Things have been developing in rather interesting ways in our “Evolution and Design” seminar. We have worked our way through all of the articles/papers and books in our required reading list, along with several in the recommended list. Before I summarize our “findings”, let me point out that for most of the summer our seminar has consisted almost entirely of registered students (all but one undergrads, with one employee taking the course for credit), plus invited guests (Hannah Maxson and Rabia of the Cornell IDEA Club). Two other faculty members (Warren Alman and Will Provine) attended for a while, but stopped in the middle of the second week, leaving me as the only faculty member still attending (not all that surprising, as it is my course after all - however, at this point I view my job mostly as facilitator, rather than teacher).

Anyway, here is how we’ve evaluated the books and articles/papers we’ve been “deconstructing”:

Dawkins/The Blind Watchmaker: The “Weasel” example is unconvincing, and parts of the book are somewhat polemical, by which we mean substituting assertion, arguments by analogy, arguments from authority, and various other forms of non-logical argument for legitimate logical argument (i.e. based on presentation and evaluation of evidence, especially empirical evidence). Dawkins’ argument for non-telological adaptation (the “as if designed” argument), although intriguing, seems mostly to be supported by assertion and abstract models, rather than by empirical evidence.

Behe/Darwin’s Black Box: The argument for “irreducible complexity”, while interesting, appears to leave almost all of evolutionary biology untouched. Behe’s argument is essentially focused on the origin of life from abiotic materials, and arguments for the “irreducible complexity” of the genetic code and a small number of biochemical pathways and processes. Therefore, generalizing his conclusions to all of evolutionary biology (and particularly to descent with modification from common ancestors, which he clearly agrees is “strongly supported by the evidence”) is not logically warranted. Attempts to make such extensions are therefore merely polemics, rather than arguments supported by evidence.

Dembski/The Design Inference and “Specification: The Pattern that Signifies Intelligence”: Dembski’s mathematical models are intriguing, especially his recent updating of the mathematical derivation of chi, his measure for “design” in complex, specified systems. However, it is not clear if empirical evidence (i.e. counted or measured quantities) can actually be plugged into the equation to yield an unambiguous value for chi, nor is it clear what value for chi would unambiguously allow for “design detection.” Dembski suggests chi equal to or greater than one, but we agreed that it would make more sense to use repeated tests, using actual designed and undesigned systems, to derive an empirically based value for chi, which could then be used to identify candidates for “design” in nature. If, as some have suggested, plugging empirically derived measurements into Dembski’s formula for chi is problematic, then his equation, however interesting, carries no real epistemic weight (i.e. no more than Dawkin’s “Weasel”, as noted above).

Johnson/The Wedge of Truth: To my surprise, both the ID supporters and critics in the class almost immediately agreed that Johnson’s book was simply a polemic, with no real intellectual (and certainly no scientific) merit. His resort to ad hominem arguments, guilt by association, and the drawing of spurious connections via arguments by analogy were universally agreed to be “outside the bounds of this course” (and to exceed in some cases Dawkins’ use of similar tactics), and we simply dropped any further consideration of it as unproductive. Indeed, one ID supporter stated quite clearly that “this book isn’t ID”, and that the kinds of assertions and polemics that Johnson makes could damage the credibility of ID as a scientific enterprise in the long run.

Ruse/Darwin and Design (plus papers on teleology in biology by Ayala, Mayr, and Nagel): Both ID supporters and evolution supporters quickly agreed that all of these authors make a convincing case for the legitimacy of inferring teleology (or what Mayr and others call “teleonomy”) in evolutionary adaptations. That is, adaptations can legitimately be said to have “functions,” and that the genomes of organisms constitute “designs” for their actualization, which is accomplished via organisms’ developmental biology interacting with their environments.

Moreover, we were able to come to some agreement that there are essentially two different types of “design”:

• Pre-existing design, in which the design for an object/process is formulated prior to the actualization of that object/process (as exemplified by Mozart’s composing of his final requiem mass); note that this corresponds to a certain extent with what ID supporters are now calling “front-loaded design”, and

• Emergent design, in which the design for an object/process arises out of a natural process similar to that by which the actualization takes place (as exemplified by Mayr’s “teleonomy”).

In addition, the ID supporters in the seminar class agreed that “emergent design” is not the kind of design they believe ID is about, as it is clearly a product of natural selection. A discussion of “pre-existing design” then ensued, going long past our scheduled closing time without resolution. We will return to a discussion of it for our last two meetings next week.

As we did not use the two days scheduled for “deconstruction” of Johnson’s Wedge of Truth, we opened the floor to members of the class to present rough drafts/outlines of their research papers for the course. It is interesting to note that both papers so presented concerned non-Western/non-Christian concepts of “design” (one focusing on Hindu/Indian and Chinese concepts of teleology in nature, and the other on Buddhist concepts of design and naturalistic causation).

Overall, the discussion taking place in our seminar classes has been both respectful and very spirited, as we tussle with difficult ideas and arguments. For my part, I have come to a much more nuanced perception of both sides of this issue, and to a much greater appreciation of the difficulties involved with coming to conclusions on what is clearly one of the core issues in all of philosophy. And, I believe we have all come to appreciate each other and our commitments to fair and logical argument, despite our differences…and even to have become friends in the process. What more could one ask for in a summer session seminar?

P.S. An open invitation to the other members of the class: if any of the statements strikes you as unrepresentative of what has been happening, please post a comment to that effect here…and thank you for keeping me honest!

… in the definition of Phi_S(T), the function Phi’(.) is applied both to T, which is a member of Omega, and to U, which is a member of Patterns(Omega). Even if patterns Omega is a well-defined set - which is far from certain - Phi’(.)…

Our server here is rather limited, and though I’ve been working on possible ways to make it a bit easier to write extensive math posts here, I haven’t met with much success. Many of you have been writing long and involved posts; but they symbols make them almost impossible to read, and the long threads, incorporating broad topics, make it difficult to follow a train of reasoning. So we’ve decided to expand, and hold our discussions of specified complexity at a new website with a bit more functionality.

This is not seperate from Evolution and Design, and the feeds for both comments and posts will be in the sidebar here (look under links). But this should help in two ways: 1)enabling clearer writing through the use of LaTeX and 2) encouraging more focused threads, by virtue of freer posting policies.

So– please visit the website and register. The way it will work: If you’ve contributed with more than seven substantive posts on the two threads discussing specified complexity here, and don’t have any strikes against you in that time period, you will automatically (i.e., as soon as we notice you’ve registered) be promoted to a writer, with the ability to make front-page posts. Class members also have posting priviliges, and everyone is welcome to comment. Feel free to repost recent comments from this thread if you feel it’ll help in the transition.

The ground rules do still apply, and if anything will be more strictly enforced there– but you can’t go far wrong when you’re talking about math, or?

You can write in LaTeX, or at least a minimalistic version thereof, by surrounding your equations with [tex] and [/tex]– an example would be tex] x^2 + y^2[/tex]. This should work both in the comments fields or if you’re writing a post. It doesn’t come out as beautifully as would be nice, but… significantly better than chi=-log_2[ M*N*phi(s)(T)* P(T|H)].

A syntax reference for the particular cgi we’re using is here, which tells you what you can and cannot do. You can play with fontsizes, but there isn’t much else besides math you can write.

We don’t have comment preview, but, instead, you’re allowed to edit your comment directly after you’ve posted it. There will be an “edit this” link next to your new comment for the first five minutes after it has been submitted, to give you a chance to fix syntax.

I know the course is almost over and I don’t know how many people will want to argue afterwards, but I figured it might be useful even for just a week– and, besides, I wanted the practice setting something like that up. :). It is probably rather buggy– mostly done over the past few nights, when I ought to have been asleep — but improvements will be made this weekend. So please email me with any and every complaint, as well as suggestions for making it work better.

Besides, where better to discuss specified complexity than in a thread title “Specified Complexity”?

On a website called “Specified Complexity”, maybe?

There were several requests on the next-to-last thread for definitions of specified complexity, so to redeem a promise and– I hope–eliminate the need for repeating the same definition ad infinitum, I’ll attempt to summarize the major points of Dembski’s paper on the subject here.

(more…)

Since this blog calls itself “informal”, I’ll be informal: the gear is stowed, the food is on ice in the cooler, the canoe is on the roofrack, and the Goonies are rarin’ to go, so we’re headed for the Adirondacks for the weekend. However, this blog (and attendant moderation duties) are in Hannah’s very capable hands, so have a great weekend and I’ll be back to posting on Monday. Next week we’ll be diving into Phillip Johnson’s The Wedge of Truth (and I will, of course, bring up the “wedge document”), so it should be an exciting and interesting week.

BTW, we have received a number of comments asking/begging/demanding that we moderators do something to censor certain commentators because they believe that they are not responding to counter-arguments and/or failing to provide references or other support (including logical arguments) for what they believe to be assertions. Well, folks, we can’t force people to identify their unsupported assertions as opinions, we can only ask them to do so. If you think that this is what is happening, then you need to provide counter-arguments (notice I didn’t say counter-assertions) that are supported by relevent citations. That way we can all identify who is really making supported arguments and who is simply arguing via assertion (or trying to change the subject). And we can do so politely, but firmly, right? Right. Good, now play nice until I get back…

“…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.

I am getting ready to take my family to a Scottish highland games in central Massachusetts (my two oldest are competing in highland dance), so this will have to be brief. Last night we finished our discussion of Michael Behe’s book, Darwin’s Black Box (DBB). The discussion ran over the end of the class period (it has been doing that pretty consistently), and it seemed that there were a number of points still under dispute, both between the EBers and IDers in the class, and within each group (i.e. we must be going something right, eh?)

Consequently, the following points are basically my own, and do not necessarily represent the concensus of the class.

(1) Behe defines “design” on pg. 194 and provides an algorithm of sorts for its detection:

“…design is evident when a number of separate, interacting components are ordered in such a way as to accomplish a function beyond the original components.

However, as I pointed out, according to this definition a thunderstorm cell (i.e. cumulonimbus cloud) would qualify as designed. We generally agreed that thunderclouds are not designed, but are rather the result of a combination of relatively simple physical (i.e. natural) properties and processes. Ergo, Behe’s definition of design is rejected, as it has a tendency to detect false positives. Furthermore, merely revising it is problematic, as this would tend to bias it toward false negatives.

(2) 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 defintion/algorithm is simply an argument by analogy, and we have already concluded that this form of argument alone is logically specious.

(3) In pages 203-205, Behe argues that all of this examples of irreducible complexity (and therefore design - eukaryotic cilia, prokaryotic flagella, mammalian blood clotting, intracellular transport, mammalian immunity, AMP regulation, and biochemical pathways in general) all have functions. But, as Ayala, Mayr, Nagel, Bedau, and others on the EB side have cogently argued, functions per se are fully compatible with evolution by natural selection. In a nutshell, genetic programs are “designers,” but there is no empirical evidence that they are themselves the result of design.

(4) In pages 206-207, Behe argues that not all biochemical systems are designed nor irreducibly complex (and using the phospholipid bilayer “unit membrane” and hemoglobin s examples). This immediately leads to a question Behe does not address: why are only some biochemical systems designed? Therefore, the “Intelligent Designer’s” motives must be an irreducible component of any comprehensive explanation of designed irreducible comlexity (DIC).

(5) From the examples cited through page 230, it is clear that DIC theory is only offered as an explanation for the origin of life from non-living materials, the origin of the genetic code, and the origin of the biochemical systems listed in #3 (above). Therefore, the whole of evolutionary theory as presented by Darwin, plus the overwhelming majority of evolutionary biology that has been investigated since 1859 are entirely unaddressed (and therefore unaffected) by Behe’s arguments.

(6) On page 176, Behe concludes that descent with modification from common ancestors is strongly supported by empirical evidence, most of it from biochemistry (specifically comparative sequence data).

(7) Therefore, since Behe accepts common descent and his arguments do not address the overwhelming majority of observations and generalizations (i.e. theories) in evolutionary biology, the whole of his argument devolves to an attack on the non-designed origin of life and biochemical pathways, which may remain forever beyond empirical verification or falsification.

In conclusion, therefore:

(8) The theory of evolution is essentially unaffected by Behe’s arguments and examples in DBB.

(9) A verifiable explanation of the origins of life, the genetic code, and selected biochemical pathways is still an open question, and may continue to remain so for the indefinite future.

(10) Given #8 and #9, neither DBB nor the components of ID theory that are based upon it will (nor indeed can) have any “revolutionary” (or even significant) effect on the science of evolutionary biology.

Which, given the essentially static, non-empirically-verifiable nature of most if ID theory, it can be concluded that ID is not, and probably will not become integrated into the empirical natural sciences.

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.

On page 231 of Michael Behe’s Darwin’s Black Box: The Biochemical Challenge to Evolution, Behe summarizes his answers to “questions about design” as follows:

The preceding are just the obvious questions that flow from a theory of design. Undoubtedly, more and better-formed questions will be generated as more and more scientists grow curious about design. The theory of intelligent design promises to reinvigorate a field of science grown stale from a lack of viable solutions to dead-end problems. The intellectual competition created by the discovery of design will bring sharper analysis to the professional scientific literature and will require that assertions be backed by hard data. The theory will spark experimental approaches and new hypotheses that would otherwise by untried. A rigorous theory of intelligent design will be a useful tool for the advancement of science in an area that has been moribund for decades. [emphasis added]

Just out of curiosity, what “area of science” is Behe referring to here? I ask because he quite clearly does not identify what area of science he is referring to. Any suggestions?

. . . 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…