“…and, in the same manner…”

Analogies. They come up all the time; useful in teaching or explaining, perhaps essential to our way of viewing the world; and yet highly problematic when too much relied upon. In his summary of Behe’s argument Allen suggests intelligent design theorists have made a fatal mistake in their reasoning, and are presenting nothing but the poorest form of logical argument, an “argument from analogy”. Is this a fair criticism?

All of the examples of design Behe provides in pages 194-204 to support his definition and design detection algorithm are clearly and unambiguously designed because they are all designed by humans, and we all agree that humans can indeed design things. However, arguing that this somehow validates his definition/algorithm is simply an argument by analogy, and we have already concluded that this form of argument alone is logically specious.

I submit that this charge is itself specious; that the design hypothesis, while based on analogies in the same way all non-deductive reasoning must necessarily be, is nevertheless a valid inductive argument; fraught with the same pitfalls as other non-mathematical inductive arguments, but neither unsound nor of inferior logic.

Our reasoning is as follows: in all situations in which we have a causal history, the presence of complex specified information (or, in Behe’s case, IC systems) unequivocally entails intelligent agency. While intelligent agency is capable of producing CSI, no other causes have been shown to have that capability. The reasonable inference, then, in those situations where we observe CSI but do not have a causal history, is to infer design by intelligent agency as the best explanation.

Allen’s charge is grounded upon the “human” element in most examples of unequivocal design; he claims that this shared property moves the argument into the camp of logically specious transductive arguments. This claim is unwarranted. In any inductive argument there is a case to be made for potential dissimilarities between the set that is observed and that to which we are generalizing; indeed, simply by virtue of having been observed, the initial set will always have some common property the extended one does not. While we may take this as a warning of the uncertainty that accompanies any inductive inference, this does not in any way invalidate the argument.

Michael Behe addresses this briefly in his response to Kitzmiller:

Cellular machines and machines in our everyday world share a relevant property — their functional complexity, born of a purposeful arrangement of parts — and so inductive conclusions to design can be drawn on the basis of that shared property. To call an induction into doubt one has to show that dissimilarities make a relevant difference to the property one wishes to explain. Neither the judge nor the Darwinists he uncritically embraces have done that in respect to intelligent design.

Nor yet, as far as I can tell, has anyone here.

First off, thanks to Elena for getting the ball rolling on class posts. I am another member of Allen’s class, and I too apologize for my ignorance of scientific theory. Nevertheless, I do have a few opinions to express on Behe’s “Black Box” and our class discussions.

Though I choose not to speculate on Behe’s possible motives (if there were any at all) for confusing the basic terminology of evolution/descent with modification/natural selection, I think it is important to note that after so much work was built on his own, which supposedly undermines evolution, he had a responsibility to define his views on the unanswered implications of his book, namely that his argument dispells “evolution”. Behe did not take the 10 year downtime between editions of Black Box to address what his book implied (that his theory overthrew evolution) whether he expressly stated it or not. Further, the fact that he wrote in the book that he believes the evidence supportes common descent is an even stronger reason for him to publically set the record straight on his views in the afterword of the new edition. Because he chose not to do so, it is difficult for me to believe he sincerely meant what he wrote on page 176.

In terms of the science behind Behe’s arguement (regarding which, as Darwin would put it, “my ignorance of the laws of biochemistry is profound”) the question to his underlying assumption is, I believe: are his examples really irreducibly complex? Well, it seems to me that depends on whether you consider any intermediate funtions of the proposed trait to be beneficial. Taking Behe’s popular example of the cilia: is it, with any aspect removed, still functional? As a whole cilia in the manner we know it now, no it is not. However, could these cilia have been functional in another way at an intermediate point in evolution? If so, then Behe’s concept of irreducible complexity doesn’t really challenge natural selection either. Though i recognize this logic is somewhat teleological, it is no more so than the concept of function/benefit in adaptations in general.

In a broader sense, I believe leaders of the ID movement (namely Behe and Dempski) are wrapped up in a similar problem to that which doomed some aspects of the modern synthesis: they focus to heavily on the micro-scale mathematical (and in Behe’s case biochemical) aspects of evolution, and in doing so tend to miss the forest for the trees. Often these minute changes do not even manifest at the level of phenotype upon which Darwin based his arguments for descent with modification and natural selection. In the same way that Fisher reduced natural selection to the level of alleles, Behe has reduced ID to the level of biochemical pathways. I believe these arguments tend to miss the significance of evolution on the level of phenotypes. Similarly, I believe Dawkin’s reductionist defense of evolution was equally as non-compelling. In my opinion, the most convincing argument for descent with modification and natural selection is still what I refer to as Darwin’s “look around you!” argument in the origin of species. Although this may not be based on hard math, I am not convinced that math and physics are the best means by which to judge biologoical processes. Though I realize this is a grossly over-generalized statement, please bare with me, as I am certainly not at the scientific level of those posting on this site. If someone with a greater degree of scientific understanding would like to explain why it is a good thing that biology be “more like physics/math” I would looking forward to reading it. Thank you.

. . . or, how not to address an argument.

I’m in major disagreement with almost everyone here, not only because of different points of view on the issues discussed, but also on the far more fundamental matter of the relevance of those issues to the whole discussion. So this is commentary and opinion, not class notes :).

We had a fun, spirited discussion; with lively participation from people on both sides. But in spite of that I maintain that we didn’t manage to make any headway at all–that, in spite of two hours of earnest discussion, our class session was singularly futile– and that this was because we couldn’t bring ourselves to address the content of the book at all.

There are three things you can do when faced with an idea with which you disagree. You can (1) ignore it, and use ad hominem attacks to explain why we shouldn’t be listening to the people who hold that idea anyway. You can (2) address it fully, and, examining its logical base, attempt to make a cogent, compelling case for why it fails. Or you can (3) use a healthy dose of imagination to decide what the disputant meant to be arguing, explain why that is illogical, and then, for good measure, lambast him for equivocating on the point he was “really, secretly” intending to make.

Our class is making– or trying to make– a strong statement against the first. But tonight we managed to get stuck in the third, and somehow failed to get to the middle one at all.

No one meant to make things up; and everyone is certain that their version of Behe is the one that matches reality. But there is something rather doubtful when everyone is so absolutely certain that they know exactly what Michael Behe thinks and intends, even if he doesn’t say it, and even if he categorically denies it several times over in the book.

What does evolution mean? The word appears on our book covers: Darwin’s Black Box: The biochemical challenge to evolution. Behe defines the way he uses the word in the preface: “a process whereby life arose from non-living matter and subsequently developed entirely by natural means.”

This is not an entirely rigorous definition, and is definitely not the way the word is used among evolutionary biologists. MacNeill will prefer the simple “evolution is descent with modification” definition. Behe doesn’t challenge descent with modification at all; in fact, he believes that common descent is well supported in biology. So is the tagline a blatant effort to mislead the public by pretending the book challenges something it can’t?

No; Behe’s tagline is consistent with his given definition, and his definition is consistent with the colloquial, commonly-used definition of evolution. This isn’t a paper in a biochemical journal, it is addressed to the layman. And– like it or not– this is the way that ordinary people consider the word evolution.

Does he use the word evolution in various senses in the book, in order to attack evolution (= natural selection) and come out having defeated evolution (= all of Darwinism, and especially descent with modification)? This charge also is hardly fair. Time and again he makes very clear which parts of evolutionary theory he rejects and which parts he sees no problem with. He rejects evolutionary mechanisms in certain parts of his field, biochemistry. He thinks “the rest” of evolutionary theory is likely true.

We can decide that he’s lying: Behe really rejects common descent, he just feels that writing a book in which he only addresses the mechanisms of evolution is the best way to support his cause right now. He is trying to get people to think that his book really destroys the case for descent with modification (the paragraphs in which he says he accepts it are meant to throw off the critics, and be ignored by the wider public).

We can, and if you want to decide someone lied and attack their supposed views you have a clear playing field in which to do it in– but none of what you say will have any relevance to the argument they actually made. The only way to deal with ideas is to give the benefit of the doubt on motives and address the arguments that were made– not their supposed intended implications.

Perhaps I feel more strongly about it because I’ve been stuck in the situation several times in the past; and I can tell you it is extremely unpleasant to make a good-faith argument for something you actually believe and then have an ugly strawman version attacked. I don’t mind being ferociously attacked– for things I actually believe. But for those just made up…

What I’m asking– yes, I know you can dream up all sorts of motivations for me, all sorts of things I “secretly believe”, and all sorts of things that I really mean to be arguing though I don’t say it. But if you want to engage my ideas you’ll have to engage more than simply your imagined boogeyman. Please, forget about it all right now, and look at what I actually argued. Can you give me an argument against that?

I’d love comments from anyone in our class who disagrees with me here. Somebody?

Or else let’s get to the ideas.

So because our class discussion tonight left me curious about several things (and thanks to Hannah’s encouragement) I’m trying out the message board for the first time… First off I just want to say, I don’t know very much about the Intelligent Design point of view, (or even if there is one standard point of view), but I’m curious about it, which is why I’m taking this class. So, if I say something that mischaracterizes it, please correct me, and also I’d be eager to get a summary of the general ID outlook/stance/point of view. Anyways, tonight we were discussing Behe’s Darwin’s Black Box and the arguments that came up included:

-What are Behe’s motives? He states several times that he believes in descent with modification, yet the cover of the book calls it a “challenge to evolution” and in many places in the book it seems he is suggesting his arguments undermine evolution, a.k.a., (as we defined it in class today) descent with modification.

-What ARE the implications of his arguments? Most everyone agreed that even if we decided to grant them all as true, it would have little bearing on 95% of evolutionary biology. Also, that questions about the origin of life are kind of a fringe area of evolutionary biology that aren’t necessary to answer in order to continue with the rest of it… and questions about how particular molecular processes came to be kind of fall into that same category with the origin of life. Even if we said, ah yes, okay, these molecular processes that Behe outlines are the instances where the intelligent designer stepped in, the vast majority of evolutionary biologists could still continue on with their research and their arguments unharmed. Hannah disagreed however, and said she did think his arguments may imply an alternate explanation to descent with modification. One of my questions is, what is this alternate explanation and how do Behe’s arguments support it? (unfortunately the discussion moved on before I got a chance to ask you about it in class, hannah)

-If, again, we accept Behe’s arguments, and say that these molecular processes are a product of intelligent design, is that a dead end? One argument was that it is, that the possibility for further research and exploration about the origin of these processes is closed. Other people said no, that it’s not an end, that it opens up other sorts of questions. Again, I’m curious, what sorts of questions do you then ask, or what research do you do, if you accept that something has been designed?

-Finally, we didn’t actually get into Behe’s actual descriptions of molecular processes and “machines”, or address his actual argument that they are “irreducibly complex” and could not have come about through any other means than design. I guess it’s true that no one in the class really has the biochemistry background necessary for the challenge, but I’m still very curious to hear the theories that more qualified people have about how these processes could have come about without being designed…

Over at the Panda’s Thumb, Dave Thomas has posted the results of another computer simulation of natural selection, this time applied to the classical “Traveling Salesman” problem. No, that isn’t the lead-in to an old dirty joke, it’s a classical problem in optimization. The basic idea is to calculate the shortest possible route for a traveling salesman to follow when visiting more than three cities (i.e. sales territories). Clearly, when there are only two cities, the solution is obvious to anyone with a knowledge of Euclidian geometry: a straight line connecting the two cities. However, as more cities are added, the number of possible solutions expands exponentially, making calculations of optimal pathways extraordinarily difficult.

This is where Dave Thomas (and a dish of soap bubbles) comes in. In his post at http://www.pandasthumb.org/archives/2006/07/target_target_w_1.html#more , Thomas first shows the classical solution to a five-node traveling salesman problem (TSP), as demonstrated by the Swiss mathematician Jakob Steiner (see http://en.wikipedia.org/wiki/Jakob_Steiner ). He then illustrates the optimal solution using a soap film generator, which uses free-standing posts and soap films to generate the optimal solution.

Thomas then goes on to formulate a “solution engine” for higher-level Steiner problems (i.e with more than five asymmetrically placed nodes), using natural selection operating on a computer-generated “TSP solver.” The results are truly astonishing: although the theoretical number of possible solutions is fantastically large, the TSP solver using simple natural selection (call it the NS_TSPS) found several optimal solutions with amazing speed. The same thing happened when Thomas tested the computer-generated solutions using soap films. Indeed, he was able to show that the NS_TSPS was actually more efficient at finding solutions than the soap film generator, a result that surprised him (and most of the commentators on the Thumb). One of the soap-film solutions took the shape of a “doggie,” a solution that the NS_TSPS didn’t find. Thomas was able to show that, although the soap-film solution was stable, it was actually sub-optimal to an alternative solution generated by the NS_TSPS (hence the title of this post)

Why is all of this important, in the context of our discussion of Dawkins’ The Blind Watchmaker? Because, unlike Dawkins’ WEASEL program, which used a pre-specified “target,” thereby opening his model to accusations that it simply “found” a pre-specified outcome (and was therefore actually an example of “intelligent design”), the NS_TSPS had no pre-specified solution at all, and found the optimal solutions the same way natural selection “finds” them in the wild: by simple trial and error, combined with preservation of partially successful outcomes.

In other words, the objections that some of us had to Dawkins’ WEASEL program have been addressed in Thomas’ NS_TSPS, and natural selection has been shown once again to be all that is necessary to “find” an optimal solution to a “problem,” even in the absence of a pre-specified outcome.

This is important to the ongoing discussion in our course for several reasons:

• It decisively undercuts the objections commonly voiced by advocates of ID, that all simulations of natural selection are actually simulating ID, as they all include pre-specified “target” outcomes.

• It shows the extraordinary (and somewhat counterintuitive) power of natural selection to “find” adaptive optima, even in the absence of pre-specified solutions.

• It reinforces a finding that has increasingly been coming out of research into computerized “genetic algorithms”: that selection processes that incorporate non-directed natural selection can find solutions to problems that are highly resistent to more “classical” targeted computation.

• It demonstrates that the common assertion by ID theorists that ID theory is logically necessary as an alternative to evolutionary theory, since the latter has failed to demonstrate empirically that it can solve such optimization problems in real time, is empirically false. That is, ID theory isn’t necessary to explain adaptation, even in cases where the computation of adaptive optima appears to be beyond the capability of any real-time computing system.

And this, in turn, emphasizes the point that I have made in several other posts to this blog: that rather than ID theory being a logically necessary alternative to evolutionary theory, it is a logically unnecessary addition to standard evolutionary theory, and one that furthermore is not supported by the empirical evidence.

There are other simulations of evolution by natural selection that are immune to the common objections voiced by ID theorists. To learn more about the most powerful one developed to date, go to: http://dllab.caltech.edu/avida/.

Cleverly drawing comparisons more or less in agreement with the creationist and/or intelligent design definition of complexity and what appears to be designed, Dawkins sets the stage for natural selection as not an alternative but the answer to the illusion of design. Yet, though he boasts, he provides no evidence or supporting arguments for his claims. In chapter two entitled Good Design, he acquiesces with the eighteen century theologian Willaim Paley and is impressed by the complexity of the sonar system bats use to coordinate themselves in space (and their respective environment). But he merely claims that Paley was wrong with no sound argument or conclusive evidence to support the modern day hypothesis that the job was done in gradual evolutionary stages by natural selection.

Granted that soft tissue (like brain) does not fossilize, we are left with guess work. We must look at various existing species of bats and using their ancestral relationships determine which form of sonar system is preceeded the other. Granted that he cannot show the transitional stages of the sonar system, he still failed to provide even a minimal basis for his confident claims. He only asserts that natural selection is the correct mechanism with no reasoning or supporting evidence by which natural selection could accomplish such an “illusion of design.” Nor does he build a strong case for natural selection in chapter three. The computer program he uses to illustrate natural selection works with a pre-determined goal oriented process - the exact opposite of natural selection!– though to his credit he acknowledges this flaw.

It seems to me that one could never expect a computer program to demonstrate the power of small changes acquired by mutation. Mutations in a grandoise sense, serves as a raw material for natural selection to work on. Considering that each mutation (roughly defined as a change in the genetic code of the individual) is unique and varies in the impact that it makes on the individual’s phenotype (it may be silent, deterimental, or a hox gene mutation with interesting results), it appears to be a mathematical impossibility to calculate the probabilities of each mutation’s effect on phenotype. To go from one stage to the next in the evolutionary process, you must recast the dice and calculate the probability of acquiring a new trait which increases your fitness value.

In the end, we are left with a book that does not satisfactorily makes an argument for natural selection, and with the impression of an “intellectually fulfilled atheist” author who’s arguments fall much below par.

In class last night Allen went over inference and his views of the boundaries of science. He gave us the example of an individual coming upon the remains of what appeared to have been a house fire in the past. Without any prior knowledge of the event or eyewitnesses to question, one might infer any of three things:

1) accidental house fire
2) arson: purposeful house fire
3) no fire at all; setup job (for film, etc.)

A tentative explanatory filter with which to distinguish between those three causes:

But he suggested there is a problem from the very beginning. The first question– was this a real fire, or a setup job? can never be definitely answered. Considering a very powerful film crew, for instance, the setup would look almost like a real fire. Extrapolating slightly, given an omnipotent “designer”, could the scene not be exactly the same as what one would expect from a housefire?

Because there is no way of giving a definite answer based on empirical evidence– to which we, as scientists, are limited– we must throw out that whole node on our explanatory filter. Everything above the dotted line, at least, is outside our realm of knowledge.

I had a quarrel with much of this reasoning, though to begin with I ought to make a strong disclaimer that I’m not at all interested in defending “setup jobs”– I think they are highly uninteresting, for one thing, and not worth spending time in. But a “right” or at least convenient answer doesn’t make the logic that goes into an argument sound.

First, can we throw a question out of the realm of science because we will never be able to get a definite answer? Scarcely anything in science will ever be proved or disproved. In general, we don’t look for certain proofs, but simply for empirical evidence that might favor one or the other, so that we can make an inference to the best explanation. If the evidence is not clear, we often make choices based on conventions, such as parsimony.

If we cannot throw it out for lack of a definite answer, can we at least throw out that node for lack of empirical evidence either way? It is true that if the scene was designed (omnipotently) so that there was absolutely no evidence there had been no real fire, science could do nothing with the question. But we cannot assume a priori that all “setup jobs” have no emperical evidence available; there are a great many other possibilities besides an omnipotent designer who works to make things exactly the same. Consider, for example Einstein’s view: “Nature hides her secrets because of her essential loftiness, but not by means of ruse.”; or in another remark: “God is slick, but he ain’t mean.”

So while we can do away with a “absolutely perfect imitation” possibility as an option that could never have any emperical grounds, that is not justification for demarcating the entire first node out of our field of inquiry. In any research project you learn quickly that things are not always as they first appear. What seems on first analysis to be the remains of a fire may turn out on further investigation to hold evidence of a set-up job. What appears to have been designed may in fact be the product of chance and necessity, and what we are used to thinking of as the products of unguided evolution may contain evidence of purposeful design.

Refusing to consider questions is never good practice; we may reject explanations for lack of warrant, but ought never reject the investigation a priori.