Saturday, January 17, 2009

A Challenge

Lately, I've found myself quoting and referring to The Design Matrix to answer questions from critics of front-loaded evolution (FLE). A lot of frustration could be avoided if the book was actually read and any references could be quickly looked up by both advocates and critics.

I also want to thank the critics here at EE by name.

Dave R.
Art Hunt
Tony Hoffman

I hold you to a high standard that I've found most critics of my TT posts do not possess.
(Please let me know if you don't want your name in this post and I'll remove ASAP).

In the spirit of a challenge given to me first by Dave R., I wish to issue a challenge to all critics who have NOT read The Design Matrix (DM). If you read DM, I'll read a book of your choice.


UPDATE 22-Jan-2009: I have one stipulation: the proposed book should be of comparable price with DM (currently just under $20 at Amazon). And kudos to Dave for taking me up on my challenge. I knew you'd be first! :)


  1. I plan on reading DM later this semester, but I haven't located a copy to borrow yet. Tell ya what, let's do a book loan. In exchange for a loan of DM, I'll loan you my copy of Sean Carroll's "Endless Forms Most Beautiful", which I think is the most accessible book on the science of evo-devo. You may need some more background reading to fully appreciate it, but I think it might give you some idea of the power of evolutionary thinking in the "design" of organisms.

    If your library can handle the loss of DM for a few weeks, send me an email.

  2. I'm glad to see you take up my challenge, Dave. I'll go you one step further. I will add "Endless Forms Most Beautiful" to my personal library as early as Friday if you're willing to buy The Design Matrix. If you don't want to keep it, you could always donate it to your local library (and possibly use it as a tax credit/write-off too). What say you, Dave?

  3. I'll have to think about it; I'd really rather just read it rather than own it. I've seen too much evidence-free blithering at TT to make me think that I want to own that book, or that I want my library to make it available to others who may not have their BS shields set high enough.

    Sorry if that disappoints.

  4. I like the book exchange thing. As soon as Dave is done and I get the DM, I'll send you, JJS P.Eng, my personal copy of this classic.

    (Yeah, yeah, two minutes for blatant self-promotion. Deal with it, we Bruins fans are pretty obnoxious lately.)

  5. Dave, it's a measly $20! You can throw it away or send it to Art if you wish. Hey, you and Art can split the cost! It ain't THAT bad down there you can't afford 10 bucks, is it? *sigh* If you're still wary, I'll get back to you Monday.

    Art, so much for the stipulation I set out, eh? (see Update in post above).

    It's OK. Bruins fans need a little sunshine after what they've gone through lately, as long as they don't choke in the playoffs ;)

    And just a friendly reminder, Art. Who beat the Bruins twice in the Stanley Cup Finals? (Yes, I am an Oilers fan, hehe, and yes, I still want MacTavish fired).

  6. LOL.

    JJS P.Eng, with my offer, you get to read a book that's a whole lot more expensive (and, if I might say so myself, has some positively sterling chapters), for much less than $20. What's wrong with that?

    But that's not why I'm chuckling. MacTavish is an alum of my undergrad school. Revenge takes strange twists.

  7. Hey, $20 will get me a good bottle of wine, and a lot more enjoyment!

  8. Art, what did MacT ever do to you that you want some sort of revenge on him? I've just had enough of 8+ years of mediocrity.

    As for your book, it would probably take me a year to read, and I'd probably go blind on the technical jargon. But hey, if you also provide the Cliff notes to your book (BTW, I like the self-promotion), I may take a stab at it.

    Dave, you're a cheapskate (and possible drunk, but I don't know you that well to say for sure). I had Endless Forms tagged for future reading, but thanks to you accepting my challenge, it's moved up the reading queue (as soon as I finish the two books I'm reading now, which won't take long to finish).

    You'll especially like the first page of writing where Mike states ID isn't science. So it ain't your typical "ID" book. It's not even an "us vs. them" book which is typical of most (if not all) ID books. In fact, it doesn't even question the legitimacy of evolution. All DM proposes is the possibility of evolution being "used". In engineering terms, it's conceptual design. No "threat" to evolution.

    So shell out the money, or start a pool so you can "spread the pain", and get the book. You can send it on a national tour or give the NCSE their very own copy. Use your imagination. ;)

  9. jjs

    If it's not science, why would I want to pay for it? If it is just more theology disguised as philosophy/woo, why would I want to pay for it?

    My whole problem with the ID "movement" is that it is long on words and short on action. I can't imagine reading more words that can't be translated into testable hypotheses and experiments. Sure, it's "possible" that living things were designed. When are you guys going to move from the "possible" to actually generating a decent testable hypothesis AND then testing it? My bet? It will never happen!

    So I just don't see any good reason to spend the money. Maybe if I actually was drunk, it would make more sense :-)

    I'll look around to see if I can find a copy. Our public library doesn't have it, nor does the university library (maybe that should be a clue...). But I can get it via interlibrary loan, so I'll do that.

    Send me your address and I'll ship you Endless Forms Most Beautiful. You won't have to part with your copy of DM at all.

  10. Hey, as a UML grad, I will never think a bad thing about MacT. The revenge quip came from the notion that some Oilers fans were less than happy with Craig as coach.

    And Cliff notes? Heck, the editors never told me I had to come up with those, too.

    Oh, wait...

    I have an answer.

  11. Sorry for the delay in commenting.

    Dave, I was planning on buying Endless Forms Most Beautiful regardless of how you obtained a copy of DM. But thanks for the offer :)

    Art, cute self-promotion of your blog. I like it ;)

  12. JJS

    i finally got a copy of DM from Interlibrary Loan today; after submitting a request almost two weeks ago. Typically our ILL staff can find a scientific article or a book in 24-36 hours; this one seems to be a tad more obscure. And it didn't come from any science library; it came from a public library in Issaquah, Washington.

    You might consider the above paragraph as a "consilience of clues" when you think about this book's place in the scientific world...

  13. Well, I'm several pages into DM, and remain unimpressed. The "Face on Mars" argument is pathetic. He argues that we can detect design without any knowledge of the designer. Left unsaid in this example is the FACT that the design detected is a HUMAN FACE. We suspect design in this instance because we are familiar with HUMANS AS DESIGNERS. This unspoken assumption applies to every ID "design detection" scheme ever formulated.

    Put another way, if there were a Face on Mars that resembled the face of a Martian, and Martians resembled nothing we have ever seen before, what methods would we use to detect design? What would be the clues, consilient or otherwise?

    The point is that design detection implicitly includes assumptions about the designer. Saying that we can detect design without considering the designer is disingenuous at best, and feeble always.

  14. More from Chapter 1 - The cell is more complex than Paley and Darwin imagined; hence it might have been designed. Like all of Gene’s arguments, this floats outside the realm of useful inquiry. Yes, this COULD be the case, but where is the evidence beyond this tentative conclusion?

  15. From Chapter 2

    Chapter 2 – Debates between teleologists and non-teleologists have been going on for centuries, dating back to Epicurus and Aristotle. The point of this seems to be that these arguments are not inherently religious, so as to deflect the current criticisms of ID as the stealth son of creationism. This approach ignores the reality that current criticisms ARE religious in nature (Democritus is rarely excoriated from the pulpit nowadays). It ignores the fact that the majority of current philosophers of science reject the teleological approach. Finally, it ignores the reality that the teleological arguments have not been buttressed by modern science, but rather have progressed more and more toward a situation where natural laws and natural processes CAN explain what we observe. So this chapter, while interesting and readable, is basically a straw man argument writ large. More unfortunately for the author, there are more complete treatments of this history elsewhere (e.g. Foster, Clark and York’s “Critique of Intelligent Design: Materials versus Creationism from Antiquity to the Present”).

    Despite the pronouncements of the radical fringes (Provine vs. standard Christian creationists), evolution and design are not necessarily incompatible. This is weak wine, and again evidence-free. Yes, teleology is a possibility. Those who maintain that it is a genuine possibility, approaching the edges of being a useful approach to science, still fail to provide evidence. Hunches are not hypotheses; clues are not data.

    An “Explanatory Continuum” can be used to address questions or disputes (e.g. solve murder cases). Again, so what? This sort of analysis, like the Face on Mars, includes an assumption that the causal agent was a human being. We know the agent from experience; we KNOW nothing about the designer. The EC is useless in detecting design or intentionality if we exclude the assumptions that include some knowledge about the agent, the tools available to that agent, the time-frame, and the techniques available to the agent. Why is this not mentioned? Perhaps because the implicit assumption of Christian denialists of evolution is that they are made in the designer’s image. Admitting that we KNOW nothing objectively about the designer would deflate all of these arguments to the hot air that they are revealed to be.

  16. Hi Dave,

    Thanks for the summary (so far)!

    Does Mike Gene ever get beyond "it looks that way to Mike Gene" as an argument or discussion? Or is that all there is?

  17. Does Mike Gene ever get beyond "it looks that way to Mike Gene" as an argument or discussion? Or is that all there is?

    So far, that is all there is. Lots of statements about how complex cells are, and how they sure do look designed, but nothing in the way of a testable hypothesis so far.

    I'll keep you posted. But it may not appear here. The forward/introduction contains this paragraph (my bolding):
    Finally, in part IV, I progressively outline a method for tentatively inferring the existence of design and helping us move beyond the suspicions - the Design Matrix. It is an open-ended method that can be used by both sides in this dispute to assess a design inference, and it is my hope that you will find it easy to understand and use. After explaining the Design matrix, I take it for a test drive to see how it scores things that are know to be designed by humans, along with various biological features. In Volume 2 that is eventually to follow, I will use it, and more, to explore the living world.

  18. More from the Design Matrix.

    Chapter 3 - Cells are really really really complex, and this is a “clue” that they were designed, because all the complex things we know about were designed. Another conclusion masquerading as hypothesis, without the intervening step (experimentation and testing) that defines the scientific method as it should be practiced.

    Metaphors of agency abound in this section (e.g. “How does the cell know…?”). This section ignores the reality that metaphors and analogies are traditional human pathways to understanding, but are often wrong. The sun does not travel around the earth, despite the analogy to Apollo’s fiery chariot. Thunder is not the action of an angry deity, despite the metaphor of Thor. And physics at the molecular level is not at all similar to the physics of the machines used as metaphors here, nor are computer programs at all analogous to the central dogma (DNA makes RNA makes Protein). Analogies are not clues; they are simply analogies. Where are the data that make support a teleological conclusion? There are none, only “clues” derived from a Judeo-Christian notion of a god who made us in his own image.

  19. More, from Chapter 4

    Chapter 4 – A standard explication of basic molecular biology, with a few over-generalizations and lots of teleology tossed in. For instance, on p. 70 we read “When I first learned about the genetic code I was totally struck by the fact that biologists behaved as if they had discovered something ordinary. In philosophy and other areas of science, people would comment on the uncanny implications of the Big Bang or quantum physics. But that life is encoded raised no one’s eyebrows.” Perhaps the author does not recall that multiple Nobel Prizes were awarded to the folks who discovered the genetic code, broke the genetic code, and unraveled the mechanisms by which DNA is transcribed and mRNAs are translated. I don’t know what he means by “raised no one’s eyebrows”, but that seminal work in the 1950’s and 1960’s was followed breathlessly by the biological science community. Clearly his surprise lies in the fact that there is an information-storing and –processing basis for life, but that fact had to be true if the observations about heredity, both ancient and modern, were true. Why be surprised at the elucidation of the mechanisms of something that had to be true? That seems rather naïve. It should indeed raise eyebrows if a conclusion that had to be true turned out to be unbased in reality.

    Then he launches into the standard ID notion that “The fact that DNA contains encoded information in the form of a one-dimensional linear string of symbols is very suggestive positive evidence for Intelligent Design behind the fabric of life. If we set aside life for the moment, then every other example of a sequence of characters representing convention is because of Intelligent Design.”

    Again, no experiment, just analogy. Conjecture becomes conclusion – "it resembles a designed thing; thus it must be designed." This unscientific approach only serves to mask the underlying argument from incredulity. Gene at al. don’t know of any information-encoding system that didn’t come from someone who thinks like they do, so they conclude that this information-encoding system MUST come from someone who thinks like they do. It certainly might be true, but an analogy is not a substitute for an experiment. They also ignore the failures of the analogy. Stop codons don’t encode for an amino acid; thus allowing an IDist to argue that this is a good design, because it allows proteins to end with any one of the standard 20 amino acids. But if that is a good design, how does the IDist explain the start codon, which does code for an amino acid, and thus constrains all proteins to start with the same amino acid? Is that also a “good design”? How do we recognize design if these two diametrically opposed strategies are able to be labeled as “good design”? This is a conundrum for the IDist, because the standard rejoinder of the previous generation of evolution-deniers (creationists) was that we can’t understand the mind of God, we just have to accept that God does things differently than we would. The IDist is denied this weaseling strategy because their whole premise rests on detecting design, and in order to detect it, we have to assume that it looks “well-designed” by our standards as well as those of the designer. Epic fail.

    Gene then launches into another canard, this time using language directly borrowed from creationism. He quotes actual scientists who concluded that the genetic code seems to be optimal, with regard to avoiding the most lethal types of coding errors. His conclusion? “Chance alone would not be expected to produce a code that was better than any other million randomly generated codes when it comes to protecting against harmful mutations.” But “chance alone” is a strawman; natural selection winnows the possibilities, and the “chance alone” strawman disintegrates. He continues with a nonsensical argument that the universality of the genetic code makes it difficult to consider natural selection as an agent here, calling this an ad hoc argument. It is, unfortunately for him, no more ad hoc than invoking a creator/designer who can do anything!

    The next argument from incredulity comes when he invokes the existence of “proof-reading” (aka DNA repair pathways, tRNA charging enzymes) as something that “underscores our intuitive suspicion of Intelligent Design”. Never mind that this is exactly what one would expect if selection worked on traits that had to be transmitted faithfully from generation to generation. Gene sees this with a teleological eye, yet still he has no experiments to propose, nor new observations to offer. Paleyism is clearly still with us, even if the data supporting it today are no more extensive than they were in the 19th century.

    Gene relates an anecdote that, according to him, shows that ID inferences are not scientific dead ends; they can act as a “research guide”. This is his “prediction” that proofreading also occurs during transcription. He predicted it from a teleological standpoint, and it turned out to be experimentally verifiable. Of course, in the spirit of ID researchers everywhere, he did not do any of the hard work; he merely hunted through the literature published by real scientists. Nevertheless, that does not stop him from exclaiming "Voila! Design can predict stuff!" Unfortunately he overlooks an important fact. Proofreading at multiple levels makes sense from an evolutionary standpoint as well. If design is going to supplant evolutionary theory in the scientific marketplace of ideas, not only will it have to be predictive, it will have to predict things that are the opposite of what evolutionary theory predicts, AND ID researchers will have to do some real work to generate these novel and paradigm-shifting observations. Gene attempts to address this problem, claiming that “Darwinian was used to explain” why transcriptional proofreading did not occur. One would like to read the papers where this “Darwinian logic” was invoked, but the only footnote for this assertion invokes an article by Mike Gene, and, his own website, is no longer to be found on the web. How convenient.


  21. Anonymous

    Thanks for the archive link. I'd actually tried to find it in archives, but since I don't know the date that Mike/Julie wrote this phillipic, I wasn't able to do it. If anyone wants to hunt it down by some other search technique, here is the link that he cites on p 87 of DM.

    Given that others have speculated that Mike/Julie did not predict this, but rather found it while searching through the literature for another topic, I'll not waste much more time on it. See the second comment by slp on this site

  22. I've finished the book. I am incredibly glad that I did not pay for it...

    Chapter 5, 6 and 7 reviews in this comment, others to follow. I'll post the entire review to Amazon sometime.
    Chapter 5 – Molecular machines! Cells are full of tiny machines! It must be design, because only designers make machines! This basically summarizes the chapter. One long argument from analogy, complete with even more incredulity

    Chapter 6 – Evolved things can resemble designed things, and vice versa. People can be fooled by their preconceptions. Still no evidence, still not a whiff of a testable hypothesis. I only marvel at the author’s ability to get so many words from such trite aphorisms.

    Chapter 7 – What if the first cells were designed, and evolution took over after that? A lovely notion, but still untestable, although the author tries to convince us otherwise. Evolutionary theory posits that mutations are random with regard to fitness. Gene says that design/teleology would posit some foresight in the mutations and thus in the variation in a population. Note again that this is pulling a rabbit out of a hat, there is no a priori reason to expect any particular behavior from a non-human super-intelligent designer. But if that ad hoc assumption is true, where does it leave us? Front-loading! The earliest cells were programmed by the designer to evolve splendidly into (what a coincidence!) the sort of cells and organisms we see today! Pure speculative baloney, begging the question, and (yet again) not a whiff of a testable hypothesis..Gene does attempt to show that the recent demonstration of genes which are related to but not identical in lower invertebrates and humans is evidence of front-loading. Unfortunately for this prediction, not only is this observation consistent with common descent and evolution, he misleads the reader into thinking that the lower invertebrates have functional forms of all genes found in humans. This is simply not true; they have proteins with related structures and different functions. Related proteins can have different functions; this is no surprise, and is also easily accommodated within evolutionary theory. He also ignores the wealth of evidence against front-loading, e.g. the vast stretches of useless derelict chunks of DNA from ancient retroviruses. Why would a designer frontload garbage into the genome?

  23. More chapter reviews


    Chapter 8 – We can detect design without knowing anything about the designer. Unfortunately his example (pp. 194-5) does not help his case. The detection of transit lightcurve signatures for planetary objects might allow us to detect intelligences at great distances in space precisely because these would be distinguishable from those signatures left by a normal planetary transit. Deviation from natural laws would allow us to detect design, just as deviation from common descent (unrelated genes inserted into an organisms genome) allows us to detect human-designed organisms. What deviations from natural laws are found in cellular life? Exactly none, to date. So where is the evidence for design from these observations? Nonexistent, per usual.

    Other aspects of this chapter are equally unrewarding. Gene argues that arguments from analogy might be suspect in this arena because the original such argument, Paley’s watch, was an attempt to prove the existence of God. Proving a designer is not the same, he would have us think. Sadly, this ruse fails. The designer of all of these Christian ID theorists is, unequivocally, the Christian God. Arguments from analogy, including this latest variation on Paley, are still bogus. Behe’s irreducible complexity (IC) argument is invoked, although it is not clear which version of IC he argues for, since Behe has moved those goalposts quite a few times recently.

    The summary for this chapter says everything you need to know about this book. From p.235 – “The suspicion of Intelligent Design can be strengthened in two ways. First, the proposed analogy between a biological feature and something known to be designed can be explored. If, for example, designed biological features known to be designed are compared with advanced versions of our own technology, we would expect that analogy between them to deepen over time. If a biological feature is designed, yet there are differences between the feature and our own products of design, we would predict that the biological feature, when properly understood, exhibits aspects of superior design.” If someone would point out to me anywhere in that passage where it is possible to tease out a testable hypothesis and do an experiment, I’d appreciate it. Suspicions are not hypotheses, analogies are not arguments, and conclusions are not justified without positive outcomes from testable hypotheses. Finally, this argument falls down in millions of cases where it can be demonstrated that a biological feature, e.g. the recurrent laryngeal nerve of the giraffe, is woefully designed. How do you explain that, using this paradigm?

    Chapter 9 – In which our intrepid author makes more arguments from analogy, engages in wishful thinking about observations which may border on becoming candidates for suspicions, but again fails to outline a single testable design-based hypothesis which could yield results supportive of teleology and incapable of being accommodated within evolutionary theory. Move along, nothing to see here.

    Chapter 10 – Finally, what we have all been waiting for, and hoping that it would make reading all those ignorant arguments worthwhile. Sadly, we are disappointed yet again. The “Design Matrix”, like the Explanatory Filter before it, fails because its assumptions are faulty. The assumption is that we can detect design by analogy with human designs; the intelligently designed feature should be superior. Yet some human designs (e.g., the wheel) are far superior to anything found in nature, and other biological features (e.g. the aforementioned recurrent laryngeal nerve of the giraffe) are wretched designs that even a kindergarten-aged engineer could readily improve. We can detect human design using this matrix; it is simply useless for its alleged purpose of detecting the intelligent designs of a superintelligent telic entity.

    The entire book is an argument from analogy, in which the author tries to elevate his hopeful “suspicions” to the rank of hypothesis. Suspicions are not hypotheses, analogies are not arguments, and conclusions are not justified without positive outcomes from testable hypotheses.

    When the ID community generates and tests a design-based hypothesis where the results are consistent with teleology and incompatible with evolutionary theory, science will pay attention. Until then, hand-waving arguments like this book, consisting of words that cannot (or at least have not) been translated into hypotheses and observations, cannot be taken seriously by scientists.

  24. "If a biological feature is designed, yet there are differences between the feature and our own products of design, we would predict that the biological feature, when properly understood, exhibits aspects of superior design.”

    A variation of a common ID theme which goes something like this. If it looks like something designed by humans, it must have been designed. However, if it doesn't look like something designed by humans, it must have been designed.

    The sad thing is that ID proponents don't understand how ludicrous this reasoning is.

  25. My entire review of DM has been posted on

    Thanks for inspiring me to read this book, JJS. I never would have known how bad it was if I hadn't experienced it for myself. I do wish that ID could come up with something that would actually be of interest to the scientific community; even cold fusion, a complete bust, generated a lot of interest and many pee-reviewed papers! But if this is the best that the Paleyists can do, science will definitely have to proceed without them.

  26. This comment has been removed by a blog administrator.

  27. LOL

    Dave, I am amazed and dumbfounded by your blindness. Mike has schooled you and made you look bad. I don't mind that you wrote an unfavourable review of DM, but at least demonstrate you got the message Mike was trying to convey through the ACTUAL TEXT, not through your narrow preconceptions. Mike made you look bad by refuting your assertions using words from DM, a book you were supposedly trying to review!

    And that Julie comment is a low blow, too.

  28. In fact, it was so low, I decided to delete it.

  29. jjs

    Thanks for the vote of confidence. If you think that "Mike made me look bad", we'll just have to disagree. Here's my perspective; I hope it can get past your "narrow preconceptions"...

    I did read those rebuttals thoroughly, and I decided to focus first on the very first of them, the Face on Mars argument. So far we haven't gotten past that one; at this rate we never will.

    I pointed out what I think is the central flaw in the ID argument as presented in that book (and elsewhere in the ID world). There is an unstated auxiliary assumption that the telic entity will produce designs that are similar to designs produced by humans. If that assumption is not true, as Mike acknowledges, his approach cannot work.

    He labels it as a "working assumption", and assumes that it is true, which is valid enough as a logical exercise. But there is absolutely no evidence that is available to support that auxiliary assumption. Despite repeated requests for some/any evidence in favor of this assumption, Mike et al. have not provided it, and seem content to wander off in discussions of suits and SETIs and other red herrings.

    In other cases where working assumptions are used in productive research enterprises, there is usually at least some evidence that the assumption is correct. Here's an example.

    In genetic engineering, the investigator has the working auxiliary assumption that the genetic code in the target organism is the standard (aka universal) genetic code. This assumption allows the investigator to use a coding sequence that should be translated to give a protein with the predicted primary sequence. There are organisms (and organelles) with non-standard genetic codes, but the working assumption is that your target organism is standard. More importantly for this discussion, there is substantial evidence that the auxiliary assumption is correct. So the work can be productive.

    Flash back to the teleologist's auxiliary assumption - telic entities design things like humans would. What is the evidence for that assumption? Zip, nada, zilch, zero. That's the point. An enterprise based on an evidence-free auxiliary assumption is on very shaky ground; one would think that it would be a very high priority for those engaged in that enterprise to find some evidence. That is not the case here. Why is that?

    Mike would like the freedom to speculate endlessly as if the assumption is true. That's fine. But in the absence of evidence that it is true, the rest of us get bored rather quickly, because nothing ever happens except the generation of more bafflegab. I am merely trying to focus attention on the logical underpinnings of the proposition of ID. I am not focused on the science, despite Mike and the minion's misreading of my words that way. There are lots of things to say on that topic as well, but so far we're stuck on this one because nobody there wants to think about it in a logical way.

    So if you want to focus on perceived personal "low blows", go right ahead. I am always disappointed in the ID community's eagerness to focus on the personal perceived insults (Is Julie a dirty word in Canada?) rather than on the substantive arguments. It is the mark of an enterprise that has no response to the substantive arguments. I'm disappointed that you censored a comment; that's not a road that leads to anywhere productive at all.

    If you want to discuss the reasons why ID gets no respect from either the philosophical or scientific communities, I'll do that any time.

  30. I may be wrong, but I'm sort of guessing that our blog host doesn't know the "Julie Thomas" story.

  31. Art

    Good point.

    JJS, look here for some of that story.