Weasels, clouds and biomorphs, part III

The Blind Watchmaker is a superb book by a masterful science writer. It's not just a book about evolution, or even about how evolution works. It's a book about how evolution explains design, and more specifically how natural selection accounts for design. As I wrote before, I consider chapter 3 to be the most important chapter of the book. The chapter is called "Accumulating small change" and it features two different computer programs that Dawkins uses to teach readers about the effectiveness of selection in evolution. Before we play with the Biomorph program in the next post, allow me to set us up by discussing the importance of the program in Dawkins' argument, and by outlining the logic of the program's design.

First let me try to convince you that chapter 3 really is the heart and soul of the book. The chapter is about gradual, step-by-step evolution resulting from natural selection. And as you might already know, natural selection is what Dawkins considers to be The Big Idea, the idea that answered Paley's seemingly insurmountable challenge. In chapter 2, Dawkins makes this clear. Here's how he starts.

Natural selection is the blind watchmaker, blind because it does not see ahead, does not plan consequences, has no purpose in view. Yet the living results of natural selection overwhelmingly impress us with the appearance of design as if by a master watchmaker, impress us with the illusion of design and planning. The purpose of this book is to resolve this paradox to the satisfaction of the reader....

–The Blind Watchmaker, page 21

Chapter 2 famously focuses on echolocation in bats, and I would buy the book just to read Dawkins' description of the engineering feat that is the little brown bat. (He gleefully recounts the utter incredulity of an audience of biologists when the mere existence of such biological phenomena was first described.) And here's his conclusion.

I hope that the reader is as awestruck as I am, and as William Paley would have been, by these bat stories. My aim has been in one respect identical to Paley's aim. I do not want the reader to underestimate the prodigious works of nature and the problems we face in explaining them. Echolocation in bats, although unknown in Paley's time, would have served his purpose just as well as any of his examples. Paley rammed home his argument by multiplying up his examples. He went right through the body, from head to toe, showing how every part, every last detail, was like the interior of a beautifully fashioned watch. In many ways I should like to do the same, for there are wonderful stories to be told, and I love storytelling. But there is really no need to multiply examples. One or two will do. The hypothesis that can explain bat navigation is a good candidate for explaining anything in the world of life, and if Paley's explanation for any one of his examples was wrong we can't make it right by multiplying up examples. His hypothesis was that living watches were literally designed and built by a master watchmaker. Our modern hypothesis is that the job was done in gradual evolutionary stages by natural selection.

–The Blind Watchmaker, page 37

Chapter 4 builds on chapter 3, and the rest of the book deals with how it might all work. Chapter 3 is Dawkins' attempt to show us the power of cumulative selection, and cumulative selection is The Blind Watchmaker. This is the heart of the matter, and Dawkins' argument (and his world) hinges on the success of this idea.

And so Dawkins tackles the concept of cumulative selection in chapter 3, and as we've already seen, he immediately faces a serious problem: the end result of an evolutionary process is the generation of design, of biological machines that are complex and, more importantly, wildly improbable. In other words, such things "can't just happen." The human mind is prone to a serious error when faced with this challenge. The error is to envision complexity arising spontaneously from chaos, in a single step, and thus to conclude that such things cannot be explained naturally. The error is in bold, and Dawkins addresses it first with the simple and effective Weasel illustration. The illustration is highly effective as a corrective for that error, but it fails as a model of evolution, as I explained in the previous post.

The Biomorph program was Dawkins' more serious attempt at modeling the development of complex structures by cumulative selection. It's important to understand just how central the program really is, and thus why it's so silly to make a big deal out of the Weasel exercise. Chapter 3 is the heart of the book, and the Biomorph program is the soul of chapter 3. The Biomorph program improves on Weasel in two very important ways:

1. It models evolutionary unfolding without a specific goal. The Weasel program "homed in" on a particular goal; the Biomorph program has no such constraint.

2. The entities that evolve in the Biomorph program, called biomorphs, "develop," and their development is controlled by a number of factors ("genes") which change (i.e., mutate) in each generation, so that mutations result in alterations to development and thus to new forms.

The biomorphs are tree-like structures, and they are drawn according to simple rules. (This post is decorated with a few that I made using a nice Java applet.) The rules control the branching of the trees (branch at a certain angle or at a certain point on the existing branch, or branch of a certain length, or whatever). The drawing of a biomorph, then, is a representation of embryonic development. And the rules represent the various processes in development.

It should be fairly easy to see how to model the effects of genes: a gene will influence a rule, by assigning a number to the rule (e.g., branch at a bigger or smaller angle). Reproduction is simple: the biomorphs are redrawn, based on the parent's structure, using the same rules influenced by the same genes. Boring? No: mutation acts to change the numeric value of the genes, randomly changing the value by either +1 or -1. The result is a set of offspring, each differing slightly from the parent by virtue of a single mutation.

So it goes like this. A parent is selected. The subroutine REPRODUCTION runs, and generates random mutations in each of the genes of the parent (there are 9 genes); the new genes are passed to the subroutine DEVELOPMENT, which draws new biomorphs based on the new genes. The result is a set of 9 offspring, each with a different version of one of the parent's genes. One is selected to be the parent of the next generation. Keep doing this, over and over and over, and you get the program EVOLUTION.

But how does selection work in this program? Recall that the major problem with the Weasel illustration was its goal-directed nature. In the Biomorph program, things are different:

...the selection criterion is not survival, but the ability to appeal to human whim. Not necessarily idle, casual whim, for we can resolve to select consistently for some quality such as 'resemblance to a weeping willow'. In my experience, however, the human selector is more often capricious and opportunistic. This, too, is not unlike certain kinds of natural selection.

–The Blind Watchmaker, page 57

Selection, in other words, is done by you, the human who is "playing God."

That's the Biomorph program. Next time: what it demonstrates about evolution.

Weasels, clouds and biomorphs, part II

Back in September I wrote about the silly preoccupation on the part of various anti-evolutionists with the so-called Weasel program, a simple exercise created more than 20 years ago by Richard Dawkins to illustrate the efficacy of cumulative selection in evolutionary scenarios. My main point was that the Weasel program had one very simple purpose (comparing "single-step selection" – which is purely random – to cumulative selection) and constitutes a trivial fraction of the argument in Dawkins' The Blind Watchmaker.

One might think that Dawkins' basic message – that random one-step flying-together of a Shakespearean phrase or a hemoglobin molecule is impossibly unlikely compared to cumulative selection of intermediate stages – is so elementary that no intelligent person would need to consider it more than once. (Once seems like a lot to me in this case, but never mind.) And yet the error (if that's what it is) is shockingly common. (It forms one pillar of poor Cornelius Hunter's whole enterprise, for example.)

Dawkins understood this problem when he wrote The Blind Watchmaker, so before he unveiled the fascinating program that forms the heart of his case for the power of selection, he took one last stab at making the basic outline clear by going back to clouds. Wait...clouds? (Fans of Hamlet are already sighing blissfully; those who don't get the connection between weasels and clouds should read either Act III, Scene II of Hamlet or Chapter 3 of The Blind Watchmaker.) Yep. Dawkins pointed back at what makes cumulative selection work: the things that are evolving must be able to generate related offspring. And that's what clouds can't do.

Clouds are not capable of entering into cumulative selection. There is no mechanism whereby clouds of particular shapes can spawn daughter clouds resembling themselves. If there were such a mechanism, if a cloud resembling a weasel or a camel could give rise to a lineage of clouds of roughly the same shape, cumulative selection would have the opportunity to get going. Of course, clouds do break up and form 'daughter' clouds sometimes, but this isn't enough for cumulative selection. It is also necessary that the 'progeny' of any given cloud should resemble its 'parent' more than it resemble any old 'parent' in the 'population'... It is further necessary that the chances of a given cloud's surviving and spawning copies should depend on its shape.

– The Blind Watchmaker, pages 50-51, italics in the original

Hence the Weasel program.

But I noted last time that Dawkins spent a tiny amount of time and text on the Weasel program, and that he declared it to be "misleading in important ways." The most important, by far, is this: the selection that drove the Weasel program was goal-directed. A better simulation of evolution would be one in which selection is more capricious, more "in the moment." (Survival can be capricious; reproduction happens rather decisively "in the moment.")

Dawkins came up with just such a program, and I mentioned it in the previous post. It's a wonderfully simple simulation of the basic aspects of selection-driven evolution: it includes development, reproduction, genes, and selection, and generates "organisms" with shapes instead of a phrase in all caps. We'll look at that program in the next and final post. But if you want to play with a modern version, you'll find plenty of nice implementations out there. So much more fun than studying...or grading.

Resurrection

So there hasn't been a post on Quintessence of Dust in three months. Here are some reasons for this.

1. We're in the midst of a distracting crisis at Calvin College right now. I won't talk about it here, but it's very serious and has already affected my relationship with the college.
2. I recently completed a major writing project, a book that I coauthored with a colleague at Calvin. Not much else to say about that at this point.
3. I've coauthored two recent review articles with my colleagues at the Van Andel Institute, and we have significantly expanded the scope of our collaboration, with a major new grant proposal in the works.

During this hiatus, I enjoyed a wonderful attack (and a flatulent followup) by a poorly-equipped ID demagogue, Cornelius Hunter. God bless him: he said I'm "the best of the worst." There's not much there, so I'll ignore his criticism and work instead on completing two interrupted series, one on deep homology & design and one on Richard Dawkins' biomorph program. Then we'll get back to regular forays into the current literature, and we'll focus on "junk DNA" a bit more. Biomorphs are next. See you soon.

Weasels, clouds and biomorphs, part I

There's usually no point in piling on when the minions of the ID movement get their just deserts after some typically brainless culture-war test launch. Consider the responses (by, most notably, Ian Musgrave at the Panda's Thumb) to the most recent rendition of the ID movement's hilariously idiotic fixation on a particular computer program written by Richard Dawkins. It seems there is little to add. But I think something important is being lost in this conversation, probably because the level of the "conversation" is the level of the ID movement. So let's start with a little quiz.

1. True or false: Richard Dawkins' 1986 classic The Blind Watchmaker used a computer model (a simulation) as a key teaching device while explaining the effectiveness of cumulative selection in evolution. The program is the main focus of chapter 3 ("Accumulating small change") of the book.

Answer: True.

2. True or false: the computer program used for this purpose was made available to the public and has since been adapted for free use on the web.

Answer: True.

3. True or false: the computer program in question is called WEASEL (or similar) and it demonstrates the stepwise generation of a famous phrase from Hamlet.

Answer: False.

Now if this surprises you, then either you haven't read The Blind Watchmaker or you haven't read it in a long time. Because even if you've been influenced by the hysterical antics of the ID crowd, you could not long believe its claims about the Weasel program if you had recently read the book. If you haven't recently read The Blind Watchmaker, you might consider a stroll through some representative ID musings on WEASEL followed by a visit to Chapter 3 of the book (and, if you have a copy from 1989 or later, a visit to the two appendices.) The experience could be jarring for those who have a positive view of these arguments by ID apologists.

But if you don't have a copy of The Blind Watchmaker handy, I can help. First, in this post, I'll discuss the Weasel program and its place in the thesis of The Blind Watchmaker – in the context of the current ID fixation on the program. Then I'll introduce the program that Dawkins really did emphasize in the book, a program called EVOLUTION (or later, when it was expanded and made commercially available, The Blind Watchmaker Evolution Simulation program) but commonly known as the biomorph(s) program. In the second post I'll talk more about the biomorph program and its usefulness.

Chapter 3 of The Blind Watchmaker is a tour de force of expository scientific writing. Called "Accumulating small change", the chapter has a single and simple thesis, laid out in the first paragraph:

We have seen that living things are too improbable and too beautifully 'designed' to have come into existence by chance. How, then, did they come into existence? The answer, Darwin's answer, is by gradual, step-by-step transformations from simple beginnings, from primordial entities sufficiently simple to have come into existence by chance. Each successive change in the gradual evolutionary process was simple enough, relative to its predecessor, to have arisen by chance. But the whole sequence of cumulative steps constitutes anything but a chance process, when you consider the complexity of the final end-product relative to the original survival. The purpose of this chapter is to demonstrate the power of this cumulative selection as a fundamentally nonrandom process.

– The Blind Watchmaker, page 43, italics in the original

Dawkins immediately tackles the crazy misconception of evolution as a process that is akin to the impossibly improbable flying-together of the parts of a machine in a single step. Echoing Isaac Asimov, he calculates the probability of the spontaneous assembly of a hemoglobin molecule in a single step, and arrives at a number of predictably indescribable magnitude. It can't just happen.

In a 1987 BBC television show , he uses a much better metaphor: the opening of a safe by entering a combination. To open the safe, a banker (or thief) must correctly enter all of the correct numbers, in order, at the same time. His point is: of course it can't "just happen." The concept that Dawkins aims to communicate is this: from an evolutionary perspective, "success" doesn't happen all at once; it is accumulated. Evolutionary change is cumulative change; it's as though the safe opens a little when one correct number is entered, and allows the banker to reach in and get a little money. ("Small change" is the topic, remember.)

This is a very basic and very important aspect of the Darwinian mechanism, and yet it is maddeningly common to see it ignored or completely misunderstood. So in the first few pages of Chapter 3, Dawkins looks for an illustration of the difference between "randomly getting the whole thing right in one fell swoop" and "accumulating random improvements till the whole thing is assembled." He starts with the old saw about monkeys, typewriters and Shakespeare. Choosing a single phrase from Hamlet, "Methinks it is like a weasel," he first calculates the probability of a random character generator (a monkey) spontaneously banging out Hamlet's phrase. The calculation charmingly indicates that there isn't enough time in the universe for such a thing to occur. Yeah, yeah, yeah. Now, it's easy enough to get a computer (even a 1986-vintage machine) to churn out 28-character strings randomly, and so Dawkins describes a program that can do this. Then he introduces the occurrence of cumulative selection in the program, to illustrate its profound effectiveness compared to mere randomness.

We again use our computer monkey, but with a crucial difference in its program. It again begins by choosing a random sequence of 28 letters... It now 'breeds from' this random phrase. It duplicates it repeatedly, but with a certain chance of random error – 'mutation' – in the copying. The computer examines the mutant nonsense phrases, the 'progeny' of the original phrase, and chooses the one which, however slightly, most resembles the target phrase... the procedure is repeated, again mutant 'progeny' are 'bred from' the phrase, and a new 'winner' is chosen.

– The Blind Watchmaker, pages 47-48, italics in the original

Dawkins shows that this procedure can get from a random monkey-phrase to "Methinks it is like a weasel" in mere seconds. And the point is simply this: cumulative selection is more effective than mere "randomness" by incomprehensibly gigantic magnitudes. Dawkins makes it very clear that the Weasel program is meant to demonstrate nothing more than that. After pointing out that single-step selection would take a near eternity to type the phrase, he reiterates the simple purpose of the comparison, and the whole weasel exercise:

Actually it would be fairer just to say that, in comparison with the time it would take either a monkey or a randomly programmed computer to type our target phrase, the total age of the universe so far is a negligibly small quantity, so small as to be well within the margin of error for this sort of back-of-an-envelope calculation. Whereas the time taken for a computer working randomly but with the constraint of cumulative selection to perform the same task is of the same order as humans ordinarily can understand, between 11 seconds and the time it takes to have lunch.

– The Blind Watchmaker, page 49, italics in the original

Folks, that's all the silly weasel thing was ever about. So what's all the fuss then?

Well, some ID partisans are all agitated about whether Dawkins' program allowed mutations in positions of the string where the correct letter had been hit upon. They wonder: if cumulative selection had gotten us "Methinks it is like a measel", could 'measel' mutate back to 'measer' and thus take the program a step away from the target? And why does this matter? Well, for Dawkins' purposes it really doesn't matter, but the ID scholars seem to think there's a big speed difference. If you're interested you can read some nice work by Wesley Elsberry or Anders Pedersen that shows clearly that it simply doesn't matter.

But. Here's what's lost in all this. Dawkins never intended the silly little weasel exercise to be a persuasive argument for evolution as it actually occurs in the world. In fact, he is quick to point out why it's deficient (remember Bohr models of the atom in grade school?), noting that it is "misleading in important ways." And at that point, he abandons the Weasel program in favor of a simulation that is far better. That simulation, the Biomorph program, is the topic of the entirety of the rest of Chapter 3 of The Blind Watchmaker (and of my next post).

The absurdity of the ID fixation on the Weasel program is hard to capture with mere words. Perhaps this table will help put the two programs into better perspective.

	Weasel	Biomorph
Number of times program is mentioned* on Uncommon Descent	444	2
Number of pages devoted to program in The Blind Watchmaker	less than 5	45, including two appendices

*All I did was Google the word 'weasel' or 'biomorph' at uncommondescent.com. The two uses of 'biomorph' were in comments by ID critics (one being Wes Elsberry). The uses of 'weasel' surely include insults that aren't references to the program.

The real focus of Chapter 3 of The Blind Watchmaker is the biomorph program. Seven figures, 23 pages, 22 more pages in two appendices which include a small user's manual for the program. The biomorph program constitutes the heart of Dawkins' book and his argument, so much so that the program is named The Blind Watchmaker. The Weasel program was a tiny stepping-stone for Richard Dawkins, a simplistic teaching tool meant to illustrate a single simple point. It's a hill to die on for the ID movement, and that says a lot about the state of that confused community.

Carnival of Evolution 14

Welcome to Quintessence of Dust and to the 14th Edition of the monthly Carnival of Evolution. Thanks for stopping by, and for supporting scientific carnivalia, members of a taxon that seems to be flirting with extinction.

One good reason to visit a carnival: brain stimulation. Brain Stimulant offers some thoughts and speculations on Free Will and the Brain, touching briefly on themes of selection and adaptation, and he doesn't charge as much as the clinic would.

Another good reason: you can bump into real scientists, the kind who actually work on evolution. Ryan Gregory has a day job as an expert on genome evolution, but somehow finds the time to blog at Genomicron. Recent entries there include fascinating pictures of ongoing field work. For this month's carnival, be sure to read two reviews of the ideas of Stephen Jay Gould, focusing on controversial papers by Gould published in 1980 and 1982. You may find that you have been misinformed about Gould's positions, and you'll surely learn more about evolution.

Michael White at Adaptive Complexity is another blogging scientist, and he writes very clearly about parasitic DNA in Selfish Gene Confusion.

David Basanta is a biologist who runs a cool blog called Cancerevo: Evolution and cancer, which is subtitled "Studying cancer as an evolutionary disease." Check it out, and don't miss his recent piece on Stem cells and ecosystems.

Zen Faulkes is a biologist who blogs at Neurodojo. That's cool enough, but the subtitle of that blog is "Train your brain." Hey, this could be a theme for the whole carnival! He recently wrote about a walking bat in New Zealand. Bat evolution...we can't get enough of that. I've written about it myself.

Brains and their origins come up in an extensive discussion of early animal evolution at AK's Rambling Thoughts. The post is The Earliest Eumetazoan Progression.

At The Loom, the peerless Carl Zimmer discusses AIDS in chimps and the relevance of the story to conceptions of scientific progress. AIDS and The Virtues of Slow-Cooked Science is engrossing and important. And John Wilkins discusses some new fossil apes in an excellent recent post at Evolving Thoughts.

John Lynch reviews a new book on Alfred Russell Wallace. Caveat lector. Brian at Laelaps takes us on a historical tour of the work of Florentino Ameghino. Are those elephants or not? Brian's discussion is typically excellent.

At The Spittoon, AnneH discusses new findings concerning both the past and the future of the mammalian Y chromosome.

Hoxful Monsters is a future host of this carnival; Nagraj recently reviewed some recent work on pattern formation in the development of spiders. Wonderful evo-devo stuff.

Someone at Wired wrote some swill about the "10 Worst Evolutionary Designs" which annoyed a few smart bloggers. At Deep-Sea News, Dr. M sets the record straight. The title is self-explanatory: Worst Evolutionary Designs? No! Brilliant Solutions to the Complexity of Nature and Constraints.

Larry Moran at Sandwalk is attending a conference entitled Perspectives on the Tree of Life. He's posted reviews of days one and two so far.

And that's our carnival. Thanks for reading, and on the way out I hope you'll look at my nearly-complete series on Notch and deep homology.

Next month's edition will appear at Southern Fried Science. To submit posts, use the submission form found at the Carnival of Evolution site. And if you like the carnival, help us promote it with a link, and/or consider hosting. More info at the carnival site.

Carnival of Evolution 14: Call for Submissions

The 14th edition of the excellent Carnival of Evolution will go up here at Quintessence of Dust this Saturday, 1 August 2009. Send submissions and links, to your own work or to good stuff you've seen elsewhere. Images welcome too!

Deep homology and design: why Notch?

The Notch signaling pathway is a golden oldie of genetics in two ways. First, it's a system that was first described at the dawn of modern genetics – named by its founder, Thomas Hunt Morgan – and used to establish some of the most basic principles of "the physical basis of heredity," as Morgan put it. (His book by that title is a founding document of modern genetics, describing in 1919 what we now call chromosomes without any knowledge of their chemical makeup.) Second, it's a system now known to be as ancient as animals themselves.

Why Notch? The name refers to the appearance of some of the first mutant fruit flies described by Morgan and his colleagues in their famous work in the early 20th century. They found flies with notched wings, and found that the trait was dominant.

Figure 1 from T.H. Morgan, "The Theory of the Gene." American Naturalist 51:513-544, 1917.

So aside from its importance in evolution and development, Notch is of historical interest to genetics. Now, Morgan was interested in Notch (the gene name is capitalized because the original trait is dominant, in case you're wondering) because of its mode of inheritance, not specifically because of its biological effects. (I mean, who cares about flies with notched wings?)

But twenty years later, things got more interesting when a different mutation in Notch was found to cause a weird (and lethal) overgrowth of the nervous system. Interesting... then, as geneticists began to probe the genetics of animal development 50 years after Morgan's initial discoveries, using the fruit fly as a model, Notch started turning up again and again. Problems in Notch signaling led to developmental problems all over the place: brain, eyes, gut, wings, bristles.

By the beginning of the 1990's, geneticists had figured out why its activity is so central to proper development: Notch controls a crucial type of cell-to-cell interaction that leads to a change in cell fate. And they had found Notch signaling in animals of every kind, including in humans, mediating the same kinds of inductive developmental interactions. It's not as complicated as it might sound – in such an interaction, two cells interact physically (they have to touch) and after the interaction one or both of the cells changes its developmental fate, choosing to become, say, a nerve cell or a skin cell. That weird brain overgrowth in the flies with no Notch activity results from a failure of cells to communicate in this way, such that all the cells on the outside of the fly's head become brain cells. (Flies, like most animals, prefer to have some skin over their brains, but in these mutants there's very little skin and lots of extra brain. Ick. See Figure 1 of this recent paper in BMC Biology for pictures; the green stain indicates nerve cells and the second animal down has the nasty trait.)

The point is that Notch signaling involves direct cell contact, and typically leads to cells making decisions about what to do when they grow up. So how does it work? Well, we know an awful lot about this particular system, and there are myriad details of mechanism and control that I'm going to skip. The very basic outline is as follows. Some cells make the Notch protein, which is a receptor. Other cells make the Delta protein, which is the signal that activates the receptor. (One useful analogy is that of locks and keys: Notch is the lock, Delta is the key.) Both proteins are displayed on the cell surface. When the two cells come into contact, the Delta protein on one cell activates the Notch protein on the other. When Notch becomes activated, it gets chopped into at least two pieces. One piece leaves the surface of the cell and travels inward to the nucleus of the cell. There, in collaboration with other proteins, it causes changes in gene expression, meaning that some genes are turned on or up and others are turned off or down.

This mode of signaling is unique and extraordinary. What we have is a signaling system that takes cell-to-cell contact and converts it directly into changes in gene expression.

Now, let's think carefully about this. We have a system of receptors and activators, in the form of Notch proteins (there are at least four in humans) and Delta proteins (there are several in humans, in a few different protein families), which serve a critical and unique purpose in cell-to-cell signaling. The function is conserved in all known animals, and that's not surprising – having cells send messages to their immediate neighbors, directing them to adopt particular fates, is key to constructing tissues and organs. I hope you'll agree that we should expect to see these inductive mechanisms in the development of complex organisms. More to the point, one should expect this regardless of one's stance on questions of "intelligent design."

Here's what is surprising. The same Notch proteins are used for this purpose in every known animal. And here's why that's surprising: as far as we know, there's no reason to insist on those particular proteins playing those particular roles. It's easy to envision – and then design and create – a set of locks and keys that bear no resemblance to Notch or Delta but that can accomplish these somewhat basic purposes just as well. There's no need for such a specific solution to a basic challenge. Why does every animal use Notch? Recall the previous post in this series and how we approached this question of common design. Here, again, are our options.

1. These inductive signaling events could only be accomplished by Notch. There is a design constraint, currently unknown, which forces that choice. It may seem that the system could have been effectively constructed using a different lock-and-key combination, but in fact it could not function (or function well) any other way.
2. These inductive signaling events could be mediated in various ways, but the choice of Notch has been forced by common ancestry. The earliest animals settled on this choice, and their descendants have used it ever since.
3. These inductive signaling events could be mediated in various ways, but an intelligent designer has repeatedly chosen Notch for reasons known only to her/him/it.

Option #1 is, in my view, unreasonable. The system is not complicated in its basic design. There are no clear constraints on the choice of lock and key. A designer who is crafting an organism from the ground up need not select that particular lock/key combination, and someone who intends to argue otherwise needs to demonstrate how that particular combination is superior.

Option #3 is, I think, perfectly reasonable. The only problem is that one must know quite a lot about the designer to begin to surmise her/his/its goals and proclivities. Without that knowledge, it is no more reasonable to assume a preference than it is to assume a constraint.

The point is not that we can ever rule out preferences or other characteristics of a creator or designer. The point is that we can rarely make explanatory use of them. Consider that while we may assert that the Creator/Intelligent Designer prefers that pine trees have needles, we would not advance that as a useful explanation for why pine trees have needles. Specifically, we would never advance that as an alternative explanation in place of one that notes that today's pine trees have the same needles that last century's pine trees had, by virtue of biological ancestry.

Notch signaling represents one of the classic examples of deep homology. It seems to me that design theorists need to deal with deep homology before they can ever be taken seriously as scientific thinkers. Deep homology is crying out for explanation, and those who believe that the biosphere cries "design" are remiss in not offering a serious design-based explanation for the fact that every animal on the planet uses the same lock-and-key mechanism to achieve basic cell-to-cell inductive communication.

Next, we'll look at a recent and very interesting example of new findings that illustrate the striking conservation of Notch-mediated developmental events – an example of deep homology that could arise from the very root of animal ancestry.

Weekly sampler 24

1. Get your genome sequenced for $48,000. I would so do this. In the meantime, we bought the Matheson family DNA test for my dad for Father's Day.

2. I'm following this series at Siris: Philosophical Sentences explained. You know the old chestnuts: Cogito ergo sum, God is dead, virtue is its own reward, cleanliness is next to godliness... heh. Brandon tells us where they came from and a little about them. Latest installment is Santayana's famous quote etched at Dachau.

3. A very cool illusion that, like all good ones, tells us something interesting about how the brain processes visual information. Don't click till you're ready to follow these instructions: display the image on your computer screen so that you can slowly back away from the screen and still see the image. The idea is to view it up close then back up at least a few meters.

4. Two of my favorite bloggers, John Lynch (of Satan's University) and John Wilkins (from Down Under) have left ScienceBlogs and set up shop independently. Lynch formerly blogged at Stranger Fruit and his new place is called a simple prop. Wilkins is an important antidote to brainless anti-religious bellowings from Coyne and like-minded simps. Both are skeptics who know a lot about evolution. Recent important posts: Lynch on The Roots of ID and Wilkins on The Demon Spencer.

5. Strangest species discovered in the last year. The ghost slug wins for weirdness, but the big news is that someday we might be able to drink decaf that's still coffee.

6. Becoming Creation is an important blog by a homeschooler, evolutionary creationist, accomplished biologist and good guy: Doug Hayworth. Up right now is an interview with Denis Lamoureux, author of Evolutionary Creation.

7. A recent piece in the Chronicle of Higher Education presents a very interesting take on teaching science in the context of religion (and other social influences). The concluding paragraph:

Science professors should explicitly engage the rich social and ethical context of the subjects that they teach, engaging new generations of students in the science that so many now fear and reject. A careful, thoughtful approach to teaching the sensitive issue of evolution represents merely the beginning of a challenging, less-traveled-by path, but one that could, nevertheless, make all the difference.

8. My research concerns some very interesting proteins called formins. Michael Behe's scholarship includes a focus on the malaria parasite, P. falciparum. A recent paper reports that a formin protein in P. falciparum is critically involved in the process by which the parasite invades red blood cells. I always knew that Professor Behe and I were destined to be collaborators.

Theistic embryology: the talk

I previously posted the abstract of a talk I gave at Calvin last month in which I test-drove my "theistic embryology" metaphor that I'll present at the North American Paleontological Convention in Cincinnati in two weeks. Now the audio and my simple slides are posted on Calvin's e-zine, Minds in the Making. Lots of jokes. And now my name's spelled right.

About halfway through, I refer to "10 dangers of theistic evolution" at Answers in Genesis. Later I read from Jerry Coyne's steaming pile. And speaking of steaming piles, I then read from one of my favorite posts in The Cesspool. In case you wanted to follow along.

Deep homology and design: common design and its implications

Consider these not-so-random samples from the animal world: a cockroach, a zebrafish, a mouse. What do these creatures have in common?

Left to right: American cockroach (Periplaneta americana), zebrafish (Danio rerio), house mouse (Mus musculus). Cockroach image from Wikimedia Commons, zebrafish and mouse from Wellcome Images.

Well, they're all animals and that means they're all eukaryotes, for example. They all have DNA-based genomes. They all like water to some extent. They all have muscles that cause them to move. And so on.

But let's think of them in a different way. Let's think of them as things that exhibit design. (Not Design. Just design.) We see similarities like the ones we just listed, and we see some dramatic differences. Insect, exoskeleton, open circulatory system. Fish, gills, egg-laying. Mammal, milk, hair, live birth, temperature control. We can see elements of common design (limbs and joints, eyes, nerves) and elements of specialized design (lungs, fins, antennae).

Now let's forget everything we know about common descent and adopt an Intelligent Design perspective. This isn't hard to do: just think of each animal as a machine that was designed to be the way it is. The machines have some common design elements and some specialized design elements. Now this is important: let's assume that each machine was designed separately, such that design decisions were made on a case-by-case basis (for each type of machine, not for each individual machine). In other words, let's think of the cockroach as designed from the ground up to be a cockroach, and the fish and the mouse likewise. Simple, right? I think so.

Now, let's look under the hood of each machine and ask detailed questions about how it's built, again with the assumption that it was designed. Not just its overall structure, but also the procedures used for its assembly. Let's look, in other words, at its molecular machinery – machinery for signaling between cells and tissues, machinery for signaling within individual cells, machinery for directing gene function during development and normal function. And let's focus specifically on the signaling systems in these creatures and in their developmental stages. What would we expect to see? Well, let's consider some basic scenarios.

1. Maybe the signaling systems will be roughly the same – or even largely the same – in all three animals. This would imply that such systems are hard to assemble and perhaps even harder to tune and maintain, and therefore we would conclude that there are very few ways to make a working system. The only other explanation would refer to preferences on the part of the designer, who was unconstrained by design limitations but nevertheless insisted on doing things a certain way.

2. Maybe the signaling systems will differ between the three animals, to such an extent that it is clear that the choice of a system is somewhat arbitrary, arbitrary in the sense that the choice of a particular system is largely independent of the context or the function that is specified. The implication is that there are plenty of ways in which cells and molecules can communicate, and no strong constraints on the designer's choices.

Now of course we may find examples of both scenarios in our analysis. Perhaps some signaling systems will appear to be highly constrained while others will be largely different among the three species. The point, though, is this: when examining machines that were separately designed, common design implies either design constraint or designer preference. Divergent design implies a lack of design constraint. There are no further options: either the designer was constrained, or she wasn't; if unconstrained, she could nevertheless choose a favorite scheme and leave the impression that she was somehow constrained.

Designer constraint could arise in various ways. It could be that a particular signaling system is uniquely suited to a particular purpose. It could be that a particular signaling system is highly robust to damage or other challenges. It could be that there are only a handful of different possibilities due to limitations in the raw materials. One variation of that last possibility would look a lot like how evolution is known to work: the designer tweaks the system a little at a time, working with the materials supplied by each generation and therefore constrained by common descent.

Design proponents can be stunningly cavalier about all this. "Common elements in animal biology? Well of course! Common design!" But wait: common design implies either design constraint (that was the best way to do it – or the only way to do it) or designer preference (she just happens to like it that way), and those are dramatically different from an explanatory standpoint.

It turns out that signaling systems in animal development are so universally conserved that they require an extraordinary explanation. The commonality of the elements is so striking that it took most biologists by surprise when it first became evident, and remains one of the most remarkable facts of developmental biology today. We'll look at some recent advances in this area of evo-devo in posts to come.

But one last thing: I'd like to try a thought experiment to illustrate how we might approach questions of signaling in animal cells and embryos. Consider a group of 50 people who have agreed to help with your experiment. You divide them into pairs and tell each pair to send one person out of the room. Then you tell the remaining people to greet their partners upon their return, using a single word of their choosing that is certain to convey the greeting. You observe that all of the people employ either "hello" or "hi" for this purpose.

Question: would you conclude that "hello" and "hi" are uniquely suited for the task, and that no other word could possibly have worked? I hope you would seek another explanation and perhaps consider trying the experiment in, say, Shanghai or Guadalajara. You would conclude, I wager, that the word itself is of little explanatory value. In other words, the choice of a word was constrained, but not by anything specific to the word itself. In Shanghai, it's "ni hao." Maybe somewhere it's "duuuuuuude." And in a matter of minutes, you could change it to "ahoy" or "blorp" or anything you want.

And if you really wanted to probe the notion of constraint in human conversation, you would ask your 25 pairs of subjects to come up with an identifying word or phrase that they could call out to find each other in the dark. You would find, of course, that the choice of that word or phrase would be almost completely unconstrained.

What does all this have to do with signaling systems and design? That's for next time. Till then, blorp.