, for example, establishes an exact lineage for human beings (almost certainly impossible - to use Dennett’s phrase, some things are “historically inert” – have lost all traces of their provenance), and research that establishes a likely trajectory for that lineage, passing near-but-not direct fossil/genetic ancestors on the way.

On your last point, I did not say that science excludes God. I said that the methodology of modern science excludes the consideration of supernatural interventions, so that, if supernatural interventions have in fact occurred, science could never know it. This is a built-in and inescapable blindness of the way science is done today. But in no way does this exclude God, because God might have chosen to work wholly through natural causes.

Yes indeed. I do not think that scientific methods can exclude God any more than they can demonstrate God. I do not think that atheism is, or can be, the inescapable conclusion of science.

Again, refer to the discussion of “tinkering” above. For God to guarantee a result under Darwinian evolution, he would have to tinker; but for God to guarantee a result under Dentonian evolution, he would not have to tinker. Modern science does not exclude a God who operates in the way that Denton suggests; it does exclude a tinkering God. And that exclusion cannot be justified by anything that modern science has “proved”. It is rather a postulate that modern scientists work from because they find it heuristically useful. And I don’t criticize that procedure, as long as modern scientists aren’t under the illusion that they have “proved” that the natural causal nexus is unbreakable. They have not proved and cannot prove such a thing. Philosophers and historians of science (who have often thought more deeply and reflectively about the nature of science than working scientists) have long been aware of this.

I think we agree fairly well on this.

I carry no brief for miraculous interventions in the evolutionary process, but biologists cannot show that such things could not have happened. What they can do is provide plausible wholly naturalistic scenarios, full hypothetical evolutionary pathways for the origin of major organs or bodily systems. The more such pathways they can describe, the stronger the case that supernatural intervention would not be necessary, and therefore would be an uneconomical hypothesis. Unfortunately for Darwinism, the fact is that there does not exist in the scientific literature even a single full (or anywhere *near* full) hypothetical evolutionary pathway such as I have called for.

Not “full” but pretty clearly indicated, just as a jigsaw puzzle with lots of pieces missing can still indicate very substantially what the picture is.

Thus, we have no demonstration that Darwinian processes, so pretty on paper when they are allowed to remain at high levels of generality such as “drift”, “mutation,” and “selection,” can actually do the job that they are required to do, which is not just to confer antibiotic resistance on a microbe, but to build a radically new body plan or system.

I often see this claimed, but I do not think it is supported. For a start, nobody claims that a single genetic change resulted in a “radical new body plan”. For a second, we know a lot about the evolution of genes that are implicated in developmental biology. The whole field of “evo devo” is burgeoning and is constantly delivering new insights. In my own field, we are starting to identify genes and alleles that govern such developmental processes as cortical folding. I simply do not accept the charge that there is something qualitatively different about the evolution of “body plans” that demands a different process from the evolution of, say antibiotic resistance, or a deeper beak.

ID people continue to remain skeptical that Darwinian processes can do that job. But skepticism about the biology of Mayr and Dobzhansky does not entail outright rejection of evolution itself. It means that it is unlikely that evolution could be driven wholly or even primarily by Darwinian processes. And on this point, ID people have been theoretically ahead of their Darwinian opponents, as the recent high-level criticisms of neo-Darwinism coming from the Altenberg group, from Shapiro and others shows.

Well, not exactly! People have been talking about the evolution of evolvability for years! Goodness, I remember putting my hand up in a high school biology class in the sixties and asking “could mutation rates have evolved?” And the biology teacher thought it perfectly possible. We both agreed that natural selection was just as logical at the level of the population as at the level of the organism. Anyway, nice to talk to you! Sorry I was so late with my response. Have a little more time this weekend for substantial replies to substantial posts! It seems we agree on quite a lot. But there is still plenty to argue about! Cheers Lizzie Elizabeth Liddle

PPS: Onlookers, you may find the ongoing discussion from here on helpful also. kairosfocus

Please, read the Weak Argument Correctives. kairosfocus

PS: Alinsky's distract, poison and dominate polarisation technique. kairosfocus

Onlookers: You will see above, that I gave KH an opportunity to examine what he did, and to reflect and correct himself. Sadly, he took opportunity of that invitation to redouble his rhetoric. It is thus now blatant that KH is not interested in reasonable discussion of issues on the merits, but in namecalling and the polarising trifecta rhetorical stratagem favoured by disciples of Saul Alinsky and his followers. THIS is what we are dealing with. In due course, I will take some time to take up what in the above is worth responding to -- by way of exposing and correcting [yes, gross and polarising error needs to be corrected] what is now blatantly materialist or materialism-influenced bigotry, talking points and prejudice sadly reminiscent of recent hate sites that have sprung up around UD. But, I suggest that in the meanwhile you will find my main responses anticipated in:

1: the UD Weak Argument Correctives that he simply will not read and reflect on soberly, 2: the ongoing UD series on ID foundations, and 3: the IOSE survey course

. . . which KH would be well advised to calm down and also read, ponder and heed. G'day, GEM of TKI kairosfocus

In what sense is the claim that the universe is not capable of forming a purpose "Scientism in action"? What evidence is there that it is? We do not otherwise attribute things without brains the capacity to devise a purpose - why should we attribute such a capacity to "the world"? Elizabeth Liddle

Elizabeth, Thank you for taking time to review my short essay from several years ago and providing your feedback. We may be talking past each other a bit with terminology, so I will endeavor to do a better job on that front. Let me point out, however, why I think your defense of Avida as a refutation of irreducible complexity is misplaced and why the main points of my original critique stand.

And thank you for taking the time to respond to my critique! This is the kind of civilised exchange of views that makes the internet worthwhile IMO. And I agree that terminology issues are important, and often crucial. So let me respond.

Programmed for Success I have argued that Avida was “programmed so that a slight, successive cumulative pathway” to the ultimate function existed. You have responded that all the changes were incremental (whether rewarded or not) “so there is no bias there.” The question is not one of bias toward functional states (which is a separate point I’ll discuss below). The question is whether a cumulative pathway exists. A large part of Behe’s point is that a cumulative pathway to a complex integrated system, such as a cilium, the bacterial flagellum, or the vertebrate eye, may not exist. Despite your protestations to the contrary, Avida does have a cumulative pathway built into the system, which may or may not reflect the real world.

Well, let’s be really clear on this. We both agree that in a Darwinian process, all changes are incremental. However, there are two aspects to this: one is whether genetic changes are all slight; the other is whether any viable changes to the phenotype that result from a genomic change will tend to be slight. These are not quite the same thing, as I’m sure you will agree. To take the question of genetic changes first. Even a slight genetic change may render the phenotype completely non-viable. For example if a gene vital to basic function is destroyed by a single insertion that shifts the reading from so that the resulting protein is nonsense, the resulting phenotype will not survive to maturity. So a slight genetic change can result in a radical phenotypic change. Moreover, radical phenotypic changes are far more likely to be disastrous than beneficial (I hope this is self-evident – if not, I will expand in a later post!) Therefore for mutations with any chance of propagating, whether by drift or because they confer some slightly reproductive advantage, the associated phenotypic changes will tend to be slight. However, some genetic changes can be huge, yet confer no, or little, phenotypic change at all. Wholesale duplication of long stretches of DNA can have no phenotypic effect whatsoever, yet are perfectly possible. So I think we can agree that Darwinian evolutionary processes must proceed by slightly phenotypic changes, though not necessarily the result of slight genotypic changes. And slight phenotypic changes that are also viable (are consistent with a successfully reproducing organism) will therefore tend to be near neutral (not disastrous, and rarely hugely beneficial). Therefore we would not expect to see, if the current evolutionary model is true, huge phenotypic changes that are beneficial in effect. We may see a huge increase in fitness resulting from a single beneficial change, but that is, I hope we agree, not the same thing. Now, Behe’s IC argument, is as you say, “that a cumulative pathway to a complex integrated system, such as a cilium, the bacterial flagellum, or the vertebrate eye, may not exist”. So what does he mean by “cumulative”? Does he mean, as I am pretty sure he means (because it makes sense!) that there is no series of incremental beneficial phenotypic changes that could have been precursors to the flagellum, or does he mean that there is no series, beneficial or otherwise, that could have been precursors to the flagellum, as perhaps you think? I suggest that the latter interpretation makes no sense. In no text of Behe that I have read does he argue that the proteins that make up the bacterial flagellum, could not have been made unless all the other proteins were also made, i.e. that a bacterium in which the gene for one of those proteins did not exist could not have manufactured the remaining proteins. It doesn’t make an biochemical sense. What he argues, explicitly, that if you disable any one of the genes that produce the flagellum, not only will the flagellum not work (hence it is “irreducibly complex” – you take away any one component and it ceases to work) but that no precursor state (some of the proteins made but not all), or, at least not enough precursor states, would have conferred any reproductive benefit, and therefore would not have propagated through the gene pool, or hung around there intact, until the remainder of the genes were in place. So I submit that Behe is not not arguing that IC structures are those for which no incremental phenotypic pathway exists (clearly any multipart structure can have independently manufactured parts), but that there is no phenotypic pathway in which each step confers increased reproductive success, whether by a minimally effective prototype of the “final” function (final as in the one we are interested in) or by serving some other useful purpose, as Matzke proposes. And in AVIDA we see that IC functions (e.g. EQU), while they are achieved, as they must, by way of incremental phenotypic changes (slight changes to the phenotype), they do not need to be changes that result in increased fitness, and can even include steps that result in reduced fitness. The changes certainly accumulate (overall – some steps may involve necessary deletions), but they do not have to accumulate by way of beneficial effects. Drift, in other words, is a potent factor in propagating neutral and even slightly deleterious changes, thus increasing the number of opportunities in which a necessary beneficial addition can convert the ashes of disaster to the roses of success (as the lovely Chitty Chitty Bang Bang song goes). This means that Nick Matzke’s proposal for a pathway consisting of beneficial steps, though intriguing, and possibly correct, is not actually necessary. We do not need to find a series of beneficial precursor steps to explain an IC structure. AVIDA shows us that many precursor steps can be neutral and even deleterious, and “IC” structures still evolve. In other words, you cannot identify any structure as IC. Thus AVIDA falsifies Behe’s entire argument.

The word “programmed” does not necessarily mean that the virtual organisms were caused to go from x to y at a particular point in time with a specific command line (although that would be one way of programming). “Programming” can also mean setting up conditions within the virtual world (in other words, within the program), whether those conditions attain inevitably or stochastically, for the population to get there. Why you don’t acknowledge that this pathway is included in Avida is strange, as the authors themselves acknowledge it: “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.” If the word “programmed” is problematic, then we can think of “established parameters” or some other term you find more appropriate. The bottom line is that the cumulative pathway is there; it exists within the virtual Avida world.

Yes, the authors set the thing up so that some complex functions could be built on simpler functions. Obviously. As they say in the sentence immediately after the one you quoted: “However, that is precisely what evolutionary theory requires, and indeed, our experiments showed that the complex feature never evolved when simpler functions were not rewarded. If no intermediate steps were beneficial, clearly the thing would not evolve. But nobody claims it would! What Behe claimed was that unless all the intermediate steps are beneficial, a feature is “IC” and therefore cannot evolve by Darwinian means. He then brought in the concept of “degrees” of IC (how many non-beneficial steps there could be on the pathway to a function and the thing still evolve), but as far as I know then backtracked on that. Last time I heard him he was back to his “mousetrap” version – if the removal of any part disables the function, the function is IC and can’t evolve. And not only were there many many non-beneficial necessary steps to evolve EQU, some of those were actually deleterious. So the thing was way more IC than Behe’s loosest definition. And yet it evolved.

So the authors are clearly aware that the program contains a cumulative pathway to the complex feature that can be built on simpler useful functions. Why would they be concerned that some readers would believe the deck was stacked? Because whether or not such cumulative pathways to complex systems exist in the real world is precisely the point in question. What is the authors’ response? “However, that is precisely what evolutionary theory requires . . .” We know what evolutionary theory requires. That is not at issue. What is at issue is whether the conditions evolutionary theory requires in fact attain in the real world. Using the authors’ logic, I can prove anything. This is very significant. I can come up with any theory, based on whatever wild or illogical parameters I want, and then write a program that “proves” my theory. All I have to do is include the parameters that my “theory requires.” Again, on such logic, nothing is out of bounds; I can prove literally anything.

My impression is that you are confused. Lenski et al tested a hypothesis, which was: given a rugged fitness landscape in which functions can only be reached by means of many neutral and even deleterious steps, can those functions evolve? And the answer is yes. They did not test the hypothesis: “given a landscape of features completely unconnected by any beneficial steps, can those features evolve?” because we know the answer to that is no. In fact, the No Free Lunch theorems tell us that – with no connections between functions, a random search will be as good as an evolutionary algorithm. Sure, if you want to falsify a Darwinian explanation for a complex feature by claiming there are NO beneficial intermediate steps, then fine. Go and find a complex feature for which there are NO beneficial intermediate steps. But not even Behe claimed that, even for his flagship flagellum. What he claimed was that when several non-beneficial mutations have to be in place before a fitness increase is gained, then the thing is IC and won’t evolve. Lenski et al showed that it can.

Whether or not evolutionary theory (in the sense of the Darwinian mechanisms we are discussing) is true is precisely the point at issue. We cannot write a program that includes – as the authors acknowledge – the parameters that are needed for the theory to be true, and then turn around later and pretend that the program has demonstrated the truth of the theory. It is entirely circular. It may be true that there is a cumulative pathway to complex features in the real world, but Avida cannot demonstrate it.

You seem to have the impression that the model was designed as a model of some biological system and so that if things could involve in the model, they could evolve in that biological system. This is not the case. The thing is not a model of a biological system. It’s a model of Darwinian processes. It makes no claim to be a model of any actual biological system. Nothing in the results of the experiment allow us to conclude that any given biological system could have evolved. Moreoever, it was not set up as a test of the hypothesis that complex functions could evolve in a landscape so rugged that no function had any beneficial intermediate step. Darwinian evolution simply does not work in that kind of landscape, as I said. And, indeed, they actually demonstrated this, but we knew that anyway. Darwin’s theory only works in a fitness landscape where there are some connections between functions, i.e. beneficial intermediaries. What it tested was the hypothesis that complex functions can evolve in a landscape rugged enough that the functions fulfil Behe’s criteria for being “IC”. And it turns out they can. As I keep saying! There is nothing circular about this at all. In fact you can use AVIDA to construct fitness landscapes of all kinds of degrees of ruggedness, and of course, the more rugged they are, the less likely the complex functions are to evolve. The interesting finding was that an IC landscape was traversable, contra Behe.

In fairness, let us pause at this point and consider the other side of the coin. As I said in my essay, “if a program were written that had no possible cumulative pathway, then the writers of that program could be fairly accused of assuming up front that the complex feature was irreducibly complex [note here that I am talking about IC in the sense of “per se irreducible complexity,” as mentioned in my paper]. Thus, evolutionary algorithms seem to be between a rock and a hard spot: assume a cumulative pathway and then you are unable to challenge irreducible complexity; assume there is no cumulative pathway and then you are unable to support irreducible complexity. And herein lies the crux of the matter. Evolutionary algorithms that assume a cumulative or non-cumulative pathway at the outset simply cannot, by definition, demonstrate whether the complex system is irreducibly complex. Such algorithms define themselves into irrelevance.”

You have made the mistake of categorising what is a continuum. In so doing you have committed the Fallacy of the Excluded Middle. A fitness landscape in which there is no pathway to any function that goes via a beneficial intermediary is a maximally rugged landscape. We know that Darwinian evolution will perform no better than random search in such a landscape. A fitness landscape, on the other hand, in which every function can be reached by a series of beneficial steps is so easily traversed that even a purely hill-climbing algorithm will do it, because to get to the functions, the population will never have to go downhill. Behe made the mistake of declaring IC any feature that could not be reached by a purely hill-climbing algorithm, and concluding that Darwinian evolution couldn’t reach it. What the Lenski paper shows is that a landscape can be considerably more rugged than the kind of tiered landscape in which every step to everywhere is beneficial (such as Weasel, in fact), and, in fact, include necessary treks over wide plateaus and even descents down deep ravines, and yet the functions still evolve. This is because Darwinian algorithms, unlike hill-climbing algorithms, can traverse rugged fitness landscapes, because they can take necessary neutral and deleterious steps as well as beneficial ones.

As a separate question, I posed to you the above hypothetical and asked whether such a program with no Darwinian pathway would invalidate the Darwinian hypothesis. You responded: “Well, no. All you would be able to conclude is that, given the parameters of your model, the thing is very unlikely to evolve. That conclusion is only as good as your model. The better (more realistic) your model, the more confident you might be that the thing in question really was unevolvable, but we can never rule out a missing parameter.” I am wholeheartedly in agreement that any “conclusion is only as good as your model.” What we need to refute Behe’s claim – the only thing that is adequate – is a faithful representation of what actually exists in the real world. And on that score, Avida leaves much to be desired.

No. All we need to refute Behe’s claim is evidence that Darwinian processes are capable of traversing rugged landscapes. He says, in effect, that they can’t, and that certain features, e.g. the bacterial flagellum sits on a peak in such a landscape. And so the rebuttal to the IC argument against a Darwinian explanation of the flagellum was couched (by Matzke) in terms of demonstrating that the landcape wasn’t really rugged. And Matzke may be correct. However, what Lenski showed is that even if Matzke is wrong, and even if Behe is right that the flagellum sits on a peak in a rugged landscape, we cannot conclude that it is unreachable by Darwinian means, because we now know that Darwinian means can reach such peaks.

Steps and Stumbling I argue that “relatively few changes are required to get from the initial organism to the complex feature.” You responded that: “Yes, it’s a model, written to establish a principle, that IC functions can evolve. Pathways to EQU ranged from 51 to 721 steps, over many thousand generations, although in principle (if intelligently directed!) it could have been done in 16 mutations. That should be indication in itself that no direction was provided.” Well, Avida may establish a principle. Unfortunately, it is not at all clear that the principle has any relevance to biotic reality. In addition, you seem to think that the “stumbling” is evidence that no direction was provided.

Well, if all you mean by “direction” is that the landscape wasn’t maximally rugged, then I guess it was “directed” but no more so than anyone is proposing for biological landscapes. And if you use the word “directed” in that sense, then the landscape in the natural world also “directs” evolution. I don’t mind whether you use the word or not, but if you use it for the virtual landscape you have to use it for real landscape because the kind of “direction” each provides is the same. But sure, the task now for those who would like to attempt to falsify the Darwinian explanation (always a worthwhile project) is to demonstrate that the actual biological landscape is too rugged for Darwinian processes to navigate. But the task is now harder, because we now know that considerable ruggedness poses no bar. Also proving a negative is always difficult.

“. . . the fact that it took them from between 51 and 721 mutations on the path to EQU, even though 16 mutations would have done it, is pretty good evidence of their “stumbling”. The[y] were helped on the way by only 8 rewarded steps, which tended to occur earlier than EQU, not surprisingly, given that they were simpler. Remember that the vast majority of mutations were either neutral or deleterious. Not surprising that they stumbled a bit.” Rather than being a vindication of the Darwinian mechanism, the real lesson from all this stumbling is that even with an easy function and a relatively short pathway to get there, the Darwinian mechanism is quite poor. The skeptic might therefore be forgiven for asking whether the stumbling might not in fact overwhelm the available resources, when translated to the real world, with functions much more difficult to achieve and pathways that may or may not exist.

Possibly. That’s why Lenski of course also conducts experiments with e-coli bacteria, and why so much lab and field work goes on with real organisms. But don’t underestimate (or misconstrue!) what the AVIDA study actually showed!

Function and Integration Another key problem with treating Avida as a refutation of Behe’s concept of irreducible complexity is that the Avida functions are too easy to attain. Behe highlights complex, integrated biological systems, like the bacterial flagellum, the cilium, the vertebrate eye. Each of these systems requires numerous proteins acting in concert, and that is ignoring the construction process itself, which is an astounding coordinated orchestra of chemical processes.

The AVIDA functions also involved multiple components acting together. That was the whole point – that’s what made them IC, because many of those components had to be acquired without conferring any benefit alone, and indeed, causing some reduction in fitness, in some cases. However, if you are now claiming that the ribosome system is IC, well, that’s another issue. Again, being IC, we now know, is not a bar to Darwinian evolution, but being very very very very ID, i.e. on a peak on a very rugged landscape, might be a problem. I don’t know much about theories of ribosome evolution (we are getting into OOL territory here), but I believe there are some. Certainly AVIDA won’t tell you just how rugged is too rugged for Darwinian evolution, nor of course how rugged any given real-world landscape is. But let’s stay on topic here. AVIDA didn’t solve every problem for evolutionary biology. But it did refute Behe’s principle. If Behe still wants to claim the flagellum is unevolvable he now has to take into account just how rugged a landscape can be and yet allow Darwinian mechanisms to reach the peaks. His old criteria (certainly the mousetrap) won’t work any more.

The Avida authors indicate that: “A single mutation distinguished the pivotal genotype from its parent in 19 populations, whereas four involved double mutations. The pivotal mutations included point mutations, insertions, a small duplication and even deletions.” Further, as you note, and as the authors describe: “The phylogenetic depth at which EQU first appeared ranged from 51 to 721 steps. In principle, 16 mutations, coupled with three instructions already present in the ancestor, could have produced an EQU-performing organism. The actual paths were much longer and highly variable, indicating the circuitousness and unpredictability of evolution leading to this complex feature.” Might the skeptic be permitted to ask whether this “complex feature” is even of the same order of magnitude as what we find in the real world?

By all means. But, as I said above, it is Behe’s principle that is falsified, not the principle that some things in biology are unevolvable. After all, in some AVIDA landscape, EQU was unevolvable. There are almost certainly some features that Darwinian mechanisms could never find (wheels in multi-cellular organisms for instance, would be my bet). And, lo and behold, they aren’t found!

How many “point mutations, insertions, small duplications and deletions” would be required to produce the systems Behe points to, which contain anywhere from dozens to hundreds of proteins acting in concert? Even assuming relatively simple proteins, we are talking about a minimum of hundreds, and likely many thousands, of “point mutations, insertions, small duplications and deletions”. Yet the ultimate Avida function, EQU, can be built with 16 mutations.

I don’t know, but Matzke has had a go at estimating them. Actually, I don’t think it was all that many from features that we know exist and which serve a beneficial function.

Avida thus ignores one of the key difficulties facing any Darwinian scenario: the difficulty of obtaining function.

No, it doesn’t! It modelled that. It had a genome that resulted in phenotypes and the phenotypes performed a function. It most certainly was not “ignored”.

By making the process orders of magnitude easier than in the real world, Avida unfortunately fails to replicate one of the key questions dogging Darwinian theory: whether chance processes would be able to stumble upon intermediate functions (or constituent parts of larger machines) in the first place.

But you are moving the goalposts here, Eric. I don’t know, and AVIDA doesn’t tell us, just how many neutral or deleterious necessary steps can intervene between one beneficial function and another and the second still evolve. What it does tell us is that, contra Behe, many can. Now what you need to do is to go out to the real world and try to count them (not an easy task, as there are many many potential pathways to any given function, as AVIDA shows, and, of course, many many ways of achieving that function, as, again, AVIDA showed, and we see in nature. But you will have to count higher than Behe did, because Behe put the number far too low.

Yet there remains an equally problematic issue: that of integration. Another key question is whether constituent parts, once they exist, can be successfully integrated into the whole. Avida completely assumes away this issue, effectively granting the organisms successful integration as soon as they come up with a successful operation. Think of it this way. Bacterium A somehow gets a new DNA sequence that codes for a functional protein (let’s assume, just so it is more believable to everyone, that this gene came from horizontal gene transfer from another bacterium, rather than arising through point mutations, replication errors or the like). Let’s further assume that the cellular machinery recognizes this gene as a legitimate gene (which is not as straight forward and certain as we have perhaps been inclined to believe in the past), translates the code and expresses the protein. Great, our cell has a new protein floating around. Now what?

Biochemistry.

In the real world it is not at all clear that the protein would perform a useful function in Bacterium A. Even if the protein has the raw capability to perform a function, it is not at all clear that the protein would be recognized by other cellular machinery, properly transported to the necessary location, and successfully integrated into a cellular machine. We simply don’t know whether this would happen in particular cases. It might be just as likely that the protein would languish, be broken down, or even gum up an existing process.

You’ve forgotten that severely deleterious mutations don’t even make it to replication. You’ve also forgotten that we are assuming that the thing is sitting on a viable spot of the landscape to begin with. And you’ve also forgotten, it seems, that in AVIDA, really quite deleterious (gum up the works deleterious) changes still propagated, providing opportunities for an ungumming change to come along and make it work. You are trying to add things that are already there, Eric! This is modelled. And if you want a real life example, read Matzke, noting that he may not even have had to try as hard as he did.

For example, if a cell somehow got a new gene to produce a dynein protein, on what basis would that protein help lead to a nascent cilium? Most proteins are significantly more complex than the intermediate operation instructions in Avida, and many additional proteins are needed, as well as a whole suite of integration and regulatory structures, in order to integrate the new protein into a working molecular machine. But in the Avida world, things are much simpler – conveniently so. Once an organism stumbles upon an intermediate operation, the integration takes place without any of the complexity or uncertainty extant in biotic reality.

Well, if you want to discuss real biology, let’s discuss Matzke’s paper. He’s around, so I’ll hand over to him. But right now we are discussing Lenski’s AVIDA paper and whether it refutes Behe’s principle, and it does. Now let’s see what the implications are for real-world biological systems.

Rewards Along the Way I mentioned that “A large part of evolutionary critics’ argument from irreducible complexity is that there is unlikely to be a functional advantage for intermediate steps.” You have pointed out that: “. . . if you follow their case study, you will read, explicitly, that a great many non-functional intermediate steps were taken along the path, including some very deleterious ones. So not only is it not true that “the Avida authors simply assume it away” but the[y] deliberately make sure that the pathways to the rewarded functions require unrewarded steps.” Further: “The authors did not set out to demonstrate [a sequence of advantageous mutations that lead to a function], which would indeed have been circular – to set up a functional feature that could be easily reached via a series of advantageous steps (like Weasel, in fact) and then claim that it proved that all functional feature could be reached by a series of advantageous steps (which Dawkins did not, of course, claim about Weasel). They set out to demonstrate that even if a functional feature could only be reached via necessary neutral and disadvantageous steps, it could still evolve.” This is an interesting point and one worth exploring. I acknowledge that my choice of wording in referencing a “beneficial continuum” was poor. Yes, there were neutral and unrewarded steps along the way to EQU. So I should not have used the word “continuum,” as that might give the impression of an unbroken chain of always positive mutations, which, as you note, would be logically problematic.

Cool. Thanks.

However, regardless of whether the chain occasionally broke (to maintain the metaphor) or the organisms were able to get back on track after veering off the trail (to mix metaphors), there was, nevertheless, a cumulative pathway, which was rewarded at regular intervals. Indeed, the authors note that: “. . . 50 populations evolved in an environment where only EQU was rewarded, and no simpler function yielded energy. We expected that EQU would evolve much less often because selection would not preserve the simpler functions that provide foundations to build more complex features.” How much less often? “Indeed, none of these populations evolved EQU . . .” despite the fact that “these populations tested more genotypes, on average, than did those in the reward-all environment . . .” I don’t dispute, and I am confident Behe does not dispute, that if relatively simple mutations in a pre-existing organism can generate a meaningful survival advantage at key intervals along the path to a later function, that such might be within the reach of Darwinian mechanisms (depending upon population size, frequency of mutations, etc.). Behe’s point is that if intermediate steps do not confer a meaningful survival advantage, then such systems are not likely to evolve via Darwinian processes. That is precisely what these last 50 populations demonstrated.

I’m sorry Eric, but this is not correct. Behe most certainly does claim that non-beneficial necessary intermediate steps will prevent Darwinian processes from finding the function. As I said, at one point he did start talking about “degrees of IC”, but he seems to have gone back on that. And in any case, the EQU function was reached via many many degrees of IC, including quite severely deleterious steps. Behe certainly did not say: as long as there are some intermediate steps, Darwinian evolution can reach a function, but can’t if there are none. We know it can’t if there are none, and nowhere that I know of has Behe claimed that for any specific function there are no intermediate beneficial steps, as well as many necessary non-beneficial steps. Perhaps you are missing out on the word “necessary”. It’s important. Weasel evolves easily, because while any given “organism” may undergo many neutral mutations before hitting a winner, none of them are necessary in order to reach the winner. On the contrary, with EQU, neutral and deleterious steps were actually necessary - had to accumulate – before EQU could be reached. This is precisely the kind of pathway Behe said was impossible for Darwinian processes to traverse, and AVIDA shows emphatically that he was incorrect.

Again, the question is not so much whether every single possible step is handsomely rewarded (as in Weasel), or whether there are occasional neutral mutations or even side-steps and/or restarts (as in Avida). Rather, the question is whether there is a rich enough reward path from A to Z. The Avida paper demonstrates that without such a path, even a relatively basic “complex” function, like EQU, is not likely to evolve. In contrast, with enough rewards along the way, a cumulative pathway becomes possible. And that is precisely the question, isn’t it? In the real world of complex, functionally-specified, information-rich, integrated biological systems, does such an intermediate reward system actually exist? Avida, whatever its other merits, unfortunately cannot answer that question.

Well, no, this is goal-post moving. Behe asked no such question. Yet again I must repeat: no-one disputes that Darwinian algorithms can traverse a maximally rugged landscape. This, incidentally, is why people have greeted Joseph’s claim to use GA’s in encryption problems with such scepticism. Encrypted codes are deliberately placed in maximally rugged landscapes precisely so that GA’s won’t find them any more easily that time-consuming random search. That’s why safes are hard to crack. Remember that to get to EQU, the virtual organisms not only had to evolve some of the other functions, but they also had to accrue necessary variations that conferred no function, and some that conferred a fitness decrement. Yet they got there.

Conclusion Avida is an interesting program that may have some utility in thinking through processes of mutation and selection. But it is clearly not (and I don’t believe the programmers have represented that it is) a faithful reproduction of any specific system in the real world, and its applicability to the real world is therefore suspect.

Agreed.

In any event, whatever the authors’ or anyone else’s pretentions, Avida certainly has not refuted Behe’s contention that some sophisticated biological systems – requiring as they do, a suite of complex parts, coordinated construction, and precise integration – lie beyond the reach of Darwinian mechanisms.

Not agreed! AVIDA has refuted Behe’s entire concept that Irreducibly Complex features (which he defines with admirable clarity) cannot evolve by Darwinian means (or are vanishingly unlikely to). Whether it remains true that some real-life biological functions are unevolvable is irrelevant. The answer obviously, in principle, is yes, because we know some hypothetical features are unevolvable by Darwinian means. But Behe claimed that we could detect them by noting whether they were IC (would function if any part were removed). He was wrong. AVIDA falsified this claim. That means that any ID claim based on the observation that a feature is IC is not justified. You have to do more than show that the feature is IC. You have to show that it is on a peak in so rugged a landscape that it is unreachable by Darwinian means. No method that I know of exists to demonstrate this. Anyway, thank you again for your generously lengthy response to my critique, and nice to talk to you :) Cheers Lizzie Elizabeth Liddle

Elizabeth, Your post 23.2.2.2.12 is a wonderful example of reductionism. Scientism in action. "I don’t think the world has a purpose". I did not expect any other answer. Thanks anyway. You can already predict my answer, I believe. No I don't think you evaded. Though I can see a deficiency of goal setting without God, but I think, yes, people are capable of setting goals for themselves. But I agree with Chris, because these goals (without God) are too shallow for humans. Eugene S

Quote 1: There is no “materialistic ideology” in science. Quote 2: Actually science is a pretty good philosophical foundation for life. To me, Quote 2 is a refutation of the statement in Quote 1. If science is understood as Quote 2, it ceases to be such and becomes an ideology. Science per se can never serve a philosophical foundation for one’s life. The role of science per se is different, quite technical and limited. And indication of this is believers and atheists doing science. Therefore science (the scientific method) alone cannot be a philosophical foundation of anyone’s life. E=mc^2 is neutral to the basic philosophical questions of purpose.

No, Quote 2 is not a refutation of Quote 1,but I could have expressed them it more clearly. I should have said that scientific principles are a pretty good philosophical foundation for life. For the reasons I gave. That does not contradict Quote 1. Scientific principles are not an ideology.

Could I ask you, Elizabeth, why do you love your close ones? What causes you to love them? Electric signals in your brain and chemistry in your body? Or maybe something else more profound that lies deeper than science can ever get to and beyond any scientific definition?

The reason I, Elizabeth, love my close ones is that the are gorgeous :) But if what you are asking is what the mechanisms are by which the biological organism we denote "Elizabeth" loves her close ones, and how she came to exist in the first place, then we might well start talking about electrical signals, and neurons, and hormones, and evolution, and chemistry, and brain networks etc. But that would be a very different question, asked from a very different stance. The intentional agent I denote by the word "I" and "me", and you denote by the word "Elizabeth" loves her loved ones because she thinks they are gorgeous. Even though they probably aren't.

What is in your opinion the purpose of the existence of the world and, there is any in your view, how does it follow from the scientific method? What is the purpose of your life or mine? Can there be an answer to this out of the scientific method? Or are we asking too much of a screw driver?

In my opinion the question "what is the purpose of the existence of the world?" is a koan. I don't think the world has a purpose, because I don't think the world, as a system, is system capable of forming a purpose. I think the ability to form a purpose is a property of things with brains, and the world isn't a brain, although it contains brains. Nor do I think that the world was created with a purpose, because that would imply a creator capable of forming a purpose, and, as a said, I think that is a property of things with brains, in other words, a property of material entities, and clearly a material entity can't be the creator of all material entities. So no, I don't think the world has a purpose, nor do I think the world was created by something for a purpose, because I don't think either the world, or its creator, whatever that was, if anything, is capable of forming a purpose. And yes, I derive that conclusion by application of the scientific method, specifically in neuroscience, which is my field, and to what are called "executive functions" - why and how we form goals, aka purposes, and manage to pursue them. However, I think people are capable of forming a purpose, and have a great many. That is always my answer to Chris Doyle, who seems to think that without God there is no purpose to life. I'm sure you will think I have evaded your question, and in a sense I have. But I have done so because from where I'm standing, the question doesn't actually make sense. My concept of a "purpose" is a goal, set by something with a brain, that governs decision-making and action. Of an entity without that goal-setting apparatus, asking about a purpose, to me, is like asking what sound is made by a one-handed clap :) Elizabeth Liddle

KF

Creationism is faith-based; Intelligent Design is empirically-based.

But you can't actually tell me any specific empirical evidence that tells me a single thing about the designer, how the design was implemented, when it was implemented or anything at all. You can't even tell me if you think the designer intervened once, many times, trillions of times or not at all.... kellyhomes

KF,

And for inference to a definitively non materialistic cause, I suggest you examine — say, starting here and footnoted linked discussions from there — the evidence pointing even through the multiverse speculations to the intelligent design of a fine tuned observed cosmos set to an operating point that facilitates C-chemistry cell based life. (In short the material universe is credibly contingent and so is not its own causal explanation. It points beyond itself to an ontologically necessary being as root cause. And such a being has no beginning and is causeless.)

So, let me get this straight. Both the above and this:

I am on repeated record that the design inference is incapable of identifying the nature of the designer of life as within or beyond the cosmos,

Can be true in your mind at the same time? So on the one hand we have a cosmos (Universe) that is fine tuned for carbon based life by an "ontologically necessary being" and on the other hand you *don't know* who or what the designer is? So, life is designed, the cosmos is designed and tuned for life but you are on the record as saying that the design inference cannot identify the designer? Can you hear a crowing in the distance? How many times have you heard it? Once? Twice? Thrice? Presumably a designer cannot be inside the thing it designed and if the cosmos was designed the designer must stand outside the cosmos. And that is what I believe you mean by "God". Yet you insist the "designer" cannot be identified. If ID does not want to be called creationism then it's people like you that cause it to be so called. After all, you are also on the record that measurements of the age of the earth are totally unreliable (were you there?) which is standard creationist fare. Creationist! kellyhomes

KF, If ID is not creationism in a tuxedo then can you tell me what makes ID different from creationism, apart from the fact that in creationism the designer == god and in ID the designer == ? Other then that, what's the difference? kellyhomes

KF,

Recall, my remarks about Venter and nanotech labs, in a current thread where you have been corrected?)

Let me as you a question. In your entire adult life have you ever you yourself been "corrected"? E.G have you taken one position then revised it in the face of new evidence? For example? kellyhomes

KF, What utter rot.

The contrast to such is INTELLIGENT cause [i/e. art].

So to you the opposite of "material" is "intelligence"? No, in fact it's not.

The process you used to post just now would be an example.

Really? So life was designed by somebody sitting at a computer typing in a forum? It was, in fact, not. Sure, we can say that intelligence was involved in the evolution of life. The intelligence of evolution. It has the ability to remember what worked, try new things, discard failures and so on. By any reasonable definition evolution is intelligent. The challenge for you is to show that life has intelligent input other then evolution. So, KF, if life was designed by INTELLIGENT case then please explain why so many women die in childbirth. Does not seen very intelligent to me. Or was that because of the fall?

I am on repeated record that the design inference is incapable of identifying the nature of the designer of life as within or beyond the cosmos,

So why the insistence on allowing a divine foot in the door?

Indeed, sadly, in some cases, we are looking at ideologically motivated willful and continued misrepresentations in the teeth of duties of care to fairness and accuracy.

I could not have said it better myself. That describes you *exactly*.

You are taking talking points of objectors who habitually misrepresent as though they were well established fact.

Again, that's you. You make claims regarding "islands of functionality" despite not having *any* idea what-so-ever of the structure of the relevant landscapes. You simple do a toy trivial calculation of all possible combination's, pick one and say "see, that would be vastly improbable to pick from that vast range of possibility" and think you've proven your case. I'll say to you what I said to PaV. Publish your claims where they can be examined by experts and then we'll see who is habitually misrepresenting their unproven claims as though they were well established fact. KF, give me a *single* example of something we see in life that is better explained by Intelligent Design then by Darwinism. A *single* thing. Bet ya can't! kellyhomes

You have publicly claimed that I have deeply misunderstood Lewontin and the elites who generally agree with him. That is a very serious thing to say and in my view — with reasons given in summary above, it is in gross error. Kindly substantiate that claim, if you can.

I have substantiated as well as I can, kf. It is, of course, my opinion only, and you are welcome to disagree. I do not think that Lewontin, or anyone else, is advocating censorship in science. I think the point is methodological That's why I asked you to give me an example of how you would test a non-materialist hypothesis experimentally. Simply repeating that equation, which tells us no more than that if an event is extremely unlikely it is extremely unlikely, does not tell me how to test a non-material hypothesis. I also tried to explain, as clearly as I could, why science has to be predicated on the assumption that nature is regular, otherwise hypothesis testing, as far as I can see, becomes impossible. Elizabeth Liddle

Quote 1: There is no “materialistic ideology” in science. Quote 2: Actually science is a pretty good philosophical foundation for life. To me, Quote 2 is a refutation of the statement in Quote 1. If science is understood as Quote 2, it ceases to be such and becomes an ideology. Science per se can never serve a philosophical foundation for one's life. The role of science per se is different, quite technical and limited. And indication of this is believers and atheists doing science. Therefore science (the scientific method) alone cannot be a philosophical foundation of anyone's life. E=mc^2 is neutral to the basic philosophical questions of purpose. Could I ask you, Elizabeth, why do you love your close ones? What causes you to love them? Electric signals in your brain and chemistry in your body? Or maybe something else more profound that lies deeper than science can ever get to and beyond any scientific definition? What is in your opinion the purpose of the existence of the world and, there is any in your view, how does it follow from the scientific method? What is the purpose of your life or mine? Can there be an answer to this out of the scientific method? Or are we asking too much of a screw driver? Eugene S

Dr Liddle You have publicly claimed that I have deeply misunderstood Lewontin and the elites who generally agree with him. That is a very serious thing to say and in my view -- with reasons given in summary above, it is in gross error. Kindly substantiate that claim, if you can. Or else, kindly EXPLICITLY retract it. And, a non materialistic cause can be easily tested, just stop imposing materialistic a prioris on science. Then, you can see clearly to test for natural causes tracing to chance and/or necessity, or to intelligent causes acting through ART and leaving empirical signs that can be evaluated for reliability. As we have highlighted and explained to you over and over for months now. Start with the equation: Chi_500 - I*S - 500, bits beyond the solar system threshold. And for inference to a definitively non materialistic cause, I suggest you examine -- say, starting here and footnoted linked discussions from there -- the evidence pointing even through the multiverse speculations to the intelligent design of a fine tuned observed cosmos set to an operating point that facilitates C-chemistry cell based life. (In short the material universe is credibly contingent and so is not its own causal explanation. It points beyond itself to an ontologically necessary being as root cause. And such a being has no beginning and is causeless.) I beg to remind you -- again -- that ever since Thaxton et al in TMLO, 1984, design thinkers have consistently held that the design of life does not by itself imply a designer necessarily within or beyond the cosmos. Observe my repeated notes on how a lab a few generations beyond Venter's could do it. Venter has given proof of concept of the possibility for the design of cell based life. GEM of TKI kairosfocus

KH: You are resorting to some very outrageous strawman tactics. Before taking you on, I ask you to re-read yourself, and then correct yourself. And BTW, on the design of life, I am on repeated record that the design inference is incapable of identifying the nature of the designer of life as within or beyond the cosmos, which is exactly what has been publicly on the table ever since the first technical design theory work, TMLO in 1984. (Recall, my remarks about Venter and nanotech labs, in a current thread where you have been corrected?) Whatever Ms Forrest or Ms Scott et al may say to the contrary, ID is not Creationism in a cheap tuxedo. the design inference is about natural causes tracing to chance and or necessity and intelligent causes acting by art, and leaving empirically detectable traces. Since you seem to have conceived a patent personal animosity and contempt to me or what I say, I direct you to the NWE article on ID, which is far better than the notorious hatchet job at Wikipedia. Please read it. Please also read the Weak Argument Correctives, in the Resources tab top of this and every UD page. You are taking talking points of objectors who habitually misrepresent as though they were well established fact. They are not. Indeed, sadly, in some cases, we are looking at ideologically motivated willful and continued misrepresentations in the teeth of duties of care to fairness and accuracy. GEM of TKI kairosfocus

"I’d argue that it allows us to know God better, not worse." To know God, the only thing that is necessary is a pure heart, nothing else. Eugene S

kf: there is no "a priori materialist censorship on science", whatever Lewontin is saying. I don't think he's saying that, but if he is, he's wrong. What there is is a method that by its very nature precludes non-material explanations. To try to break the logjam, kf, let me ask you something: How would you devise a scientific experiment to test a non-materialist hypothesis? Elizabeth Liddle

Try here for starters. kairosfocus

And, BTW, please read the weak argument correctives before resorting to the creationists in a cheap tuxedo caricature. kairosfocus

Material causes as used on our side denotes chance and/or necessity [i.e. nature]. The contrast to such is INTELLIGENT cause [i/e. art]. The process you used to post just now would be an example. And, a tested, reliable sign of such is FSCI, such as in your post. Please do not try to force-fit design thinkers into the STRAWMAN templates set up by the more agenda driven objectors. kairosfocus

KF, Just for clarity, can you please describe one of these "non-material causes" and how it can be investigated, given that we can only investigate material causes as we are material beings in a material world and I am a material girl (HT Madonna). If you think otherwise, that non-material causes can be investigated by science, please describe to me how I'd go about investigating such a non-material cause. I can't think how I would, but you seem so desperate to get that divine foot in the door you *must* have some idea of what you'd do once it was there! Don't you? Don't tell me it's all been a bluff all along! The "non-material causes bluff" I think I'll call it. Railing against science and it's exclusion of non-material causes but then unable to actually articulate what it is that such an investigation into said non-material causes would consist of when asked. kellyhomes

KF,

This extends to trying to redefine science and to revisionise its history propagandistically.

Which is exactly what you are trying to do yourself! So if you want to redefine science to allow the divine foot in the door you are free to do so. All you have to do is give *a single example* of that explaining something that materialistic science cannot. Then scientists around the world, seeing the fruitfulness of your methodology will copy you and you'll get the worldwide revolution that you want. I don't know if you've noticed but scientists like things that generate results. So generate some results already! It seems to me that when I ask "well, how does ID explain the origin of bodyplans" you say "It was designed, all the signs point to it". So if you allow that divine foot in the door you can then add the detail "It was designed by god". Not much difference really. So, tell me KF, what advantage does allowing the divine foot in the door bring? Give me a *single* example of that advancing the cause of human knowledge? Just a *single* example. Go on, dare you. And if you say that Newton was a creationist and he created the laws of motion because of that then I'll ask you where in his equations he allows a divine foot in the door! kellyhomes

KF,

we are forced by our a priori adherence to material causes

Ok, let's allow that divine foot in the door. Now what? Where, specifically, do we say "ah, that was God" then? Is the reason why you are so reluctant, going off into multiple diversions, to talk about the actual "design" in "Intelligent design" and how it was done? As you really think it was god but know that saying such makes a mockery of the idea that the designer is not the Christian God? Why do you want to allow the divine foot in the door KF? What advantage does it bring? What can it explain that materialistic science cannot?

while in fact Wernher von Braun, the man who sent the Apollo rocket to the Moon was a Christian and a Creationist.

Perhaps you could show me where in the work of sending Apollo to the moon divine causes were referenced? If you can't what possible relevance does his beliefs have? Sure, if the rocket went wrong they might have cracked open the manual and read "pray" but other then that, what? So, and I don't expect a short answer to this nor an answer actually relevant to the question asked but here goes anyway: What changes once "materalist science" allows "a divine foot in the door"? What will we investigate and say "oh, we can't invesitgate that any more as that's divine"? What specifically do you have in mind? And what relevance does all this (it's one of your favorite subjects judging by the number of times you've re-used that quotemine) have to ID anyway? If the "designer" is simply responsible for the "design" you see in life that does not make it god. So what does it matter to you if science disallows divine causes as ID does not claim that the design of life was a divine event in any case. So what gives KF? Is the designer not study-able because of sciences refusal to allow the divine into science? If so then you've obviously already decided the "designer" is in fact god. When it could well be aliens, remember? Pathetic. kellyhomes

Ah boy: I missed the correct "Reply" point and so my response to Dr Liddle's claim that I do not correctly understand Lewontin is out of place, here. Pardon. kairosfocus

Dr Liddle: Please, just READ what is being said. Do you have any phil background, if not just take in here as a background primer. Now, please look at the -- frankly, sophomoric (this generation of scientists is nowhere near as sophisticated that way as the generation of Bohr and Einstein) -- worldview and epistemological-logical assertions and inferences that cannot stand serious scrutiny, noting that this is a report by a member of the elites, on the views of the elites (one backed up here on by no less than three other cites, including by the US NAS and the US NSTA, the American Scientific Academy and the national science teachers body: ______________ >> . . . to put a correct view of the universe [1 --> a claim to holding truth, not just an empirically reliable, provisional account] into people's heads we must first get an incorrect view out [2 --> an open ideological agenda] . . . the problem is to get them to reject irrational and supernatural explanations of the world, the demons that exist only in their imaginations [3 --> a declaration of cultural war], and to accept a social and intellectual apparatus, Science, as the only begetter of truth [ 4 --> this is a knowledge claim about knowledge and its possible sources, i.e. it is a claim in philosophy not science; it is thus self-refuting]. . . . To Sagan, as to all but a few other scientists, it is self-evident [5 --> a self evident claim is that this is true, must be true and its denial is patently absurd. But actually, science and its knowledge claims are plainly not immediately and necessarily true on pain of absurdity, to one who understands them; this is another logical error, begging the question, confused for real self-evidence] that the practices of science provide the surest method of putting us in contact with physical reality [6 --> Science gives reality, reality is naturalistic and material], and that, in contrast, the demon-haunted world rests on a set of beliefs and behaviors that fail every reasonable test [7 --> i.e. an assertion that tellingly reveals a hostile mindset, not a warranted claim: if you reject naturalistic, materialistic evolutionism, you are ignorant, stupid, insane or wicked, by direct implication] . . . . It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world [8 --> redefines science as a material explanation of the observed world], but, on the contrary, that we are forced by our a priori adherence to material causes [9 --> another major begging of the question . . . by imposition of a priori materialism as a worldview that hen goes on to control science as its handmaiden and propaganda arm that claims to be the true prophet of reality, the only begetter of truth] to create an apparatus of investigation and a set of concepts that produce material explanations, no matter how counter-intuitive, no matter how mystifying to the uninitiated. [10 --> In short, even if the result is patently absurd on its face, it is locked in, as materialistic "science" is now our criterion of truth!] Moreover, that materialism is absolute [11 --> i.e. here we see the fallacious, indoctrinated, ideological, closed mind . . . ], for we cannot allow a Divine Foot in the door. [12 --> Hostility to the divine is embedded, from the outset, as per the dismissal of the "supernatural"] The eminent Kant scholar Lewis Beck used to say that anyone who could believe in God could believe in anything. [13 --> a slightly more sophisticated form of Dawkins' ignorant, stupid, insane or wicked, certainly, irrational. This is a declaration of war! Those who believe in God, never mind the record of history, never mind the contributions across the ages, are dismissed as utterly credulous and irrational, dangerous and chaotic] To appeal to an omnipotent deity is to allow that at any moment the regularities of nature may be ruptured, that miracles may happen. [14 --> Perhaps the second saddest thing is that some actually believe that these last three sentences that express hostility to God and then back it up with a loaded strawman caricature of theism and theists JUSTIFY what has gone on before. As a first correction, accurate history -- as opposed to the commonly promoted rationalist myth of the longstanding war of religion against science -- documents (cf. here for a start) that the Judaeo-Christian worldview nurtured and gave crucial impetus to the rise of modern science through its view that God as creator made and sustains an orderly world. Similarly, for miracles -- e.g. the resurrection of Jesus -- to stand out as signs pointing beyond the ordinary course of the world, there must first be such an ordinary course, one plainly amenable to scientific study. The saddest thing is that many are now so blinded and hostile that, having been corrected, they will STILL think that this justifies the above. But, nothing can excuse the imposition of a priori materialist censorship on science, which distorts its ability to seek the empirically warranted truth about our world.] [[From: “Billions and Billions of Demons,” NYRB, January 9, 1997.] >> ____________ Do you see my fourteen main points of concern in the clip? And if you go to the immediately linked, you will see a following note that raises much more, e.g Lewontin's caricature of the woman who thought the TV broadcasts form the moon were fake because she could not get Dallas on her set; while in fact Wernher von Braun, the man who sent the Apollo rocket to the Moon was a Christian and a Creationist. There is even more in the onward linked full article. Read the above, work your way throughte4 fourteen points, then come back to me and show me how I have misunderstood what Lewontin "really" meant. Kindly, do. For, I fear that I have only just begun to understand the full depth of what this notorious article reveals about a hostile agenda that can only be exposed and broken, not reasoned with. In particular, do please explain to me how I am to deal with those who are redefining truth question- beggingly in a way that shows that they do not even understand that a claim to be the provider of knowledge is inevitably a phil claim not a scientific one, the criteria of truth likewise, the nature of science, refuse to be corrected even by reductio ad absurdum, and are openly declaring that people like me are ignorant and/or stupid and/or insane and/or wicked, menaces to reason and to science and to society. If that is not a declaration of cultural war under the false flag of scientific progress, I do not know what more would have to be said to be that. Ten, please go back to the link and read down on Coyne, on the NAS and the NSTA. Then, please come back to me and explain to me how I have profoundly misunderstood what is being said. GEM of TKI kairosfocus

I would agree with you if I did not know that the founding fathers of European science of modern age all believed in God.

You seem to have missed my point entirely, Eugene. Yes, they probably did. Many scientists today also believe in God. That does not mean they will let the Divine Foot in the door of science. If you do, it ceases to work. Science is all about abstracting regularities, not irregularities. By definition, the supernatural is an irregularity.

I think it is fair to say that the likes of Pascal or Newton or Kepler understood more about science than either you or I do.

Depends what you mean. In some senses they did. In some senses both you and I know more science than they did. A lot more.

It is their interpretations of what science can or cannot, should or should not do, I am ready to take as first-hand scientific knowledge, not a materialistic ideology in the cloak of science.

There is no "materialistic ideology" in science. There is a method. That method deals with the material, or, at least, the natural. It cannot deal with the supernatural. Newton made his biggest mistakes when he tried to write God into his orbital equations.

You seem to be saying things that are 95% correct (I do not mean your evolutionary stand, which is another matter), but this 5% is what makes it all miss the target. In my opinion, science without God is like a 2D black and white picture in comparison with a 3D full colour model. Science without God is incapable of delivering really deep insights. By itself, science is incomplete. If everything happens by fluke, then why bother finding out how?

Because "happens by fluke" is a complete misrepresentation of the scientific model! On the contrary, as Lewontin says, if we allow the Divine Foot in the door of science, anything can happen - predictability goes out of the window. Science, on the other hand, is all about predicting what will happen, not by "fluke" but the opposite - by natural law. I don't know where this weird idea came from that somehow scientists think that the world happens "by chance". It's a meaningless statement anyway, but it appears to be presented as the only alternative to: happens "on purpose". There is a vast excluded middle there! Yes, one thing we have discovered in the last century is that there is (or appears to be) a fundamentally stochastic element to the universe. Indeed, it is gpuccio's position that this stochastic "window" is the access point for divine influence. But the goal of the scientific model is to find out why things happen, which is not the same as asking "for what purpose" they happen, but nor is it the same as claiming that they happen "by fluke"! Quite the opposite.

All materialist motivations for science are aimed at building an “earthly heaven” without God.

This is a completely unsupported and unwarranted assertion, Eugene. I do not know of a single scientist whose motivation is "building an "earthly Heaven" without God". Sure, many scientists are motivated by the desire to make the world a better place - and so they should be. Others are motivated primarily by sheer curiosity. Nothing to do with "without God" whatsoever.

In the best case, the proposed motivation is to help people in their daily lives. That would be fine, if materialists did not want to make a religion out of science.

Who does? None of my acquaintance.

Science by itself has no more right to become a philosophical foundation for our life than a sledge hammer or a screw driver has.

Well, no. This is apples and oranges. Actually science is a pretty good philosophical foundation for life. Rational, evidence-based decisions uninfluenced by superstition or irrational behavioural precepts (stoning adulterers; covering women's faces; forcing celibacy on gays) seem pretty sound to me. But a scientific philosophical foundation does not preclude belief in God. I'd argue that it allows us to know God better, not worse. After all, if God made the universe, wouldn't understanding how it works increase our understanding of its Maker?

However, science was turned into an ideology. And this is exactly where Darwinism and Communism have a lot in common, in my opinion.

I find this assertion unsupported and unwarranted. Elizabeth Liddle

23.2.2.2.6 Elizabeth, I would agree with you if I did not know that the founding fathers of European science of modern age all believed in God. I think it is fair to say that the likes of Pascal or Newton or Kepler understood more about science than either you or I do. It is their interpretations of what science can or cannot, should or should not do, I am ready to take as first-hand scientific knowledge, not a materialistic ideology in the cloak of science. You seem to be saying things that are 95% correct (I do not mean your evolutionary stand, which is another matter), but this 5% is what makes it all miss the target. In my opinion, science without God is like a 2D black and white picture in comparison with a 3D full colour model. Science without God is incapable of delivering really deep insights. By itself, science is incomplete. If everything happens by fluke, then why bother finding out how? All materialist motivations for science are aimed at building an "earthly heaven" without God. In the best case, the proposed motivation is to help people in their daily lives. That would be fine, if materialists did not want to make a religion out of science. Science by itself has no more right to become a philosophical foundation for our life than a sledge hammer or a screw driver has. However, science was turned into an ideology. And this is exactly where Darwinism and Communism have a lot in common, in my opinion. Eugene S

Thanks for the background, kf, and perhaps I can now understand why that passage has made such an extraordinarily deep impression on you. But, as I have said several times, I don't think it means what you think it means. In fact I'm sure you are misinterpreting it. What Lewontin clearly means (and he says so explicitly) is that the entire scientific method is predicated on the assumption that the universe is predictable. That doesn't mean it is but that science can only proceed on that assumption. There is no indoctination here - because no doctrine. Science does not teach the doctrine that there is "no Divine Foot". What it teaches is that scientific methology must exclude that possiblity because otherwise the entire system collapses. To be specific: science proceeds via hypothesis testing, as I am sure you will agree. To test a hypothesis, you make a prediction. Then you collect appropriate data and see whether your prediction is confirmed. If it is, your hypothesis is supported. If it is not, you retain the null. If we "allow a Divine Foot in the door" we are unable to test our hypotheses, because all bets are off. Sure, we might get data that support our hypothesis, but how could we tell that it wasn't just the Divine playing Footsie with us? We couldn't. Ditto if our hypothesis is not supported. Does that mean we are off on the wrong tack? Who knows! Perhaps the Divine Foot kicked the data into touch whilst we weren't looking! That's why we keep the Divine Foot out. Not because we have to believe there is no God, but because the possiblity that God interferes with our data makes a nonsense of the entire project. And the project itself is extraordinarily successful. Perhaps, nonetheless, God does intervene from time to time, to add a flagellum to a bacteria, or raise someone from the dead, or make the sun wobble in the sky. But we are unable to take that into account in our scientific methodology. Elizabeth Liddle

PS: I know both relativity and gravitation. Darwinism is very different, and the sort of a prioris just mentioned are pervasive, usually implicit but sometimes explicit. This extends to trying to redefine science and to revisionise its history propagandistically. kairosfocus

Dr Liddle: I went to a marxism-dominated 3rd world university. I saw marxist indoctrination in action formally and as subtly pervading the general environment. What I have seen in the five or six years since I first took up discussing ID in online fora as a thought exercise [and then saw that it had something serious in it], is all too familiar, and it fits in with what ES saw. If you doubt the ideological framing, cf Lewontin et al. Try here on. Think about ideas like a priori, seeming self-evident, only beggetter of truth, and absolute commitment. All of this is ever so familiar to me. And to ES. We've both seen it before. GEM of TKI kairosfocus

Dr Liddle, please read the four clips here on, with particular reference to Lewontin's "all but a few" [recognising, he speaks of the reigning elites]. As one from the UK, you may not be aware of surveys of the NAS and of evolutionary biologists and the like vs the bulk of working grunts. Toss in the medically trained and the disjoint between the elites and ordinary scientifically trained people becomes even more clear; to the point where suspicions of glass ceilings etc are warranted, in light of some recent incidents of career busting even at STUDENT level. Joseph is correct about the reigning elites, their party-line, and their promoters. kairosfocus

Elizabeth, Thank you for taking time to review my short essay from several years ago and providing your feedback. We may be talking past each other a bit with terminology, so I will endeavor to do a better job on that front. Let me point out, however, why I think your defense of Avida as a refutation of irreducible complexity is misplaced and why the main points of my original critique stand. Programmed for Success I have argued that Avida was “programmed so that a slight, successive cumulative pathway” to the ultimate function existed. You have responded that all the changes were incremental (whether rewarded or not) “so there is no bias there.” The question is not one of bias toward functional states (which is a separate point I’ll discuss below). The question is whether a cumulative pathway exists. A large part of Behe’s point is that a cumulative pathway to a complex integrated system, such as a cilium, the bacterial flagellum, or the vertebrate eye, may not exist. Despite your protestations to the contrary, Avida does have a cumulative pathway built into the system, which may or may not reflect the real world. The word “programmed” does not necessarily mean that the virtual organisms were caused to go from x to y at a particular point in time with a specific command line (although that would be one way of programming). “Programming” can also mean setting up conditions within the virtual world (in other words, within the program), whether those conditions attain inevitably or stochastically, for the population to get there. Why you don’t acknowledge that this pathway is included in Avida is strange, as the authors themselves acknowledge it: “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.” If the word “programmed” is problematic, then we can think of “established parameters” or some other term you find more appropriate. The bottom line is that the cumulative pathway is there; it exists within the virtual Avida world. So the authors are clearly aware that the program contains a cumulative pathway to the complex feature that can be built on simpler useful functions. Why would they be concerned that some readers would believe the deck was stacked? Because whether or not such cumulative pathways to complex systems exist in the real world is precisely the point in question. What is the authors’ response? “However, that is precisely what evolutionary theory requires . . .” We know what evolutionary theory requires. That is not at issue. What is at issue is whether the conditions evolutionary theory requires in fact attain in the real world. Using the authors’ logic, I can prove anything. This is very significant. I can come up with any theory, based on whatever wild or illogical parameters I want, and then write a program that “proves” my theory. All I have to do is include the parameters that my “theory requires.” Again, on such logic, nothing is out of bounds; I can prove literally anything. Whether or not evolutionary theory (in the sense of the Darwinian mechanisms we are discussing) is true is precisely the point at issue. We cannot write a program that includes – as the authors acknowledge – the parameters that are needed for the theory to be true, and then turn around later and pretend that the program has demonstrated the truth of the theory. It is entirely circular. It may be true that there is a cumulative pathway to complex features in the real world, but Avida cannot demonstrate it. In fairness, let us pause at this point and consider the other side of the coin. As I said in my essay, “if a program were written that had no possible cumulative pathway, then the writers of that program could be fairly accused of assuming up front that the complex feature was irreducibly complex [note here that I am talking about IC in the sense of “per se irreducible complexity,” as mentioned in my paper]. Thus, evolutionary algorithms seem to be between a rock and a hard spot: assume a cumulative pathway and then you are unable to challenge irreducible complexity; assume there is no cumulative pathway and then you are unable to support irreducible complexity. And herein lies the crux of the matter. Evolutionary algorithms that assume a cumulative or non-cumulative pathway at the outset simply cannot, by definition, demonstrate whether the complex system is irreducibly complex. Such algorithms define themselves into irrelevance.” As a separate question, I posed to you the above hypothetical and asked whether such a program with no Darwinian pathway would invalidate the Darwinian hypothesis. You responded: “Well, no. All you would be able to conclude is that, given the parameters of your model, the thing is very unlikely to evolve. That conclusion is only as good as your model. The better (more realistic) your model, the more confident you might be that the thing in question really was unevolvable, but we can never rule out a missing parameter.” I am wholeheartedly in agreement that any “conclusion is only as good as your model.” What we need to refute Behe’s claim – the only thing that is adequate – is a faithful representation of what actually exists in the real world. And on that score, Avida leaves much to be desired. Steps and Stumbling I argue that “relatively few changes are required to get from the initial organism to the complex feature.” You responded that: “Yes, it’s a model, written to establish a principle, that IC functions can evolve. Pathways to EQU ranged from 51 to 721 steps, over many thousand generations, although in principle (if intelligently directed!) it could have been done in 16 mutations. That should be indication in itself that no direction was provided.” Well, Avida may establish a principle. Unfortunately, it is not at all clear that the principle has any relevance to biotic reality. In addition, you seem to think that the “stumbling” is evidence that no direction was provided. “. . . the fact that it took them from between 51 and 721 mutations on the path to EQU, even though 16 mutations would have done it, is pretty good evidence of their “stumbling”. The[y] were helped on the way by only 8 rewarded steps, which tended to occur earlier than EQU, not surprisingly, given that they were simpler. Remember that the vast majority of mutations were either neutral or deleterious. Not surprising that they stumbled a bit.” Rather than being a vindication of the Darwinian mechanism, the real lesson from all this stumbling is that even with an easy function and a relatively short pathway to get there, the Darwinian mechanism is quite poor. The skeptic might therefore be forgiven for asking whether the stumbling might not in fact overwhelm the available resources, when translated to the real world, with functions much more difficult to achieve and pathways that may or may not exist. Function and Integration Another key problem with treating Avida as a refutation of Behe’s concept of irreducible complexity is that the Avida functions are too easy to attain. Behe highlights complex, integrated biological systems, like the bacterial flagellum, the cilium, the vertebrate eye. Each of these systems requires numerous proteins acting in concert, and that is ignoring the construction process itself, which is an astounding coordinated orchestra of chemical processes. The Avida authors indicate that: “A single mutation distinguished the pivotal genotype from its parent in 19 populations, whereas four involved double mutations. The pivotal mutations included point mutations, insertions, a small duplication and even deletions.” Further, as you note, and as the authors describe: “The phylogenetic depth at which EQU first appeared ranged from 51 to 721 steps. In principle, 16 mutations, coupled with three instructions already present in the ancestor, could have produced an EQU-performing organism. The actual paths were much longer and highly variable, indicating the circuitousness and unpredictability of evolution leading to this complex feature.” Might the skeptic be permitted to ask whether this “complex feature” is even of the same order of magnitude as what we find in the real world? How many “point mutations, insertions, small duplications and deletions” would be required to produce the systems Behe points to, which contain anywhere from dozens to hundreds of proteins acting in concert? Even assuming relatively simple proteins, we are talking about a minimum of hundreds, and likely many thousands, of “point mutations, insertions, small duplications and deletions”. Yet the ultimate Avida function, EQU, can be built with 16 mutations. Avida thus ignores one of the key difficulties facing any Darwinian scenario: the difficulty of obtaining function. By making the process orders of magnitude easier than in the real world, Avida unfortunately fails to replicate one of the key questions dogging Darwinian theory: whether chance processes would be able to stumble upon intermediate functions (or constituent parts of larger machines) in the first place. Yet there remains an equally problematic issue: that of integration. Another key question is whether constituent parts, once they exist, can be successfully integrated into the whole. Avida completely assumes away this issue, effectively granting the organisms successful integration as soon as they come up with a successful operation. Think of it this way. Bacterium A somehow gets a new DNA sequence that codes for a functional protein (let’s assume, just so it is more believable to everyone, that this gene came from horizontal gene transfer from another bacterium, rather than arising through point mutations, replication errors or the like). Let’s further assume that the cellular machinery recognizes this gene as a legitimate gene (which is not as straight forward and certain as we have perhaps been inclined to believe in the past), translates the code and expresses the protein. Great, our cell has a new protein floating around. Now what? In the real world it is not at all clear that the protein would perform a useful function in Bacterium A. Even if the protein has the raw capability to perform a function, it is not at all clear that the protein would be recognized by other cellular machinery, properly transported to the necessary location, and successfully integrated into a cellular machine. We simply don’t know whether this would happen in particular cases. It might be just as likely that the protein would languish, be broken down, or even gum up an existing process. For example, if a cell somehow got a new gene to produce a dynein protein, on what basis would that protein help lead to a nascent cilium? Most proteins are significantly more complex than the intermediate operation instructions in Avida, and many additional proteins are needed, as well as a whole suite of integration and regulatory structures, in order to integrate the new protein into a working molecular machine. But in the Avida world, things are much simpler – conveniently so. Once an organism stumbles upon an intermediate operation, the integration takes place without any of the complexity or uncertainty extant in biotic reality. Rewards Along the Way I mentioned that “A large part of evolutionary critics’ argument from irreducible complexity is that there is unlikely to be a functional advantage for intermediate steps.” You have pointed out that: “. . . if you follow their case study, you will read, explicitly, that a great many non-functional intermediate steps were taken along the path, including some very deleterious ones. So not only is it not true that “the Avida authors simply assume it away” but the[y] deliberately make sure that the pathways to the rewarded functions require unrewarded steps.” Further: “The authors did not set out to demonstrate [a sequence of advantageous mutations that lead to a function], which would indeed have been circular – to set up a functional feature that could be easily reached via a series of advantageous steps (like Weasel, in fact) and then claim that it proved that all functional feature could be reached by a series of advantageous steps (which Dawkins did not, of course, claim about Weasel). They set out to demonstrate that even if a functional feature could only be reached via necessary neutral and disadvantageous steps, it could still evolve.” This is an interesting point and one worth exploring. I acknowledge that my choice of wording in referencing a “beneficial continuum” was poor. Yes, there were neutral and unrewarded steps along the way to EQU. So I should not have used the word “continuum,” as that might give the impression of an unbroken chain of always positive mutations, which, as you note, would be logically problematic. However, regardless of whether the chain occasionally broke (to maintain the metaphor) or the organisms were able to get back on track after veering off the trail (to mix metaphors), there was, nevertheless, a cumulative pathway, which was rewarded at regular intervals. Indeed, the authors note that: “. . . 50 populations evolved in an environment where only EQU was rewarded, and no simpler function yielded energy. We expected that EQU would evolve much less often because selection would not preserve the simpler functions that provide foundations to build more complex features.” How much less often? “Indeed, none of these populations evolved EQU . . .” despite the fact that “these populations tested more genotypes, on average, than did those in the reward-all environment . . .” I don’t dispute, and I am confident Behe does not dispute, that if relatively simple mutations in a pre-existing organism can generate a meaningful survival advantage at key intervals along the path to a later function, that such might be within the reach of Darwinian mechanisms (depending upon population size, frequency of mutations, etc.). Behe’s point is that if intermediate steps do not confer a meaningful survival advantage, then such systems are not likely to evolve via Darwinian processes. That is precisely what these last 50 populations demonstrated. Again, the question is not so much whether every single possible step is handsomely rewarded (as in Weasel), or whether there are occasional neutral mutations or even side-steps and/or restarts (as in Avida). Rather, the question is whether there is a rich enough reward path from A to Z. The Avida paper demonstrates that without such a path, even a relatively basic “complex” function, like EQU, is not likely to evolve. In contrast, with enough rewards along the way, a cumulative pathway becomes possible. And that is precisely the question, isn’t it? In the real world of complex, functionally-specified, information-rich, integrated biological systems, does such an intermediate reward system actually exist? Avida, whatever its other merits, unfortunately cannot answer that question. Conclusion Avida is an interesting program that may have some utility in thinking through processes of mutation and selection. But it is clearly not (and I don’t believe the programmers have represented that it is) a faithful reproduction of any specific system in the real world, and its applicability to the real world is therefore suspect. In any event, whatever the authors’ or anyone else’s pretentions, Avida certainly has not refuted Behe’s contention that some sophisticated biological systems – requiring as they do, a suite of complex parts, coordinated construction, and precise integration – lie beyond the reach of Darwinian mechanisms. Eric Anderson

There you go again, Joseph: "there isn't any evidence...." Yes, there is, lots. You just don't accept that it is evidence. Most people do. The reason they do is that the model fits the evidence. Elizabeth Liddle

Joseph: your posts are evidence to support that claim :) Eugene: Darwinism doesn't have an "ideological base". It is no more atheistic than the theory of relativity or the theory of gravity. If it was taught in the USSR as an ideology then it was mistaught. It is not an ideology. Elizabeth Liddle

Neither palaeontology nor genetics help you. Ya see there isn't any evidence from genetics that demonstrates the transformations required are even possible- no way to test it. The theory of evolution relies on our ignorance and vast eons of time. And there isn't any confirmatory evidence for Darwinism- all we observe says darwinian mechanisms break things. Joseph

Well, yes, there is, Joseph. There's all of palaeontology and genetics. And yes, you can test it without assuming it. And there is no reason to "assume" that any theory is true until you get at least some confirmatory evidence. And while I tend to assume Darwinism is probably true, given all the confirmatory evidence, my reasoning has nothing to do with whether I'm a "materialist" or otherwise. I've been persuaded by Darwinism all my life. I've only been a "materialist" for a couple of years. Elizabeth Liddle

There isn't any evidence that living things diversed fromn a very simple common ancestor and there isn't any way to test the claim without first assuming it. And the only reason to assume darwinism or neo-darwinism is if you are a materialist... Joseph

Elizabeth,

You are profoundly misunderstanding the methodology of evolutionary biology.

Maybe I am. Maybe I'm not. Does it matter, if an uneducated child can be trained to draw the same conclusions in five minutes? ScottAndrews

Darwinism is not "a materialistic way of thinking". It's simply a theory of how living things could have diversified from a very simple common ancestor, as the evidence suggests they did. Scientific theories can sit quite comfortably with most ideologies, as long as that ideology is not anti-science. Unfortunately, many are. And I recall that Stalin didn't think much of Darwinism, promoting Lysenkoism instead, with appalling consequences for Soviet agriculture. When ideology trumps science, disaster too often results. Elizabeth Liddle

Elizabeth, BTW I did not mention Marxism. Communism was taught as a materialistic way of thinking, of which Marxism and Darwinism were only parts. Darwinism sat there quite comfortably. Eugene S

I agree, Scott, which is why I would call both GAs and Evolution undirected. As I said, it's perfectly possible to program a GA with a randomly selected fitness function, so the fitness function itself need not be "designed". In practice, of course, we use them for evolving solutions to problems we actually want to solve. So we design the fitness function - the "environment" in which our population will evolve, so that critters that at least partially solve our problem breed better. But we needn't. Or, we could choose a problem that the environment itself naturally "sets". For example, you could set up a GA to evolve a solution to water resistance - an optimal shape, perhaps. Yes, we would have "directed" the evolution of an optimally efficient shape in water, but it would be no different from the "natural" "direction" set by an aquatic environment to an evolving penguin, say. The environment, whether natural or artificial, simply sets the parameters within which the evolving population adapts. If one is directed, so is the other. If one is undirected, so is the other. GA fitness functions and natural environments are exactly equivalent. Elizabeth Liddle

I was not saying they were the same. I said they were similar. I think so because they share the same ideological base, i.e. atheism. "Theistic evolution" is a pathetic attempt to serve two masters. Children in the USSR were indoctrinated into both from a very young age in all years at school. Eugene S

Well Elizabeth I find it strange taht all evos can do is say IDists don't understand the theory of evolution but NEVER produce anything to support that claim. Joseph

The theory of evolution is nothing like the teaching of Marxism. geez. One of the most interesting thing I've found here is just how little most ID proponents actually know about the theory of evolution. Yes, I know, the same goes for me about ID. But the fact that on each "side" we see ignorance about "our" theory from the "other side" speaks volumes about why we so vehemently disagree with each other. Elizabeth Liddle

Scott, That would be a nice thing to try! It's been a long time since Darwinism became a monopoly in science. I have no doubt all this nonsense will be over eventually. I was born in the USSR and I remember the times of Scientific Communism (it used to be taught at universities, with elements taught at schools). I remember studying Lenin's works at school. Luckily by the time I became a university student it had been thrown away. What amazes me is how terribly similar TOE is to it. "The teaching of Marx is omniponent because it is true", said Lenin. Any objection, and the next evening a black van would come after you. How similar is that to evolutionary story telling! You dare doubt in chance/necessity?! It needs no proof, it is self-evident, it is how science works! Little wonder, due to its atheistic roots Scientific Communism relied on Darwinism to claim its own legitimacy. Nonetheless they both are of equal zero scientific worth. Eugene S

Do I sense some desperation in the above posts, Eric and Joseph? It seems to me you are both trying to find a loophole. What Joyce did was huge. He demonstrated (as I said in my original comment) that Darwinian processes work spontaneously at the chemical level, given a set of designed molecules that could replicate to produce slightly varying copies of the original individuals, and that recombinant variants that replicated better came to dominate the population, to the extent that they hugely outnumbered the originals. The fact that it the original molecules were designed, that the cross-replicated rather than cloned themselves, that they needed to be supplied with special "food" in the form of matching molecules means that, as Joyce says, this is not the spontaneous evolution of life. But it is a powerful demonstration that given the Darwinian essentials, even with nothing more than (fairly) simple chemistry, a population of replicators evolves into a population of better-replicators. Elizabeth Liddle

According to ID organisms DO decide- and also according to Dr Spetner. What selection criteria? Natural selection is non-exietent in populations over 1000. SIPS? SIPS do not represent biological reality. EQU does not represent reality as no organism is so reqarded by surviving. But anyway all GAs are directed towards the goal. Joseph

How could one possibly “over interpret” your words, when you make a blanket sweeping statement that “Darwin’s postulated mechanism works”?

You accused me of "spreading false information". Nothing I said was false. Darwin's postulated mechanism does indeed work as you concede below:

Sure, Darwin’s mechanism works if we are talking about simplistic, easily found, minor variations at the macroevolutionary level, like peppered moth populations and finch beaks (although we are learning that much of what goes on, even at that level, has little to do with Darwin’s variation + selection mechanism).

No, we are not "learning that much of what goes on, even at that level, has little to do with Darwin’s variation + selection mechanism" unless you are talking about the role of drift, but in the case of both peppered moth and finch beaks, there is a clearly observed environmental correlate. Moreover, it is the power of drift, previously underestimated, that allows IC features to evolve, as in AVIDA. So drift mechanisms are a major problem for ID icons - and hugely support evolutionary biological models.

Blind, undirected processes have not been demonstrated to do all that you claim, so it is simply false. For example, you linked to an article, which says in its opening paragraph “A new molecule that performs the essential function of life – self-replication – could shed light on the origin of all living things.” We’re calling BS on this, as it is not self-replication in any real-world sense of the word.

OK, I am happy to add the caveat that it was cross-replication, not self-replication. It makes no difference to the principle. Tell me, do you regard sexually reproducing species as self-replicators or cross-replicators?

Let’s set aside the materialistic cheerleading pom-poms for a moment and put on an engineer’s hat. What would actually be necessary for a self-replicating molecule? From an engineering perspective, what would be required for such a molecule (or system) to function by itself in the real world? What does the Joyce paper say? They have two enzymes that catalyze a single bond between pre-formed substrates. Sorry, but it doesn’t matter how easily impressed you are with this; it is not self-replication in any meaningful sense of the word. I stand by my assessment that you are spreading false information if you continue to assert that it is.

What would be necessary to result in self-replication? Well, the simplest system would be a double chain, with cross bonds. If the chain then splits, and re-bonds with new molecules to form new cross bonds, then you will end up with two copies of the original. But I am perfectly happy to concede that in a literal sense, the molecules did not "self-replicate". They did not clone. Nor do we. Cross-replication works just as well for evolution (actually, better). Elizabeth Liddle

You are profoundly misunderstanding the methodology of evolutionary biology. Elizabeth Liddle

Yikes, hit the wrong key and it posted before I could proofread. Obviously, I meant "micro"evolutionary in the second paragraph . . . Eric Anderson

How could one possibly "over interpret" your words, when you make a blanket sweeping statement that "Darwin's postulated mechanism works"? Sure, Darwin's mechanism works if we are talking about simplistic, easily found, minor variations at the macroevolutionary level, like peppered moth populations and finch beaks (although we are learning that much of what goes on, even at that level, has little to do with Darwin's variation + selection mechanism). Blind, undirected processes have not been demonstrated to do all that you claim, so it is simply false. For example, you linked to an article, which says in its opening paragraph "A new molecule that performs the essential function of life - self-replication - could shed light on the origin of all living things." We're calling BS on this, as it is not self-replication in any real-world sense of the word. Let's set aside the materialistic cheerleading pom-poms for a moment and put on an engineer's hat. What would actually be necessary for a self-replicating molecule? From an engineering perspective, what would be required for such a molecule (or system) to function by itself in the real world? What does the Joyce paper say? They have two enzymes that catalyze a single bond between pre-formed substrates. Sorry, but it doesn't matter how easily impressed you are with this; it is not self-replication in any meaningful sense of the word. I stand by my assessment that you are spreading false information if you continue to assert that it is. Eric Anderson

Petrushka,

If selection could cause populations to adapt, there would be a lot fewer extinctions.

Does anything cause populations to adapt? Or do they do it for no reason whatsoever. Take whatever that cause is, and you've just refuted it. If [insert here] could cause populations to adapt, there were would be a lot fewer extinctions. I couldn't do it without you. :)

ScottAndrews

Here's something you can do with your family for fun. If you're still convinced that it requires an iota of scientific education or method to make up natural selection stories then just try it yourself. Get the kids. Make some popcorn. Everyone pick an animal out of the book and imagine the reason why one of its features or behaviors was selected. Then, for extra credit, get your eight-year-old to tell some PhD genius what he just read in a book and see if he questions it. How many of you darwinists honestly think that half the biology professors out there would think twice or question a child who presented them with their own made-up natural selection narrative if the child said he read it in science book? Be honest. ScottAndrews

Ever since school they have heard hundreds of stories about how some environmental condition or predator or prey caused this animal or plant to evolve into its unique state. They think that maybe someone must know this somehow, or else they wouldn’t say it on the Discovery Channel.

If selection could cause populations to adapt, there would be a lot fewer extinctions. Petrushka

Elizabeth,

Natural selection doesn’t select- it is a result.

Everything that happens is a result of something. The current form of any population is the result of something. Is it always a result of natural selection? What other causes are there? If I asked you why leopards have spots, would you agree that no one knows and that there is not even a provisional explanation? If there is a provisional explanation, what is it? That spots were selected, and anyone's guess why is good? Or is there a door number three? In any given case the reason is, "it was selected," because according to the circular logic, selection explains everything. Then you just have to guess or make up reasons why it was selected. The conclusion comes first, and then you just use your imagination to fill in the evidence. I point this out for the sake of however many people read this stuff but never post. Some of them don't believe the nonsense they hear and maybe they wonder if something is wrong with them. Maybe they are fools because they can't see the emperor's new clothes. Ever since school they have heard hundreds of stories about how some environmental condition or predator or prey caused this animal or plant to evolve into its unique state. They think that maybe someone must know this somehow, or else they wouldn't say it on the Discovery Channel. But in every single case, natural selection was the assumption, the starting point. The rest is literally made up. Why do anteaters have long tongues? Because it's too hard to get to the ants with short tongues. And that's it. They have long tongues because they needed them, so natural selection worked its magic. It sounds nice, but that's beside the point. As nice as it sounds, somebody just made it up. You can probably make up several in one minute. It's like a factory that can manufacture thousands of pseudoscientific explanations running only on imagination. ScottAndrews

"What exactly do you think was “fixed”, and where are you reading this?" From the quote at 14.2.1.1.3, the quote you used to locate the paper: "Lenski has estimated that only 10 to 20 beneficial mutations achieved fixation in each population." What evidence is there that 10 beneficial mutations achieving fixation in each population was more or less probable than 20. The range appears equiprobable, there is no tail. The Lenski paper does not say if it is flat or Gaussian, if he did it would not then be my hunch. The variables however, suggest flat. junkdnaforlife

Yes, Joseph, which is why I put it in scare quotes. I usually use the phrase "self-replication with heritable variance in reproductive success in the current environment" which amounts to the same thing. But as you seemed to be missing my point, I put it in what I thought might be slightly more familiar language. And no, the organism do not "decide". Nobody "decides" as you point out. But the selection criteria are determined by the environment, not by the organism, which is what it is, and bears whatever genome it inherited, with whatever novel variants resulted from its conception. With a GA, usually the designer has her own agenda, sure. But needn't. I've written GAs where the fitness criteria were randomly selected. The GAs still evolve so as to maximise their reproductive success within the randomly chosen environment. From the PoV of the virtual organisms, all that matters is survival. The virtual critters in AVIDA don't "care" about whether they can perform logic functions or not, all they "care" about is the SIPS they receive for doing so. Elizabeth Liddle

I am not "spreading false information" Eric. I simply said, in response to Joseph, that "blind, undirected processes" could do the things I claim, both in simulations and in actual chemistry. Please do not over-interpret my words and then accuse me of "spreading false information". Joyce did the equivalent, in many respects, in chemistry, that GA writers do with "virtual organisms". They designed a self-replication (or at least cross-replicating, the difference is neither here nor there) RNA molecule that replicated with variance (the variance arising from recombination, as is also often done in GAs) and the result was an increase in prevalence of those variants that happened to reproduce better in the environment provided, i.e. the evolution of a population better adapted to its environment. No, it isn't artificial life, and neither I nor Joyce have claimed that it is. GAs are not "artificial life" either. But both demonstrate that given a population of self-replicators (or cross-replicators) that replicate with variance, e.g. point mutations or recombination, the variants that happen to have some feature that enhances their reproductive chances in the current environment will become more prevalent. i.e. that Darwin's postulated mechanism works. Elizabeth Liddle

Elizabeth, stop spreading false information. The Joyce experiment *did not* demonstrate self-replication in any normal sense of the word. There was no copying of genetic information from free-standing nucleotides. The enzymes were created, the substrates were created, and then the enzymes simply catalyzed a bonding reaction between substrates. Joyce has done good work. Let's recognize it for what it is. But you lose all credibility when you make sweeping pronouncements about things that have been "demonstrated" about your beloved theory that have not in fact been demonstrated. Eric Anderson

Elizabeth,

either GAs and evolution are both “directed” by the environment, or neither are.

This is only true if we modify the work "direct" until it is meaningless. Whatever the outcome of a GA, that it should have some output and hopefully a useful one is at least intended. Its design and operation could be called "direction." In the sense that you apply it to evolution it becomes tautological. Birds fly because it fit the environment. The lizards they lived next to do don't fly but they change colors because it fits the environment. It is a meaningless post hoc explanation. It retroactively predicts everything. It makes the expression "was directed" equal to "happened." It's vacuous. I could say that my bowling ball was directed to fall on my toe by gravity. How do I know that it was so directed? Because it fell on my toe, silly. It's tautological. ScottAndrews

Elizabeth:

If the target is “a solution to the problem” then so is natural evolution “directed”, as “natural selection” “selects” variants that best “solve” the “problem” of survival presented by the environment.

Natural selection doesn't select- it is a result. But you are right, survival is all there is to solve. And again in real life behaviour is the best option for survival. waiting for the right mutation will get you nothing but dead. IOW the organisms decide, not the environment. Again you are confused over what really happens. With a GA there is a goal/ target that is trying to be achieved- something beyond mere survival. And that is how GAs are directed. Joseph

Elizabeth:

Well, do you call it “self-replication” when you have children? Or “cross replication”?

I call it sexual reproduction. And what Joyce did isn't that. And again nothing new- faster replication is not new, just something different. And obviously that wasn't good because they ran out of "food" sooner. And then nothing! Yeah that's just great. Joseph

If there is a target/ goal then it is directed.

If the target is "a solution to the problem" then so is natural evolution "directed", as "natural selection" "selects" variants that best "solve" the "problem" of survival presented by the environment. Just as in a GA. So, Joseph: either GAs and evolution are both "directed" by the environment, or neither are. But saying that one is "directed" and the other is "undirected" is trying to have your cake and eat it. In both cases, the environment is what "decides" which variants will reproduce best. However, in neither case is the variant that reproduces best a "target", and in both cases the variant that reproduces best is totally unknown in advance, therefore not "designed".

And just how does one write the code to do a blind search? Can you post a line or two of that code?

You copy "parent" virtual organisms to produce "offspring", randomly (using a random number generator) introducing changes into the virtual genome. You can also "mate" pairs of "parents", and randomly splice bits of their genome to produce novel genomes. Then you let the resulting enlarged population "compete" on your fitness function, and cull the worst performers. I could post some code, but not till the weekend as it's on my other computer.

You really should stop with your ignorant nonsense. There ARE solutions to HOW to encrypt- I didn’t write or use tehm to break encryption and I didn’t imply that I did.

OK, I confess to ignorance about how you use GAs in encryption. That's why I asked you. Perhaps you could explain how you use them. Elizabeth Liddle

Petrushka (18.1.2.1): You could not have read *Nature's Destiny* with care, or you would not say that Denton's view is "indistinguishable from mainstream biology." "Mainstream biology," if by that you mean mainstream evolutionary theory, has been neo-Darwinian (occasionally spiced up with other elements, but primarily neo-Darwinian) for about 75 years. Denton's book made a frontal assault on neo-Darwinian theory by insisting that evolution was teleological. You have not read my posts carefully. I did not say that Shapiro believed in intervention. Indeed, if you were paying attention, you would see that I have not been championing "intervention" at all, and have tried to show Elizabeth that ID does not require it. As for whether Shapiro departs from "mainstream biology," again, if by that you mean "mainstream evolutionary theory," i.e., neo-Darwinism, he does depart significantly from it. He regards evolution as a fact (as does Denton), but like Denton, he thinks the standard explanation for evolution is very inadequate, and proposes some alternative notions (though not identical with the alternative notions of Denton). Keep in mind the context. In all her comments here, Elizabeth is defending a very standard, mainstream, population-genetics-centered understanding of evolution, essentially the Modern Synthesis (or neo-Darwinism, as it is popularly called). Her theoretical explanation of evolution is not much different from what people like Mayr were writing 35 years ago. It is precisely that understanding which Shapiro and other leading new theorists are challenging. And it is no coincidence that religious unbelievers like Shapiro and some of the members of the Altenberg group (and in another direction, Margulis) have some of the same criticisms of neo-Darwinism that ID does. The problem is not (as Panda's Thumb and the NCSE would tell the story) that crazed creationists under the guise of ID are trying to overthrow all of biological science. The problem is that the old guard of evolutionary biology (Coyne, Lewontin, Dawkins, Eugenie Scott, etc.) are stubbornly resistant to major theoretical change, even when it comes from secular, humanist scientists like themselves. But there is nothing that can stop the change from coming, because the weaknesses of neo-Darwinism are too glaring. In retrospect, the ID people, at least regarding the negative half of their project (the critique of Darwinism), will 50 years from now be seen as being on the right side of scientific history. T. Timaeus

Well, do you call it "self-replication" when you have children? Or "cross replication"? I don't mind what you call it - the point is that your originals are replicated, with variance. And what was the increase in replication efficience if not "a new function"? I think I've found your quotation by the way:

Joyce says that only when a system is developed in the lab that has the capability of evolving novel functions on its own can it be properly called life. "We're knocking on that door," he says, "But of course we haven't achieved that."

http://www.sciencedaily.com/releases/2009/01/090109173205.htm my bold. Clearly the whole process was heavily assisted, with "food" provided in the form of specific mirror rna molecules. However, the evolution of better replicators was not "directed" - they occurred through non-designed recombination with the "wrong" "food" molecule, resulting in variants that then outcompeted the originals. As I said. Elizabeth Liddle

Well it sure as heck is NOT self-replication. And I will take Joyce's word that nothing evolved- no new function was achieved- and that only ONE bond was created. Joseph

“There is absolutely no reason to think that the distribution wasn’t Gaussian.” How exactly is it not flat?

I don't know "how" it was not flat, junkdnaforlife, because they didn't say what the distribution was. But there's no reason to think it was flat. Very few distributions are, as you agree below.

“The distribution is not, in fact given in the paper, and flat-topped distributions are extremely unusual.” Exactly. But a flat distribution is exactly what we find based on the fixed beneficial mutation rates of the 12 isolated populations. After 10^8 + mutations, according to Lenski, all possible mutations that could have mutated, mutated, and all 12 populations had their fixed beneficial # fall exactly within 10-20. You are right: that is extremely unusual. And flat. Where are the tail/s?

No, it is not "flat", or at least we are not told that it is. You just agreed that the distribution was not given, only the range. For all we know, 10 and 20 are tails of a Gaussian.

“And, again entirely consistent with the ToE, the rate of increase in fitness tended to decline.” I’m concerned specifically with the fixed beneficial/neutral mutation distribution rates of isolated Avida colonies after 10…50+ generations vs. Lenski

What do you mean by "fixed beneficial/neutral mutation distribution rates"? What exactly do you think was "fixed", and where are you reading this?

But I wonder, however, if the Avida program incorporated the diminishing return evidenced by Lenski?

Well, yes, by definition, because, being a model, once a virtual organism could perform all nine (?) functions, there were no further dimensions along which to gain fitness. And once an organism could perform EQU, any other functions still to be accomplished produced smaller returns. EQU produced the biggest jump in fitness.

“It does not say what you think it says, and even if it did, it would not mean what you seem to think it would mean!” I wager it does in fact “say what I think it says”. However, “what it means” is another issue entirely.

I cannot find anywhere in the paper that says that the distribution of beneficial mutations was "flat". Can you find the page number where you think it does so? Elizabeth Liddle

"There is absolutely no reason to think that the distribution wasn’t Gaussian." How exactly is it not flat? "The distribution is not, in fact given in the paper, and flat-topped distributions are extremely unusual." Exactly. But a flat distribution is exactly what we find based on the fixed beneficial mutation rates of the 12 isolated populations. After 10^8 + mutations, according to Lenski, all possible mutations that could have mutated, mutated, and all 12 populations had their fixed beneficial # fall exactly within 10-20. You are right: that is extremely unusual. And flat. Where are the tail/s? "And, again entirely consistent with the ToE, the rate of increase in fitness tended to decline." I'm concerned specifically with the fixed beneficial/neutral mutation distribution rates of isolated Avida colonies after 10...50+ generations vs. Lenski. But I wonder, however, if the Avida program incorporated the diminishing return evidenced by Lenski? "It does not say what you think it says, and even if it did, it would not mean what you seem to think it would mean!" I wager it does in fact "say what I think it says". However, "what it means" is another issue entirely. junkdnaforlife

Well, it's called "cross-replication". A bit like sexual reproduction. The result is the same - lots of slightly variant copies of the originals. And some variants reproduce better than either, and come to dominate the population. i.e. the population evolves. Elizabeth Liddle

Elizabeth, They took TWO DESIGNED RNA strands, added other designed strands and then those first two started using the others tio make more- it was always TWO and there was NEVER and SELF-replication. Joseph

Thanks for the link to the actual paper. From the abstract:

Populations of various cross-replicating enzymes were constructed and allowed to compete for a common pool of substrates, during which recombinant replicators arose and grew to dominate the population

My bold. Elizabeth Liddle

Elizabeth:

If a person designs a program to evolve a solution to a problem by a blind and undirected process, then it does it by a blind and undirected process.

If there is a target/ goal then it is directed. And just how does one write the code to do a blind search? Can you post a line or two of that code?

I am intrigued that you use them to solve encryption problems, as encryption problems are the kind of problem not readily solvable by GAs – because there are no part-solutions.

You really should stop with your ignorant nonsense. There ARE solutions to HOW to encrypt- I didn't write or use tehm to break encryption and I didn't imply that I did. Joseph

Elizabeth, You are soooo confused. They did NOT self-replicate as it takes TWO strands to make ONE. One strand was the template and one was the catalyst that made ONE and ONLY ONE bond. Ya see they cheated with the other parts too as RNA starnds were used, not individual nucleotides. And they did not evolve any new functions as the new RNA did the same thing as the original. Self-Sustained Replication of an RNA Enzyme I can also pull a quote from Joyce as he was interviewed by SciAm and I am sure I have the copy, I just need to find it. He said nothing new evolved... Joseph

If a person designs a program to evolve a solution to a problem by a blind and undirected process, then it does it by a blind and undirected process. And that is what GAs do. Joseph, I asked you about your own GAs. I am intrigued that you use them to solve encryption problems, as encryption problems are the kind of problem not readily solvable by GAs - because there are no part-solutions. So if you are solving encryption problems by what you call a GA, then you are probably have in mind something very different from an actual evolutionary algorithm. Elizabeth Liddle

Yes, they self-replicated, and yes they evolved new functions, as self-replicators will if they replicate with heritable variance in reproductive success. They evolved functions that enhanced their ability to self-replicate (in other words they evolved by natural selection), thus exhibiting sequence changes that were reflected in phenotypic advantages. Yes, the original self-replicating molecules were designed, but the form they eventually took, in which they self-replicated far more efficiently than the original designed molecules, was not designed. It evolved.

“There was a day that it all happened,” said Dr. Joyce, namely Oct. 1, 2007, when as he puts it, the replicators “went critical,” and their population began growing exponentially. The game, as he likes to say, was on. And it has never stopped. Dr. Joyce and his colleagues next proceeded to engineer a sort of March Madness for molecules. They synthesized 12 versions of the replicators, which could mutate and evolve to improve their ability to reproduce. The experimenters threw these into the pot, along with the appropriate “food” segments, to compete. “They just go at it,” Dr. Joyce explained. By the end, the winning molecules were doubling their numbers every 15 minutes. Mistaken swaps had produced combinations, mutations, that had not been in the mix at the start. Most of the original versions almost completely disappeared. In short, the molecule evolved. “Evolution is not a theory for us chemists,” Dr. Joyce said. “It’s what molecules do when they have the property to replicate and transmit information from parents to progeny.”

http://www.nytimes.com/2011/07/28/science/28life.html?_r=1&pagewanted=all Elizabeth Liddle

If a person designs a program to do something AND IT DOES IT, then there isn't anything blind and undirected about it. If you think there is then you need some serious help. As for the theory of evolution, well I would bet I have a better understanding of it than you. However it is a safe bet that you do not understand Intelligent Design. BTW no one knows what constrains evolution- and IF anything does it would be information. Joseph

Except they didn't evolve- no new functions- and they didn't even self-replicate. And no new complexity- nothing- you lose (yes a sequence change but no evolution, which requires something different besides just the sequence) Joseph

Thank you for your substantial response. I will try to get to it at the weekend :) Elizabeth Liddle

So if you follow the posts and comments of people such as that, along with the core readings suggested above, you and I should end up on the same page regarding what ID is.

You mention Michael Denton's "Nature's Destiny" which is a fine tuning argument. Denton's view is indistinguishable from mainstream biology. He states this explicitly. Shapiro, in his new book, does not depart from mainstream biology. He has an extreme position on evolvability, and he might personally think the game of evolution is rigged by fine tuning, but he invokes no hint of intervention. He explicitly denies that any such thing is necessary or indicated. Petrushka

Elizabeth: Thank you for your reply in 18.1. Regarding your first point, you have to distinguish between ID as a coherent theoretical position and a whole host of things which ID enthusiasts might say about ID. If you want to see ID as a coherent theoretical position, I would recommend that you focus mainly on the writings of Behe, on Dembski's No Free Lunch, on Dembski and Wells's Design of Life, on Denton's Nature's Destiny, and on some of the articles on the Discovery web site where a short, pithy definition of ID is articulated. Remember that on an open-for-comments website such as UD, you get comments from scores of people, some of who know the ID literature extremely well, and others who know it less well, and you get comments from scores of people whose interest is more in religious apologetics than in theories of design detection. So in some of the comments here you are bound to get a blurring between design theory proper and religious applications of design theory, just as on some other websites you will get a blurring between arguments for evolution and anti-religious polemics allegedly based on evolution. You have to take the time to sort out the core assertions of ID from the peripheral material. That said, there are many commenters here who understand the core assertions of ID very well, including Vincent Torley, Gil Dodgen, scordova, nullasalus, Cudworth, and StephenB, to name just a few. So if you follow the posts and comments of people such as that, along with the core readings suggested above, you and I should end up on the same page regarding what ID is. It is possible to assert ID without raising battle-cries against atheism and without launching into Christian apologetics. Those of us who have studied the history of philosophy and the history of science in some depth know that the modern debate between ID and Darwinian theory has ancient pre-Christian parallels. We have in the debates between the Epicureans, on one hand, and the Platonists, Aristotelians, and Stoics, on the other hand, many passages which (adjusting for the archaic scientific vocabulary) look as if they could have been pulled out of ID-Darwinist debates. The Epicureans argued that it was perfectly plausible that complex order, including the order of living things, could have come about through the unguided interaction and combination of blind, non-foresighted particles, and the others argued that this was nonsense, that order on the highest level cannot come from disorder, that a designing mind must have been involved, etc. And none of the participants in these debates had read Genesis or were concerned to attack or defend the Bible. So if you want to understand the theoretical core of ID, think of those pre-Christian debates. What ID does is to update the anti-Epicurean side, and what The Modern Synthesis does is to update the Epicurean side. The Bible and Christian theology ought to be kept out of it, as far as the basic theoretical debate goes. And in ID at its theoretically most pure, this is exactly what we find: the Bible and Christian theology are kept out of it. You don't find arguments from the Bible or theology in Behe's books, for example, or in No Free Lunch by Dembski. And when Darwin is criticized by Behe or Denton, he is not criticized for being an atheist (which he probably wasn't, anyway), or for being responsible for Hitler or eugenics or the moral depravity of modern America, etc.; he is criticized for proposing a flawed evolutionary mechanism. (Of course, by that mechanism they have in mind not simply Darwin's ideas, but Darwin's ideas as updated and polished by the Modern Synthesis.) So you have to keep your eye on the ball, and ignore the extraneous religious flak. If you want to disagree with Behe or Dembski about this or that biological claim, that's fine. But don't try to characterize ID as a doctrine of divine tinkering, when its core theoretical writings do not argue for or discuss divine tinkering. Second, regarding your statement that you are entitled to express any theological opinion that you want, I agree. So if you object to "God as tinkerer" -- though it is unclear to me why such a view would bother you, since, if I understand previous statements you have made elsewhere, you don't believe in God in the first place -- you can of course protest this notion. But it is pointless to bring up the inadequacies of God as tinkerer as a criticism of ID when ID as such does not affirm God as tinkerer. Denton has explicitly denied that God tinkers, and Behe, when the question has been put to him directly, has denied that tinkering is a necessary implication of ID. If an individual ID proponent, speaking for himself as a religious believer, affirms that God is a tinkerer, then you can of course sensibly raise your objection then. But such an objection is irrelevant if you are pretending to characterize ID as a pure theoretical position. The correct formulation is in fact that ID does not exclude the possibility of divine tinkering, but does not require it. A designer could achieve his end either by constantly modifying a pre-existing design, but could also set things up so that the design would unfold by an automatic process. So the designer could be something like a tinkerer, but could also be something like a computer programmer. Denton's designer is a sort of cosmic computer programmer, with the set of evolutionary outcomes being the output of the program. You wrote: "Yes, you do have “one possible interpretation of evolution from an ID perspective”. It’s the very one I suggested myself in my post you quoted. However, that interpretation does not emerge from, for example, Dembski’s argument, and does, interestingly, emerge from Darwin’s, who famously said: "'There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.' "The ID case, as I understand it, is that Darwinian evolutionary processes cannot account for the evolution of “endless forms most beautiful and most wonderful” from “so simple a beginning”. I think that case is fundamentally flawed." There is confusion here. The form of evolution that I was indicating was Dentonian. You here identify what I was talking about with Darwin's form of evolution. But the two are quite different, even though in both cases only natural causes are involved. The Dentonian form is driven by an inbuilt teleology, whereas the Darwinian form is resolutely anti-teleological, both in its original Darwinian form and in its later version in the Modern Synthesis. Keep in mind that ID in its pure form is not anti-evolutionary but only anti-Darwinian. The debate between ID and Darwinism is not over evolution but over teleology. (And yes, I know, there are many ID proponents who are not just anti-Darwin but also anti-evolution. But anti-evolutionism is merely compatible with ID, not essential to ID. Again, one must keep one's eye on the pure theoretical position.) So yes, ID proponents do deny the capacity of Darwinian processes to accomplish the results claimed for them; but this is not an inherently anti-evolutionary position, since non-ID evolutionary biologists like Margulis and Shapiro also deny the same thing. That's all I have to say about the mischaracterization of ID. I now turn to your response to my final point, about the nature of modern science. You wrote: "Science is all about finding regularities in the universe, not about accounting for every single individual phenomenon. We know why meteor craters form. We cannot trace the trajectory of a single meteor." Two points. First, your first sentence is true of experimental or "operational" science; it is not true for historical sciences such as cosmology, geology and evolutionary biology. The latter necessarily affirm the occurrence of particular contingent events, and cannot dispense with detailed accounts of how those events might have happened. Second, even in the case of experimental or operational sciences, while it is not necessary to trace particular causal paths in all cases, it certainly is necessary to do so in some cases. For example, when scientists concern themselves with predicting whether a certain rogue asteroid is going to hit the earth X years from now, and contemplate how a nuclear device might be sent up to intercept it, they must indeed be able to trace the trajectory of the of the rogue asteroid, and they can in principle do this using their knowledge of celestial mechanics. (For that matter, the same knowledge enables them to land craft safely on Mars within a few dozen feet of the projected target.) On your last point, I did not say that science excludes God. I said that the methodology of modern science excludes the consideration of supernatural interventions, so that, if supernatural interventions have in fact occurred, science could never know it. This is a built-in and inescapable blindness of the way science is done today. But in no way does this exclude God, because God might have chosen to work wholly through natural causes. Again, refer to the discussion of "tinkering" above. For God to guarantee a result under Darwinian evolution, he would have to tinker; but for God to guarantee a result under Dentonian evolution, he would not have to tinker. Modern science does not exclude a God who operates in the way that Denton suggests; it does exclude a tinkering God. And that exclusion cannot be justified by anything that modern science has "proved". It is rather a postulate that modern scientists work from because they find it heuristically useful. And I don't criticize that procedure, as long as modern scientists aren't under the illusion that they have "proved" that the natural causal nexus is unbreakable. They have not proved and cannot prove such a thing. Philosophers and historians of science (who have often thought more deeply and reflectively about the nature of science than working scientists) have long been aware of this. I carry no brief for miraculous interventions in the evolutionary process, but biologists cannot show that such things could not have happened. What they can do is provide plausible wholly naturalistic scenarios, full hypothetical evolutionary pathways for the origin of major organs or bodily systems. The more such pathways they can describe, the stronger the case that supernatural intervention would not be necessary, and therefore would be an uneconomical hypothesis. Unfortunately for Darwinism, the fact is that there does not exist in the scientific literature even a single full (or anywhere *near* full) hypothetical evolutionary pathway such as I have called for. Thus, we have no demonstration that Darwinian processes, so pretty on paper when they are allowed to remain at high levels of generality such as "drift", "mutation," and "selection," can actually do the job that they are required to do, which is not just to confer antibiotic resistance on a microbe, but to build a radically new body plan or system. ID people continue to remain skeptical that Darwinian processes can do that job. But skepticism about the biology of Mayr and Dobzhansky does not entail outright rejection of evolution itself. It means that it is unlikely that evolution could be driven wholly or even primarily by Darwinian processes. And on this point, ID people have been theoretically ahead of their Darwinian opponents, as the recent high-level criticisms of neo-Darwinism coming from the Altenberg group, from Shapiro and others shows. T. Timaeus

oops: that should read (third last paragraph) "the GA designer's problem is also solved". Elizabeth Liddle

Yes, they do, Joseph. In a GA (at least in the ones I am familiar with) the mutations are completely blind, and no more likely (less likely in most cases) to result in a variant with better chances of reproductive success than no change, or worse. That's what we mean by "blind" in evolution and in that sense, GAs are blind. Nor are they "directed" except in the sense in which evolution is "directed" by the simple truism that variants that reproduce well in the current environment will leave more copies of themselves than variants that reproduce less well. The "current environment" in both GAs and in nature, consists of a set of hazards and resources. In a GA these are often chosen in such a way that when the population of virtual organisms evolves to reproduce well within that environment, the GA designer's program is also solved. But the solution is not directed in the very slightest, in either GAs or nature. What constrains evolution is the hazards and resources of the environment. If you don't understand this, Joseph, you either don't really understand GAs, or you don't really understand the theory of evolution. Elizabeth Liddle

Yes, they designed the molecules - the starting population. Which then evolved, by blind, undirected processes. I win :) Elizabeth Liddle

Elizabeth:

not only that but at least one experiment has shown that this happens in chemistry: http://www.newscientist.com/ar.....e-lab.html

BWAAAAAHAAAAHAAAA- you ARE cofused- they DESIGNED the molecules and nothing evolved- you lose. Joseph

Elizabeth:

And GAs demonstrate that blind undirected (except by the environment) processes can do the things I claim;

Except that GAs have nothing to do with blind, undirected processes. Joseph

I love probability calculations, Joseph, and I'm running one right now. And GAs demonstrate that blind undirected (except by the environment) processes can do the things I claim; not only that but at least one experiment has shown that this happens in chemistry: http://www.newscientist.com/article/dn16382-artificial-molecule-evolves-in-the-lab.html I'm not the one whining here, Joseph :) And nonsense is not established by majority opinion. Elizabeth Liddle

Note to evolutionists: If you do not like probability calculations then perhaps you should get to work and actually demonstrate that blind, undirected chemical processes can do the things you claim. In the absence of that it appears that all you have is child-like whining. And that is why the majority of people think your position is nonsense. Joseph

Elizabeth, Until YOU start supporting YOUR assertions do not ask me to support something that is a common fact. again we do not know how Stonehemge came to be.

Yes, we do.

According to the archaeologists who have studied it, we do not know how it was built.

We know what it is made of, and therefore where and how the stones were formed.

Umm stones can be formed in many ways. One is that MAN made them.

We know they were not local, so we can infer they were transported by some mechanism.

Thanks for supporting my claim-> transported by some mechanism? loL!

We know that people lived at the time it was most likely built, which we can infer from other artefacts and cross-reference to artefacts found on other sites, and we know a lot about their culture, and the other kinds of things they built.

The people could have just found it.

Please supply equivalent information for the ID you postulate as the designer of biological organisms.

You didn't provide anything about how Stonehenge was built. And all we do know came from INVESTIGATING Stonehenge, just as I said.

Please also note that in the case of Stonehenge, we know it does not reproduce, and in the case of biological organisms, they do.

Question-begging. Ya see there still isn't any evidence that blind, undirected chemical processes can produce reproduction.

I may be “full of something” Joseph, but it may be something you might like to try for yourself.

No thank you. What you have is detrimental to the health and well-being of the planet. Joseph

But you still haven't told me what you mean by "probability" in the context in which you are using it. How are you computing your "extremely small probabilities"? Not by frequentist methods, clearly, so, how? Let me take your post line by line, and see if I can pinpoint what I am seeing as the problem with your line of argument:

I mean, given probabilistic resources,

I'm assuming you mean something like the number of events estimated to have occurred in the universe since the Big Bang. Please correct me if I'm misunderstanding you.

the statistical observation

What is a "statistical observation"? Again, I'm not trying to be difficult here, I'm really trying to understand what you are saying. In usual statistical parlance we talk about "observations" and then we produce summary statistics that describe them. For example, we might calculate the mean value, or plot them on a frequency histogram and calculate the probability distribution, so I'm assuming you mean something like the latter. But (nitpick) the observations are not "statistical". Statistical stuff is what we infer from the observations. At least in "inferential statistics" which I take it we are talking about here.

that certain events with extremely small probabilities

And this is what I want to know - what "certain events" are we talking about, and how have you calculated their probabilities?

(i.e. those below the universal plausibility bounds)

OK, the probability is small, given the number of "trials" or "opportunities". But how is this calculated?

of occurring actually never occur in practice.

But again, that's circular, or, at best, backwards. Things that never occur in practice (are never observed) clearly have "extremely small probabilities of occurring", by definition (at least by a frequentist definition). But, as you say:

life has occurred indeed

and so it does not have an extremely small probability by frequentist calculations. So what is it that does have an "extremely small probability"? Let me help you out here :) I think what you are trying to say is that: Under the null hypothesis of "no design" the probability of observing life is "extremely small" and, in fact, so small that it is unlikely to have occurred in the lifetime of the universe. And so, we must infer an alternative explanation from the undoubted fact that life exists, namely "design"? If this is indeed what you are trying to say, my question to you becomes: How are you calculating the "extremely small" probability that life could have occurred in the absence of design? Because your entire argument hangs on that calculation :) Elizabeth Liddle

Most do.

Please support this assertion.

again we do not know how Stonehemge came to be.

Yes, we do. We know what it is made of, and therefore where and how the stones were formed. We know they were not local, so we can infer they were transported by some mechanism. We know that people lived at the time it was most likely built, which we can infer from other artefacts and cross-reference to artefacts found on other sites, and we know a lot about their culture, and the other kinds of things they built. We know that people are capable of building things out of stone. Please supply equivalent information for the ID you postulate as the designer of biological organisms. Please also note that in the case of Stonehenge, we know it does not reproduce, and in the case of biological organisms, they do. I may be "full of something" Joseph, but it may be something you might like to try for yourself. Harrumph. Elizabeth Liddle

Elizabeth:

So some Darwinists infer that God does not exist.

Most do.

A great number of Darwinists make no such inference, and many are theists.

Yet there is no difference between their "god" and no god at all. Strange.

If you want ID to be taken seriously as objective science, then stop implying that Darwinism is equivalent to atheism,

DARWINISTS SAY IT IS. And BTW I can infer from what I read. People who say./ write do the implying.

And, having dropped the assumption that your ID is God, try to find evidence as to what kind of being he/she/it actually is, and how he/she/it executed the alleged designs.

You are confused. In the absence of direct observation or design input the ONLY possible way to make any scientific determination about the specific design mechanism used is by studying the design in question. Heck we still don’t know how Stonehenge was built but we can say it is an artifact.

No. We also use information about how the “design in question” came into existence.

We can only do that by studying ten design- again we do not know how Stonehemge came to be.

However, if the thing was born from a parent, then we have to hand an alternative mechanism to an Intelligent Designer, namely Darwinian processes.

Yet darwinian processes have NEVER been observed to create new, functional multi-part systems. IOW you are full of something that isn't science.

If Stonehenge was observed to spawn baby henges one morning, the inference that it was designed by humans would have to be dropped.

Yup you are full of something... Joseph

Elizabeth, ok, thanks. I am using it in the following sense. I believe I have said that already elsewhere. I mean, given probabilistic resources, the statistical observation that certain events with extremely small probabilities (i.e. those below the universal plausibility bounds) of occurring actually never occur in practice. That life has occured indeed means that according to this statistical observation, it must not have had an extremely small probability. What was it that caused it to emerge? The only empirically warranted cause is design. Eugene S

So some Darwinists infer that God does not exist. A great number of Darwinists make no such inference, and many are theists. Just because some Darwinists are atheists and draw support for their atheism from Darwinism doesn't mean that Darwinism is equivalent to atheism, or even leads to it. If you want ID to be taken seriously as objective science, then stop implying that Darwinism is equivalent to atheism, otherwise the corollary is that ID is equivalent to theism. And, having dropped the assumption that your ID is God, try to find evidence as to what kind of being he/she/it actually is, and how he/she/it executed the alleged designs.

You are confused. In the absence of direct observation or design input the ONLY possible way to make any scientific determination about the specific design mechanism used is by studying the design in question. Heck we still don’t know how Stonehenge was built but we can say it is an artifact.

No. We also use information about how the "design in question" came into existence. Was it born from a parent? would be a first question. If not, then, could biological organism have built it?" would be a second. Then "do we know of any biological organisms with the competence to do such a thing?" would be a third. However, if the thing was born from a parent, then we have to hand an alternative mechanism to an Intelligent Designer, namely Darwinian processes. If Stonehenge was observed to spawn baby henges one morning, the inference that it was designed by humans would have to be dropped. Elizabeth Liddle

What was IC about Thorton’s example? Elizabeth:

It was reached via neutral and even slightly deleterious pathways.

Non-sequitur. I ask AGAIN: What was IC about Thorton’s example? How many components, ie proteins, does it contain? Joseph

Elizabeth:

Yes, I know ID people keep saying this ad nauseam. And yet this site is absolutely full of posts and comments that conflate “Darwinism” with “atheism” and “materialism”. So I don’t find the protestations very convincing.

Except it is the materialists/ Darwinists that say their position = atheism. Geez just read Dawkins, Dennett and Provine.

More to the point: what is wrong with ID IMO, and this has nothing to do with theological inferences, merely with scientific methodology, if you want to infer design, you also have to consider the mechanisms of both design and execution.

You are confused. In the absence of direct observation or design input the ONLY possible way to make any scientific determination about the specific design mechanism used is by studying the design in question. Heck we still don't know how Stonehenge was built but we can say it is an artifact.

We have an alternative candidate to an Intelligent Designer, which is self-replication with heritable variation in reproductive success.

Question-begging as you have no idea that can mimic a designer.

This also results in complex structures that serve to enhance both the survival of the individual and the survival of the population.

Unfortunately that has NEVER been observed- no complex structures have ever been observed to come from reproduction with heritable variants.

So to differentiate between the two candidate processes, it is necessary to provide evidence for the postulated Intelligent Designer, or at least, for mechanisms by which he/she/it executed the designs.

We already know the power of targeted searches. OTOH we don't have any evidence for the claims of your position. All we have are your bald declarations. Strange. Ya see the design inference is based on our knowledge of cause and effect relationships whereas your position is based on the battle-cry "anything but design!"

It is not sufficient merely to say: oh, but it looks designed, because evolved things look designed too.

As I just said. ID is not anti-evolution, so thanks for the equivocation. There still isn't any evidence that blind, undirected chemical processes can design anything.

As I am continually told that Darwinism is equivalent to atheism,

Me too, by DARWINISTS!!!!!! Read for yourself:

In other words, religion is compatible with modern evolutionary biology (and indeed all of modern science) if the religion is effectively indistinguishable from atheism.1

…

The frequently made assertion that modern biology and the assumptions of the Judaeo-Christian tradition are fully compatible is false.2

…

Evolution is the greatest engine of atheism ever invented. Naturalistic evolution has clear consequences that Charles Darwin understood perfectly. 1) No gods worth having exist; 2) no life after death exists; 3) no ultimate foundation for ethics exists; 4) no ultimate meaning in life exists; and 5) human free will is nonexistent.3

As the creationists claim, belief in modern evolution makes atheists of people. One can have a religious view that is compatible with evolution only if the religious view is indistinguishable from atheism.4

click here for a hint:

‘Let me summarize my views on what modern evolutionary biology tells us loud and clear … There are no gods, no purposes, no goal-directed forces of any kind. There is no life after death. When I die, I am absolutely certain that I am going to be dead. That’s the end for me. There is no ultimate foundation for ethics, no ultimate meaning to life, and no free will for humans, either.’ 5

Thank you for your honesty Will Provine. 1- Academe January 1987 pp.51-52 † 2-Evolutionary Progress (1988) p. 65 † 3- “Evolution: Free will and punishment and meaning in life” 1998 Darwin Day Keynote Address 1 2 † 4- No Free Will (1999) p.123 5- Provine, W.B., Origins Research 16(1), p.9, 1994.

But my point is that if you probe ID, you find tinkering is the inevitable inference. I have p[robed it and you are wrong. Ya see I also understand what a targeted search is- apparently you have absolutely no clue how targeted searches work.

Joseph

Eugene, I wasn't trying to be difficult. I asked if you could define probability as you are using it in that sentence. The wiki article does not tell me that. But let me try to explain why I am asking: If an event does not occur in practice, then it has never been observed. Therefore, if we plot a frequency histogram of observed comparable events, it won't appear on the histogram, i.e. it has a frequency of zero. So when we compute the probability of its occurring in the future based on past frequencies (a "frequentist" approach to probability estimates) it will have probability of zero, or, if, as we should, we regard our observations as a sample rather than as a population, we can say that the probability is vanishingly small. It is thus backwards to say: "events with extremely small probability do not occur in practice". It is rather that: "events which have not occurred in practice are considered to have extremely small future probability". Now, life occurred in practice, so we cannot say that it has "extremely small probability". So you cannot be using "probability" in its frequentist sense. So, in what sense are you using the term in the context of your sentence? Elizabeth Liddle

"Could you define probability" Please see here. Eugene S

"Events with exteremely small probabilities do not occur in practice" Could you define "probability" as you are using it in that sentence? Elizabeth Liddle

Elizabeth, you wrote: “In fact, if the ID argument was that only a God could have invented a universe that could bring forth Chopin, I’d be almost fine with it. What I’m not fine with is the idea that the only possible God is one who had to tinker with his/her creation from time to time in order to ensure that Chopin turned up. The theory that the universe actually works without outside interference seems infinitely more marvellous to me than one that requires a maintenance engineer It is also, IMO, one that is supported by overwhelming evidence.” 1. “The ID argument” isn’t about God at all. It’s about inferring design. You may object, saying that many ID proponents identify the designer with the God of their religion. But that identification is not part of ID per se, as ID people have been saying ad nauseam for 15 years now. I’m not going to bother to find you quotations for this. If you are a responsible critic of ID, i.e., if you read what ID proponents say for themselves as opposed to rumors spread about them by their opponents, you will have seen many statements like the one I have just made.

Yes, I know ID people keep saying this ad nauseam. And yet this site is absolutely full of posts and comments that conflate "Darwinism" with "atheism" and "materialism". So I don't find the protestations very convincing. But whether ID is only about design detection or not, I am perfectly entitled to say what I think about any theological inference, and my own view is that if you are going to make a theological inference from evidence for design, it doesn't seem to me that a tinkerer ID is a very good candidate for god-hood. More to the point: what is wrong with ID IMO, and this has nothing to do with theological inferences, merely with scientific methodology, if you want to infer design, you also have to consider the mechanisms of both design and execution. We have an alternative candidate to an Intelligent Designer, which is self-replication with heritable variation in reproductive success. This also results in complex structures that serve to enhance both the survival of the individual and the survival of the population. So to differentiate between the two candidate processes, it is necessary to provide evidence for the postulated Intelligent Designer, or at least, for mechanisms by which he/she/it executed the designs. It is not sufficient merely to say: oh, but it looks designed, because evolved things look designed too. Indeed they are, but not by a foresighted process, and, as the evidence suggests that living things did not emerge from a foresighted process, then the Darwinian explanation, especially given the lack of any evidence for an actual Intelligent Designer, or for any mechanism by which the Designers designs could be implemented, like the likelier solution. Certainly the more parsimonious one.

2. To speak about “the only possible God” is to speak theologically. ID is not theology; it is branch of the information sciences, applied to biology (and sometimes also to cosmology). I have not heard leading ID proponents make statements about “the only possible God” in their theoretical writings about design detection. And even in the case of *some* ID proponents, who write about God in popular apologetic works, I haven’t heard them speaking of “the only possible God” — they merely defend their own conception of God. I don’t know where you are pulling up this phrase, but it either never or only rarely appears in literature written by ID proponents.

I didn't "pull it up". As I am continually told that Darwinism is equivalent to atheism, and that Christian Darwinists are sorely misled, it seems that there is a lot of opposition on this site to the idea that God could operate by means of setting up a universe in which intelligent life could evolve, and an insistence that s/he must tinker with the process to make sure it did. I'm not sure why. There seems to me nothing essentially atheist about Darwinism, any more than there is something essentially theistic about ID. If you agree, I have no quarrel with you, only with ID science. But in that case, let's hear less from IDist of the Divine Foot, and how science is wrong to exclude it!

3. It is not an inherent part of ID that the designer has to “tinker” with anything. Some ID proponents may personally believe that the Designer did in fact “tinker” with nature, but tinkering is not part of ID per se. You here fall into the same confusion that most ID critics fall into. You think that ID is about affirming supernatural interventions as against purely natural causes. It isn’t. It’s about affirming design as against chance. And a design can be implemented through purely natural causes, through a chain of events in which there is no divine intervention.

But my point is that if you probe ID, you find tinkering is the inevitable inference. And while I would agree with you that that inference is faulty (if you do agree), that is IMO because the design inference itself is faulty. It sets up ID as the only alternative to "Chance" which is fallacious as it has a huge "Excluded Middle", not least because "Chance" is not, in fact, an "explanation" at all.

Have you ever played the game “Mousetrap”? Everything that happens once the “boot” kicks the sign is purely natural; there is no intervention by the player. Yet the whole sequence is designed by the game manufacturer. Substitute “first life” or even “Big Bang” for the action of the boot, and you have one possible interpretation of evolution from an ID perspective. In fact, that is exactly the interpretation of evolution you will find in Michael Denton’s second book. No miracles. No interventions. And Michael Denton is definitely a design theorist, at least “id” if not “ID”.

Yes, you do have "one possible interpretation of evolution from an ID perspective". It's the very one I suggested myself in my post you quoted. However, that interpretation does not emerge from, for example, Dembski's argument, and does, interestingly, emerge from Darwin's, who famously said: "There is grandeur in this view of life, with its several powers, having been originally breathed into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved." The ID case, as I understand it, is that Darwinian evolutionary processes cannot account for the evolution of "endless forms most beautiful and most wonderful" from "so simple a beginning". I think that case is fundamentally flawed.

4. Whether or not something seems more marvellous to someone has nothing to do with its truth. The world of revealed religion seems more marvellous to most people than does the world postulated by atheism, but I don’t think you would agree that this is an argument for revealed religion against atheism.

Indeed.

5. Your notion of “overwhelming evidence” is curious. We don’t even understand 1% of what happens in the universe, and you are confident that “the universe works without outside interference”? We don’t have even one complete hypothetical evolutionary pathway for the origin of any major organ or system, and you are confident that evolution works without outside interference? I guess people trained in philosophy are much more skeptical than those trained in biomedical fields, because I don’t have your confidence.

Science is all about finding regularities in the universe, not about accounting for every single individual phenomenon. We know why meteor craters form. We cannot trace the trajectory of a single meteor. We know Darwinian processes work to produce novel solutions to difficult problems, and we have observed adaptation (i.e. evolution by means of natural selection) in both lab and field. We know a great deal about the mechanisms of inheritance, reproduction, development of the phenotype from the genotype, the mechanisms of mutations and the mechanisms of repair processes. We have both palaeontological and genetic evidence for descent with modification and for a vast branching tree-of-life, in which the further back you grow, the more merging of later species we find, so that we can identify ancestral population of multiple later, divergent populations. We also have growing evidence for the pathways by which the earliest self-replicators may have emerged from non-self-replicating molecules. I find that overwhelming evidence to support the "regularity" that Darwin proposed.

For all I know, all events may indeed happen without any “outside interference”; but I certainly do not think the evidence for such a claim is “overwhelming.” In fact, I don’t think such a claim arises primarily out of “evidence” in the first place. The claim is primarily an operational postulate of modern scientific research, not something that has been proved by modern scientific research. There isn’t a single event, no matter how strange or miraculous-seeming, that a modern scientist wouldn’t try to find a natural cause for. If Jesus rose from the dead today, the laboratory staff would be all over him, grabbing blood and tissue samples and putting his brain through a scan and so on, trying to isolate the natural cause of his resurrection. Thus, any possible counterevidence to naturalistic assumptions is simply turned into a new question for naturalistic science to answer. Modern science is methodologically blind to supernatural events, even if they do occur. So to speak of “overwhelming evidence” is to misconstrue the nature of modern scientific practice. Modern science could never find evidence that would count against its own inescapable assumptions. T.

heh. So ID is not about God, but the problem of science is that it excludes God? Do you really not see why the claim that ID has nothing to do with God rings hollow? Elizabeth Liddle

14.2.2.4.4 LastYearOn Re your question regarding past improbable events. Please see Emile Borel, "Probabilities and Life". Events with exteremely small probabilities do not occur in practice. Sound scientific research should take that observation into account. Eugene S

You seem very reluctant to provide the actual citation! Not to worry, I found the wiki page by putting your quotation into google, and that got me to the original paper: http://myxo.css.msu.edu/lenski/pdf/2004,%20Plant%20Breeding%20Reviews,%20Lenski.pdf Read page 251. There is nothing to suggest that the "perhaps 10 or 20 beneficial mutations" that occurred in each population had a flat distribution. The distribution is not, in fact given in the paper, and flat-topped distributions are extremely unusual. There is absolutely no reason to think that the distribution wasn't Gaussian. But even if it was flat, why would that mean a "wall"? A wall against what? I think you are confused. What they did find is that over all 12 populations, the average fitness increased relative to the ancestral population, indicating, as the theory of evolution proposes, adaptation to the lab environment (see figures 8.1 and 8.2). And, again entirely consistent with the ToE, the rate of increase in fitness tended to decline. This may be what you are regarding as a "wall". But it's only a "wall" in the sense of a ceiling for that environment. In other words, the population optimises itself for that environment. However, recall that the Lenski experiment is on bacteria which are cloning organisms, not sexually reproducing organisms. While bacteria are extremely useful for studying population genetics, because they replicate so rapidly, there is no way (or no systematic way) for a beneficial mutation in one lineage to mix'n'match with a beneficial mutation in another lineage, nor to shed any deleterious "hitch-hikers" that it has acquired on the way. This is not the case in sexually reproducing populations, in which successful alleles can propagate independently through the population. So I suggest that before you too far with your "hunch" you read the original Lenski paper thoroughly! It does not say what you think it says, and even if it did, it would not mean what you seem to think it would mean! Elizabeth Liddle

That’s wonderful. Now use that to explain where buildings come from.

Well take a look at your side's favorite links. The evolutionary changes required to distinguish one vertebrate from another require none of the difficult inventions that Behe and Axe talk about -- the invention of new proteins. You have your understanding of actual complexity backwards. Petrushka

Petrushka,

Nearly every every living thing in the world is a microbe or virus. By number, by weight, by variety. Why the obsession with evolving into something else?

I don't know, maybe because I am something else. And I tried obsessing with the stuff that didn't evolve into something else, but it's rather boring. By the way, are those the same bacteria that adapted to new food sources by means of loss of function mutations? This has been covered a thousand times. You might get some immediate benefit, but it doesn't explain large-scale evolution. It's like taking a wrecking ball to a building and smashing an accidental hole in the side. Everyone agree that they could use the extra entrance/exit, and now the employee of the month can drive his car to his desk. It's beneficial. Except for the weakened structure and higher AC bills. That's wonderful. Now use that to explain where buildings come from. ScottAndrews

Elizabeth, you wrote: "In fact, if the ID argument was that only a God could have invented a universe that could bring forth Chopin, I’d be almost fine with it. What I’m not fine with is the idea that the only possible God is one who had to tinker with his/her creation from time to time in order to ensure that Chopin turned up. The theory that the universe actually works without outside interference seems infinitely more marvellous to me than one that requires a maintenance engineer It is also, IMO, one that is supported by overwhelming evidence." 1. "The ID argument" isn't about God at all. It's about inferring design. You may object, saying that many ID proponents identify the designer with the God of their religion. But that identification is not part of ID per se, as ID people have been saying ad nauseam for 15 years now. I'm not going to bother to find you quotations for this. If you are a responsible critic of ID, i.e., if you read what ID proponents say for themselves as opposed to rumors spread about them by their opponents, you will have seen many statements like the one I have just made. 2. To speak about "the only possible God" is to speak theologically. ID is not theology; it is branch of the information sciences, applied to biology (and sometimes also to cosmology). I have not heard leading ID proponents make statements about "the only possible God" in their theoretical writings about design detection. And even in the case of *some* ID proponents, who write about God in popular apologetic works, I haven't heard them speaking of "the only possible God" -- they merely defend their own conception of God. I don't know where you are pulling up this phrase, but it either never or only rarely appears in literature written by ID proponents. 3. It is not an inherent part of ID that the designer has to "tinker" with anything. Some ID proponents may personally believe that the Designer did in fact "tinker" with nature, but tinkering is not part of ID per se. You here fall into the same confusion that most ID critics fall into. You think that ID is about affirming supernatural interventions as against purely natural causes. It isn't. It's about affirming design as against chance. And a design can be implemented through purely natural causes, through a chain of events in which there is no divine intervention. Have you ever played the game "Mousetrap"? Everything that happens once the "boot" kicks the sign is purely natural; there is no intervention by the player. Yet the whole sequence is designed by the game manufacturer. Substitute "first life" or even "Big Bang" for the action of the boot, and you have one possible interpretation of evolution from an ID perspective. In fact, that is exactly the interpretation of evolution you will find in Michael Denton's second book. No miracles. No interventions. And Michael Denton is definitely a design theorist, at least "id" if not "ID". 4. Whether or not something seems more marvellous to someone has nothing to do with its truth. The world of revealed religion seems more marvellous to most people than does the world postulated by atheism, but I don't think you would agree that this is an argument for revealed religion against atheism. 5. Your notion of "overwhelming evidence" is curious. We don't even understand 1% of what happens in the universe, and you are confident that "the universe works without outside interference"? We don't have even one complete hypothetical evolutionary pathway for the origin of any major organ or system, and you are confident that evolution works without outside interference? I guess people trained in philosophy are much more skeptical than those trained in biomedical fields, because I don't have your confidence. For all I know, all events may indeed happen without any "outside interference"; but I certainly do not think the evidence for such a claim is "overwhelming." In fact, I don't think such a claim arises primarily out of "evidence" in the first place. The claim is primarily an operational postulate of modern scientific research, not something that has been proved by modern scientific research. There isn't a single event, no matter how strange or miraculous-seeming, that a modern scientist wouldn't try to find a natural cause for. If Jesus rose from the dead today, the laboratory staff would be all over him, grabbing blood and tissue samples and putting his brain through a scan and so on, trying to isolate the natural cause of his resurrection. Thus, any possible counterevidence to naturalistic assumptions is simply turned into a new question for naturalistic science to answer. Modern science is methodologically blind to supernatural events, even if they do occur. So to speak of "overwhelming evidence" is to misconstrue the nature of modern scientific practice. Modern science could never find evidence that would count against its own inescapable assumptions. T. Timaeus

You said it takes a brief time. How many times has it been tested, and what have these bacteria evolved into?

They evolved into bacteria adapted to a new food source. Nearly every every living thing in the world is a microbe or virus. By number, by weight, by variety. Why the obsession with evolving into something else? It's not what TOE predicts. Petrushka

"...10 and 20 was equiprobable and no other number occurred, which seems vanishingly unlikely to me." This is exactly what happened. All beneficial fixed mutations fell within 10 and 20 for all 12 isolated populations. It does appear that no other number occurred. "Although the bacteria in each population are thought to have generated hundreds of millions of mutations over the first 20,000 generations, Lenski has estimated that only 10 to 20 beneficial mutations achieved fixation in each population, with less than 100 total point mutations (including neutral mutations) reaching fixation in each population." Concerning fixed beneficial mutations (10-20), this is not Gaussian distribution. With a 100 total fixed cap. This is flat. I wager the Avida distributions are Gaussian. In fact many of the examples on youtube often cited are normal bell curve. However, the lenski e-coli seems to be flat, indicating a wall. If this is true, than the Avida results are not representative of what is evidenced by the largest evo field study to date. I have never seen the Avida data. But I have a hunch based on other sim results I have seen. junkdnaforlife

There is a terrible abuse of the word "probable" in the above exchanges! Probability is, essentially, a measure of uncertainty. Once something has happened, all uncertainty is ended. Bearing this in mind, try reading through the above posts :) Elizabeth Liddle

Petrushka, In response to

Every possible state of the universe is astronomically improbable.

You said

The fallacy is that evolution doesn’t test every possible state in the universe.

You're crossing discussion points. As I said before, I get it. Almost everyone gets it. Evolution tests the surrounding points. You said this before and I believe I acknowledged it.

A population of bacteria, even a small population, can buy every possible lottery ticket.

What is this fixation with lottery tickets? Is there some magic correlation between lottery odds and evolution? Which lottery are you even talking about? Nonetheless, you're making my point very well for me. Lenski is giving those bacteria every opportunity to buy as many lottery tickets as they can, and where exactly has it gotten them?

The Lenski experiment demonstrates that all the one step changes can be sampled by a small population in a very brief time.

Really? So after that very brief time, the modified bacteria were now searching from a new "point," one step from where they were. What happened after the next brief time when they searched the points that were nearest to them in their modified state? What happened the next time, and the next? You said it takes a brief time. How many times has it been tested, and what have these bacteria evolved into? Let me guess: The search spaces available within single-step increments don't get them very far. They are still living the same bacterial lives as their distant ancestors. Why do you keep making the point that you intend to argue against? The only meaningful tests ever conducted indicate that evolution is real, it produces variations, and it appears to have limits. ScottAndrews

Lastyearon, One more note on this:

can you think of one past event(not related to biology/evolution) that was too improbable to be plausible?

As I have repeatedly pointed out, plausibility is subjective. It is not a measurement of probability, much less possibility. I think you're confusing plausible with possible. Plausible is a film plot or a homework excuse. If someone told you that you were going to get struck by lightning on five different occasions during your lifetime, you would probably say that they were crazy. It's not plausible. It is highly improbable, but it is not impossible. Improbable and impossible will never be the same thing. Getting hit by lightning 1,000 times in a lifetime is improbable. But it's improbable enough that we safely rule it out. Where exactly do you draw that line? Even that is subjective. But can you see the difference between acknowledging that an improbable event might happen, acknowledging that one has happened, and using a series of improbable events that you can't even define as an explanation? Look for a better explanation, or realize that you don't have one and leave it at that. ScottAndrews

Lastyearon, Are you just throwing stuff to see what sticks?

You contradicted yourself in your last paragraph. First you said that “Every possible state of the universe is astronomically improbable”. And then you said, “within that reality, some events are probable”. How can some events be probable if every state of the universe is astronomically improbable?

When you consider any two events, the general improbability of the state of the universe applies to either of them. You can factor it out. Yes, given the state of the universe five billion years ago, its present state is one of many possible states, and is therefore improbable. Does that mean that when you throw a rock in the air it's not more likely to fall than to fly into space or turn into a whale? How can I make this any simpler? Probability is a rough measurement. It measures which things are more or less probable. What does it say about your point of view if it requires you to first undermine and negate the very concept of probability? Isn't that a giant red flag? ScottAndrews

Lastyearon, That's a nonsensical question.

can you think of one past event(not related to biology/evolution) that was too improbable to be plausible?

Probability or the lack thereof can apply to past events. Plausibility cannot. A thing either happened or it didn't. ScottAndrews

Every possible state of the universe is astronomically improbable.

The fallacy is that evolution doesn't test every possible state in the universe. For the most part it tests those states that are one point mutation away from the current state. There are, of course, many minds of genomic changes in addition to point mutations, but these basically shuffle existing sequences without changing them. The Lenski experiment demonstrates that all the one step changes can be sampled by a small population in a very brief time. A population of bacteria, even a small population, can buy every possible lottery ticket. Petrushka

Scott, You contradicted yourself in your last paragraph. First you said that "Every possible state of the universe is astronomically improbable". And then you said, "within that reality, some events are probable". How can some events be probable if every state of the universe is astronomically improbable? lastyearon

some [events] are too improbable to be plausible

Scott, can you think of one past event(not related to biology/evolution) that was too improbable to be plausible? lastyearon

The problem with the Powerball/lightning strike analogy is that that it compares the probability of more probable events to that of less probable events. Measurements of probability exist precisely to distinguish between the two. If 50 million tickets out of 500 million combinations is comparable to 1 in 10^100, then the very concept of probability is meaningless. Every possible state of the universe is astronomically improbable. Let's just put that out there and acknowledge it. Now, do we throw away the concept of probability, or do we accept that within that reality, some events are probable, some are less probable, and some are too improbable to be plausible? It's a valid concept or it's not. You can't acknowledge it and then use meaningless comparisons to negate it when it's inconvenient. ScottAndrews

would you acknowledge that Behe’s irreducible complexity is a real principle in biology and that some *existing* systems are simply out of reach of Darwinian evolution?

Things are not out of reach because of Behe's principle. Anything that requires a succession of improbable events is out of reach if you are trying to predict the future, but not necessarily so if you are trying to discern the past. We have a communication problem regarding probability. Any specific event can be incredibly unlikely (getting hit by a meteorite, winning Powerball, your parents getting together and conceiving you). And yet things happen, despite the incredible odds against. This is why we can't predict the future in detail. From my perspective, ID makes the mistake of looking at the odds against Joe winning Powerball after he has won. Dembski has actually written a paper on this in which he uses his explanatory filter to decide whether elections were deliberately rigged by placing candidates on a ballot in a certain sequence. There's also an interesting recent case of a woman statistician who has apparently figured out how to win scratch-off card games. The evidence is that she has math skills, and she has won a lot of money over a long period of time. There are uses and misuses of this process. It seems so intuitive, and yet it is subject to all kinds or reasoning errors. When you are trying to figure out whether an election has been rigged or a lottery is not random, you are deciding between likelihoods of competing theories. This is a Bayesian analysis (something Dembski used in the election analysis). You have to know something about the situation and the possible ways in which a particular end could be achieved. In order to rig an election, you have too have physical access to some aspect of the ballot process. In order to "cheat" at scratch-off cards, you have to have access to some aspect of the cards. Apparently in the case of the cards, there were clues in the card serial number. I believe in an older case of Lotto cheating, the winners were related to people who did the drawings. Returning to Behe's principle, the problem is he is astonished that certain sequences of change have occurred, but he offers no particular reason why they shouldn't have. He offers what I consider a rather disingenuous argument that we cannot predict the course of future evolution. I consider this equivalent to asserting we cannot predict the names of the next three Powerball winners. And yet there will be three winners. Behe's principle hinges on what is known as Dollo's Law. Originally it dealt with the irreversibility of a particular evolutionary path. It has been generalized to argue that any particular path is improbable. Having three lotto winners, one cannot expect that a rerun of the drawings would produce the same winners. But one cannot say the winners were specified in advance. And in evolution, one cannot say that the particular size, shape, color or decorative feature of an organism was specified in advance. One thing established by the Lenski experiment is that given a population of bacteria, all possible point mutations will occur. There is no bias toward useful mutations. This is interesting for another reason, and that is that a relatively small population of bacteria, in the course of a couple decades, can explore the entire functional landscape of incremental changes. A third interesting finding is that a change that confers no immediate benefit, and some slight harm, can be preserved in a population, and can eventually become useful when combined with further mutations. This has been a hypothesis for half a century, but has now been observed. Petrushka

Are you asking me what existing systems couldn't evolve?

So with that clarification and if such a computer program were written, would you acknowledge that Behe’s irreducible complexity is a real principle in biology and that some *existing* systems are simply out of reach of Darwinian evolution?

Let me check I understand your question. You originally asked:

If I were to write a computer program based on the idea that some biological systems are irreducibly complex and that a Darwinian pathway would not be able to achieve them, and after running the program, sure enough, the Darwinian approach did not achieve them, would you be willing to publicly acknowledge that Behe’s irreducible complexity is a real principle in biology and that some systems are simply out of reach of Darwinian evolution? If not, why not?

Are you proposing that your hypothetical Darwinian computer model is of an actual existing biological system? And that if a virtual version of that system couldn't evolve within your evolutionary model, then we would have to conclude it was out of reach of evolution? Well, no. All you would be able to conclude is that, given the parameters of your model, the thing is very unlikely to evolve. That conclusion is only as good as your model. The better (more realistic) your model, the more confident you might be that the thing in question really was unevolvable, but we can never rule out a missing parameter. Indeed, many of the great breakthroughs in science have been in finding missing parameters - finding a key overlooked factor that explains otherwise "unexplainable" phenomena. But there's another problem: in a system as complex and varied as biological systems, the changes of a specific "target" feature evolving is very small, although the chances of a feature that performs some target function may be quite high (this is true of AVIDA, by the way: what is "rewarded" is not a specific algorithm, but one that performs a specific function - many possible algorithms may do this). So if, in your model system, your virtual organisms evolved a motility system involving, say, some kind of jet propulsion principle that doesn't happen to exist in nature, when what you were trying to model was, say, some kind of rotary engine principle (like the bacterial flagellum) - would you conclude that flagella were unevolvable? Or might you rather conclude that motility systems tend to evolve, but that the probability of any one system evolving is quite low (just as the probability of any hand of cards is 1, while the probability of any given hand of cards is vanishingly small)? Elizabeth Liddle

If, as the theory of evolution proposes, adaptation of populations to their current environment is via incremental changes, each of which may be only slightly beneficial (or, it turns out, neutral or even slightly deleterious), but which accumulate via selection and drift to provide adaptive "solutions" to the current environment, centaurs (hexapods) would have to diverge from the lineage that produced tetrapods long before tetrapods evolved forelimbs that served as arms with hands. Evolutionary processes can only build on what goes immediately before. The one sort-of exception is hybridisation, but that is still only possible up to a certain point after speciation. Even if you crossed a horse with a human, you wouldn't end up with a centaur, because neither parent has genotypic information that specifies six limbs. Now it's possible that in the remote future, hexapods might evolve from our current fish population, and six-legged vertebrates with hoof-like hind limbs and hand-like forelimbs might be one form they take, but the probability that the hind-limbs might bear more than a passing resemblance to a horse, and the forelimbs more than a passing resemblance to a human, that it should have mammal-like hair and sets of mammary glands between each pair of limbs, mammalian jaws and ear bones, and language function is simply vanishingly unlikely. Convergent evolution does occur, but only extremely rarely does the same body-part evolve similar functions in both cases, and the probability that many would do so, in a completely different lineage, is obviously infinitessimal. Never mind a rabbit in the pre-cambrian, a centaur (a breeding population of centaurs, anyway), anywhere, would simply not fit into any Darwinian phylogeny. Elizabeth Liddle

It was reached via neutral and even slightly deleterious pathways. Elizabeth Liddle

Well, from where I am sitting, it is you who are confused. Certainly the starting population was designed, as was the fitness landscape. What was not designed were the evolving virtual organisms themselves. Each mutation was completely blind; the vast majority were neutral or deleterious; Moroever, the "rewarded" i.e. beneficial mutations were both rare and separated by necessary but non-beneficial step; therefore there was no direction. Therefore the evolution of each function was both blind and undirected, thus simulating biological evolution. You appear to have made a mistake. Elizabeth Liddle

Evaluation of neo-Darwinian Theory using the Avida Platform. Part 1. Evaluation of neo-Darwinian Theory using the Avida Platform. Part 2. Joseph

As for EQU- what is the evidence that EQU can arise via blind, undirected physical processes? Joseph

Perhaps you can show how self-reproduction arose via blind, undirected physical processes. Joseph

But anyway you still have issues with the fact that ID is not anti-evolution and things that are designed to evolve. evolve by design are in no way connected to darwinism.

I look forward to the day when you flesh out that statement.

Genetic algorithms already "fleshed it out", duh.

It makes no sense to me.

Typical. Ya see organisms could be evolving by design- as in they were designed to evolve, meaning that evolution is directed as opposed to blind and undirected. Joseph

Ummm Behe argues only against blind and undirected processes producing IC. And AVIDA does not simulate that. Game over... Joseph

Elizabeth:

Yes, I know it is, Joseph. But, it turns out Behe is wrong. And so are you. AVIDA demonstrates that even blind and undirected process can result in the evolution of IC functions.

No, it does not do that. You are confused. AVIDA does not simulate biological evolution, you lose. With AVIDA EVERYTHING was DESIGNED- the starting organism, the resources, the reward- it does NOT reflect/ simulate blind and undirected physical processes. Joseph

What was IC about Thorton's example? Joseph

Please could you provide the actual citation. What you are saying is profoundly unclear. For a start, "exactly 15 +-5" is not the nomenclature for a flat distribution, unless you are saying that every number between 10 and 20 was equiprobable and no other number occurred, which seems vanishingly unlikely to me. And even if it was, I'm not seeing your point. Could you be specific? Elizabeth Liddle

If intermediate steps are deleterious but nonetheless in the long run they lead to benefit in terms of survival, they are not deleterious.

Your are playing word games. There are several ways in which deleterious changes can become fixed in a population. In humans sickle cell trait is recessive and is beneficial unless it is homozygous. Another way is for the change to occur in a duplicate gene, in which case it may have little or no effect. Another way is for it to occur after a compensating change. Another way is for it to be nearly neutral. Another way is for it to deleterious in its original environment, but beneficial in its current environment. Another way is for it to hitchhike on a beneficial mutation. You may wish to ignore all this, but the compensation scenario has has in fact been tested in pathetic detail by Thornton. Petrushka

Let us step back a bit and think. If intermediate steps are deleterious but nonetheless in the long run they lead to benefit in terms of survival, they are not deleterious. Consequently, everything is beneficial, and therefore we haven't explained anything. In this case, is impossible to substantiate extinction or non-existence of fairy tale creatures. My point is that it is possible to "prove" anything with this kind of logic. Generally speaking, I believe that a system of statements allowing anything to happen (positive, neutral and deleterious) is trivial and delivers zero information. In which case the notions of positive, neutral and deleterious lose their distinctive meanings. Eugene S

BTW, you didn't respond to the point of my question. I'm not talking about fairy tale creatures we know don't exist. It's easy to admit Darwinian evolution can't account for them because they don't exist; thus your theory is rhetorically protected. How convenient. Of course I'm talking about real biology, so I apologize if you misunderstood my question to think I was talking about fairy tale creatures that don't exist. Just put the word "existing" in front of "systems." So with that clarification and if such a computer program were written, would you acknowledge that Behe’s irreducible complexity is a real principle in biology and that some *existing* systems are simply out of reach of Darwinian evolution? If not, why not? Eric Anderson

What principle of evolution dictates that centaurs cannot evolve? Can you articulate an objective principle flowing from the concept of mutations + selection that would prevent the formation of any particular organism? Eric Anderson

"If you just compare the receptors in modern humans, the evolutionary events by which they could have evolved are not obvious. It may look as if the complex functions of each protein evolved independently," said Thornton, an HHMI early career scientist and professor in the UO's Center for Ecology and Evolutionary Biology. "But when we traced these proteins from their ancestor through time, we saw how evolution tinkered with the ancestral form, producing an incredible diversity of protein functions and the ability to interact with many different chemical signals."

http://uonews.uoregon.edu/archive/news-release/2010/10/evolutionary-tinkering-produced-complex-proteins-diverse-functions Petrushka

Thornton demonstrated an historical example of an IC system evolving. the debate with Behe continues: http://blogs.discovermagazine.com/loom/2009/10/15/the-blind-locksmith-continued-an-update-from-joe-thornton/ Petrushka

12 isolated populations, after 5*10^4 + generations, all mutations that could have mutated, mutated (numbers in the millions according to lenski), and every population lands at exactly 15 +-5 fixed beneficial mutations. Where is the tail liz? That seems like a flat distribution to me. Data comes from: wiki+lenski+e-coli. junkdnaforlife

What "flat distribution rates"? I'm not even sure what you mean by this term. Can explain, and give a citation? Elizabeth Liddle

Yes, of course I would. I am sure that some systems are out of reach of Darwinian evolution. Centaurs, for instance. Indeed it is the absence of such things that is one of the evidence for Darwinian evolution - there really are limits to evolution and those limits are evident in the distribution of observed features, namely the nested hierarchies that Linnaeus delineated. But here we have a One Black Swan situation. If it can be shown (as AVIDA shows) that complex features can in fact evolve via deeply IC pathways, and do so regularly and reproducibly, the argument that any observed complex feature for which only deeply IC pathways can be postulated cannot have evolved is refuted. Elizabeth Liddle

Thanks :) I'm going to be busy myself for the next few days, but I'll check back later. cheers Lizzie Elizabeth Liddle

You don't need a computer sim for this, we can simply look at the flat distribution rates of the fixed beneficial mutations along with the flat distributions of neutral "drift" mutations from the 12 isolated e-coli Lenski colonies and compare to simulated results. I wager they will not support one another, just as Gil has said over an over concerning the problems of sim vs field. junkdnaforlife

Oh, in the meantime, if you could respond to the following question, I think it would help a lot in focusing our attention on the key issues: If I were to write a computer program based on the idea that some biological systems are irreducibly complex and that a Darwinian pathway would not be able to achieve them, and after running the program, sure enough, the Darwinian approach did not achieve them, would you be willing to publicly acknowledge that Behe's irreducible complexity is a real principle in biology and that some systems are simply out of reach of Darwinian evolution? If not, why not? Eric Anderson

Elizabeth, thank you for taking time to look through my essay of a few years ago. I probably won't have time to respond to your critique tomorrow, but hopefully in the next day or two I can give you a worthy response. Eric Anderson

Eric, I have just read your paper, linked to by Gil. Let me point out what I think are your fundamental errors. You go through the "assumptions" you think the AVIDA designers make. First you say:

Avida was programmed so that a slight, successive cumulative pathway to the ultimate complex function existed. In other words, the researchers assumed that the ultimate complex feature was not irreducibly complex, and wrote their program in such a way as to guarantee that it would not be irreducibly complex, before they even ran the very first simulation.

This is an error. AVIDA was not "programmed so that a slight, successive cumulative pathway to the ultimate complex function existed". AVIDA was programmed so that the virtual organisms (I will stick with the standard terminology) were subject to slight random variation in their genomes. This means that any change, whether in the direction of either greater or decreased fitness, was incremental. Therefore all pathways in AVIDA are incremental (slight, successive). And that, clearly, by definition, includes any pathways that might exist to the various rewarded functions. Equally it includes any pathways to non-rewarded states. So there is no bias there. Far more importantly, far from "assum[ing] that the ultimate complex feature was not irreducibly complex" they deliberately ensured that all their complex features were irreducibly complex, in that none could be achieved by a series of advantageous mutations from the initial state. And it turns out that EQU, the most complex function, was not only irreducibly complex (would not function if any parts were removed) but that its necessary precursors included changes that were actually substantially deleterious. So you have simply misunderstood this, and it is absolutely critical. Lenski et al set out to show that IC functions could evolve. To do this, they set up an algorithm in which all rewarded functions were IC. All evolved.

Relatively few changes are required to get from the initial organism to the complex feature

Yes, it's a model, written to establish a principle, that IC functions can evolve. Pathways to EQU ranged from 51 to 721 steps,over many thousand generations, although in principle (if intelligently directed!) it could have been done in 16 mutations. That should be indication in itself that no direction was provided.

There are regular and closely spaced fitness plateaus in proceeding from one function to the next.

This claim is quite bizarre. You later say, in support, that:

The Avida researchers initially approach the intermediate functions as though there were a beneficial continuum from one function to the next, although it is far from clear that this would be the case in the real world. A large part of evolutionary critics’ argument from irreducible complexity is that there is unlikely to be a functional advantage for intermediate steps. What good is a cornea without a lens? What good are a cornea and a lens without the retina? And what good are all of these without an exceedingly complex and interconnected nervous system to carry the information to the brain? This is in fact one of the key areas in question in the debate over irreducible complexity, but the Avida authors simply assume it away.

No they do not! I'm not even sure what you mean by "the Avida researchers initially approach the intermediate functions....". They certainly do not provide (let alone assume) "a beneficial continuum from one function to the next". On the contrary, they took pains to ensure there was not. Indeed, they designed their fitness landscape to reflect precisely what "evolutionary critics" assume, that there is unlikely to be a functional advantage for intermediate steps. And, indeed, if you follow their case study, you will read, explicitly, that a great many non-functional intermediate steps were taken along the path, including some very deleterious ones. So not only is it not true that "the Avida authors simply assume it away" but the deliberately make sure that the pathways to the rewarded functions require unrewarded steps. Bizarrely you then say:

In other words, Avida’s cumulative pathway to EQU was elastic enough to allow an unrewarded function to be preserved until the organism got lucky enough to mutuate a further rewarded function and get back on track to its EQU goal.

So it isn't as though you haven't noticed that the pathways include neutral steps! The "elasticity" you mention isn't some cheat algorithm that the authors somehow smuggled in - it's evidence to support their prediction - that even with neutral - and deleterious - steps, in other words even along IC pathways, complex functions can evolve! Then you say: <blockquote? Certainly, there is some possibility that neutral mutations in nature could hang around pending final assembly of a complex feature, but such an approach takes us completely out of the slight-successive-mutations-preserved-by-natural-selection mode and back into a reliance on pure chance. Exactly. Which Behe claims won't work. And Lenski shows does. Although, as you yourself noted earlier, if there are no rewarded steps, then EQU won't evolve. The point is that they can be quite sparse, and separated not just by "plateaux" but by quite deep troughs.

Thus, this finding is not supportive of the authors’ attempt to demonstrate a cumulative pathway, and is not further addressed in the Avida article.

And here is a clue as to where your misunderstanding comes from. You seem to be conflating "cumulative" in the sense of "a sequence of advantageous mutations that lead to a function" with "cumulative" in the sense of "a sequence of any mutations, advantageous, neutral or disadvantageous that are necessary on the pathway to a function". The authors did not set out to demonstrate the first, which would indeed have been circular - to set up a functional feature that could be easily reached via a series of advantageous steps (like Weasel, in fact) and then claim that it proved that all functional feature could be reached by a series of advantageous steps (which Dawkins did not, of course, claim about Weasel). They set out to demonstrate that even if a functional feature could only be reached via necessary neutral and disadvantageous steps, it could still evolve. And succeeded, thus refuting Behe's argument that IC functions cannot evolve by incremental steps.

Each functional advantage is promptly rewarded.

Yes, this ignores stochastic aspects of selection that we find in nature. It could easily be included though. But under the same heading you say:

It is entirely an open question whether a particular functional advantage in isolation would be able to integrate successfully into the organismic whole.

But the AVIDA fitness function required this. Each organism was only rewarded for one performance of each function, and so a function that knocked out another function couldn't compensate by performing the other function more often. So integration was required, and was accomplished.

“The benefits increased exponentially with the approximate difficulty of each function.” In other words, each step closer to the complexity goal (wait a minute, what is that word “goal” doing in an alleged evolutionary mechanism!) is rewarded in a way that makes that step more advantageous vis-à-vis previous steps.

Ahem. The word "goal" does not appear anywhere in the paper! There is, of course, no "goal" (apart from the researcher's goal of demonstrating that complex IC functions can evolve, contrary to Behe's claim), so this is a straw man. The "other words" are yours, and are not what the authors either said, or meant. What they meant is what they said - more complex functions reap bigger rewards (you can run it yourself with different reward schedules). But remember, the organism doesn't get the reward until it performs the function, and the mutations are blind, so the rewards do not act as an "incentive". "Benefits" would have been a better word. All that is happening is that some mutations are "beneficial" just as in nature. But the beneficial mutations, in this case, require non-beneficial precursors, and even some deleterious ones. You say:

What the Avida authors have done is slip a goal, a design if you will, in through the back door. Rather than turning the organisms loose to stumble upon the ultimate complex system in a realistic environment, the researchers have carefully established a specific pre-determined goal and then incessantly flogged the population up the back of Mount Improbable.

This is quite false. As I've said, now, several times, not only is the population not rewarded for steps it takes up Mount Improbable, several of those steps are actually penalised. Only very few steps are "rewarded" on the way, and some of these are actually reversed before the most advantageous function is reached. I think your metaphors have misled you. Something has, anyway. This paragraph is the exact reverse of the truth. The organisms were, in fact, contrary to your assertion, "turned loose" in the environment, and the fact that it took them from between 51 and 721 mutations on the path to EQU, even though 16 mutations would have done it, is pretty good evidence of their "stumbling". The were helped on the way by only 8 rewarded steps, which tended to occur earlier than EQU, not surprisingly, given that they were simpler. Remember that the vast majority of mutations were either neutral or deleterious. Not surprising that they stumbled a bit. Nonetheless they made it, even though all the beneficial functions were IC.

It is the result of assuming that each step along the way toward the goal has an increased advantage.

No. They neither assumed it, nor built it in. Each step along the way did NOT have an increased advantage, as should be clear to you by now. Many necessary steps were neutral, and some were deleterious. That will do. I think I have demonstrated that your critique is absolutely flawed; you seem to have fundamentally misunderstood AVIDA, and Lenski et al's finding. Oddly, you seem also to have fundamentally misunderstood the claim (Behe's: that some functions are IC, therefore cannot have evolved by incremental steps) that the paper soundly refutes. I rest my case :) Elizabeth Liddle

Only in biology does it equal ability to reproduce.

Perhaps you can supply an example of self-reproduction from outside biology. Petrushka

I hope I've addressed this in my other response to you, but let me make a couple of points here:

NormO, the reason for bringing Weasel into the discussion is that I’m trying to get everyone back to basics and on the same page so that we can have a rational discussion about Avida. People tend to swoon when they see a slightly complicated program that affirms their beliefs, so thus (on this thread, for example) we’ve seen nothing but absolute praise for Avida from the Darwinists, without so much as a hint of willingness to even consider the possibility that Avida might have serious problems.

Possibly because there aren't any? As for me, I'm perfectly willing, but all the problems that have been pointed out seem to be based on a misunderstanding of it.

With Weasel, it is simple enough to see that it has problems, so that was a start. But even there I was able to ascertain that not everyone was thinking about the key issues. For example, Elizabeth thought the problem with Weasel was that it has a single solution.

I don't think it's "the problem" with weasel. But that feature renders it misleading when you generalise to algorithms where the problem, solution are not identical. As a result, many people seem to have conflated the desired output of the evolving organisms with the organisms as output. The first is coded in (as the fitness function) but the second is not (and is what evolves).

As a result, she thinks that Avida, with more than one solution, doesn’t suffer from some of the same issues as Weasel.

Well, it doesn't, but not simply because there are multiple solutions. The much more important difference is that there is a distinction between the organism's output and the organism as output. In Weasel, they are coterminous.

Had she correctly understood that the circularity problem with Weasel has absolutely nothing to do with a single solution and everything to do with the fact that there is an initial target built in and that the program is set up to converge on the solution, then we might have been able to take the discussion and apply it to Avida.

There is no circularity problem with Weasel.

Yes, Weasel is a joke, but sometimes we have to go back to the basics and regroup.

So much of a joke that there were vigorous arguments at one stage that it could only work because it "latched". It need not, and does not latch, and, by not latching, demonstrated that latching is not required for Weasel to evolve. It was a small point, but an important one. Even jokes have their uses. Elizabeth Liddle

Elizabeth, let’s parse the wording, and we will see that either (1) you have misunderstood, or (2) you are purposely trying to hide the issues.

The last is certainly not the case. The first is possible. There is a third, which is that you have misunderstood the issue. I will not give a fourth ;)

You quote Lenski et al. as saying the following: “The evolution of a complex feature, such as EQU, is not always an inexorably upward climb toward a fitness peak, but instead may involve sideways and even backward steps, some of which are important.” Do you see that word “always”? Do you see the term “upward climb”? The only thing Lenski is saying is that the pathway toward EQU might not be a straight line. Behe never claimed there had to be a straight line, and I certainly didn’t either. Let’s look at what Lenski actually say:

Yes, Lenski is saying that the pathway toward EQU is often not a straight line, by which he means there are necessary steps that involve no increase, or a decrease, in fitness. This is exactly what Behe means by "Irreducibly complex". He did not say "there had to be a straight line" - what he said was that if there is NOT a "straight line" (i.e. if necessary precursors are non-advantageous or deleterious) then the thing can't have evolved by Darwinian processes. His poster child analogy is the mousetrap. His case for the bacterial flagellum is that it could not have evolved by Darwinian processes because its necessary precursors are non-advantageous or deleterious. I think you have misunderstood. As for the word "always" - there may well be a straight path to EQU, I don't know (I don't think I've seen one demonstrated). That doesn't matter. The point is that EQU can, and does, evolve by paths that are IC. Therefore things can evolve by paths that are IC. Therefore Behe is wrong.

“The benefit increased exponentially with the approximate difficulty of each function.” “The most complex function, EQU, evolved only when several simpler functions were also useful.” “At the other extreme, 50 populations evolved in an environment where only EQU was rewarded, and no simpler function yielded energy. We expected that EQU would evolve much less often because selection could not preserve the simpler functions that provide foundations to build more complex features. Indeed, none of these populations evolved EQU, a highly significant difference from the fraction that did so in the reward-all environment.” The last quote is the real lesson from the “experiment” and is an excellent support of Behe’s point.

Not at all. Nobody is claiming that stepwise evolution of complex features can occur without some selected precursor steps. This is a straw man, and Behe is too smart to attack it. What Behe argues, indeed it's his whole IC concept, and one I've frequently seen here, is that some functions are on "islands" that cannot be reached by a series of advantageous steps. AVIDA shows that these "islands" can indeed by reached - that the intervening steps can be both neutral and deleterious.

It is amazing to me that you are defending Avida tooth and nail without even demonstrating a willingness to consider the possibility that the program is flawed. Can you even stop for a moment and consider that Avida might not be the knock-down proof of Darwinian evolution you think it is?

Certainly I could. But I'm not seeing that it isn't, and your counter argument seems to be based on a) a misreading of Behe and b) a misunderstanding of what evolutionary theory claims.

You seem very impressed with the idea that there is a set of possible solutions, rather than one solution. I hope, based on what I wrote in my other response to you yesterday, you now realize that is not the issue.

It's an issue when talking about Weasel. But as Weasel is irrelevant, I'm happy to leave it to one side.

Do you deny that there was a step-by-step process to get to EQU? Do you deny that there were regular rewards along the way? Do you deny that the program was written in such a way to move the populations toward EQU?

Of course there was a step-by-step process!!!! The point is not whether there were steps (we all think that there were steps) but that not all the steps were advantageous, even when they were necessary, and that some were quite seriously deleterious, i.e. EQU is IC!!!!! And yes, I "deny that the program was written in such a way to move the population towards EQU" except in the sense that it was written to demonstrate that even IC functions would evolve as long as some steps are rewarded. Not a single step in AVIDA is "designed to move the population towards EQU" and the vast majority of steps are neutral (don't move at all) or deleterious (make the individual less likely to breed). The only "moving" is done by the fitness landscape, just as in the natural world. But far from designing a landscape in which EQU would evolve easily, it was deliberately designed to be extremely rugged, with all rewarded functions IC, and EQU very IC. Yet all regularly evolved, thus refuting Behe.

Avida demonstrates that even in an extremely simple context (17 steps to EQU) populations won’t get to a complex function without regular rewards along the way. That is precisely Behe’s point and it stands. Avida most certainly did not refute Behe. Any statement to that effect is either clueless or purposely deceptive.

No, it is not Behe's point. If that were Behe's point he'd be part of the evolutionary establishment, because that's what everyone thinks. What Behe's point is is that you won't get to a complex function by an incremental process if the complex function is IC, i.e. requires precursor steps that are neutral or deleterious. That's the definition of IC (if you take any part away, it doesn't function, therefore many neutral or deleterious steps are required for it to evolve, which won't therefore happen). AVIDA shows that even when many neutral or deleterious steps are required, when you have a function that requires many non-advantageous parts to function at all, it nonetheless evolves. I am not deceptive (and get pretty cross when people suggest I am) nor am I clueless, as I hope is now clear to you. You yourself have made an error. IMO that doesn't make you "clueless", but it does make you wrong. Elizabeth Liddle

Elizabeth, let's parse the wording, and we will see that either (1) you have misunderstood, or (2) you are purposely trying to hide the issues. You quote Lenski et al. as saying the following: "The evolution of a complex feature, such as EQU, is not always an inexorably upward climb toward a fitness peak, but instead may involve sideways and even backward steps, some of which are important." Do you see that word "always"? Do you see the term "upward climb"? The only thing Lenski is saying is that the pathway toward EQU might not be a straight line. Behe never claimed there had to be a straight line, and I certainly didn't either. Let's look at what Lenski actually say: "The benefit increased exponentially with the approximate difficulty of each function." "The most complex function, EQU, evolved only when several simpler functions were also useful." "At the other extreme, 50 populations evolved in an environment where only EQU was rewarded, and no simpler function yielded energy. We expected that EQU would evolve much less often because selection could not preserve the simpler functions that provide foundations to build more complex features. Indeed, none of these populations evolved EQU, a highly significant difference from the fraction that did so in the reward-all environment." The last quote is the real lesson from the "experiment" and is an excellent support of Behe's point. It is amazing to me that you are defending Avida tooth and nail without even demonstrating a willingness to consider the possibility that the program is flawed. Can you even stop for a moment and consider that Avida might not be the knock-down proof of Darwinian evolution you think it is? You seem very impressed with the idea that there is a set of possible solutions, rather than one solution. I hope, based on what I wrote in my other response to you yesterday, you now realize that is not the issue. Do you deny that there was a step-by-step process to get to EQU? Do you deny that there were regular rewards along the way? Do you deny that the program was written in such a way to move the populations toward EQU? Avida demonstrates that even in an extremely simple context (17 steps to EQU) populations won't get to a complex function without regular rewards along the way. That is precisely Behe's point and it stands. Avida most certainly did not refute Behe. Any statement to that effect is either clueless or purposely deceptive. Eric Anderson

everything to do with the fact that there is an initial target built in and that the program is set up to converge on the solution, then we might have been able to take the discussion and apply it to Avida.

It is quite easy to build a GA that doesn't converge on a target. In fact, I've done it, and I have rather limited programming skills. You can start with the same seed and it will produce different output every time, even though the fitness landscape remains unchanged. Run a travelling salesman GA and you will get different results every time. In fact, there is no way to know the best solution if you use enough stops. The point is that there are open ended landscapes that cannot be explored except by GAs. Landscapes having 10^150 points or more. Petrushka

Yes, I know it is, Joseph. But, it turns out Behe is wrong. And so are you. AVIDA demonstrates that even blind and undirected process can result in the evolution of IC functions. In AVIDA, the evolution is both blind (no variant is selected for what it might be useful for later, merely for what it is currently useful for) and undirected (the variants are complete random; they are not biased in the direction of usefulness - most are either neutral or deleterious, and only a very small fraction advantageous). And all the functions that evolve in AVIDA are IC, EQU being, additionally, complex, and, apparently requiring necessary deleterious precursors. Behe's claim is that only systems with foresight can evolve IC functions. In AVIDA, without using foresight, IC functions evolve. Therefore AVIDA refutes Behe. Elizabeth Liddle

NormO, the reason for bringing Weasel into the discussion is that I'm trying to get everyone back to basics and on the same page so that we can have a rational discussion about Avida. People tend to swoon when they see a slightly complicated program that affirms their beliefs, so thus (on this thread, for example) we've seen nothing but absolute praise for Avida from the Darwinists, without so much as a hint of willingness to even consider the possibility that Avida might have serious problems. With Weasel, it is simple enough to see that it has problems, so that was a start. But even there I was able to ascertain that not everyone was thinking about the key issues. For example, Elizabeth thought the problem with Weasel was that it has a single solution. As a result, she thinks that Avida, with more than one solution, doesn't suffer from some of the same issues as Weasel. Had she correctly understood that the circularity problem with Weasel has absolutely nothing to do with a single solution and everything to do with the fact that there is an initial target built in and that the program is set up to converge on the solution, then we might have been able to take the discussion and apply it to Avida. Yes, Weasel is a joke, but sometimes we have to go back to the basics and regroup. Eric Anderson

Actually, what Behe says is right here: http://www.evolutionnews.org/2011/10/wheel_of_fortune_new_work_by_t051621.html And Elizabeth's summary is accurate. It's not about whether the direction is blind. It's about whether evolution can reach a state that requires neutral or deleterious intermediate steps. Petrushka

But anyway you still have issues with the fact that ID is not anti-evolution and things that are designed to evolve. evolve by design are in no way connected to darwinism

I look forward to the day when you flesh out that statement. It makes no sense to me. Perhaps you could start a thread on the topic. Petrushka

Umm Behe's IC argument is that blind and undirected chemical/ physical processes cannot produce it. And AVIDA does not simulate blind and undirected processes. Buy a vowel... Joseph

Elizabeth:

When you set up an evolutionary algorithm, it has several components, including a virtual environment and a starting population of virtual organisms that replicate with variance, some of which results in variable reproductive success within that virtual environment. This whole set up is designed so as to allow the population of virtual organisms to evolve.

Evoled by design/ designed to evolve- same thing. Thanks.

These later members are not “designed” – they evolved within a designed system, but nobody designed them.

The original population was designed to evolve and evolved by design. Umm GA = genetic algorithm and those are designed. The final thing was designed by the program.

Right, but not by the designer of the program.

I never said nor implied the designer of the program designed the final population- not necessary. But anyway you still have issues with the fact that ID is not anti-evolution and things that are designed to evolve. evolve by design are in no way connected to darwinism Joseph

Yes it is bogus - do you have a dictionary? Look up the word "fitness". Only in biology does it equal ability to reproduce. I also see you failed to respond to my reasoning of why the biological definition is bogus- very telling, that... Joseph

No, it's not "bogus", Joseph - it's what the word means. If you want to critique evolution, you really have to understand what the theory is! Elizabeth Liddle

Elizabeth:

Designed to evolve is not the same as “evolved by design”.

What is teh difference? Please be specific.

I've already been specific. When you set up an evolutionary algorithm, it has several components, including a virtual environment and a starting population of virtual organisms that replicate with variance, some of which results in variable reproductive success within that virtual environment. This whole set up is designed so as to allow the population of virtual organisms to evolve. And they do. In the end, the population of virtual organisms is quite different from the starting population, and its members can perform functions that none of the members of the starting population could perform. These later members are not "designed" - they evolved within a designed system, but nobody designed them. And the designs are often extremely surprising to the people who designed the environment in which they evolved.

Obviously the virtual organisms in a GA are “designed to evolve” – what is designed are the conditions under which this will happen.

You say things yet you never support them. Strange.

I do, did, and have, again.

But the final GAs are not “designed” The GA creator does not even know what they will look like.

Umm GA = genetic algorithm and those are designed. The final thing was designed by the program.

Right, but not by the designer of the program. The designer of the program simulates a starting population in a virtual environment. Within that environment, the population evolves - acquire function that maximise its reproductive success within that environment. What its evolved members will look like is completely unknown in advance by the designer of the environment. Indeed, sometimes the virtual organisms do something quite unintended by the designer of the environment - they "cheat" in other words. A bit like harmless snakes that evolve to look like poisonous ones, without having to go to the bother of evolving venom :) Elizabeth Liddle

Elizabeth:

OK, so you accept that natural selection (i.e. heritable variation in reproductive success) results in adaptation, but you argue that the variance must be directed?

Natural selection is 1- an oxymoron as nature does not select and 2- a result of three processes. Adaptaion? Anything is possible.

And I’m defining “fitness” as “reproductive success within the current environment”.

And that is still the most bogus definition, perhaps ever. I say that because it is all AFTER-THE-FACT- you cannot tell which individuals will outreproduce the others in any given population in which all can mate. In real-life the "reward" is mere survival. That said if there is a target then it is directed evolution, period, end of story. The antenna example is a perfect illustration of that. And AVIDA has been laid bare by many others. Joseph

Elizabeth:

Designed to evolve is not the same as “evolved by design”.

What is teh difference? Please be specific.

Obviously the virtual organisms in a GA are “designed to evolve” – what is designed are the conditions under which this will happen.

You say things yet you never support them. Strange.

But the final GAs are not “designed” The GA creator does not even know what they will look like.

Umm GA = genetic algorithm and those are designed. The final thing was designed by the program. Joseph

Continuing:

*All* of the key questions about what would make a Darwinian process actually work in the real world were *assumed* in the Avida program, not demonstrated by it. Simple fitness landscape, easy to traverse from one point to the next, regular rewards along the way, increasing rewards the closer you get to the goal, short pathway to a complex function, and on and on. There is a real, genuine, scientific, observational question about whether these things are true in the real world of biology. Avida simply assumes them all.

No, it does not. The fitness landscape is not "easy to traverse", and the rewards along the way are not only sporadic, but are interspersed, often, with severe penalties. There is no "short pathway" to a complex function; there isn't even a "short pathway" to a simple function: even the simplest function is "irreducibly complex" in that several unrewarded steps are required before it is achieved. I think you may have seriously misread the paper!

People are easily impressed because it is a “program” and gee, it seems to work kind of automatically once you finish writing all the details and press “start”. But we have to remember, anything a program can do, we can do with paper and pen.

Well, yes. You could, in principle, given the lifespan of Methusalah, render AVIDA in hand written binary symbols, or even black and white stones, but the medium is irrelevant. What matters is the execution of the program logic.

And what would that pen-and-paper description look like? Well, if we assume all the key points in question, then our theory will work.

Well, if the theory is right, the program will work. But that isn't circular, it's a test of the theory. If Lenski et al had been wrong, and irreducibly complex functions can't evolve, then EQU wouldn't have evolved, because it turns out to be irreducibly complex.

Sure. Of course. But that is *not a demonstration of the efficacy of our theory,* it is simply a restatement of it, in computer format, rather than with pen on paper. Avida is entirely circular.

No, it is not. If every step required on the pathway to EQU was rewarded, it would have demonstrated that natural selection can work if all steps are rewarded. But every step was not rewarded, and some steps were penalised. And in fact, EQU emerged many times, from many lineages, all of which involved many neutral and some deleterious steps. That means that natural selection works even if the function in question is irreducibly complex.

Indeed, the primary lesson of the Avida progam was that even with a simple function and an easy landscape, the program couldn’t get to the complex function without regular rewards along the way. That is precisely what Behe said!

Except that that is not what Lenski et al found. They found that the program could get to the complex function despite many unrewarded, but necessary, steps, and some penalised, but necessary, steps. Which is the exact opposite of what Behe said!

Avida is a toy, just as Weasel is.

It is indeed. All models are "toys" - that's why we call them "models". They aren't The Thing Itself. But if they fit the data, or emulate the data, then we can infer that they are good models of The Thing Itself.

Oh, it has a few more steps and a few nuances that have to be parsed through to see what is actually going on. And some people who have an a priori inclination to accept the result without asking the hard questions about how the result came about are easily impressed by the smoke and mirrors.

I have "asked the hard questions" and received very satisfactory answers, mostly simply by reading the paper itself. I have also played with AVIDA, and also taken part in a fascinating thread on IIDB, in which Richard Hoppe conducted his own case study, and posted the results as he went along. He confirmed the findings of the paper, which is that EQU regularly evolves but seems to require substantial sequences of unrewarded and even substantially deleterious steps. He also confirmed the obvious, which is that if there are no rewards along the way (no simpler functions that enhance reproduction) that EQU will not evolve. But no-one is claiming this - Darwin's theory was that, given rewards for slight variants, adaptation will occur. Behe's point that some things appear to have necessary but non-advantageous precursors, and therefore could not have evolved by Darwinian processes. AVIDA shows that even functions with necessary but non-advantageous precursors do evolve by Darwinian processes, as long as at least some of the steps are rewarded.

But it is a toy, no more relevant to biology than Weasel and no more able to demonstrate the efficacy of the Darwinian creation theory.

On the contrary, it is a model of evolution that simulates a natural fitness landscape (by rewarding phenotypic functions with "energy" to breed, just as a biological phenotype that is able to exploit an environmental resource gains energy to breed), and it demonstrates that Darwin was wrong, in a sense, and so was Behe: that the incremental necessary changes on the pathway to a complex function do not have to all be beneficial; even when neutral and deleterious changes are necessary precursors, the complex function can still evolve. Elizabeth Liddle

To be specific: you claim that:

Lenski et al. say: “No! Behe is wrong! If there is a step-by-step incremental pathway with regular fitness rewards along the way, Darwinian processes might produce such a system.”

In fact, Lenski et al say the exact opposite:

The evolution of a complex feature, such as EQU, is not always an inexorably upward climb toward a fitness peak, but instead may involve sideways and even backward steps, some of which are important.

In other words that rewards are not required at every step, and that in some cases, deleterious steps are important. Unless your claim is merely that there have to be some rewards along the way, which is of course true. But Behe's "irreducible complexity" argument is that any non-advantageous step to a function renders the thing is "irreducibly complex" and and thus on an "island" that cannot be reached by evolutionary processes (hence the mousetrap argument). He did at one point talk about "degrees of" irreducible complexity, depending on the number of non-advantegous steps in the lineage, but many EQU-performing organisms in AVIDA have high degrees of irreducible complexity (many steps that are non-advantageous, including deleterious steps) in their lineage. And, in any case, he seems to have reverted now back to his mousetrap case. So AVIDA does indeed refute Behe's core claim, and you seem to have misunderstood Lenski's :) Elizabeth Liddle

Where do Lenski et al say such a thing? What AVIDA, interestingly, shows is advantageous functions may be reached by way of many neutral, even deleterious, steps. In other words, EQU for example, is "irreducibly complex" in that it doesn't work if you take away any part, and, moreoever, we can check back and show that it was actually reached by paths that included neutral and deleterious steps. So it refutes Behe not by claiming that nothing is "Irreducibly complex" but by demonstrating the irreducible complexity is not a bar to evolution. Elizabeth Liddle

I mean the final GA virtual organisms - it is important to distinguish between the virtual organisms within a GA and the GA itself, which is the setup in which the virtual organisms can evolve Elizabeth Liddle

Designed to evolve is not the same as "evolved by design". Obviously the virtual organisms in a GA are "designed to evolve" - what is designed are the conditions under which this will happen. But the final GAs are not "designed" The GA creator does not even know what they will look like. Elizabeth Liddle

OK, so you accept that natural selection (i.e. heritable variation in reproductive success) results in adaptation, but you argue that the variance must be directed? OK. But we see from GAs that undirected variance (variations in the virtual genomes are randomly selected) also leads to adaptation, so it appears that no direction at the level of the mutation is required for adaptation to occur. But then you seem to argue that direction at the level of the environment must occur. Well, in a GA, clearly, the environment is usually designed to solve a human problem, and so the fitness function criteria reflect the degree to which the output from the virtual organisms matches the target output. But that's no different from a natural environment, in which the "target output" is simply something that will enhance reproduction, for, example, better camouflage, or more effective foraging. Those "targets" are just as "built in" to the environment as they are to a fitness function, it's just that they are naturally ocurring targets. Hence the term "natural" selection. And I'm defining "fitness" as "reproductive success within the current environment". By the way: bear in mind that in a GA, the fitness function merely specifies the output from the virtual organism - it doesn't specify how the organisms must produce that output. That's the whole point, and that's why we use them - to evolve solutions that will give us the output we want. Elizabeth Liddle

6.2.1.1.12 Dr Bot, That the space has many dimensions is not why EAs work well. EAs are just a kind of local (non-systematic) search. They are as good as any other local search algorithm in general (e.g. tabu search, guided local search). In particular instances where we do not know much about the problem domain, they may be good because we don't know better. There are problem classes where hybrid search is better (non-systematic and systematic), i.e. where we can exploit our knowledge about the problem structure and efficiently propagate our knowledge as search progresses. You see, there are various types of search. Typically, people who work with one type tend to advocate it. I have seen people arguing for swarm intelligence, EAs, Tabu, you name it. In general, a search algorithm (as anything else) suffers from dimensionality not benefits from it because of combinatorial explosion: the neighbourhood size grows exponentially with the number of dimensions. Eugene S

OK, thanks for the clarification. You say:

I have a theory that there is no indirect Darwinian pathway from point x to y. I write a computer program, *building in the fact that there is no possible indirect pathway from x to y.* I run the program, and sure enough, none of my fake “organisms” make it from x to y through an indirect pathway. Would you say that the program has demonstrated the veracity of my theory? Or would you say that the program is an exercise in circular reasoning?

What I'd say is that it is very difficult to prove a negative, but you could say that the probability of a direct pathway, given your parameters, is very low. And if you'd selected the parameters deliberately in advance so that they would render the probability low, then what you would have done is confirm this. That's not necessarily circular - if you had simply hypothesised that, given your parameters, Y is very unlikely, your model is a test of that hypothesis. That's the point of stochastic models of non-linear systems. Unlike the pre-computer days when you could prove something with "pen and paper", we often do not know, until we run a model, whether our model fits the data,and the answer may be a p value rather than a "yes or no" answer. So I think we are not quite on the same page, although establishing this may nonetheless be useful! I am certainly not of the opinion that because a computer model is designed by a programmer, the answer must be known in advance, and conclusions from its output therefore circular. Anyway, I look forward to your critique of AVIDA :) Elizabeth Liddle

Oh, it refers to a mechanism, all right. It's just misleading to call "it" an agent. What I'm saying is neither an "admission" nor contrary to any "Darwinist Claim". Heritable variance in reproductive success (aka "selection") is the mechanism by which genotypic variants that confer reproductive success in the current environment become more prevalent in the population, i.e. is the mechanism by which populations adapt to their environment. What is less obvious, at least to Darwin, was the mechanism by which traits were inherited (we know know that it's mostly genetic), and the mechanisms by which novel sequences are introduced into the genome (there are many, point mutations, deletions, insertions, and recombination being the most important). So lots of mechanisms are involved at the level of generating heritable variance. Evolution occurs when this heritable variance results in changes in allele frequency in a population, and adaptation occurs when the heritable variance is reflected in reproductive success in the current environment. Elizabeth Liddle

Fake but accurate. material.infantacy

The Weasel program was intended to demonstrate the power of cumulative selection vs. a purely random search. And it does exactly that. I'm not sure why certain people got so hung up about it, but I think that says more about them than it does about the Weasel program and what Dawkins intended it to demonstrate. NormO

Elizabeth,

Firstly, Dawkins didn’t “go wrong” with Weasel. It was simply never intended to be anything other than a toy to demonstrate a very simple point. It is not a simulation of evolution in any sense but that simple point.

Dawkins acknowledged the limitations of Weasel and how it differs from evolution. But then why use the illustration at all while admitting that it doesn't fit? All it did was get people even more hung up on this half-crazy idea that random variation and selection can come up with something as simple as a coherent 28-letter sentence. Of course, this is coming from a guy who thinks monkeys really do write Shakespeare. Getting them into shape takes a few million years, and then the rest is easy. ScottAndrews

Mine too I've noticed. Perhaps fingers have a bad sense of context, or are a little lazy. material.infantacy

oops, site=sight. Why do fingers type homophones? Elizabeth Liddle

Firstly, Dawkins didn't "go wrong" with Weasel. It was simply never intended to be anything other than a toy to demonstrate a very simple point. It is not a simulation of evolution in any sense but that simple point. Secondly, "EQU" is not "programmed into" AVIDA. The fitness function rewards functions that perform "EQU" but that is based on the output of the evolving functions, not whether or not the functions themselves match a preset solution - indeed there is no "preset solution". The functions that evolve are different on every run. And of course EQU won't evolve unless it is "rewarded"! That's the Whole Point! In order for evolution to occur there needs to be heritable variance in reproductive success. A simulation that did not build this in would not be a simulation of evolution. In the case of AVIDA, what determines reproductive success is whether the critter can perform certain functions, just as, in nature, whether a critter can perform certain foraging functions will determine whether it thrives long enough to breed. The populations were not "coaxed towards EQU every step of the way". In fact, one of the reasons EQU is slow to evolve is that in many cases, both neutral and deleterious mutations are important precursors. EQU functions, in other words, tend to be "irreducibly complex". Nonetheless, functions that perform EQU regularly evolve! The idea that in evolutionary algorithms "information" is "smuggled in" is a fundamentally mistaken one. No "information" is "smuggled in". It is there, in plain site, in the fitness function, just as it is there, in plain site, in the natural environment. Hot sun "smuggles in" the information that organisms need to find a solution to "keeping cool"; "large seeds" smuggle in the information that organisms need to find a solution to "opening beaks wider". "EQU rewards" smuggle in the information that AVIDA organisms need to find a solution to "performing EQU". In other words, there is no "smuggling" at all. The environment is what it is, and critters evolve to thrive within what it offers in terms of resources and hazards, whatever they may be. And what they may be determines the functions they evolve to tackle. Just as in AVIDA. Elizabeth Liddle

Thanks, Elizabeth. We're getting closer to the heart of the matter, so let's keep going for a bit. Elizabeth: "No, the solution was not “programmed in from the beginning”. What was programmed in from the beginning was the problem, which happens to have a single solution. Posing a problem with a single solution is not the same as “programming in the solution”." You are correct that a problem with a single solution is not the same as programming in the solution. However, Weasel did *not* simply pose a problem. It contained the information for the output solution *in the program itself* as a target string. The "generations" of letters were then compared against this specified information *which was already in the program,* and accepted only to the extent that the letters approached the goal. Yes, there was only one solution, but that is not the problem. The problem is how it arrived at that solution -- the fact that the solution was slipped in the back door and the program was written to converge on the solution. We could have substituted any other target string, from something simple like "Hi there" to something more complex, like the Gettysburg address, and the program would have inevitably convereged on the solution. Elizabeth: "Or, if you insist that in the case of an evolutionary algorithm that poses a problem with a single solution that it is legitimate to say that the solution is “programmed in . . ." No. Again, whether there is a single solution is not the issue. It doesn't matter whether there is a single "correct" answer or whether there is a range of potential answers, or some stochastic result whereby we expect a certain percentage of the program runs to arrive at a solution. The problem is whether the solution is carefully slipped in the back door and whether the program is geared to converge on a solution -- again, that convergence could be inevitable (like Weasel) or stochastic (more like Avida). The key is that if the program drives the process toward a solution, then by definition, the information about the solution was contained in the program itself. This has nothing to do with evolutionary mechanisms; this is purely a question of programming, logic and information theory. Now we all can see what Dawkins did wrong. Does a similar problem beset Avida? Setting aside for a moment all the other significant problems with Avida, let's focus on this particular issue. EQU is a solution that is contained in the program itself. It is a known target, just like Weasel. You seem to think this is not an issue because, well, perhaps the program wouldn't have necessarily converged on EQU, you might say. But that is simply a misunderstanding of the program. The fact that Avida is more complex than Weasel, includes more steps, and is stochastic, rather than a single solution, does not change the fact that the target is set in the program from the outset and that the program is geared to move the populations inevitably toward EQU. It takes a bit more finesse to see what is going on with Avida, but in terms of containing a target sequence that the population is *programmed to converge on* it is fundamentally no different than Weasel. Indeed, when the authors tried to get EQU in the 50 populations they ran without the incremental rewards (think Weasel with the target sequence getting closer), the populations couldn't get to EQU. Thus, even in a relatively simple situation, the populations couldn't come up with the solution, *unless they were coaxed along toward the pre-determined and pre-programmed solution.* This is the real takeaway of the Avida program, and is consistent with the monkey-typewriter experiments and with Behe's review of functional gain from mutations. Now, there are lots of other issues with Avida, which I point to in my paper and which others have discussed, but we need to be very clear about this key problem. The EQU target was contained in the program from the beginning; the pathway to get to EQU was contained in the program from the beginning; the rewards to get to EQU were set up from the beginning; the populations were carefully coaxed toward EQU nearly each step of the way. All of the information content relevant to EQU and how to get there was in the program from the outset. Don't let the fact that there are lots of "organisms" fool you. Don't let the fact that there are "populations" rather than a single "entity" fool you. Don't let the fact that we are dealing with statistical curves and percentages and stochastic outcomes, rather than a single solution, fool you. The solution was programmed in from the beginning and the populations were driven inevitably toward it. Eric Anderson

As a GA, the Weasel program would consist of, in parts, a randomization procedure (a mutator), an evaluation routine (score keeper), and a fitness function (Hamming oracle). The fitness function would determine a Hamming distance between the target string and the mutated progeny, and feed that score to the evaluation routine, which would score each progeny, only allowing the most successful to reproduce. In this regard, the target string in the fitness function would be pre-programmed, unequivocally. Any target could be substituted, and the program would consistently converge on the solution without fail, given appropriate tuning for generation size and mutation rate. The output of the program would demonstrate the conservation of information; the information content of the final output would be less than or equal to the information content of the initial input. We could modify the fitness function to score against two target strings, say "methinks it is like a weasel" and "abcdefghijklmnopqrstuvwxyzab" and we would see convergence on either of the strings (at random) but nothing more. Keep adding target strings and we would see convergence on any one of them, but nothing more. The information input into the system would determine its output. String length, generation size, mutation rate, and target space would all determine how and if a solution was found, but the output would never wander beyond the constraints of the input. Do what you will to the fitness function. The output won't exceed the input (technically by more than 500 bits). material.infantacy

One additional source of confusion regarding Weasel is that in most evolutionary algorithms, the fitness function - the criteria that determines how likely a critter is to reproduce - does, unlike Weasel, simply match the critter against a "target". Instead, the critter performs some function, for example taking input and producing output, and it is the output that is matched against the "target" criteria. How that output is produced is "up to" the critter, and when you get a population of critters that regularly manage to match the output, you can peek inside, and see how it does it. In other words, the evolved critters embody the solution to your problem - the fact that you "programmed in" the problem does not mean you "programmed in" the solution. Elizabeth Liddle

In the special case of the Weasel program, problem, solution, and fitness function are the same thing - a specific letter sequence. If you want to call that "programming in the solution" I suppose you could, but it would be a non-generalisable observation, a bit like inferring that because the sqrt of 1 is 1, taking the sqrt of a number doesn't change it. Elizabeth Liddle

EL, are you suggesting that the Weasel program did not contain the target string "methinks it is like a weasel" and that the program did not test each generation against this target string? How was the problem modeled to have a single solution that didn't include comparison with a predefined target? material.infantacy

Elizabeth, please respond to the central question. Elizabeth: “In weasel, the problem is trivial and there is only one optimal solution (the sequence of letters that spell “methinks it is like a weasel). So it does not demonstrate that Darwinian algorithms can find unknown solutions to non-trivial problems.” Yes, these are problems with the weasel program, but you are skirting the primary issue. The question was whether the solution was programmed in from the beginning. This is important to the circularity issue we have been discussing from the beginning.

No, the solution was not "programmed in from the beginning". What was programmed in from the beginning was the problem, which happens to have a single solution. Posing a problem with a single solution is not the same as "programming in the solution". Or, if you insist that in the case of an evolutionary algorithm that poses a problem with a single solution that it is legitimate to say that the solution is "programmed in", then please do not generalise from that completely atypical example to any other evolutionary algorithm. The Weasel is a toy. Useful evolutionary algorithms pose problems to which there may be multiple solutions, none of which are known in advance. So they are certainly not "programmed in".

Do you or do you not acknowledge that the solution was programmed in from the beginning?

Only in the above, extremely limited and not generalisable, sense. Elizabeth Liddle

“Name an unconnected island” Organs of vision, for example. There is no known path of successive modifications that connect no-vision to vision. The famous diagram is too scanty to be able to show that in satisfactory detail. Behe points out that the curvature of the retina recess alone requires a complex protein-protein interaction to be fine-tuned.

Yes, there are known paths of successive modification to organs of vision. Not only that, but all stages of the path are actually found in extant living things. But let's not get on to too much of a tangent - my point is that the irreducible complexity argument is quite different from the Information Can't Be Created By Computer Simulations argument. And also quite different from the "Reaching Islands of Complexity is Highly Improbable" argument. Complex designs evolve within Evolutionary Algorithsm, so we know the sytem can produce complex novel solutions to the problems posed by the environment. Nobody argues that Darwin's theory accounts for "Reaching Islands of Complexity", so probability arguments don't work either. The only remaining argument is: Some things couldn't have evolved by stepwise increments. Which is simply an arguments from lack of a model, not an actual model. And, in the case of vision, we actually have a good model. Where we don't as yet have a good model is getting to a DNA-based life-form. But that's no reason to infer "Design" (nor of course, reject it). Elizabeth Liddle

6.2.1.1.14 "Name an unconnected island" Organs of vision, for example. There is no known path of successive modifications that connect no-vision to vision. The famous diagram is too scanty to be able to show that in satisfactory detail. Behe points out that the curvature of the retina recess alone requires a complex protein-protein interaction to be fine-tuned. Eugene S

Dr Bot, I am not an expert on ID. An even better example to show what you intended to show is synthetic life. Here is what I think about this. Obviously, information gets generated. As to how much and whether it can be described as CSI, I don't know. IN fairness, even if it is CSI, what remains to be seen is: 1. how you got the initial setup for the system to generate CSI. This is by no means the same as the problem of origins, so I am not switching the problem. The problem we are talking about is enabling optimisations within a (sufficiently small) set of allowed configurations. 2. Quantitatively, how much (CSI) information have been generated: - i.e. whether it is beyond the quantitative CSI threshold (500 bits) 3. Qualitatively, it remains to be seen whether the explanatory filter can give out the "design" answer. Dembski does address the criticism of Fibonacci series observed in nature, in the same vein: yes, natural systems produce Fibonacci series "naturally" (and not only Fibonacci, but other things like the golden ratio of parts to the whole, on mass). But what does that exactly mean? To me it would mean that design is involved at some stage here anyway. Eugene S

I think we're getting off in the weeds a bit. There are two primary points. (1) The Avida paper failed to do what it was intended to do, namely refute the concept of irreducible complexity. Here is what happened with the famous Avida paper: Behe says, in effect: "Darwinian processes are unlikely to produce a functionally integrated system unless there is a step-by-step incremental pathway with regular fitness rewards along the way." Lenski et al. say: "No! Behe is wrong! If there is a step-by-step incremental pathway with regular fitness rewards along the way, Darwinian processes might produce such a system." Anyone see an issue with their response to Behe? [Note, this isn't an evolution test, just a simple logic test.] ----------- (2) *All* of the key questions about what would make a Darwinian process actually work in the real world were *assumed* in the Avida program, not demonstrated by it. Simple fitness landscape, easy to traverse from one point to the next, regular rewards along the way, increasing rewards the closer you get to the goal, short pathway to a complex function, and on and on. There is a real, genuine, scientific, observational question about whether these things are true in the real world of biology. Avida simply assumes them all. People are easily impressed because it is a "program" and gee, it seems to work kind of automatically once you finish writing all the details and press "start". But we have to remember, anything a program can do, we can do with paper and pen. And what would that pen-and-paper description look like? Well, if we assume all the key points in question, then our theory will work. Sure. Of course. But that is *not a demonstration of the efficacy of our theory,* it is simply a restatement of it, in computer format, rather than with pen on paper. Avida is entirely circular. Indeed, the primary lesson of the Avida progam was that even with a simple function and an easy landscape, the program couldn't get to the complex function without regular rewards along the way. That is precisely what Behe said! Avida is a toy, just as Weasel is. Oh, it has a few more steps and a few nuances that have to be parsed through to see what is actually going on. And some people who have an a priori inclination to accept the result without asking the hard questions about how the result came about are easily impressed by the smoke and mirrors. But it is a toy, no more relevant to biology than Weasel and no more able to demonstrate the efficacy of the Darwinian creation theory. Eric Anderson

Elizabeth, please respond to the central question. Elizabeth: "In weasel, the problem is trivial and there is only one optimal solution (the sequence of letters that spell “methinks it is like a weasel). So it does not demonstrate that Darwinian algorithms can find unknown solutions to non-trivial problems." Yes, these are problems with the weasel program, but you are skirting the primary issue. The question was whether the solution was programmed in from the beginning. This is important to the circularity issue we have been discussing from the beginning. Do you or do you not acknowledge that the solution was programmed in from the beginning? Eric Anderson

DrBot:

Take a real example, evolving a logic circuit: One experiment used a genotype of 1800 bits, specifying the configuration of a 10×10 section of a field programmable logic array (FPGA). With a suitable fitness function the evolutionary algorithm was able to configure those 1800 bits, starting from a totally random population, to produce circuits that could discriminate between square waves of 1kHz and 10kHz.

Designed to evolve/ evolved by design. Thank you for proving our point. Joseph

And on top of that, the GA has the enormous benefit of not knowing or caring whether the antenna it "designs" ever gets manufactured. Real world evolution has to design and manufacture simultaneously. The GA is conveniently freed from solving that problem, passing it off to who? Intelligent designers. ScottAndrews

DrBot, Evolved antennas and evolved electronics are optimizations of designed functionality. Sure, GAs are handy way to quickly explore possible optimizations, but this has no bearing on the creative powers attributed to evolution. This example sums it up quite well.

Here we describe our work in using an evolutionary algorithm (EA) to automatically design an antenna for NASA's Space Technology 5 (ST5) mission. ST5 is one of NASA's New Millennium Program missions to launch multiple miniature spacecraft to test, demonstrate and flight-qualify innovative concepts and technologies in the harsh environment of space for application on future space missions.

What role does an evolutionary algorithm play in launching a miniature spacecraft? Does it identify the need for miniature spacecraft or the benefit? Does it design the spacecraft from raw materials? Does it invent a propulsion system? Does it determine that the spacecraft may need to send and receive signals? Does it conceive how such signals might be transmitted, received, and interpreted? Does it determine that sending and receiving such signals would require an antenna? None of the above. When the heavy lifting is done it shows up and optimizes the antenna after it's told what to do and what to look for. It's a good application of computer science, but it doesn't make a case that evolutionary processes can invent anything. ScottAndrews

The TARGET is programmed in. Elizabeth:

Well, the problem is programmed in. Not sure what you mean by the “target”. The “target” as in “a solution to the problem” is not programmed in, as you agree. So what are you calling the “target”?

The target is what it is you are trying to accomplish. That is the "problem" you are trying to find a "solution" to. How do I get X starting with something that isn't X.

We are talking about Darwinian evolution which pre-supposes a minimally complex self-replicating population.

But the origin of that directly impacts any subsequent evolution. And the resources and means to reach the target is also programmed in.

Well, the “resources” are simply part of the environment,

Not entirely. The resources also include the stuff necessary to reach the goal of the program. In biology this would be the genome/ whatever it is that makes an organism what it is- which we don't know what that is yet (yes we know what genomes are but there isn't any evidence that an organism is a sum of its genome).

What they do demonstrate is that given these two prerequisites, namely critters that replicate with modification and an environment that provides resources and hazards, adaptation (evolution of the population to fit its environment) will occur.

You are confused- ID is not anti-evolution. Rather it argues that the changes that lead to adaptation are directed via some internal programming. ALL genetic algorithms mimic ID not blind, undirected processes.

They mimic blind probes of nearby fitness space.

Fitness space? How are you defining "fitness"? And what GA does this and what is your evidence for that? Joseph

That's ok. In fact, yes I was :) By the initial conditions I mean not only the parameter values but the whole configuration for the experiment to run that, I believe, takes us to an island of functionality where a meaningful experiment is possible. Eugene S

The question is how this game was put together or how we got to that functional island.

Again, that is a different issue to the question: Can a GA produce CSI A GA clearly has CSI, but I would say there are tons of examples to show that they can generate more CSI. It makes no sense to demand that evolutionary mechanisms be used to explain the origin of evolutionary mechanisms! DrBot

6.2.1.2.1 DrBot Unfortunately I can't say at the top of my head whether CSI has been generated here. It is down to detailed analysis but the question is interesting. I accept that some information can be generated spontaneously, the question is how much. E.g. a double coincidental error introduction/correction in a message, however the original meaningful message has an intelligent cause in practice. In any case, this has been a very interesting discussion indeed, thanks to you and Elizabeth. I'll think of this question. Eugene S

Sorry, I just realized I misread when you referred to the example - thought you were responding to my example ;) DrBot

6.2.1.1.15 Dr Bot, Thanks for the example. Yes I know of capabilities of GAs. But that misses the target. Here GAs are working in an intelligently setup environment. This environment is not a simple sum of components sporadically put together. We are already in a target zone amenable to GAs. GAs have to have something that discriminates between "good" and "bad" and the other rules of the game, the fitness may be changed adaptively, etc. But again it is us who control the action of GAs. The question is how this game was put together or how we got to that functional island. Eugene S

You can have more example like that but they are glossing over inherent levels of complexity and choosing the “right” set of initial conditions.

In that example the initial conditions were random. Unless you are still switching the question to the origins of the evolutionary system rather than the operation and products of that system? I gave an example of an evolutionary system that I think generates CSI - can you explain, if you believe it doesn't, why it doesn't? DrBot

Dr Bot, You can have more example like that but they are glossing over inherent levels of complexity and choosing the "right" set of initial conditions. At a suitable abstraction level everything works fine until you actually get involved in the technical detail, which such illustrations lack. Tell me which is easier, to tune a bike or an internal combustion engine? Eugene S

“why are macrochanges not the sum of microchanges?” They are not because of the simultaneous presence of many parameters needing tuning. The cumulative effect of components may not always be a simple arithmetic sum of their individual independent inputs.

Indeed. There will also be powerful non-linearities. But this would seem to support my side, not yours :) Small genetic changes can indeed lead to large phenotypic changes, particularly when, as DrBot points out, we consider development. So things can move quite rapidly at times. But that doesn't mean it isn't incremental - it just means that even small genetic changes will often be substantial enough that they affect the fitness landscape to which other traits must adapt.

Take for example, resonanse: it will only occur if an eigen-frequency of an oscillating system is near enough to the frequency of external force.

Sure, but I don't see your point. Elizabeth Liddle

To illustrate this, lets start from the beginning. Say, an abstract system has N parameters.

Take a real example, evolving a logic circuit: One experiment used a genotype of 1800 bits, specifying the configuration of a 10x10 section of a field programmable logic array (FPGA). With a suitable fitness function the evolutionary algorithm was able to configure those 1800 bits, starting from a totally random population, to produce circuits that could discriminate between square waves of 1kHz and 10kHz. DrBot

Elizabeth, Somewhere you asserted that the higher the number of dimensions the more opportunities exist. What makes you assume that? Common sense and engineering practice tells me it is the other way around in too many real world cases. You need purposeful fine-tuning of parameters to make sure the system functions as appropriate, that all control circuits operate normally.

What do you mean by "as appropriate"? You are stuck in the paradigm of human purpose! Sure, if you are using an EA to design an antenna, you don't want the thing haring off because along another dimension it could make an excellent clothes drier! But the great thing about a purposeless system, or rather one in which the only intrinsic purpose (I am not talking about moral or personal purpose here) is to survive to breed, then anything that increases that probability will be "appropriate". So that even if a wing evolved to be "appropriate" to flying, if another dimension opens up in which adaptation in the direction of flipperdom offers increased reproductive chances, then there is no pesky Intelligent Engineer to say: hey! we need to retune that parameter or we are going to end up with a penguin!

To illustrate this, lets start from the beginning. Say, an abstract system has N parameters. Each parameter has a domain of values D. So, theoretically you have |NxD| configurations where “x” means the Cartesian product. In the universal scale this is a huge number. Suppose then that only a subset of those parameter values are viable, the others lead to fatalities or malfunction. In the overall set N x D such viable configurations are so tiny and isolated (as to why “and” in the biological contexts, see works by Douglas Axe e.g.), given the size of N and D, that they represent islands in the vast sea of possible configurations.

Oh, there are islands already. Centaurs are on an island. So are griffins. And those are precisely the places evolution cannot, and does not, reach. Having lots of dimensions doesn't mean there are no islands. It means that there is far more mainland.

Evolution cannot present a tenable mechanism of how you get to those islands in the first place. Once you are there, it is a different matter. I am somewhat familiar with combinatorial optimisation and I can therefore understand quite well how tiny these islands can be in relation to the overall config space. No evidence exists to assure everyone that islands representing biological functionality are in fact connected.

Name an unconnected island :)

The likelihood of getting to those islands by chance without intelligent guidance is below operational possibilities in the grand scale of our Solar system or our universe.

Yes, we agree. I don't know why this keeps being brought up. Nobody thinks you can get to an unconnected island through evolution. Evolution posits that all the places living things have reached are not islands, i.e. are connected by incremental steps. So saying "evolution can't reach islands" is non-controversial. What you have to do is to demonstrates that islands have been reached. I don't see any compelling evidence for this, merely arguments from gaps in detailed incremental accounts.

Now I envision the common evolutionary argument, that evolution allegedly does away with a lot of those no-good configurations by means of co-evolving everything and thus making it far easier. Kauffman asserts this for instance. But again I can see no solid evidence for such hypotheses.

You can't? There seems to be a fair bit of it to me :) Elizabeth Liddle

Elizabeth, "why are macrochanges not the sum of microchanges?" They are not because of the simultaneous presence of many parameters needing tuning. The cumulative effect of components may not always be a simple arithmetic sum of their individual independent inputs. Take for example, resonanse: it will only occur if an eigen-frequency of an oscillating system is near enough to the frequency of external force. See my response 6.2.1.1.10. Eugene S

Common sense and engineering practice tells me it is the other way around in too many real world cases.

Actually no, one reason EA's are popular with some engineers is their ability to navigate very high dimensional search spaces - they tend to be better than people in some instances. That doesn't imply that just having more dimensions will always help but there are plenty of papers out there on the topic of dimensionality and evolutionary search. DrBot

We don’t have evidence of this.

I'm sorry but we do. It can be directly observed in artificial evolutionary systems. Look at evolved antennas, or evolved electronics. The system being evolved in each case starts out with minimal function and increases in functional complexity as it evolves - functional complexity in both cases can include the pattern of information in the phenotype and the length of the phenotype. In the case of an antenna you can start with a genotype containing just three variables (the end point (x,y,z) of a segment relative to the antenna base) and if the EA allows for random insertion of new variables so the number of segments in new generations of antenna will grow if selection favors variants with multiple segments. If you want to talk about it in bits of CSI then lets say you start with three 8 bit integers for each x,y,z 'gene'. You start then with 24 bits describing the proto-antenna (which can be totally random) and the evolutionary mechanism can then incrementally grow the number of bits that describe the antenna, and tune their specificity. (BTW, I'm not saying this is the best way to specify an antenna genotype, an L system for example could be better) DrBot

6.2.1.1.7 Elizabeth, Somewhere you asserted that the higher the number of dimensions the more opportunities exist. What makes you assume that? Common sense and engineering practice tells me it is the other way around in too many real world cases. You need purposeful fine-tuning of parameters to make sure the system functions as appropriate, that all control circuits operate normally. To illustrate this, lets start from the beginning. Say, an abstract system has N parameters. Each parameter has a domain of values D. So, theoretically you have |NxD| configurations where "x" means the Cartesian product. In the universal scale this is a huge number. Suppose then that only a subset of those parameter values are viable, the others lead to fatalities or malfunction. In the overall set N x D such viable configurations are so tiny and isolated (as to why "and" in the biological contexts, see works by Douglas Axe e.g.), given the size of N and D, that they represent islands in the vast sea of possible configurations. Evolution cannot present a tenable mechanism of how you get to those islands in the first place. Once you are there, it is a different matter. I am somewhat familiar with combinatorial optimisation and I can therefore understand quite well how tiny these islands can be in relation to the overall config space. No evidence exists to assure everyone that islands representing biological functionality are in fact connected. The likelihood of getting to those islands by chance without intelligent guidance is below operational possibilities in the grand scale of our Solar system or our universe. Now I envision the common evolutionary argument, that evolution allegedly does away with a lot of those no-good configurations by means of co-evolving everything and thus making it far easier. Kauffman asserts this for instance. But again I can see no solid evidence for such hypotheses. Eugene S

We don’t have evidence of this.

Are you saying that virtual organism with no function except reproduction that evolves within an Evolutionary Algorithm and ends up able to perform quite complex logic operations doesn't possess increased CSI? Obviously I haven't done the computation, but it seems to me it almost certainly does!

We don’t have evidence that fruit flies or bacteria can acquire genuine novelty that would translate into an increase in CSI.

What are your criteria for "genuine novelty"? It seems to me that there is plenty of evidence for novelty. Why wouldn't it translate into an increase in CSI?

I simply do not believe evolution as a principle can ever be able to account for that.

Well, you are entitled to your beliefs:)

An indirect sign of this is overloading of evolutionary terminology rendering the whole theory too complex.

What is "too complex"? Why shouldn't a theory be complex? Especially when it is covering a very complex set of phenomena, encompassing many mechanisms, molecules and systems? The remarkable thing, however, is that Darwin's basic principle remains at its core; what has happened Darwin's day is increasing knowledge of how it works, mechanistically, and in specific instances.

It can reliably account only for microchanges, Darwin’s finches, lengths of limbs, degree of hairiness, different camouflage &c.

It certainly can and does account for these, but why are macrochanges not the sum of microchanges? If microchanges over a short time scale are possible, why not macrochanges over a longer time scale? Back to those algorithms - going from inability to perform not a single logic function to being able to perform a complex one seems pretty "macro" to me, and also "novel" and yet is the result of a long series of "microchanges". Elizabeth Liddle

True the solution isn’t programmed in- that would be dumb and defeat the purpose.

Exactly.

The TARGET is programmed in.

Well, the problem is programmed in. Not sure what you mean by the "target". The "target" as in "a solution to the problem" is not programmed in, as you agree. So what are you calling the "target"?

The starting point is programmed in.

Yes. That part is the equivalent of OOL. We aren't talking about OOL, right? We are talking about Darwinian evolution which pre-supposes a minimally complex self-replicating population.

And the resources and means to reach the target is also programmed in.

Well, the "resources" are simply part of the environment, which obviously is designed in a computer simulation, but has a direct analog with the physical environment in real life. The "means" are simply self-replication with modification - in other words the equivalent of OOL. Darwin's theory does not attempt to explain either OOL, or why the environment has scarce resources and life-threatening hazards. The first of these remains unsolved, the second seems pretty easy to answer. Evolution algorithms do not demonstrate an explanation of these either. What they do demonstrate is that given these two prerequisites, namely critters that replicate with modification and an environment that provides resources and hazards, adaptation (evolution of the population to fit its environment) will occur.

IOW it is design all the way down.

Nope. You left out the bit in the middle.

ALL genetic algorithms mimic ID not blind, undirected processes.

They mimic blind probes of nearby fitness space. The fitness space itself provides "direction" but only in the manner that a hillside provides "direction" to a stream. In some sense they also mimic intelligent thought, which also works on a related principle, with the big difference that intelligent agents are able to model the consequence of a given step before executing it, and feed the result back into the selection process. Evolution, and evolutionary algorithms do not do this (and EAs are sometimes frustrating to watch! They can take very circuitous routes before reaching a solution).

It is unbelievable that some people really think that GAs support the current theory of evolution…

It remains true :) For good reason. Elizabeth Liddle

6.2.1.1.6 Dr Bot, I was with you almost to the end of your post, namely up until the point where you say: "so we can say that evolutionary mechanisms can increase the CSI of a system." We don't have evidence of this. We don't have evidence that fruit flies or bacteria can acquire genuine novelty that would translate into an increase in CSI. I simply do not believe evolution as a principle can ever be able to account for that. An indirect sign of this is overloading of evolutionary terminology rendering the whole theory too complex. It can reliably account only for microchanges, Darwin's finches, lengths of limbs, degree of hairiness, different camouflage &c. Eugene S

DrBot has responded eloquently, but I'll add my two pence or so:

Elizabeth, I am saying that evolutionary algorithms are designed. They are designed to find solutions, not to evolve.

Yes, clearly the whole caboodle is "designed"! You can't build a simulation without designing it! But you can design it to evolve, and that is exactly what they do. The environment, which is a modelling of the problem, is designed, and so is the basic starting critter, complete with its reproductive system. What is not designed by the computer modeller are the critters you end up with - they evolve as critters best fitted to survive in the environment you design. So the computer modeller designs A) the starting critter and B) the environment. What evolves is C) the final critter. A is the analog of OOL B is the analog of the actual environment C is the analog of evolved creatures. In the simulation, C is not designed, only A and B. And it is only C that is at issue. Yes?

As an aside, evoalgorithms just like any other non-systematic search algorithms are prone to getting stuck in local optima, which may preclude the system using them from exploring more opportunities depending on the landscape and on the initial solution.

Yes indeed. And so do actual critters, which is why we still have critters that seem very like their ancient ancestors (so called "living fossils") alongside critters that have travelled much further from the ancestors we share. However, in the living world, two important factors are present that are usually absent, or impoverished in the computer simulations. One is that in the natural world, the environment is much richer. This means that it is far higher-dimensioned than most mere human-designed environments, and the higher-dimension a fitness landscape, the more opportunity there is for escaping from a local optimum. The second is that the environment is not only constantly changing (or populations constantly change their location) but that the evolving population itself forms part of the environment, so that powerful feedback loops occur. Both these things can be simulated to some extent, and, indeed, evolutionary algorithms are powerful design tools, but they have only a fraction of the power of the real thing.

Do we have any evidence of evolving computer viruses that are clearly able to replicate themselves? No. They behave as they are programmed to behave.

Well, they do replicate themselves, of course, which is why they are called "viruses" but to my knowledge they are not designed, on the whole, with genotypes that spontaneously mutate and still produce viable phenotypes. Unless you have self-replication with heritable variability in reproductive success then you won't get evolution. And if all almost all variants are fatal, then you won't get evolution either. Though I wouldn't put it past a clever virus designer to design a virus that did have a variable genotype that gave rise to differential reproductive success within cyberspace, and thus evolve into something that the designer did not design :)

You are claiming that evolutionary algorithms are not only capable of adapting to the environment (here we agree) but also of introducing advantageous novelty, which is equivalent to spontaneous injections of complexity or islands of functionality (and here we disagree, you even deny the existence of the problem of novelty isolation in config spaces).

As DrBot says, these two things are not equivalent. Not in the least. The reason virtual organisms in an evolutionary algorithm do adapt to their virtual environment is precisely because they introduce advantageous novelty, by which I mean exactly that - new capacities that are reproductively advantageous within that environment. They are new because they weren't present in the founder population, and it's because they are advantageous that population "adapts". But these adaptations are incremental - they do not "leap" between islands, or, at least, not very far. Just because something is new doesn't mean it is an "island". A single step can be in a new direction. A substantial number of incremental steps may result in a complex function that started simple. No abrupt "injection of complexity" is required or implied.

ID uses design inference based on solid evidence of systems where such information injections are a result of intelligent agency.

Well, I disagree that the evidence for "information injections" is solid. It seems to me to be simply an inference from ignorance. Just because we don't know the incremental pathway doesn't mean we can infer there wasn't one, and we certainly can't then infer that therefore there must have been an intelligent agency. In fact it's worse than that - if we can posit a plausible incremental pathway, even if we don't know that it was in fact the pathway, then we should certainly not infer that there cannot have been such a pathway, and only if we have grounds to infer that there cannot have been such a pathway must we infer a non-incremental mechanism. I know of no evidence of a biological feature for which there cannot have been an incremental pathway. Certainly not the flagellum illustrated (in a somewhat misleading rendering!) at the top of this page, for which a plausible pathway has been proposed. It could be wrong - and probably is, given that several are possible - but the fact that any plausible pathway can be postulated means that we cannot infer that none is possible.

No evidence exists suggesting that complex specific information can be gained spontaneously.

Well, what do you call the solutions given by evolutionary algorithms, if not "complex specific information"? And if they were arrived at by Darwinian process (which they are), in what sense were they not gained "spontaneously"? Elizabeth Liddle

To date, the only credible and demonstrable way of getting CSI into systems is intelligent intervention/initial setup.

I would agree that initial setup is an important question - but it is not one that the theory of evolution was created to address!

Evolution does not answer that question adequately enough.

Because it is not a theory of the origin of life.

The chance of getting CSI spontaneously generated is so ridiculously small that it is fair to say it is is operationally impossible.

I've never seen any realistic calculation of those odds - we don't know nearly enough yet to even have a chance at calculating them, but again this is an OOL question, not an evolutionary theory one.

the only credible and demonstrable way of getting CSI into systems is intelligent intervention

Or an evolutionary mechanism, as we can observe in the lab and the field. They only work on systems that already contain a certain type of CSI though - the ability to reproduce with variance - so we can say that evolutionary mechanisms can increase the CSI of a system. DrBot

6.2.1.1.4 Dr Bot, Thanks for your response, esp. regarding phenotype/genotype distinction. I think that you underestimate the importance and scale of the complexity argument. The major controversy nonetheless stands out: how complex specified information gets into biosystems? To date, the only credible and demonstrable way of getting CSI into systems is intelligent intervention/initial setup. Evolution does not answer that question adequately enough. The chance of getting CSI spontaneously generated is so ridiculously small that it is fair to say it is is operationally impossible. All we require is evidence not theoretical discourse, that CSI can be produced by evolution. Eugene S

I am saying that evolutionary algorithms are designed. They are designed to find solutions, not to evolve.

This seems to illustrate your misunderstanding of the whole topic. Evolutionary algorithms generate evolution - evolution is the result of these algorithms in action. If we relate it back to biology then the evolutionary algorithm is a minimal model of observed mechanisms in the real world - Inheritance with variety resulting in differential reproductive rates in a variable environment. Pointing out that the simulation - the model running on a computer which is an instantiation of the algorithm - is designed is just a failure to understand the point of creating a simulation. Any model of observed phenomena must be designed, the real question would be how did the observed phenomena come about, but in the case of evolution it is a two part question - how did a universe in which evolution could occur come to exist, and how did self replicators capable of evolving come to exist. Both these questions are about the origins of things, not their operation once they actually exist. Evolution is not a theory of the origin of life, nor is it a theory of the origin of the universe

You are claiming that evolutionary algorithms are not only capable of adapting to the environment (here we agree) but also of introducing advantageous novelty,

The means by which an evolving agent adapts is by the generation of novelty.

which is equivalent to spontaneous injections of complexity or islands of functionality (and here we disagree, you even deny the existence of the problem of novelty isolation in config spaces).

No it isn't. The topography of the fitness space depends a great deal on the system that is evolving. As EL has pointed out already, not all landscapes are navigable but the evidence suggests that the biological one is. Don't forget that biological systems have a developmental period, they grow. A minor change to the genotype can result in major changes to the phenotype because of the way genes influence the developmental cycle. You don't have genes to describe each finger on your hand, what you have are genes that regulate an iterative growth process, making whole extra fingers possible through very minor changes to the genome. That is not to say that every possible solution can be reached from any other point. Have you ever wondered why we don't see powered wheels in biology? They are, I suspect, a real example of an irreducibly complex system. DrBot

6.2.1.1.2 Elizabeth, I am saying that evolutionary algorithms are designed. They are designed to find solutions, not to evolve. As an aside, evoalgorithms just like any other non-systematic search algorithms are prone to getting stuck in local optima, which may preclude the system using them from exploring more opportunities depending on the landscape and on the initial solution. Do we have any evidence of evolving computer viruses that are clearly able to replicate themselves? No. They behave as they are programmed to behave. You are claiming that evolutionary algorithms are not only capable of adapting to the environment (here we agree) but also of introducing advantageous novelty, which is equivalent to spontaneous injections of complexity or islands of functionality (and here we disagree, you even deny the existence of the problem of novelty isolation in config spaces). ID uses design inference based on solid evidence of systems where such information injections are a result of intelligent agency. No evidence exists suggesting that complex specific information can be gained spontaneously. Eugene S

Elizabeth:

In an evolutionary algorithm, the solution is not programmed in from the beginning. The problem is programmed, but not the solution. The whole point of using such algorithms is to find novel solutions.

True the solution isn't programmed in- that would be dumb and defeat the purpose. The TARGET is programmed in. The starting point is programmed in. And the resources and means to reach the target is also programmed in. IOW it is design all the way down. ALL genetic algorithms mimic ID not blind, undirected processes. It is unbelievable that some people really think that GAs support the current theory of evolution... Joseph

So what is the question, Eugene? You agree, then, that evolutionary algorithms can find solutions to problems that have solutions? But you argue that they can't find solutions to - what? Problems that don't have solutions? You seem to be conflating knowledge of the problem with knowledge of the solution. If I want to know how to distinguish between brain activity in a patient, and brain activity in a healthy volunteer, I know the problem ("what brain activity patterns distinguish between the two?) but not the solution (I do not know what those brain patterns are). But an evolutionary algorithm can find me the solution to my problem. I don't "design" the problem so that it can be found. I had the problem and I ask my evolutionary algorithm to find a solution. And it does. Exactly the same thing happens in nature. The environment "sets" a problem for the evolving population to solve: that problem is "how do you reproduce in this environment, given these resources and these hazards?" which is exactly the problem I set my evolutionary algorithms, except, that because I have my own agenda, I design the environment in such a way that in order solve their problem (of reproduction), the critters must evolve a solution to mine (how to distinguish between a patient brain and a healthy one). Obviously a program that only prints out "Hello world" won't evolve into a program that solves some much more complex problem unless, firstly, you ensure that it reproduces with variance, and secondly, you embed it in an environment in which some variants will reproduce more successfully than others (by, for instance, arranging it so that part-solutions to your problem increase the probability of replication). But that isn't "circular" - it is simply setting up the equivalent of what happens in the natural world: creatures that happen to inherit a trait that confers environmental advantage (better camouflage, say) will stand more chance of handing on their traits to the next generation. BTW: one problem I think besets these discussion is failure to distinguish between genotype and phenotype. Throwing some error at machine code level into, say, a higher level coding that displays "hello world" and letting the ones that do something interesting as a result, replicate, isn't going to get you very far, because considering machine code as the genotype is a very poor way of modeling what DNA does. What you have to do, of course, is set up your virtual critter/program so that it has a mutatable genotype and a resulting mostly-viable phenotype, just as biological critters are fairly robust to minor changes in genotype. It won't work if you do not simulate that robustness. Elizabeth Liddle

Elizabeth, Let us stop beating about the bush. The question is not about microadaptations i.e. solutions that evoalgorithms are designed to be able to find. The question is rather about whether evoalgorithms which assume a lot of things in order to function as they are expected to function (I can tell you that as a programmer using GAs at work), can really develop themselves, not merely find solutions. Here by development I mean the said algorithms aquiring new functionality spontaneously on their own without the software engineer taking part. Something like a program that can only print out "Hello, world" developing into a finite element analysis tool by itself. Eugene S

In weasel, the problem is trivial and there is only one optimal solution (the sequence of letters that spell "methinks it is like a weasel). So it does not demonstrate that Darwinian algorithms can find unknown solutions to non-trivial problems. But other evolutionary algorithms do. There are many solutions to the problems "set" by AVIDA, including the most difficult (an algorithm that performs EQU), and different runs produce different solutions. Dr Bot knows about examples that solve real-life coding problems; others have found novel engineering designs, for example for antennae; in my field they find classifier algorithms to distinguish between brain patterns. All these are problems without a single solution, for which we need a good solution, and for which the solution is not known in advance. Evolutionary algorithms find them for us, just as they find solutions for populations to the problem of how to thrive in a given environment. Elizabeth Liddle

Do you acknowledge that Dawkins’ “Methinks” program had the solution programmed in from the beginning?

Of course it is. Why do people keep talking about WEASEL. It is a pedagogical example from a popular science book designed to illustrate selection, and in that sense it is not a 'simple early algorithm' but an educational toy. Please can you choose an early example of a proper GA from the academic literature, not a coffee table book. There are tens of thousands of academic publications relating to genetic algorithms dating back decades and whole journals dedicated to the subject of evolutionary computing. As far as I'm aware Dawkins has not published anything in any of them. DrBot

Elizabeth. Let's come back to Avida in a moment when we're sure we have some basic common understanding. So let's start with a very simple and early algorithm: Do you acknowledge that Dawkins' "Methinks" program had the solution programmed in from the beginning? Eric Anderson

"Well, I’m not sure what an “indirect Darwinian pathway” is, but sure, you can’t use a computer program to show that something is impossible if you write the code in such a way that it is impossible!" Nothing fancy in my terminology. An indirect pathway just means that you get from A to Z through intermediate points, say B-Y, rather than jumping straight from A-Z. Just the general Darwinian idea of change from A to B to C and so on. "Although generally speaking, showing that something is impossible is difficult, and scientific methodology isn’t set up even to attempt it." Fair point, but it is tangential -- let's not get hung up on the "impossible" terminology. We could build a program that makes it highly improbable or exceedingly unlikely or whatever else you want to say that is short of impossible. The problem with such a program would be that it is circular, correct? As a result it hasn't proved anything. It hasn't corroborated my theory. It hasn't refuted anyone else's theory. All I have done is create a virtual representation of my theory (which I could have done just as easily with pen and paper before the days of fancy computers), incorporating as a premise the very thing I am allegedly trying to prove. Let me know if we're on the same page thus far, and then we'll see if the same principle applies to Avida. Eric Anderson

In an evolutionary algorithm, the solution is not programmed in from the beginning. The problem is programmed, but not the solution. The whole point of using such algorithms is to find novel solutions. Elizabeth Liddle

Thanks! I should have spotted it.

Elizabeth, see my comment above. All the key issues about the Darwinian mechanism are *assumed* as premises and programmed into the system. It is entirely circular, 100%. If you doubt this, then please answer the following question: I have a theory that there is no indirect Darwinian pathway from point x to y. I write a computer program, *building in the fact that there is no possible indirect pathway from x to y.* I run the program, and sure enough, none of my fake “organisms” make it from x to y through an indirect pathway. Would you say that the program has demonstrated the veracity of my theory? Or would you say that the program is an exercise in circular reasoning?

Well, I'm not sure what an "indirect Darwinian pathway" is, but sure, you can't use a computer program to show that something is impossible if you write the code in such a way that it is impossible! Although generally speaking, showing that something is impossible is difficult, and scientific methodology isn't set up even to attempt it. Which is why it's much harder to show that a drug is safe than show that it is dangerous. Elizabeth Liddle

Elizabeth, my bad. The question is in comment 2.2.1.1. Eric Anderson

Eugene: Darwinists claim that big increases in complexity did not occur, therefore do not have to be explained, i.e. that all increases in complexity, or, to put it better, all increases in fitness, are incremental. That's my point - to keep arguing that Darwinism cannot explain big leaps is a straw man, because Darwinism doesn't try to. What it argues is that there are only tiny steps, but that enough tiny steps amount to a very large distance. Elizabeth Liddle

Elizabeth, since you apparently have very little understanding/experience with computer programs and the problem of circularity, let’s step back a bit. Please just answer my question from 2.1.1.1. Would such a program prove that Darwinian evolution is false, or would it be an example of circular reasoning?

Could you give a link to your post, Eric? Or perhaps re-pose your question? 2.1.1.1 appears to be by Charles. As for my experience, in fact you are incorrect. I have substantial experience with computer programs, and, indeed, with evolutionary algorithms. Elizabeth Liddle

Double post uoflcard

DrBot

But is not just features of a system, like gravity, aerodynamic characteristics, etc. The solution it looks to prove is programmed in from the beginning. That is the the question-begging circularity that Eric speaks of.

No it isn’t.

What isn’t? The solution being programmed in from the beginning, or that being the question-begging circularity that Eric speaks of? uoflcard

DrBot

But is not just features of a system, like gravity, aerodynamic characteristics, etc. The solution it looks to prove is programmed in from the beginning. That is the the question-begging circularity that Eric speaks of.

No it isn’t.

What isn't? The solution being programmed in from the beginning, or that being the question-begging circularity that Eric speaks of? uoflcard

DrBot

You mean more substantial than “seems to have been designed”? Can ID offer any evidence beyond this?

Observation: Functional, complex, specified information Proven causes of Observation: Intelligence/Design, none others Inference to best explanation: Intelligence/Design That is why it "seems" to have been designed. How much evidence could you possibly want that this fCSI can be generated by intelligence? Every word you type is further evidence of this. The evidence that is lacking is that anything besides intelligence is capable of generating fCSI. That's all this debate boils down to, really. Can you offer evidence rather than assertions and apriori assumptions? Your view was accepted as fact long before this problem was ever known, and we still are not to the bottom of the complexity of life. uoflcard

DrBot, Have I made an ID-related claim regarding the mammalian inner ear? If I don't have anything substantial then I won't make a claim. That's good advice for anyone. I'm still free to point out that someone else's claim that the mammalian inner ear "seems to have evolved" is insubstantial, which it still is, just in case anyone got distracted. ScottAndrews

If there is something more substantial than “seems to have evolved,” use that to establish the premise.

You mean more substantial than "seems to have been designed"? Can ID offer any evidence beyond this? DrBot

But is not just features of a system, like gravity, aerodynamic characteristics, etc. The solution it looks to prove is programmed in from the beginning. That is the the question-begging circularity that Eric speaks of.

No it isn't. DrBot

Elizabeth, since you apparently have very little understanding/experience with computer programs and the problem of circularity, let's step back a bit. Please just answer my question from 2.1.1.1. Would such a program prove that Darwinian evolution is false, or would it be an example of circular reasoning? Eric Anderson

Petrushka, After mentioning the mammalian inner ear, you say, "We can easily demonstrate the adequacy of that kind of change. Breeders exploit it all the time." Are you saying that one could breed a new type of inner ear or some similar change? You are saying that. Perhaps it's the difference between the length of legs and having legs in the first place and knowing how to use them that we need to focus on. By your own words you indicate great uncertainty about how the mammalian ear might have evolved. If there is something more substantial than "seems to have evolved," use that to establish the premise. Right now the assertion that no such pathway has ever been observed stands unchallenged. It's what we know, and it carries far more weight than what someone things might have happened but can't explain in any specific detail. ScottAndrews

Not a single person here doubts that the Darwinian mechanism works when this pathway is present. But we have no evidence that such a pathway has ever existed for any complex, specified, functional feature/mechanism/object/information that has ever been observed. None.

There are two major categories of change. Those that affect protein coding and those that affect developmental pathways. The mammalian middle ear seems to have evolved purely by the route that changes development, things like leg length in dogs. In the case of the ear, it appears to have affected the size and timing of bone development. We have fossil evidence that it was incremental. We can easily demonstrate the adequacy of that kind of change. Breeders exploit it all the time, and did so long before Darwin. Petrushka

DrBot

You appear to be arguing that it is wrong to include features of a system in a simulation of that system if you are attempting to establish what effect those features have on the system.

But is not just features of a system, like gravity, aerodynamic characteristics, etc. The solution it looks to prove is programmed in from the beginning. That is the the question-begging circularity that Eric speaks of. Taking your analogous simulation, let's say I want to run a simulation to see if a freely falling object's flight path (let's say, a feather) can spell out the word "Hello" in cursive. Would it be misleading to program in a powerful jet stream that just happened to spell out the word "Hello" in cursive? Seems obvious to me, and it also seems that this is exactly what Avida does. It is programmed to succeed. uoflcard

But Eric, the whole point of the AVIDA simulation is to show that if a feature is “rewarded” it will evolve! That’s the Darwinian mechanism! And it works! It’s not circular to demonstrate that the mechanism you propose works, works! It’s just successful!

But it entirely misses the point of the primary challenge to Darwinism, which is the question "IS there a bit-by-bit, functionally increasing pathway to any complex, specified, functional system?" This pathway is guided every step of the way in these "simulations". Not a single person here doubts that the Darwinian mechanism works when this pathway is present. But we have no evidence that such a pathway has ever existed for any complex, specified, functional feature/mechanism/object/information that has ever been observed. None. That is the point. I have personally seen it described to you on this website dozens and dozens of times, and have done so myself many times (three times in this thread, in fact) and have never seen an evidence-based reply. Great, AVIDA proves that the Darwinian mechanism works (as long as we figure out the one challenge ID has been talking about for the last 10+ years). Similarly, I will run a one-step simulation to show that I am rich: uoflcard's Bank account = $50,000,000 See, I'm rich! (Once I actually get the $50,000,000) uoflcard

you’ve got a neutral sequence hanging around (from duplication or whatever your preferred approach is). Even if you have complete and total freedom to tweak the sequence all you want, you simply are not likely to stumble upon a functional protein sequence.

I think you are wrong. What Axe did was start with modern functional sequences and explore the possibility of finding adjacent functional sequences, without breaking functionality. What others have done is start with completely novel sequences, ones having nothing in common with living things, and explore the possibility that they might have function. And some do. So the issue is not whether you can improve on existing proteins, but whether you can find new, minimally functional proteins. It matters that duplication and other genomic changes provide sequences that are "off line" so to speak. Mutations in non-necessary genes are neutral, so it is possible to cross to other islands. But the really interesting thing being revealed by sequencing technology is that genes are very old, and most predate multi-celled organisms. Petrushka

The existence proof is down to you, guys. ID claims a big enough increase in complexity cannot be done spontaneously simply *because it has not been observed*. I would like to ask you a few things. 1. Do you acknowledge the fact that between System A that has vision of any kind (no matter rudimentary or not) and System B which doesn't there is a complexity gap. 2. Do you appreciate how big this complexity gap is? 3. Do you appreciate the likelihood of such a spontaneous advantageous complexity increase given our universe? Eugene S

Elizabeth- what is this alleged "Darwinian hypothesis"? Also there isn't any evidence that all mutations/ genetic changes are Darwinian processes- that is the point of what Eric said. Scientists just ASSUME all changes are Darwinian. That said ID is NOT anti-evolution and is OK with reproduction, heritable variation and an envirnment. ID just posits the variation is directed via internal programming. Geez you anti-ID types are so clueless it is painful. Joseph

Dr Liddle: Kindly cf my current discussion of the underlying issues here in an update post. GEM of TKI kairosfocus

All the key issues about the Darwinian mechanism are *assumed* as premises and programmed into the system. It is entirely circular, 100%.

No, all the key observations are modelled in the simulation - all the mechanisms that are observed to exist. The output of the simulation confirms the hypothesis - that given heritable variation in reproductive success within an environment, adaptation will occur. If not then which of the following aspects of the simulation are not observed to exist in reality: >> Reproduction. >> heritable variation. >> an environment. DrBot

And that is the wrong answer. Enough has been said here at UD and elsewhere that there are. But that obviously does not count…

No it doesn't - you need evidence, not just claims. DrBot

No, they are not "assumed as premises", Eric. You really are confused! It tests the Darwinian hypothesis that given heritable variation in reproductive success within an environment, adaptation will occur. And it does. The "solutions" to the "problems" posed by the environment are not assumed at the outset, either in nature or in AVIDA. But in both, the problems are given as survival problems, and the evolving populations finds solutions that are, a priori, unknown. The reason it may seem "circular" to you is that it is so self-evidently true. That was the beauty of Darwin's insight. Elizabeth Liddle

Eric, I'm not sure you have understood. You appear to be arguing that it is wrong to include features of a system in a simulation of that system if you are attempting to establish what effect those features have on the system.

Is there a route from point a, to b, to c to get to our final function? Avida is programmed to assume that there is. (2) ...

Let me paraphrase the argument. I want to study the effect of an aerodynamic feature on a free falling object and hypothesize that the feature will allow the object to drift a given distance in relation to the drop altitude. So I create a simulation that includes gravity, air, and the aerodynamic feature I am studying. You are claiming that it is circular to include these features? Can you tell us how you would create an experiment to test the hypotheses that AVIDA was created to test without the circularity you allege?

In other words, if I assume all of the key points about my theory, then I can demonstrate the veracity of my theory.

Then you create a model and see how well the model matches observed data. . . If you propose pixies as a feature then you need to demonstrate that they exist and how they operate, not just claim that they do. DrBot

Liz, I'll just leave you with these thoughts: Do you ever marvel at the beauty of the laws of physics which govern the universe and that appear to be fine-tuned for the emergence of life? Do you think about the fact that these laws can be represented by equally elegant and beautiful mathematical equations, and that the human mind has uncovered these profound relationships? Do you ever think, deep in your soul, about the profound discontinuity between human and animal life, and where that might have come from in a geological instant? Are you completely convinced that your materialistic worldview can account for Chopin's piano concerto? If your worldview is correct (and I find it superbly irrational) then nothing ultimately matters. We are just meat-machines, and all of the discussion on this forum is a completely pointless waste of time, as is your life, and as is mine. GilDodgen

Elizabeth, see my comment above. All the key issues about the Darwinian mechanism are *assumed* as premises and programmed into the system. It is entirely circular, 100%. If you doubt this, then please answer the following question: I have a theory that there is no indirect Darwinian pathway from point x to y. I write a computer program, *building in the fact that there is no possible indirect pathway from x to y.* I run the program, and sure enough, none of my fake "organisms" make it from x to y through an indirect pathway. Would you say that the program has demonstrated the veracity of my theory? Or would you say that the program is an exercise in circular reasoning? Eric Anderson

Elizabeth: “But Eric, the whole point of the AVIDA simulation is to show that if a feature is “rewarded” it will evolve! That’s the Darwinian mechanism! And it works! It’s not circular to demonstrate that the mechanism you propose works, works! It’s just successful!” Well, I posted a long comment earlier today, but apparently it went into the ether. Briefly, the Avida paper demonstrates purely circular question-begging reasoning. Let’s look at some of the key questions about the alleged Darwinian mechanism. (1) Is there a route from point a, to b, to c to get to our final function? Avida is programmed to assume that there is. (2) Does each point along the route confer a functional advantage? Avida is programmed to provide such advantage. (3) Is there an end-looking goal to the progress? Avida supplies the end “goal”. (4) Would organisms be rewarded more for getting closer to the goal? Avida includes an increasing award along the way. (5) Does it only take a small number of changes to get from point x to y? Avida is programmed with a short, simplistic path. (6) Is it easy for mutations to achieve each step along the way? Avida is programmed with that assumption. Those are off the top of my head, and we could probably think of others if we took a few minutes. In other words, if I assume all of the key points about my theory, then I can demonstrate the veracity of my theory. Congratulations. Guess what, I can prove my theory about pixies creating all the trees in the forest too. All I have to do is assume that pixies exist and regularly create trees in the forest and, voila, I have shown my theory! Let’s be very clear, in addition to all the problems that arise from the fact that Avida doesn’t mimic anything close to biotic reality, the primary Avida paper Darwinists love to point to as a demonstration of Darwinian principles in action is nothing but question-begging circularity. As a demonstration of Darwinian evolution having the ability to evolve irreducibly complex features (which was the point of the exercise), it is fatally flawed and logically invalid. Please take some time to think through this issue before jumping on the Avida bandwagon. Darwinism isn’t proven wrong just because of the Avida circularity, so it’s OK for you to acknowledge that Avida is circular. :) Eric Anderson

"The Darwinian answer is "no"." And that is the wrong answer. Enough has been said here at UD and elsewhere that there are. But that obviously does not count... Eugene S

This really does betray a complete misunderstanding of both AVIDA and evolution on both your parts! The reasoning is not "circular" at all. The hypothesis is that if you have self-replicating critters that reproduce with variance, and that the variance results in differential reproduction in a given environment, the population will tend to adapt to that environment, meaning that its members will tend to have features that enhance its chances of surviving and reproducing in that environment. All the AVIDA simulation does is specify the environmental constraints on survival. In nature, these simply exist. Thus, AVIDA simulates a toy version of nature, in which populations evolve to survive environmental hazards and exploit resources. In AVIDA the environmental resources are exploited by critters that can perform logic functions. In life they are exploited by critters that can perform foraging functions. No circularity at all. Elizabeth Liddle

But Eric, the whole point of the AVIDA simulation is to show that if a feature is "rewarded" it will evolve! That's the Darwinian mechanism! And it works! It's not circular to demonstrate that the mechanism you propose works, works! It's just successful! Elizabeth Liddle

Indeed. So the issue is: are there islands? The Darwinian answer is "no". Elizabeth Liddle

would hope you would appreciate this by now, but it bears repeating. First, bad design is not a valid argument against design.

No, it isn't, but it would be an argument against a good designer.

Second, the bad design nonsense, from Darwin to modern times, enjoys an extremely poor track record — nearly 100% negative.

I didn't say the giraffe's neck was "badly" designed (although I would say our own backs were, also female pelvises). I said it looked incrementally designed - retrofitted from an earlier model. Why else would the recurrent laryngeal nerve take such a hugely circuitous route? But the point about incremental retrofitting is that however successful the result (and incremental modification is often an excellent way to proceed), it tends to leave a "paper trail", as in the recurrent laryngeal nerve. Or what are called "skiamorphs" in human design. Elizabeth Liddle

gene duplication and fusion seem to always pop-up when i read about new genes. Starbuck

Uoflcard, It is so clear and obvious, isn't it? Trouble is they will never agree with this, maybe some individuals will, but not the entire cohort. They will keep on repeating that Windows 7 bit by bit can come spontaneously out of "Hello, world!" or that long messages can appear by chance as a result of letters spontaneously sticking together in words and then in sentences. And that meaning can emerge out of chaos by itself... Eugene S

Elizabeth: “But Gil, the range of “existing” information in any given population that is “mixed and matched” is itself the result of mutations!” If you simply mean that mutations are happening and changing existing information, then sure (although they wouldn’t be changing it for the better, see below). If you mean that mutations are responsible for the functional complex specified information that is in organisms in the first place, then your statement is an unsupported article of faith.

Well, we need a clear definition of information in order to continue with this conversation. If a mutation results in a viable phenotype that nonetheless bears brand new alleles, we can say there is "new" information - we now have a DNA sequence that "tells" the other molecule in the cell to do something new. There is no reason to think that this wouldn't be something "better", but more likely it is something that is neither better nor worse, simply slightly different. If it is disastrously worse, it probably won't get passed on to many offspring, if any, and will quickly drop right out of the gene pool. If neutral, it may propagate through the population, and if better, it is more likely to do so. Once it has become prevalent, and most members of the population bear it, to their advantage, we say that the population has "adapted", in that it now mostly consists of individuals that have a new feature that fits it better for the current environment. So in this sense the population genome, and the prevalence of the new allele represents population-level "information" about what works in the current environment. As for "the functional complex specified information that is in organisms in the first place" then it depends what you mean by "in the first place". Why should we assume that "in the first place" the "information" was particularly complex? We know that Darwinian processes (heritable variance in reproductive success) results in information, on at least two levels (the organism and the population), and that this information tends to accumulate. What 's to prevent it starting simple and becoming more complex?

“Mutations – novel sequences – are constantly being drip-fed into the population . . .” Again, if you mean that mutations can change sequences, sure. If you mean that mutations bring about new functional complex specified information, then this statement is unsupported.

I mean that mutations result in brand new alleles. These represent new information in the sense that they build and/or maintain an organism in a new, if tiny, way. They also represent variety in the population gene pool. This means that the population can adapt, as you would agree it does, which means that it represents "information" from which "nature" "selects" what "works" in the current, or changing environment. If you mean something else by "new functional specified information" then please say what. I have just supported my own statement.

“Especially as we know from simulations that this is exactly what happens!” Not clear what you mean by “this.” What is it you think is happening in computer simulations? If you are referring to the fact that simulations are programmed to keep the “helpful” changes and cull the bad ones, then we are simply talking about a circular programming logic.

Computer imulations of evolutionary processes simulate the natural process by which "helpful" changes are bred from and the poorer ones are "culled" by hazard. That's not "circular programming logic" it's simply the implementation of the very mechanism that Darwin proposed, and it works.

If you are suggesting that simulations produce new functional complex specified information, that is simply false. No computer simulation has ever done so.

Lots of simulations have done so. That's why we use them - to gain "new functional, complex, specified information" about how to solve a problem. Quite literally. Sometimes the information is a piece of computer code; sometimes it is a novel design (antennae, for instance); sometimes it is a classifying algorithm. All are new (they didn't exist at the beginning of the run); functional (they do a useful job); complex (in the sense of being highly unlikely to be generated by a random draw of components, although sometimes more elegantly simple than human designs); and specified (one of a sub set of possible patterns), and they tell us something we didn't know (so they contain information). Elizabeth Liddle

I'm aware of the problems of pumping blood to the giraffe brain. But the fact is that when legs get longer, many systems have to get longer. How do you suppose all that is coordinated? Petrushka

Are you seriously arguing that the giraffe’s neck supports a gradualistic evolutionary scenario and counts as evidence against design because it is designed poorly? If so, you need to do two things: (i) read up on what is involved in the engineering of the giraffe’s neck, (ii) think through what would be involved in changing it, before making assertions based on simplistic notions of what you think the design should be.

What do you suppose is involved in engineering the difference between a basset hound and a greyhound? You suppose selection could manage that? Petrushka

Elizabeth: "In fact the giraffe’s neck is an excellent example of incremental adaptation being a more likely explanation than intelligent design . . ." Are you seriously arguing that the giraffe's neck supports a gradualistic evolutionary scenario and counts as evidence against design because it is designed poorly? If so, you need to do two things: (i) read up on what is involved in the engineering of the giraffe's neck, (ii) think through what would be involved in changing it, before making assertions based on simplistic notions of what you think the design should be. I would hope you would appreciate this by now, but it bears repeating. First, bad design is not a valid argument against design. Second, the bad design nonsense, from Darwin to modern times, enjoys an extremely poor track record -- nearly 100% negative. Almost without exception (so-called vestigial organs, the supposed backwards wiring of the vertebrate eye, junk DNA, etc.) once we learn more about the system in question it turns out to be an example of exquisite design, including often ingenious engineering constraint tradeoffs. People who make the bad design arguments invariably never offer any detailed engineering explanation for how the system could be engineered better. The argument always grovels at the base level of "gee, this looks kind of strange to me, so it must not have been designed." Eric Anderson

Petruskha: "I’m addressing the Douglas Axe paper in which he argues that sequence space is so sparse that you can’t evolve a new protein by gradual accumulation of mutations from an old one. This is a non-problem. I don’t have the pathetic level of detail, but no one thinks that you can modify an existing protein coding sequence substantially while it is still needed for its old function." You are missing Axe's point. He is not primarly talking about changing a protein while it is still needed for old function (although that would further complicate things). His work shows that *even assuming* you've got a neutral sequence hanging around (from duplication or whatever your preferred approach is). Even if you have complete and total freedom to tweak the sequence all you want, you simply are not likely to stumble upon a functional protein sequence. Eric Anderson

Elizabeth: "But Gil, the range of “existing” information in any given population that is “mixed and matched” is itself the result of mutations!" If you simply mean that mutations are happening and changing existing information, then sure (although they wouldn't be changing it for the better, see below). If you mean that mutations are responsible for the functional complex specified information that is in organisms in the first place, then your statement is an unsupported article of faith. "Mutations – novel sequences – are constantly being drip-fed into the population . . ." Again, if you mean that mutations can change sequences, sure. If you mean that mutations bring about new functional complex specified information, then this statement is unsupported. "Especially as we know from simulations that this is exactly what happens!" Not clear what you mean by "this." What is it you think is happening in computer simulations? If you are referring to the fact that simulations are programmed to keep the "helpful" changes and cull the bad ones, then we are simply talking about a circular programming logic. If you are suggesting that simulations produce new functional complex specified information, that is simply false. No computer simulation has ever done so. Eric Anderson

[q]I think we have a language problem here. “Natural selection” doesn’t “act” at all. It’s just the name we give to what happens when variants have differential reproduction in a given environment, and the resulting increased prevalence in the population of those variants that do best in that environment is what we call the adaptation of the population to that environment. That is the sense in which I was using the word “adaptation”.[/q] Liz, et.al. Its nice to see someone from the Darwinian camp admit to this. I've been saying for quite some time that NS is not a mechanism contrary to the claims of Darwinists that NS is one of the main mechanisms of evolution. It is just as you say, little more than a label given after the fact to certain observations we make. But if NS isn't the mechanism, then what is? That, it seems to me, is part of the issue...evolution doesn't really seem to have a mechanism. DonaldM

For record, moving around WITHIN a landscape of complex function, is utterly different from FINDING the islands in which those landscapes live, in the wider space of configs. kairosfocus

DLH You are of course right, but the problem is not cogency but listening. We have people who refuse to see a difference between moving about within an island of complex and specific function, and getting to such an island in a vast config space without intelligent guidance. You cannot extrapolate from the one to the other, but that is not recognised. The same people use intelligence to compose messages, and who see that you cannot compose anything of consequence by trial and error, want to imagine that in the special case of life, that happened. The implied appeal to repeated miracles of chance -- a cull on differential reproductive success across sub-populations is REMOVING not adding info -- pass right over their heads without their noticing. I have seen this before, with Marxists. So, I conclude: we are seeing a priori commitments and indoctrination in action. It is going to take an internal collapse of the evolutionary materialistic paradigm for many minds to change. But, already, alarming cracks are springing up in the foundations of the scheme. At this point, we need to note for record, observe on the implications of the symptoms, and move on. Twenty more years, is my guess. Back in 1980, few would have predicted that by 1990 - 91, Communism would be dead. (Never mind how it keeps on trying to stir and rise from its shallow grave. Von Mises and von Hayek put the fatal stake through the heart.) GEM of TKI kairosfocus

ScottAndrews: "Even that gets you only as far as variation, perhaps changes in beak sizes and shapes. It does not extrapolate to beaks, birds, or vertebrates." Elizabeth: "Why not?" Elizabeth, here is the fundamental, critical question you need to ask yourself: What if the microevolutionary changes we see don't lead to large-scale macroevolutionary changes? Once you are willing to sincerely ask this question and escape from the assumption that everything is all part of a the same long process of evolution, you find yourself free to examine the evidence in a whole new light. This mindset -- that all reality is just different manifestations of the one overarching reality of evolution -- is one of the principle barriers to being able to evaluate the evidence in an impartial manner. Eric Anderson

Elizabeth,

It’s just the name we give to what happens when variants have differential reproduction in a given environment, and the resulting increased prevalence in the population of those variants that do best in that environment is what we call the adaptation of the population to that environment.

Which is it? Differential reproduction or adaptation? How do you know whether differential reproduction has anything to do with the environment at all? It's circular. Differential reproduction results from a better fit to the environment, and a better fit to the environment is determined by differential reproduction.

you determine that it becomes fixed in the population faster than predicted by drift, and then you figure out by what mechanism it is conferring advantage.

That's better, although the dots between the specific benefit of the variation and the differential reproduction would have to be connected quite well. What appears to be selection could be epigenetic.

Even that gets you only as far as variation, perhaps changes in beak sizes and shapes. It does not extrapolate to beaks, birds, or vertebrates.

Why not?

I stand corrected. Such an extrapolation is at best a guess, so who am I to say what you may or may not imagine? ScottAndrews

Natural selection (according to theory) acts on individual variations, not adaptations. It is parts, not sums.

I think we have a language problem here. "Natural selection" doesn't "act" at all. It's just the name we give to what happens when variants have differential reproduction in a given environment, and the resulting increased prevalence in the population of those variants that do best in that environment is what we call the adaptation of the population to that environment. That is the sense in which I was using the word "adaptation".

Well, you have to do it statistically – if a variant becomes more prevalent in a population, then it is probably conferring some systematic reproductive advantage.

How can natural explanation explain anything when you cannot identify when it has occurred?

You can identify it, but only in the aggregate. This is true of lots of phenomena.

In order for the theory to be meaningful you must observe an individual variation, determine that it is advantageous, and observe that it leads to differential reproduction and becomes fixed in the population.

Or backwards: you determine that it becomes fixed in the population faster than predicted by drift, and then you figure out by what mechanism it is conferring advantage.

I honestly don’t find the idea that controversial, but that doesn’t mean it should get a free pass right on to being the cornerstone of biology without which nothing in biology makes sense, etc.

Sure, it shouldn't. I'm not suggesting it should.

Even that gets you only as far as variation, perhaps changes in beak sizes and shapes. It does not extrapolate to beaks, birds, or vertebrates.

Why not?

To say after the fact, that well, it’s prevalent in the population therefore it’s possible that it was advantageous and possible that it was selected, or maybe not, is meaningless. Less than meaningless.

Well you have to first compute the probability under the null of neutral drift, and if that is low, find the mechanism that seems to be conferring reproductive advantage. Elizabeth Liddle

Elizabeth,

It’s what natural selection is – the adaptation of a population to its environment by means of the differential reproduction of heritable variants within that environment.

Natural selection (according to theory) acts on individual variations, not adaptations. It is parts, not sums.

Well, you have to do it statistically – if a variant becomes more prevalent in a population, then it is probably conferring some systematic reproductive advantage.

How can natural explanation explain anything when you cannot identify when it has occurred? In order for the theory to be meaningful you must observe an individual variation, determine that it is advantageous, and observe that it leads to differential reproduction and becomes fixed in the population. I honestly don't find the idea that controversial, but that doesn't mean it should get a free pass right on to being the cornerstone of biology without which nothing in biology makes sense, etc. Even that gets you only as far as variation, perhaps changes in beak sizes and shapes. It does not extrapolate to beaks, birds, or vertebrates. To say after the fact, that well, it's prevalent in the population therefore it's possible that it was advantageous and possible that it was selected, or maybe not, is meaningless. Less than meaningless. ScottAndrews

Dr Liddle, the problem persists that in nothing you say is there anything of the rise of semiosis/information. I know its a broken record for materialists, but unforatunately its also the central figure in living systems. Without it, the prolific assumptions begin at the very start. Please point me to a materialist paper that doesn't simple assume a material reason for a combination of chemical compounds throwing off the shackles of entropy which ALL other material things must endure - only to forge unbelievable complex function in its place. Function? Can you point me to a single peer-reviewed article that calls this assumption into question in a serious manner. How many times has it been cited by others as a serious challenge to this assumption? Has it been buried? Why is not such a paper(s) heralded as being a logical benchmark in the search for OOL; why is it not in constant discourse among scientist attempting to explain the utterly astounding presence of biosemiotic LIFE in a universe of constant degradation and entropy? Or, in place of another round of meaningless answers to these questions, I would settle for your answers in regard to this conversation: https://uncommondescent.com/intelligent-design/science-and-freethinking/comment-page-2/#comment-401695 Upright BiPed

Liz, Let me preface my comments with some accolades. You have tremendous courage coming on this forum and defending your position with decorum and civility.

You are very gracious, Gil, but no courage on my part is required :) If I persuade you of my case, that is fine - if you persuade me of yours - well, I shall also regard that as fine! After all, in that case I will presumably regard my change of view as an improvement :)

But Gil, the range of “existing” information in any given population that is “mixed and matched” is itself the result of mutations!

This is a completely unverified assumption based on an a priori assumption that random errors — which universally and consistently degrade complex functionally integrated systems — can produce the exact opposite.

It's an extremely well-verified "assumption" - which is why evolutionary algorithms actually work! Random copying "errors" (scare quotes used because of course they are not "errors" - an EA wouldn't work without them), in other words, replication with stochastically introduced variation do not "consistently" and certainly do not "universally" degrade complex functionally integrated systems. They do if the system is not robust to variation (by definition) but not all complex functionally integrated systems are vulnerable to variation, and biological organisms are demonstrably robust to variation, which is why most of us are healthy despite the huge number of alleles found in the human population.

In addition, even the most trivial mathematical calculation of the probabilistic resources that would be required relegates all of this speculation to the realm of magical thinking, in my opinion.

Required for what? Could you show your calculation, and show me what you are calculating?

I no longer visit Darwinist websites because of the vilification and outright pathological hatred and vitriol displayed against me and those of my persuasion.

Well, I can understand that. It's one of the reasons I set up my own site.

I am especially offensive to such people, because my interest and expertise in science, engineering, mathematics, computation, and information theory — all of which they thought would support their worldview — convinced me that they have everything wrong.

But there are many people with interest and expertise in science, engineering, mathematics, computation and information theory who are just as convinced that you have "everything wrong"! I'd argue many more, in fact. I'd even include myself :)

The point of my post is that the creative potential of the proposed Darwinian mechanism is based on completely unverifiable assumptions (and even empirically falsified assumptions), which contradict everything we have learned in the information age.

Well, I'm not sure what "unverifiable assumptions" you mean, but it seems to me that it is perfectly verifiable that organisms are robust to genetic variation, and, moreover, that even though in a well-adapted population, more new variants will be less good than even better, those that are less good will tend to drop out of the gene pool. So far from contradicting "everything we have learned in the information age" that "assumption" is entirely consistent with it, and, moreover, underlies much information theory, including neural science, and certainly including the development of evolutionary algorithms.

Natural selection does nothing to mitigate the probabilistic hurdles that must be overcome.

Well, first I'd like to know what these "probabilistic hurdles" and then I'd like to know why "natural selection does nothing to overcome" them. Natural selection is not, of course, an agent, and it can be misleading to use it as the subject of a verb. Natural selection simply means, no more and no less, than the simple fact that in populations that replicate with heritable variance in reproductive success, the probability is high that variants that confer some phenotypic feature that enhances reproductive success will become more prevalent than those that those without that feature. In other words, far from being "improbable", adaptation becomes highly probable, once you have that self-replicating population.

NS is a garbage-disposal system. Garbage disposals don’t create anything new.

Not really. Natural selection is simply differential reproduction. If a new variant reproduces better in a given environment, or even if an old variant reproduces better in a new environment, that is natural selection. What produces something "new" is the drip feed of near neutral variation. What builds these new variants into some new function is the accumulation, over generations, of variants of variants each of which confer increased reproductive success in the current environment. Which can be observed readily in any Evolutionary algorithm, and is observed both in the lab and in the field.

Finally, I refer you to my link here: http://www.youtube.com/watch?v=UEQbgJ2J9D4 If Darwinism is true we must believe that random errors (with the bad errors thrown out by natural selection) created the mind of Chopin who composed his beautiful piano concerto.

Natural selection does not throw out bad errors. Natural selection is, as I said, no more than heritable variation in reproductive success. Obviously if a new variant is incompatible with reproduction it will be "thrown out" in the sense that it will not join the gene pool. Much more important is that any change in the environment will tend to result in a change in the prevalence of existing variants within the pool, a pool that is being constantly drip-fed by near-near neutral variants that drift kaleidoscopically across it. As the environment fluctuates and changes, these variants shift in "selection coefficient" - fluctuate from being slightly advantageous to neutral to slightly disadvantageous and back again, sometimes simply around a mean, sometimes, if the change in the environment is rapid (and remember that the environment includes the evolving population itself, so there are feedback loops and resulting non-linearities) in a consistent direction along some fitness dimension. So why should this not result eventually in Chopin? Why should our primate ancestors not have moved systematically along the dimension of greater and greater intellectual and imaginative power, given the benefits that it provides?

It also must explain the invention of the musical instruments, the skill and dedication of the musicians, and the passion and beauty of this wonderful art.

Well, no. It must explain the capacity to invent musical instruments. But once you have cultural vectors for the transmission of behaviour as well as genetic ones, we are beyond Darwin (except in the sense of "neural Darwinism", which is important, and relevant, but not what Darwin was talking about). Nobody thinks that Chopin's music evolved by Darwinian mechanisms (apart from neural Darwinism), merely that people with the capacity to develop a culture that enabled some to write music on a par with Chopin's did.

I’m sorry, but there is no way I could possibly muster up enough irrational blind faith to believe in such a thing.

And I hope you never will :) What is required is not "irrational blind faith" but insight into just how well the universe actually works :) In fact, if the ID argument was that only a God could have invented a universe that could bring forth Chopin, I'd be almost fine with it. What I'm not fine with is the idea that the only possible God is one who had to tinker with his/her creation from time to time in order to ensure that Chopin turned up. The theory that the universe actually works without outside interference seems infinitely more marvellous to me than one that requires a maintenance engineer :) It is also, IMO, one that is supported by overwhelming evidence. Elizabeth Liddle

I'm addressing the Douglas Axe paper in which he argues that sequence space is so sparse that you can't evolve a new protein by gradual accumulation of mutations from an old one. This is a non-problem. I don't have the pathetic level of detail, but no one thinks that you can modify an existing protein coding sequence substantially while it is still needed for its old function. But there are many sources of emergent proteins, ones with minimal functionality, arising from duplicated genes or from other genomic changes. We can track these through lineages. Someone else on this forum asserted there were 22 proteins separating humans from chimps. This was supposed to be an argument in favor of ID. But 22 proteins is eleven each for the two species, about 2 per million years since divergence. That seems about right for evolution and not particularly fast for a designer. More pathetic detail is no doubt needed. It would be interesting to see and compare the coding sequences. Petrushka

sorry about messing up the quote tags! Elizabeth Liddle

Natural selection is the selection of individual variations.

Well, it's the increase in prevalence, in a population, of those heritable variants that tend to confer reproductive success.

The concept of natural selection does not include adaptation.

? Yes it does! It's what natural selection is - the adaptation of a population to its environment by means of the differential reproduction of heritable variants within that environment.

You could argue that an individually selected variation is an adaptation, but above you distinguished the two by stating that one leads to the other.

Well, if it's "selected" that means it was adaptive! Unless I'm misunderstanding what you mean by "individually selected variation". Variants aren't exactly "individually selected". No active "selection" of course takes place at all. "Natural selection" simply refers to the self-evident fact that variants tend to reproduce better in a given environment will become more prevalent in that environment (by definition!) The other name for that is "adaptation" by a population, to its environment, i.e. the increased prevalence of variants that do well (are well "adapted") to that environment

Is every inherited variation a selected one?

No. "Selected" variations are those that become more prevalent in a population because they confer some kind of reproductive advantage in that environment (better camouflage, for instance, or more efficient foraging). Most variants will be neutral with respect to the current environment.

Can a variation be inherited but not selected?

Of course. Any variant that is passed on to an organism's offspring is "inherited". Only when, and if, organisms with that variant tend to reproduce better in that environment than other variants do we say they are "selected".

It seems that in order to know the difference one would have to determine that a single variation was directly responsible for differential reproduction. How does one do that?

Well, you have to do it statistically - if a variant becomes more prevalent in a population, then it is probably conferring some systematic reproductive advantage. However, some fluctuations in prevalence are simply drift, so you'd need to demonstrate that the rate of increase in prevalence is sufficiently rapid that it is unlikely to be due to drift alone. And of course all inferential statistics come with confidence limits. Also, de novo mutations are fairly unlikely to be advantageous ("selected") at time of first appearance - the vast majority of de novo mutations are near-neutral in effect, and some of them drift right out of the population straight away while others drift across it. Those that become prevalent by drift contribute to the richness of the gene pool, so that when the environment changes, the population is able to adapt. In populations that get too small, this richness of course is reduced, and extinction becomes more likely.

Elizabeth Liddle

There isn't any evidence that demonstrates any organism is a sum of its genome. And although genes may influence development they do not determine it. As for gene regulation, well Darwinism can account for that either. Joseph

But why would new proteins be needed for any of those things? Ciphertext: a regulatory sequence is a DNA sequence of that may or may not code for a protein, but does code for the expression of genes that do code for proteins, according to incoming signals, either from internal or external environment. Genes are expressed both during development, to build the organism, and throughout the lifetime of the organism, to enable it to maintain itself and to function. Every time you move, or think, genes are switched on and off, so that they express, or stop expressing, proteins. When and where they do so is what makes you physically different from other people (even your identical twin!), from other species, and from yourself yesterday. Elizabeth Liddle

Except nature does not select and natural selection is just an output of three processes. Joseph

One doesn’t need new proteins to make a longer neck. Changes in size are regulatory changes, and one doesn’t have to have separate genetic changes to take care of muscles and bones. Development takes care of coordinating the separate systems.

Those are pretty bold assertions! No, usually an offspring with a longer neck does not need new proteins to accomplish that. Let's say I have a 5.0" neck and my child grows up and has a 5.3" neck. I would feel safe with your assertion that no new proteins were developed for him/her to have the 0.3" longer neck. But at some point during giraffe evolution, many new features were required to prevent catastrophe: pressure sensors along the arteries, valves throughout the veins to control returning blood flow, along with the larger heart, thicker arteries, etc. I'm not saying you're definitely wrong, but I would tend to be more cautious when saying "no new proteins are needed to make a longer neck". uoflcard

Well, that’s the irreducible complexity argument.

No, it's not. It's the fCSI argument.

But it’s based simply on the assertion that these “canyons” exist.

It's not an assertion, it's an observation. It's an observation from every time we have ever witnessed something complex, functional and specified being created; it has always involved leaps in information, not piece-by-piece increases in functionality. The burden of proof is on you to show that this is possible. You are the one making unsubstantiated assertions. And incremental modification does not conflict with ID. It just depends on what how big the "increments" are. Many ID advocates believe in descent with modification, in one way or another. So many would agree with you for why the laryngeal nerve is where it is. Others say it serves, or may serve, purposes we're not yet fully aware of. You could fill a 500-page text book with the cases where neo-Darwinian evolutionists completely underestimated a biological feature as "bad design" when it was accomplishing something no one had foresaw. uoflcard

Elizabeth Liddle Re: "Mutations – novel sequences – . . .Why shouldn’t this produce a continously operating homeostatic system that constantly optimises the population . . .?" Excellent question that strikes to the core of the issue. 1) The very high probability that mutations systemically degrades the genome much faster than any probability of fixing "beneficial" mutations. 2) Any benefit of "beneficial" mutations is swamped by the load of harmful mutations since the organism can only pass them all on to the next generation, negating any possibility of beneficial "natural selection". 3) This overwhelming degenerating process very strongly prevents the first viable self reproducing cell from ever forming. These degeneration statistics are similar to that of the overwhelming probability of the 2nd law of thermodynamics. For a popular presentation with technical appendix see John Sanford, Genetic Entropy and The Mystery of the Genome ISBN-13: 978-0981631608. To see the effective consequence of such mutations, check out: Mendel's Accountant. That gives you full control over all the mutation parameters and gives you quantitative statistics from actual forward mutation runs. All Darwinian arm waving is not in the remotest sense credible against the overwhelming statistics of mutational degradation. Arthur Eddington declared:

if your theory is found to be against the second law of thermodynamics I can give you no hope; there is nothing for it but to collapse in deepest humiliation.”

Gifford Lectures (1927), The Nature of the Physical World (1928), 74 Ivan Pavlovich Bazarov (1916-2005) observed:

“The second law of thermodynamics is, without a doubt, one of the most perfect laws in physics. . . . . It is not possible to find any other law (except, perhaps, for super selection rules such as charge conservation) for which a proposed violation would bring more skepticism than this one.

The statistical probability of overcoming this systemic mutational degradation of the genome is in the same class as the probability of violating the 2nd law of thermodynamics. Any attempt to overcome it is laughably futile. DLH

Liz, Let me preface my comments with some accolades. You have tremendous courage coming on this forum and defending your position with decorum and civility.

But Gil, the range of “existing” information in any given population that is “mixed and matched” is itself the result of mutations!

This is a completely unverified assumption based on an a priori assumption that random errors -- which universally and consistently degrade complex functionally integrated systems -- can produce the exact opposite. In addition, even the most trivial mathematical calculation of the probabilistic resources that would be required relegates all of this speculation to the realm of magical thinking, in my opinion. I no longer visit Darwinist websites because of the vilification and outright pathological hatred and vitriol displayed against me and those of my persuasion. I am especially offensive to such people, because my interest and expertise in science, engineering, mathematics, computation, and information theory -- all of which they thought would support their worldview -- convinced me that they have everything wrong. The point of my post is that the creative potential of the proposed Darwinian mechanism is based on completely unverifiable assumptions (and even empirically falsified assumptions), which contradict everything we have learned in the information age. Natural selection does nothing to mitigate the probabilistic hurdles that must be overcome. NS is a garbage-disposal system. Garbage disposals don't create anything new. Finally, I refer you to my link here: http://www.youtube.com/watch?v=UEQbgJ2J9D4 If Darwinism is true we must believe that random errors (with the bad errors thrown out by natural selection) created the mind of Chopin who composed his beautiful piano concerto. It also must explain the invention of the musical instruments, the skill and dedication of the musicians, and the passion and beauty of this wonderful art. I'm sorry, but there is no way I could possibly muster up enough irrational blind faith to believe in such a thing. GilDodgen

Your last paragraph is almost as predictable from you as your "conversion from atheism" story. Yet you never give any evidence. Some time ago you said that your high school math showed you why "Darwinism" is wrong: when are you going to share the math with us? Grunty

What would constitute a regulatory sequence? Is that a sequence of genes? If so, I gather that the use of the term "sequence" indicates that there is a significance in the order of the genes comprising the sequence. So perhaps you don't need new genes (folded proteins), but you would need a previously unrecorded sequence? So you have a specific set of proteins/genes to operate upon which represent a reduced set of the larger, possible proteins in configuration space. I wonder what the possible sequences could be? Can they repeat or is that a "no no"? What are the other term limiting factors? Something like I have a "G" so that means the next term could be a "C" or an "A" but not a "T". That could further reduce the config space per term, but probably not in total. ciphertext

That's interesting - I didn't realise that people thought that having a longer neck required new proteins. Elizabeth Liddle

It really depends on the landscape. I think the Douglas Axe paper muddies the water by assuming that evolution is mostly about making new proteins. This seems to be the focus of Behe's Edge also. But most morphological evolution, including most of what separates one mammal from another, is accomplished in regulatory sequences, not in protein coding sequences. One doesn't need new proteins to make a longer neck. Changes in size are regulatory changes, and one doesn't have to have separate genetic changes to take care of muscles and bones. Development takes care of coordinating the separate systems. If this weren't true, then sizes differences within species would be mostly fatal. Petrushka

Well, that's the irreducible complexity argument. But it's based simply on the assertion that these "canyons" exist. Why should the giraffe's neck not have been due to incremental adaptation? It's not as though anyone is proposing that suddenly a generation of giraffes had 8 foot necks and then had to wait around hoping for the right kind of arterial support. In fact the giraffe's neck is an excellent example of incremental adaptation being a more likely explanation than intelligent design - why else would its recurrent laryngeal nerve have to take such an enormous detour rather than a short cut, if not because it is the result of incremental modification from a short-necked ancestors in which the routing is less of a problem (though still a problem, and for us too), and, which in turn resulted from incremental change from yet more remote ancestors with no necks at all? Elizabeth Liddle

Why shouldn’t this produce a continously operating homeostatic system that constantly optimises the population as the environment changes, and maintains it at an optimum when it stays the same? Especially as we know from simulations that this is exactly what happens!

Sounds good, except you forgot the whole problem about complexity, in which life is rich. It works great when you don't need complex novelty, just optimization in the variety. For instance, Darwin's finches. It also works with make-believe, middle school biology explanations for things like giraffe's necks. Long ago, ancestors to giraffes had much shorter necks (among other differences). There was competition for the available foliage. Some orangisms' necks were longer than others. The longer their necks, the higher the vegetation they could reach, where there was less competition. These were more likely to reproduce than the average pre-giraffe, so the average neck length of the population drifted upward. This continued until we have the giraffe's of today! Nevermind that multiple phenotypic canyons had to be crossed, which required loads of new information to prevent the organism from passing out, arteries from rupturing, etc. None of this information could seemingly be pieced together bit-by-bit with gradually increasing fitness, just as the code for Windows 7 can't be generated bit-by-bit with increased functionality at each step. Simulations are great at showing that functional, complex specificity can only be generated by intelligence, either all at once or piece-by-piece with an end goal in mind. It's like saying my car can drive from here to Disney World all by itself (as long as I make velocity [speed and direction] corrections at certain points). uoflcard

Elizabeth, I'm just jumping in at random, but this simply isn't so:

Natural selection is most certainly a “meaningful principle” and a very straightforward one, which is that heritable variation in reproductive success will lead to adaptation.

Natural selection is the selection of individual variations. The concept of natural selection does not include adaptation. You could argue that an individually selected variation is an adaptation, but above you distinguished the two by stating that one leads to the other. Is every inherited variation a selected one? Can a variation be inherited but not selected? It seems that in order to know the difference one would have to determine that a single variation was directly responsible for differential reproduction. How does one do that?

ScottAndrews

But Gil, the range of "existing" information in any given population that is "mixed and matched" is itself the result of mutations! Mutations - novel sequences - are constantly being drip-fed into the population, while others, including those least advantageous in the current environment, constantly leaking out. Why shouldn't this produce a continously operating homeostatic system that constantly optimises the population as the environment changes, and maintains it at an optimum when it stays the same? Especially as we know from simulations that this is exactly what happens! Elizabeth Liddle

Natural selection is most certainly a "meaningful principle" and a very straightforward one, which is that heritable variation in reproductive success will lead to adaptation. For it to happen, you have to have some mechanism for producting heritable changes in phenotypic characteristics that will affect an organism's probability of reproduction, and we know what this mechanism is - slight variations in DNA sequences as they are transmitted from one generation to the next. And no, they don't "do much of significance" usually, at least alone, or for the organism in which they appear de novo. Which is why they tend to just drift, or not, through the population, those that do enriching the pool of variance from which, as we know from direct observation, "nature" "selects" those variants that do turn out to be useful when the environment changes. Elizabeth Liddle

Natural selection (to the extent it is even a meaningful principle) does not operate to create new systems. All it does is apply a label to the fact that some creatures died out before their characteristics got fixed in the population, while their more fortunate siblings survived. The "creative" part of Darwinism is just random, slight, successive variations. Then there is the growing realization that random mutations might not do much of significance anyway . . . Eric Anderson

"But this is not what Darwinism ultimately claims. It claims that random errors ... can explain all of biology, including the evolution of a primordial single cell into the mind of Mozart." No. You left out natural selection. All that the random mutations do is produce the raw material that gets filtered out by natural selection. It isn't a straight-line path that says one radom mutation will propagat all the way. What happens is that many organisms will be generated, with many different random mutations, from which nature will select. Grunty

Eric, This entire discussion elucidates the essential difference between the ID inference to the best explanation (design) and Darwinian materialistic philosophy, which is hopelessly mired in the ignorance of the 19th century. Randomness is universally, progressively, and inexorably destructive. It always eventually degrades, and never ultimately produces, except in the pathological circumstances Behe has identified, and even there, randomness does destroy, although with a temporary survival advantage. As I mentioned, the notion that random errors -- of whatever variety, and whether or not filtered by natural selection -- can produce something like the following from a primordial single cell http://www.youtube.com/watch?v=UEQbgJ2J9D4 should be considered by any logical person to be preposterous on its face. This is snake-oil salesmanship of the highest order. (My apologies to snake-oil salesmen, since snake oil might actually have some beneficial properties.) GilDodgen

Thank you. The [what Avida paper?] answer I'd hoped for was "The evolutionary origin of complex features" Regardless, your quote above from that paper enabled me to find it. Charles

I discuss it in passing in my paper Gil linked to below. The specific sentence arises in the discussion portion of their paper, in the same breath where they attempt to wave off the obvious circularity problem in their arguments. They state: "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, and indeed, our experiments showed that the complex feature never evolved when simpler functions were not rewarded." It is the last phrase that is particularly telling, and demonstrates that the entire Avida exercise they undertook is a question-begging circular argument. The fact that the complex feature never evolved unless the program was systematically nudged toward the end target is, in my view, the real lesson of the Avida exercise. Namely, that complex features are not likely to arise without some kind of forward-looking target in mind. This coincides nicely with Behe's concept of irreducible complexity, as further elucidated in his later book "The Edge of Evolution" where he looks at just how much (or little) variation plus selection is actually able to accomplish. Undertsood properly, without Darwinian blinders on, the Avida results actually support Behe, rather than being a refutation of Behe, as they were intended. Eric Anderson

Eric, You wrote a superb essay deconstructing Avida. UD readers might like to check it out here: http://www.iscid.org/papers/Anderson_BitByte_020305.pdf I particularly enjoyed this paragraph:

What is more astonishing, is that the authors are aware of their circular reasoning, but blithely dismiss it. In the final discussion section, they state, “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 . . .” Say what?? In other words, we have adopted as our premise the very conclusion we are trying to reach. In a particularly Darwinian display of twisted logic, the researchers seem oblivious to the fact that this circular reasoning invalidates their entire conclusion, and cheerfully waive it aside as an inconsequential technicality. At best such an approach manifests questionable judgment, at worst, self-deception.

GilDodgen

Indeed, there is a sentence in the Avida paper that is extremely telling To what Avida paper do you refer, please? A title or a link would be most helpful. Charles

...random variation followed by natural selection... An important distinction needs to be made here. The mixing and matching of existing biological information can produce substantially different outcomes, within the limits of that information. Any parent with two or more children can tell you that. But this is not what Darwinism ultimately claims. It claims that random errors (whether point mutations or other stochastic events, which flow endlessly from the fertile imaginations of Darwinists) can explain all of biology, including the evolution of a primordial single cell into the mind of Mozart. This is an extraordinary claim, which should require extraordinary evidence, not speculation and silly computer programs like Avida. GilDodgen

...what particular simulation of the Darwinian mechanism are you criticizing? All of them, insofar as they have any relevance to biological reality. The point is that computer simulations of the Darwinian mechanism in biology are completely irrelevant. They are completely detached from the reality they attempt to simulate, and are based on so many unverified assumptions that they should not be taken seriously by anyone with any legitimate scientific integrity. The only empirical evidence we have for the creative power of the Darwinian mechanism of random errors in biology has been elucidated by Michael Behe, and that is the partial destruction of existing systems to provide a survival advantage in a pathological environment. The extrapolation of this phenomenon to explain the origin of complex information-processing machinery should be rejected as superbly illogical and completely unwarranted on any legitimate scientific grounds. GilDodgen

NormO, I'm not sure I'd tell them to go back to school in a particular case. But we certainly could tell them to go back and look at the program again, carefully this time, to see if they can tell (from a programming standpoint, not a Darwinian wishful thinking standpoint) at precisely what point the particular specified information was first put into the program. The results will be telling. Eric Anderson

Gil, you make some valuable points about the need for precise, quantifiable, calculable inputs in order for simulations to produce useful results that match real-world situations. As far as organismal evolution, we aren't even close to being able to put a handle on what is going on biologically, and certainly can't program a reliable simulation at this stage. I happen to have been reading one of Bill Dembski's old essays today and was reminded of another fact that is, in my humble opinion, more central to the problem of many evolutionary algorithms. Specifically, whenever there is a target (whether Dawkins' "methinks it is like a weasel" or more recent efforts such as ev and Avida), anything within the programming that nudges the program to converge on the target, necessarily and by definition, increases the probability -- often to something nearing 1. By definition, this increased probability means that there is less contingency in the outcome, and, therefore, less complexity in any specification. These kinds of evolutionary algorithms give the appearance of being complex, but they in fact are largely deterministic. As a result, they simply cannot, as a matter of principle, produce complex specified information. Indeed, there is a sentence in the Avida paper that is extremely telling, which I view as the primary lesson behind Avida but which Darwinian proponents like to overlook. It is an acknowledgement that when they didn't carefully nudge the program in the right direction, it couldn't seem to get there on its own. And then there's the whole issue of the no free lunch algorithms, which, as I understand it, were specifically proposed in the context of evolutionary-type computer simulations to help properly recognize the conservation of information and avoid inadvertently attributing "new" information to the simulation when it in fact was programmed in at the beginning. Eric Anderson

Well this is all great Gil but what particular simulation of the Darwinian mechanism are you criticizing? I mean, if someone tries to convince me that a computer simulation has validated the creative power of the Darwinian mechanism of random variation followed by natural selection, should I just tell them to go back to school, or should I actually address the the particular weaknesses in their specific simulation? In other words, what the heck is the point of this post? NormO