Sympathy for the Devil's Chaplain (Part I)

Well, I guess I should start with some contrition. I have gotten cheap laughs referring to Richard Dawkins as an idiot, such that students of mine have twice referred to him simply as 'The Idiot,' knowing they'd be perfectly well understood. The context of this classroom slander is his infamous conflation of Christian belief and natural theology, an obnoxious habit for which he has been amply excoriated (e.g., by Michael Ruse and Alister McGrath). Years ago, when I first read his 1995 Scientific American piece "God's Utility Function," I was astonished by the banality of the argument, and for years thereafter I had him pegged as the anti-Phillip Johnson, the yin to scores of creationist yangs. After all, when Dawkins talks about religion, he tends to make an ass of himself. (Some of his friends can see this, and they note it ruefully. I'm not sure what's going on with those who rise to his defense.)

Now, I'm not at all sorry about observing that the Professor with the Overlong Title frequently makes atheists look like ignorant thugs. But the whole 'idiot' thing... well, here's the problem. I've recently read some of Dawkins' other work, the stuff that made him famous enough to be able to publish swill like The God Delusion on something other than, say, a blog. :-) And this work is just flat brilliant -- I mean over-the-top fantastic -- and now I'm feeling a little sheepish about suggesting that Dawkins is a simpleton. So, I have two aims in these next two posts: 1) in the current post, to reflect on (and strongly recommend) the book that Dawkins himself identifies as his best work; and 2) in the next article, to give the Professor with the Overlong Title credit for at least some of his many claims that are fully correct -- claims that are, in some cases, proof texts cited repeatedly by Christian critics.

So: let's see if you can guess which of these Dawkins masterpieces has been identified by the author as his best (or at least his most important):

• The Blind Watchmaker
• The Selfish Gene
• The God Delusion

...time's up! Well, if you picked any one of the above, you're wrong! Nyaahahahaha! (Unfair! Unfair! Unf--ooof!)

Uh, seriously, here is an excerpt from the preface of the Oxford Paperback Edition of The Extended Phenotype:

I suppose most scientists -- most authors -- have one piece of work of which they would say: It doesn't matter if you never read anything else of mine, please at least read this. For me, it is The Extended Phenotype. In particular, the last four chapters constitute the best candidate for the title 'innovative' that I have to offer.

That preface was written in 1989, after The Blind Watchmaker, but admittedly before The God Delusion. Perhaps the Devil's Chaplain doesn't think his most recent work is an embarrassing joke, but plenty of his fellow evolutionists/scholars/atheists do, and so I'm willing to bet that Dawkins hasn't changed his mind about The Extended Phenotype. (None of his other works from 1990 on seem to come close, but I'll gladly accept nominations from those who feel otherwise.)

Originally published in 1982, The Extended Phenotype has three main sections:

1. An introductory section in which Dawkins answers criticisms and objections to the "gene's-eye view" of life that he first put forth in The Selfish Gene;
2. A longer middle section in which he advances arguments for the primacy of the "genetic replicator" as the so-called unit of selection; and
3. The final four chapters, "the heart of the book," in which Dawkins describes the concept of the extended phenotype, nicely summarized in the 1989 edition's subtitle: "The long reach of the gene."

I won't review the whole book here. Instead, I'll offer some highlights from those three sections.

Section 1: Dealing with objections to the gene's-eye view of selection

I'm a huge fan of Stephen Jay Gould. I once got to talk to him on a call-in radio program in Boston. (The Connection, then with Christopher Lydon. Maybe you heard me...the show was national. The topic was evolution for some reason, and it was Opening Day 1998 or 1999.) And Gould was, as you might know, one of Dawkins' most bitter rivals. I still count Gould as one of my favorite authors (he was, among other things, the pre-web incarnation of the ultimate blogger), but his well-intentioned vendetta against "genetic determinism" sometimes led to oversimplification. And one of his main beefs with Dawkins' ideas was this one: that too strong an emphasis on genes as targets of evolutionary selection can lead to a sort of biological Calvinism:

If we are programmed to be what we are, then these traits are ineluctable. We may, at best, channel them, but we cannot change them either by will, education, or culture.

-- from Ever Since Darwin, quoted in The Extended Phenotype, p. 10

This is, in fact, a typical objection to any sort of "determinism," and who could disagree? Gould is talking about genes here, but I think the problem can crop up at almost any level of natural explanation. Christians (or worse, Calvinists like me) love to worry about this sort of thing, since we are understandably preoccupied with moral agency.

Dawkins deftly answers the challenge by first attacking the idea that genes are any more "deterministic" than other influences. He notes at the outset that biological "determinism" (read: causation) is a statistical -- not absolute -- matter.

For example, the claim that "smoking causes cancer" is understood by most to mean this: smoking increases one's risk of getting lung cancer. A genetic influence, Dawkins argues, should be viewed in exactly the same way. So, if you know that a certain adult has a Y chromosome, then you might bet that this person would be larger or stronger than a certain adult without Y chromosomes, and you would be unwise to bet the other way. And yet you wouldn't be utterly flummoxed when you learned that sometimes your bet was wrong.

Then he explodes the myth that genetic influences are any less modifiable than are other influences on a person's traits:

People seem to have little difficulty in accepting the modifiability of 'environmental' effects on human development. If a child has had bad teaching in mathematics, it is accepted that the resulting deficiency can be remedied by extra good teaching the following year. But any suggestion that the child's mathematical deficiency might have a genetic origin is likely to be greeted with something approaching despair: if it is in the genes 'it is written', it is 'determined' and nothing can be done about it; you might as well give up attempting to teach the child mathematics. This is pernicious rubbish on an almost astrological scale. Genetic causes and environmental causes are in principle no different from each other. Some influences of both types may be hard to reverse; others may be easy to reverse. [...] The important point is that there is no general reason for expecting genetic influences to be any more irreversible than environmental ones.

-- The Extended Phenotype, page 13

Dawkins then offers two ideas regarding how and why genes acquired "their sinister, juggernaut-like reputation." This one is worthy of serious reflection: genetic inheritance, which is famously inflexible and inexorable, is easily confused with the expression of genetic characteristics in an individual person (or other organism), which is maddeningly variable. Adding to the confusion, surely, is the fact that most people are aware that learning and achievement don't change one's genes (this is the heresy of Lamarckianism), and this knowledge probably makes it difficult to understand that the expression of those genes, and their influence on a person's life, has much to do with learning and achievement.

There's so much more, just in that second chapter, that is worthy of consideration (musings about variation in human intelligence, careful discussion of the meaning of adaptation, explanation of the importance of differences as the focus of adaptive evolution), but you have other blogs to read. Seriously, if you've read The God Delusion, you'll be astonished to learn that the same guy wrote Chapter 2 of The Extended Phenotype. At least that's how I felt.

Section 2: Genetic replicators as the "units of selection"

I hope you can tell that some of the ideas in The Selfish Gene were controversial in their time; the first section of The Extended Phenotype deals with objections of a serious nature (i.e., not creationist objections). The complaints about determinism and adaptationism, however, are not as central to Dawkins' thesis as are objections like this one, again from Stephen Jay Gould:

No matter how much power Dawkins wishes to assign to genes, there is one thing that he cannot give them -- direct visibility to natural selection. Selection simply cannot see genes and pick among them directly. It must use bodies as an intermediary. A gene is a bit of DNA hidden within a cell. Selection views bodies.

It [selection] accepts or rejects entire organisms because suites of parts, interacting in complex ways, confer advantages. The image of individual genes, plotting the course of their own survival, bears little relationship to developmental genetics as we understand it.

-- The Panda's Thumb, pages 90-91

Now, at first blush I found Gould's objection quite compelling. In fact, if you know a little about developmental biology, or especially if you know a lot about developmental biology, you might be cheering out loud. As before, it sure seems like he has a good point. But here's what Dawkins writes at the end of Chapter 6 ("Organisms, Groups, and Memes: Replicators or Vehicles?"):

Of course genes are not directly visible to selection. Obviously they are selected by virtue of their phenotypic effects, and certainly they can only be said to have phenotypic effects in concert with hundreds of other genes. But it is the thesis of this book that we should not be trapped into assuming that these phenotypic effects are best regarded as being neatly wrapped up in discrete bodies (or other discrete vehicles). The doctrine of the extended phenotype is that the phenotypic effect of a gene (genetic replicator) is best seen as an effect on the world at large, and only incidentally upon the individual organism -- or any other vehicle -- in which it happens to sit.

-- The Extended Phenotype, page 117 (italics in original)

Now I hope you can see what the book is about. It's about establishing the gene as the unit of selection, by showing that only the reference point of the gene is ultimately helpful in understanding selection -- because genes can exert influences outside of the organism in which they exist. Even before I toss you a few of Dawkins' examples, see if you agree with me that Gould's objection is already in serious trouble.

Chapter 4, "Arms Races and Manipulation," is a feast for anyone who thinks biology is interesting. Dawkins notes that organisms have much to gain by manipulating other organisms. Just think: you're a bug or a bird, competing with other bugs and birds for resources and opportunities, and you find out that you could have someone else gather your food, build your house, raise your kids. Selfish, even evil, but...smart. Could such behaviors arise through evolution? In other words, can such manipulation be evolutionarily stable? Wouldn't the organisms getting ripped off fight back, evolutionarily speaking? What, after all, could be more evolutionarily insane than spending your life as a slave, feeding someone else's offspring? Dawkins explains why manipulation can be, and is, evolutionarily stable, and even commonplace.

The basic idea is illustrated by the moral of one of Aesop's fables: the rabbit runs faster than the fox, because the rabbit is running for his life, but the fox is only running for his dinner. Manipulation is predicted to lead to an evolutionary "arms race," because the manipulated species will "fight back," but the outcome can be stable if there are large asymmetries in costs and benefits. In other words, if species A has a lot to gain from the manipulation of members of species B, but members of species B have little to lose by being exposed to this risk, species A can "get away with" the manipulation of members of species B. The turning point of Chapter 4 is here:

If the individual manipulator has more to lose by failing to manipulate than the individual victim has to lose by failing to resist manipulation, we should expect to see successful manipulation in nature. We should expect to see animals working in the interests of other animals' genes.

-- The Extended Phenotype, page 67

And what are the best examples? So-called brood parasites, the cuckoo being the classic example. Cuckoos lay their eggs in other birds' (warblers') nests, and the victims slavishly feed the baby cuckoo, even after it kicks their own babies out of the nest, growing far bigger than its "adoptive parents." Some ant species use mysterious chemical signals to fool entire colonies of ants of another species into raising the raider's kids. Other species are slavers, carrying off babies of other species and "forcing" them to work for the advancement of their own colony. These are fascinating, weird stories, and there are cooler and weirder tales in Chapter 12, "Host Phenotypes of Parasite Genes." These accounts overwhelmingly make the point: individual organisms sometimes work to advance the replication of genes in someone else's body. Focusing on genetic replicators provides explanatory power, and whimpering about "determinism" or swatting "plotting genes" strawmen just doesn't get it done.

Chapter 7, "Selfish Wasp or Selfish Strategy?" is interesting to me, because in reading it I became aware, for the first time, that Richard Dawkins used to be a pretty good scientist. This probably sounds obnoxious, and it's really not meant to be an insult. Dawkins is a fantastic science writer, but it's not accurate, in my view, to call him a scientist. He's not what I would call a "practicing scientist" -- he hasn't contributed to the primary research literature in decades. And when he did, he worked as an ethologist (one who studies behavior) and not strictly as an evolutionary biologist. I surely don't mean to suggest that he's not right about evolution (see the next post). I just happen to think that actually doing science can keep one honest in ways that Richard Dawkins (and some others I can think of) clearly needs.

Well, in that chapter Dawkins uses his own research to illustrate precisely why a gene's-eye view of selection can be helpful "on the ground" in formulating and testing hypotheses. It's wonderfully interesting -- and, to me, just a little sad -- to read.

Section 3: The doctrine of the extended phenotype

This final section contains some riveting scientific writing. Chapter 11, "The Genetical Evolution of Animal Artefacts," serves an obvious purpose in Dawkins' quest to liberate the analysis of genetic effects from the confines of the bodies in which the genes are found, by pointing out that the effects of some genes are clearly manifested outside of that body. Dawkins notes that the causal connections between genes and their phenotypic expression are often utterly byzantine, and no one is surprised by that. So, "further extensions of the concept of phenotype should not overstretch our credulity." What follows is a tour de force of scientific persuasion. If a spider's hairy exterior is genetically influenced, via some poorly-understood interplay of genes, development and environment, then mightn't the spider's web be similarly influenced, similarly under the control of genes and, therefore, similarly acted upon by natural selection?

By whatever embryological routes the genes may work in detail, the small extra step from behaviour to web is not any more difficult to conceive of than the many causal steps which preceded the behavioural effect, and which lie buried in the labyrinth of neuroembryology.

-- The Extended Phenotype, page 199

The point, again, is this: genes don't have to act on bodies per se. They act on the "world at large." And more specifically, genetic effects which are the subjects of natural selection need not be exerted within the body that hosts the genes in question. The phenotype, which is the output of evolutionary interest, is not tied to the organism itself.

The final chapter, "Rediscovering the Organism," seeks an explanation for why organisms are a good vehicle for genetic replicators. It might seem like a weird question, but given the centrality of genetic replicators and their phenotypes as objects of selection, it's a fair one. Organisms occupy a prominent place in the order of biological creation. Why?

One idea that Dawkins explores is the role of cyclical development in the evolution of complex (multicellular) organisms. He maintains that such prodigies of creation are only possible in the context of a "complex developmental sequence." Specifically, he proposes a definition of an organism as:

...the unit which is initiated by a new act of reproduction via a single-celled developmental 'bottleneck.'

-- The Extended Phenotype, page 258 (italics in original)

According to Dawkins, the doctrine of the extended phenotype leads to this explanation for the utility of organisms and their developmental trajectories:

An organism is the physical unit associated with one single life cycle. Replicators that gang up in multicellular organisms achieve a regularly recycling life history, and complex adaptations to aid their preservation, as they progress through evolutionary time.

-- The Extended Phenotype, page 258

In other words, the regular re-start associated with developmental life cycles creates the opportunity for evolutionary adaptation. Interesting ideas for fans of evo-devo like me.

Okay, so I hope I at least got you to see the brilliance of Dawkins' thinking, at least as it stood in 1982. He birthed interesting new ideas, and handled his critics with grace that is undetectable in his current screeds. He's not an idiot, or at least he wasn't one back then.

But one more thing. The idea of selfish replicators has been linked (correctly) with the existence of "junk DNA," especially since animal genomes are nearly overrun with seemingly parasitic elements that look exactly like "selfish genes." (Dawkins would call them "outlaws;" see page 163.) Referring to plasmids and other DNA fragments that insert themselves into host genomes, Dawkins writes:

It is impossible to imagine a more intimate parasite. 'Selfish DNA' itself is not more intimate, and indeed we may never know how many of our genes, whether 'junk' or 'useful', originated as inserted plasmids. It seems to follow from the thesis of this book that there is no important distinction between our 'own' genes and parasitic or symbiotic insertion sequences. Whether they conflict or cooperate will depend not on their historical origins but on the circumstances from which they stand to gain now.

-- The Extended Phenotype, page 226

Compare that reflection on "junk DNA" (or the longer discussion in Chapter 9, "Selfish DNA, Jumping Genes, and a Lamarckian Scare") to the simplistic claims of anti-evolutionists who think that finding "functions" for "junk DNA" is somehow a problem for evolutionary theory. It's not, and I'll take that up sometime soon. But first, part II of my contrition for the Idiot Episode.

"And your horse now would make him an ass"

Well, first of all, I wanted to get "My kingdom for a horse" into the title, but I couldn't think of anything that made any sense. The title instead comes from this nifty exchange, which I found by searching for the relevant term in the Oxford Shakespeare:

Sir Toby Belch. He shall think, by the letters that thou wilt drop, that they come from my niece, and that she is in love with him.
Maria. My purpose is, indeed, a horse of that colour.
Sir Andrew Aguecheek. And your horse now would make him an ass.
Maria. Ass, I doubt not.
Sir Andrew. O! ’twill be admirable.

-- Twelfth Night, Act II, Scene III, The Oxford Shakespeare

Horse evolution has been ricocheting through the blogosphere recently, because the author of Laelaps (who claims to be an individual human being; I'm still skeptical) has posted an excellent review of the history of the paleontology of the horse. I'm just as interested, however, in his followup article on creationist work on the subject. The author ably dismantles the largely propagandistic work of Jonathan Wells and AIG's Jonathan Sarfati, among others. Then he ends by noting a relative silence on the subject of horse evolution among anti-evolution partisans:

To be entirely honest, I was rather surprised by the overall paucity of creationist literature as pertaining to horse evolution. Given its prominence in textbooks and museums (and even though many books and institutions still present such evolution incorrectly) I would have expected at least a semi-rigorous creationist explanation for horses, but they seem content to merely criticize the work of Marsh and Huxley, praising Richard Owen for not associating the European Hyrcaotherium with living horses. Even in the one book (Icons of Evolution) that specifically targets horse evolution, the phylogeny is only a set up in order to allow Wells to attack Darwin and Dawkins, hinting that orthogenesis should still be considered as being a good hypothesis for evolution.

I have two comments. First, I'm not surprised to find that bodies of strong evidence for common descent are poorly covered by anti-evolution writers. In fact, I'd like to do some research on the coverage of particular topics by opponents of evolution. Do you think you can learn about pseudogenes at discovery.org? Or read a detailed analysis of natural selection in guppies at Answers In Genesis? It would be interesting to quantitate their verbiage.

But second, I'd like to add a couple of additional creationist commentaries to the mix. One is by Keith Miller, of Kansas State University, who is the same kind of creationist as I am: an evolutionary creationist. (The full expression of my position would be something like "old-earth-descent-with-modification-selection-acting-on-variation creationist," but that's too long to type.) His article "Taxonomy, Transtional Forms, and the Fossil Record" has been a fixture on the ASA website for ten years. It includes a superb overview of the horse evolution story. If you've heard that horse evolution is a fib, and you want to hear the other side from a Christian, read Miller's paper. (Then read all the rest of his papers, and the book he edited, and anything he recommends.)

The other creationist work on horses comes from the Real Thing, a young-earth creationist, and a scientist more worthy of the title than many of evolution's most boisterous apologists. He's Todd Wood, from Bryan College, president of the BSG, which describes itself as "an affiliation of biologists and other researchers dedicated to developing a young-age creation model of biological origins." I'll mention these folks occasionally, and comment on their work at length some other time. For now, I just want to note the integrity of their work and their approach. (Todd and I appeared together in a symposium at Calvin last year, and I think he enjoyed his visit as much as I enjoyed meeting him.)

Todd and his coworkers have addressed the horse evolution story with sophistication and integrity that is wholly undetectable in the work of the Jonathans mentioned above. In fact, they've used some interesting statistical tools to examine the relationship between fossil age and changes in form. Their work confirms the pattern inferred by evolutionary biologists, though of course they interpret it somewhat differently. (This isn't sarcasm; these folks believe in evolution, big time. They think it happens FAST. And you know, sometimes it does.) And these neocreationists (their chosen descriptor) aren't afraid to reflect on how things are going and how their ideas can interact with mainstream science. (Check out their About page; these are not your parents' creationists.) I think they're wrong, because I don't believe that biblical Christianity commits me to a young earth. But some of these neocreationists do science (unlike some of the best-known science bloggers), they do it well, and they seem to love it. Hear hear!

Say cheese! Or, evidence that facial muscles are the puppet-strings of the soul

Souls will come up regularly in this blog, for lots of reasons. For one, disembodied spirits (wandering souls, I presume) are everywhere in Shakespeare, and his very conception of death seems to be the separation of the soul from the body. I can't very well bring up Shakespeare without conjuring ghosts or visions thereof. Such visions are utterly commonplace in Western literature and thought, and Shakespeare certainly didn't cook them up (I recall spirits fluttering out of dead warriors in the Iliad, and that little piece of work was conceived just a few millenia before the Bard). The picture of someone "giving up the ghost" (hilariously pictured in "Who Framed Roger Rabbit?", if you remember that little gem) obviously inspires Romeo:

Now, Tybalt, take the villain back again
That late thou gav’st me; for Mercutio’s soul
Is but a little way above our heads,
Staying for thine to keep him company:
Either thou, or I, or both, must go with him.

--Romeo and Juliet, Act III, Scene I (The Oxford Shakespeare)

We need souls in our poetry, even when our poetry has no soul. Hamlet without souls? No such thing.

And of course, we need souls in Christianity. We're essentially dualists, meaning that we believe in everlasting souls encamped (or entrapped) in mortal bodies. Right?

Well, actually, no. I'm just a biologist, but some of my best friends are philosophers, Christian philosophers, and darn good ones at that. It's a story for another time, but suffice it to say for now that many hard-thinking Christians are advancing a physicalistic (or "materialistic") view of human persons, some while claiming that biblical evidence for belief in immaterial souls is quite thin.

But whether or not you're an agnostic on immaterial souls, you should find the notion of "embodied emotion" interesting, because:

• It's cool science, and of course you love cool science;
• You're a human, and humans, it seems to me, are dualistically inclined;
• Souls are linked to various cognitive phenomena, including emotion;
  
• You're reading a blog called Quintessence of Dust, for heaven's sake.

The 18 May 2007 issue of Science features a "Behavioral Science" theme, and includes a brief review of some new applications of theories of embodied cognition to the study of human emotion. The author, Paula M. Niedenthal, contrasts such theories with traditional models of human cognition built around the image of brains (and minds) as computers, and identifies the following assertion as distinctive of theories of embodied cognition:

...that high-level cognitive processes (such as thought and language) use partial reactivations of states in sensory, motor, and affective systems to do their jobs. Put another way, the grounding for knowledge -- what it refers to -- is the original neural state that occurred when the information was initially acquired. If this is true, then using knowledge is a lot like reliving past experience in at least some (and sometimes all) of its sensory, motor, and affective modalities.

The idea, then, is that when you think, you are in some ways reenacting the scenario or the information itself. You are thinking with your whole body, not just with the meat-based computational soul-center in your skull. (As cool as that thing is.) If you are, like I am, a fan of Antonio Damasio and his ideas, then you're already familiar with this type of thinking and theorizing, and with the connection he makes between emotion and consciousness.

So...body is connected with emotion, emotion with cognition...doesn't this mean, then, that your body -- muscles, bones, tendons, mundane animal machinery -- can influence, even control, your cognition? Hello, Professor Descartes? If you just smile, can that make you happy?

Well, consider some of the wild stuff in this article. In one experiment, subjects were registering their perception of a projected image by moving a lever. When they saw the image, they were to quickly move the lever. The participants surely thought the experiment was measuring their reaction time, and they were partially correct. But they probably couldn't have discerned the variable of interest: whether the lever was pulled, toward the body, or pushed away. In the experiment, images were flashed, some that would be emotionally positive, some negative. Subjects who were pushing the lever away responded more quickly to negative images, and vice versa.

Maybe I'm the only one, but that kind of thing really messes with my dualistic impulses. (And I'm not a body-soul dualist.) But there's more. The author describes some of her group's work, in which activity in 4 facial muscles was recorded while subjects were judging the emotional content of certain words. Here's her synopsis of the results:

...individuals embodied the relevant, discrete emotion as indicated by their facial expressions...in the very brief time it took participants to decide that a "slug" was related to an emotion (less than 3 seconds), they expressed disgust on their faces.

The author also describes the elegant control experiment: the subjects looked at the words in print and determined whether they were written in all caps. No such embodiment was detected in the facial muscle recordings.

You might think, "gee, it must take a lot of time to do all that embodying work when making decisions." You'd be right: the author describes experiments that show timing costs associated with switching systems (or modalities):

They are slower to verify that a "bomb" can be "loud" when they have just confirmed that a "lemon" can be "tart" than compared to when, for example, they have just confirmed that "leaves" can be "rustling."

And you might wonder whether we could alter your emotional state by forcing you to embody a particular state. Suppose we force you to smile; will this make you happier? Call me silly, but my initial response to this hypothesis is to scoff. But wait: inspired scientists are testing hypotheses very much like this one.

In the last experiment described by Prof. Niedenthal, each subject was asked to determine whether a sentence described something pleasant or unpleasant, while holding a pen in his or her mouth. Huh? Have a look at Figure 1 (you don't need a subscription to Science): holding a pen with the lips precludes smiling, and even seems to embody the opposite; holding a pen with the teeth forces the lips into a smile. I suppose you know what's coming:

Reading times for understanding sentences describing pleasant events were faster when participants were smiling...sentences that described unpleasant events were understood faster when participants were prevented from smiling.

"Smile and laughter comes thereafter." Pretty corny stuff; it can still make me faintly nauseous (another embodied emotion, clearly). But maybe it's true. And if the eyes are the windows of the soul, what does that make the jaw muscles?

Not-quite-endless Forms Most Beautiful, or Wormholes Through Morphospace

The jaw-dropping diversity of life begs for explanation, but at the same time it defies description, so much so that it has inspired hyperbole, even hyperbole of the finest variety. (Cf. Annie Dillard's Pilgrim at Tinker Creek.) You might say that the human description of biological diversity has been extravagant, well-nigh endlessly so:

The result of the various, quite unknown, or dimly seen laws of variation is infinitely complex and diversified. It is well worth while carefully to study the several treatises published on some of our old cultivated plants, as on the hyacinth, potato, even the dahlia, &c.; and it is really surprising to note the endless points in structure and constitution in which the varieties and sub-varieties differ slightly from each other. The whole organisation seems to have become plastic, and tends to depart in some small degree from that of the parental type.

-- Darwin, On the Origin of Species, 1st Edition, page 12

And I think everyone's heard the famous last sentence in the Origin:

There is grandeur in this view of life, with its several powers, having been originally breathed* into a few forms or into one; and that, whilst this planet has gone cycling on according to the fixed law of gravity, from so simple a beginning endless forms most beautiful and most wonderful have been, and are being, evolved.

-- Darwin, On the Origin of Species, 1st Edition, page 490

(You may have seen it with three extra words, inserted at the * in the 2nd Edition and all subsequent editions. Some other time.)

Now, I know that Darwin didn't really mean 'infinite' when he wrote 'endless,' but it sure does sound like it, and his awe on contemplating the biosphere is certainly understandable. There are, after all, some really weird organisms out there (there are even 4-leaf clovers). Naturalists, of all people, should be excused for blurting out, "Now I've seen everything." The creations we see are indeed wonderfully beautiful, and their forms seem to be endless.

But they're really not endless, or even nearly so. Of the truly endless forms that are possible in living things, a tiny subset has actually come to be (on Earth, at least).

The 'forms' we're discussing here, by the way, are structures, architectures, what biologists call morphology. A particular type of structure might be called a morph, and the complete set of possible structures would be called a morphospace. A morphospace exists for any type of structure: butterfly wing spots, number of limbs in an animal, twisting shape of a snail's shell.

In fact, sometimes it is the lack of diversity in form that is more remarkable. In other words, sometimes the question faced by evolutionary or developmental biologists is this: why, given all the possibilities, do we only see these few forms? Why not more, or for that matter, why not fewer?

In the 8 June 2007 issue of Science, Prusinkiewicz et al. tackle this very problem, focusing on plant development using tools well-suited to understanding the development and evolution of form. Specifically, they analyzed the development of inflorescences. The inflorescence is the branching section of a plant stem upon which flowers form. Inflorescences take their shape through a process by which the growing part of the stem (the meristem) forms branches that either turn into a flower (and thus stop branching) or turn into another meristem (which can keep forming new branches). It's a pretty simple process geometrically, and perhaps you can see that it could generate an effectively infinite number of possible forms. Even if you don't have access to Science, you can look at their diagram in Figure 1, where you'll see six different types of inflorescence forms. The top three forms (selected, it seems, at random from a gigantic set of possibilities) do not occur in nature. The bottom three represent the three types of forms that are actually seen on Earth. Three! Three?! Three.

Six flowering plants, all with a different type of compound inflorescence. Chromolithograph, c. 1850. farbendruck und verlag von C. C. Meinhold & Söhne, Dresden Courtesy of Wellcome Images, Creative Commons license.

What's more, there seems to be some kind of developmental or evolutionary barrier between two of the forms (E and F in Figure 1). Groups of related species rarely display both forms; a given group will be all one form or the other. So in other words, examination of inflorescence architectures reveals two curious aspects of this part of the living world:

• the vast morphospace of inflorescence structure is almost completely unoccupied, with all known forms crowded into three neighborhoods; and
• forms are distributed among species in a pattern suggesting the presence of significant constraints on their development.

Before setting out to address these related questions, the authors explain how they began their quest:

Previously, distinct developmental models have been postulated for different inflorescence types leading to a fractured view of phenotypic space. From an evolutionary perspective, however, inflorescence types should be related to each other through genetic changes. A developmental model that encompasses different architectural types within a single parameter space is thus needed.

In other words, the authors are claiming that previous work on these forms has failed to take into account the background of common descent. According to evolutionary theory, flowering plants have a common history, and are therefore all related to each other through common ancestors. The distinct forms we see today must have arisen through modification of the forms from which they descended. And that means that the different forms should arise developmentally through a common set of functions and components, what the authors call a common "parameter space."

In my view, this is an extraordinary example of evolutionary thinking that drives a specific experimental analysis. The authors sought an encompassing developmental model precisely because they noted that the reality of common descent necessitates such a model. So if you've heard that evolutionary theory doesn't make testable predictions or is of no use in modern biology, here's one more demonstration of the falsity of those claims. "Design" considerations sure didn't produce the key insight; on the contrary, the denial of common ancestry that is sadly typical in the ID camp would have precluded the authors' approach.

The authors proceed to craft a developmental model that can account for the growth patterns that yield the three forms. It's elegantly simple, and its power is magnified significantly by the authors' demonstration that the processes involved are accounted for by the actions of known genes.

We could stop here, noting that a complete and testable model for inflorescence development arose from the introduction of evolutionary bases for new hypotheses.

But the authors went one step further. First, note that their model can be visualized as an "exploration" of the inflorescence morphospace (Figure 3). The developmental processes that make up the model drive the form of the inflorescence down just a few potential pathways; myriad alternative forms in the morphospace remain untouched by the "exploration." Now, evolution can be viewed as a similar exploration, not of morphospace but of a fitness space, or a "fitness landscape." ('Fitness' being defined here as advantageous adaptation.) In a fitness landscape, the peaks are forms or morphs of high fitness, as shown in Figure 5. By varying the parameters of their model to reflect known scenarios faced in evolution (different habitats, for example), the authors show that certain forms are optimal under certain conditions. In other words, the highest fitness peak under some environmental conditions, for example, might be form A, while under another set of conditions, it would be form B.

Interestingly, their fitness landscape models provide an explanation for why forms E and F in Figure 1 are nearly mutually exclusive: in the most common fitness landscapes, those two forms occupy peaks that are separated by a low-fitness valley. An evolutionary exploration from E to F would require a trip through an area of significantly suboptimal structure/function relationship. (Look at Figure 5D, for example: the two forms are the red peaks on either side of the landscape, each at the end of a "ramp," separated by a low fitness point at the bottom where the two "ramps" begin.) Not surprisingly, that doesn't happen very often.

Why, though, does it happen at all? Well, the last two graphs in Figure 5 show what is revealed when the fitness landscape incorporates a third dimension, either environmental variation or longevity of the plant. Have a look: the red boxes represent the high-fitness regions of what is now a 3-D fitness landscape. The red paths in those two graphs connect all three of the main forms. In other words, certain evolutionary influences can facilitate the kind of change that seems impossibly unlikely when looking at a simpler 2-D fitness landscape. The authors call the linkages pictured in Figure 5 "evolutionary wormholes," presumably since they seem to represent an unseen path that belies an initial conviction that "you can't get there from here."

If you've gotten this far, and you've heard/read a lot of ID claims, then you should be able to see why I think this article is important to consider in the context of ID challenges to evolutionary theory. After all, "you can't get there from here" is a reasonable paraphrase of a lot of ID challenges to evolutionary theory.

From a simple insistence on an evolutionary viewpoint, to a simple but elegant model for the development of plant architectures, through some molecular genetics, to wormholes through fitness landscapes. Wow! Can "design" do that?

Article(s) discussed in this post: Prusinkiewicz, P., Erasmus, Y., Lane, B., Harder, L.D. and Coen, E. (2007) Evolution and development of inflorescence architectures. Science 316:1452-1456.

[Looks around] Wow. [Looks around some more] Wow.

If you are a professional scientist, then perhaps you felt like I did when you went to your first scientific meeting. My first meeting was a meeting of the Society of Toxicology, but the one I really remember was the 1988 Annual Meeting of the Society for Neuroscience. It was a watershed in my life; there in Toronto I was Seduced By The Dark Side and elected to pursue a Ph.D. and a career in academic science. The rest is history although, alas, my student loans are not.

What I can still clearly recall is that giddy rush that comes from seeing all those smart and talented people, all as geeked out as I am about the brain, and all as happy as I was to be in the presence of 12,000 other brain geeks. (Neuroscience, as the meeting is called, is far bigger nowadays; 25,000 or so.) The elation was always tempered by the aching sense of loss and regret that resulted from being physically unable to attend 98% of the talks and 99% of the posters. (Hundreds of posters, and dozens of platform talks and symposia, occur simultaneously. Even Hermione's Time-Turner would be no help.)

And that's what I'm feeling now, as I have been welcomed into the blogosphere. Omigosh, there are HUNDREDS of fantastic blogs out there, and mere finitude (not to mention my cool day job) makes it impossible to consume them all. But the rush...look at all these smart people, so geeked out by evolution, faith, Shakespeare...wow.

Well, if you're interested enough in such topics to be reading this, then you'll find some of the following blogs to be worth a visit (or a permanent feed). I'll start a new label, since I'm sure I'll want to add to this list regularly.

I can probably leave theology alone on my blog, because Steve Martin's An Evangelical Dialogue on Evolution is superb. Great links, excellent articles, and now...guest columnists. His first guest is Gordon Glover, the author of a recent and well-reviewed book on science and creation, which was recently recommended on the ASA listserv. Wisdom and dialogue, without the sickening bile of Uncommon Descent. Go.

Profs at Rutgers University don't assign nearly enough homework. How do I know this? I've been to Laelaps, a blog full of wit and paleontology, written by an undergrad (!) at Rutgers. Wow. (Secret note to author of Laelaps: I went to Rutgers a long long time ago, and yes, we had the RU Screw then. Ah, stasis.)

Mobile genetic elements are a favorite topic of mine. Retroviruses (and other retroelements) are fascinating examples (and useful to cell biologists like me). And of course some talented technician-turned-grad-student (who evidently doesn't need 8 hours of sleep) has a whole blog on the topic. Free education!

And now you've decided that there's no point in going to bed, since you feel crappier on 3 hours of sleep than on none. Okay, then get to Siris, described thus:

A Golden Chain from Tar-Water to the Trinity, With Thoughts Relating to Philosophy, Christian Theology, and the Universe Generally.

Sleep?! HA!

Good night.

Which came first, the bird or the smaller genome?

It’s easy to think of a genome as a collection of genes, perhaps because so many of the metaphors used to explain genes and genomes (blueprint, book of life, Rosetta Stone) can give one the impression that everything in a genome is useful or functional. But genomes are, in fact, packed with debris. Many genomes contain huge collections of fossil genes: genes that have been inactivated by mutation but were never discarded, sort of like the old cheap nonfunctional VCRs in my basement. And many genomes contain even more massive collections of another kind of fossil-like DNA: mobile elements, or their remnants. The human genome, for example, contains over 1 million copies of a single type of mobile genetic element, the Alu transposon. Together, the various types of mobile genetic elements comprise nearly half of the human genome.

Think about that. Almost half of the human genome is made up of known mobile elements, pieces of DNA that can move around, either within a genome or between genomes with the help of a virus. This extraordinary fact -- and many of the specifics surrounding it -- constitutes one of the most compelling sources of evidence in favor of common descent, the kind of data for which only common ancestry provides a complete (or even reasonable) explanation. I’ll come back to this topic regularly.

Now it turns out, not surprisingly, that differences in genome size among types of organisms are determined primarily by the numbers of these mobile elements, and not by the number of genes. In fact, there is wild variation in genome size among types of organisms, and the variation has little to do with the numbers of genes expressed by those organisms. Consider birds, the subject of this week’s Journal Club (“Origin of avian genome size and structure in non-avian dinosaurs,” Organ et al., Nature 446:180-184, 8 March 2007).

Birds have remarkably small genomes, averaging 1/2 to 1/3 of the size of typical mammalian genomes. (The chicken genome, for example, is less than half the size of the mouse genome.) Why might this be? In other words, how might we explain this difference? The authors point to two important ideas. First, the chicken genome has been fully sequenced and analyzed, and it contains far less of the debris mentioned above. It seems that the processes that create (or multiply) mobile genetic elements are significantly less active in birds than in mammals and other vertebrates. Second, small genome size is intriguingly correlated with flight. Bats, compared to other mammals, have small genomes, and flightless birds, compared to other birds, have larger genomes. This has led to the proposal that small genome size might offer a selective advantage to flying animals, by reducing the energy cost associated with hauling all that debris around. So, it seems that a smaller genome is advantageous for flying vertebrates, and that genome size can be reduced by restraining the production of mobile genetic elements. And this raises several interesting questions, including this one: did the reduction in genome size accompany the origin of bird flight, or did it happen in advance? In other words, we can propose at least two alternative scenarios:

• 1) flight drove the genome change, by favoring small genomes, or
  
• 2) the genome change happened first, and helped to get flight off the ground. ;-)

How can we even hope to distinguish between these possible explanations? We would need, somehow, to look at the genomes of the ancestors of birds. And all evidence indicates that the relevant ancestors of birds are dinosaurs; in fact, today's birds are considered to be flying dinosaurs. The recent description of protein sequences from T. rex bone provided strong confirmation of the birds-from-dinosaurs hypothesis, but no DNA was recovered from the samples, and no information about genome structure can be inferred from those otherwise fascinating studies. If only, a la Jurassic Park, we could get some dino DNA...

Enter Organ et al. with a wonderfully creative idea. It turns out that, in organisms alive today, cell size is strongly correlated with genome size. In other words, organisms with large genomes tend to have larger cells. This relationship was first described in red blood cells, but Organ et al. show that it holds quite well in bone cells as well. Using bones from living species, they created a statistical model that enabled them to infer genome size by looking at the size of bone cells. Then they combined their model with measurements of bone cell size from fossilized bones of long-extinct animals, and were able to estimate the genome size of dozens of extinct species, including 31 dinosaur species and several extinct bird species. Their results are remarkable: small genomes are found in the entire lineage (with one interesting exception, Oviraptor) that gave rise to birds, all the way back to the theropod dinosaurs that are the typical reference point in the dinosaur-to-bird story. Here's how the authors put it: "Except for Oviraptor, all of the inferred genome sizes for extinct theropods fall within the narrow range of genome sizes for living birds." Even if you don't have access to Nature, you can have a look at the cool family tree in Figure 2, which shows small genomes in red and larger ones in blue. It's a compelling image.

The results suggest that small genomes arose long before dinosaurs took to the air, and raise some interesting questions about the interplay of physiological function (e.g., energy consumption associated with flight) and genome structure. Certainly scenario #1 above is not favored by these findings: flight apparently arose in organisms that already had much smaller genomes than many of their earthbound cousins. The relationship between flight and small genome size, then, remains unclear and even mildly controversial. Organ et al. acknowledge that the two characteristics did not arise together, but after reference to the larger genomes in flightless birds, they conclude their paper by noting that "the two may be functionally related, perhaps at a physiological level." And they postulate that small genome sizes may have been favored by warm-bloodedness and its associated energetic demands. But a minireview of the paper raises several criticisms of these hypotheses, and it is clear that the evolutionary forces acting on genome size are complex and yet poorly understood.

Notwithstanding the unanswered questions regarding genome evolution, this paper is the kind of scientific article that should be carefully considered by those who deny common descent. Following are some aspects of the story that create interesting questions for creationists and/or design advocates.

Consider the results presented in Figure 2. Outside of common ancestry, how are we to account for these data? The strong correlation between flight and small genome size in living organisms might look like some kind of "design" to someone who favors that sort of thinking, but Organ et al. have conclusively uncoupled genome size and flight. Of course those of us who see the universe as a creation will be happy to marvel at the advantages presented by small genomes to flying organisms, and perhaps we'll all think of these wonders as evidence of brilliant "design." But it seems to me that "design" does not serve a significant explanatory role here. On the contrary, I maintain that the work of Organ et al. demonstrates the following: in dinosaur lineages, the best way to predict genome size in an extinct species is to know the ancestry of the species. Common design aspects don't help. Common descent explains the pattern.

And yet, I think it gets much worse than that for anti-evolution thinkers. I regularly see certain old-earth creationists (e.g. the folks at Reasons To Believe) and design proponents (e.g. William Dembski) arguing that "junk DNA" (which includes, but is not limited to, the 45% of the human genome composed of mobile elements and their debris) is not "junk" but can have important functions. (The arguments of these critics are flawed in several ways, which I'll detail some other time.) While it's true that mobile elements have contributed to the formation of new genes from time to time, and are thought to be significant sculptors of genomic evolution, it's also true that mobile elements are indiscriminate in their jumping, and their continued hopping about is a documented cause of harmful mutation. Here, though, is a significant quandary for a design advocate considering a bird genome: if these mobile elements have important functions in the organism, then how is it that birds can get by with 1/4 as many of them as, say, squirrels? Why, if these elements have important functions in the organism, do bats seem to need far fewer of them than, say, rats? (The genome of the big brown bat is 40% the size of the genome of the aardvark. Hello!) It seems to me that these facts are best understood when one considers the possibility that most of this DNA is essentially parasitic, and that some types of organisms have benefited by restraining its spread. A "design" perspective with regard to genome size is just not helpful, and if that perspective insists on excluding common ancestry, then it's worse than worthless.

Article(s) discussed in this post: Organ, C.L., Shedlock, A.M., Meade, A., Pagel, M. and Edwards, S.V. (2007) Origin of avian genome size and structure in non-avian dinosaurs. Nature 446:180-184.

Introducing me: on common descent and explanation

What is the evidence for common descent?

To even ask the question, it seems to me, is to suppose that common descent is a proposal, or a hypothesis, and that a certain body of evidence supports the proposal. And that, of course, is quite true: common descent is a scientific theory, and a certain body of evidence supports that theory. But it is my view, and one of the themes of this blog, that the theory of common descent does not derive its main strength, its immense scientific success, from the collection of evidence that supports the proposal that organisms alive today are related through ancient common ancestors. In other words, I think that to claim that “there is a lot of evidence for common descent” is to significantly understate the strength of the theory.

The strength of the theory arises not from the evidence that supports it, although one can certainly build an overwhelmingly compelling case on that basis alone. The strength of the theory arises from its vast explanatory power. The data that make common descent so scientifically compelling are not just the data that “support” the theory. To really understand why common descent is such a powerful theory, one must focus on data that are explained by the theory, findings that just don’t make sense without an explanatory framework of common ancestry.

So I find common descent to be a scientific explanation with extensive and pervasive explanatory power, an explanation that allows data from widely varying areas of biology to just make sense. There is no competing scientific explanation for these data. Many of my weekly journal article reviews will deal with recent scientific findings that are beautifully explained by common ancestry.

But wait: this idea of explanation can be tricky. One can offer various explanations for a particular event or phenomenon, and no single explanation need be identified as the only explanation, or even as the best one. John Haught has famously noted this fact, using an illustration originally created by John Polkinghorne. Suppose someone walks into my kitchen and discovers a tea kettle boiling, then asks, “why is the water boiling?” I could offer several explanations: 1) the water is transitioning from a liquid to a gas, under certain kinetic or thermal influences; 2) an intense blue flame is burning beneath the kettle; or 3) I wanted to make a pot of coffee. (Haught prefers tea. I had to change something.) All of these explanations are correct, and none is better than any of the others. If the question was “why is the water boiling?” then a perfectly true answer can take many forms.

So, when I claim that common descent has no competition as a scientific explanation, I am focusing on the scientific nature of the explanation. If we want to know, for example, why there are highly conserved retroelements at homologous locations on certain mammalian chromosomes, the best scientific explanation is common ancestry. Might there be other true explanations? I can think of several alternative explanations, among them this one: “Because God made the chromosomes that way.” And that’s certainly true. So that alternative explanation is correct, but it’s not an explanation that competes with common ancestry. After all, it doesn’t say how God made the chromosomes that way. And what about this one: “The chromosomes are that way because God made them that way, de novo and without common ancestry, and the evidence for common descent is contrived or illusory.” That’s an interesting explanation, with lots of problems, one of which is this: it’s not a scientific theory in my view. In a future article, I’ll unpack some of the issues here for Christians. Suffice it to say for now that I see that last proposal as an alternative explanation, but not as a competing scientific explanation.

And do I really mean that the theory has no scientific competition at all? Well, no, for in fact there are perhaps innumerable scientific explanations that could account for the observations in question. Maybe, for example, there are unknown and utterly mysterious scientific laws that govern the formation of living things, such that every species acquires its unique characteristics independently of other species. The problem with this proposal is not so much that it isn’t scientific, but that it’s scientifically vacuous. It explains the observations, but has no basis within them. It’s an explanation, but it’s a worthless one.

And yes, that does mean that science employs an interesting and largely unseen set of values, a collection of assumptions and criteria by which explanations are judged. We all know that some explanations are better than others, in that they provide an account that we all judge to be superior to those of other explanations. How does this work? Maybe that question will come up occasionally in my articles or in the discussion.

So that’s what I think about common descent and scientific explanation. And what about natural selection? I’m a big fan of Darwin’s big idea, for sure, but I think the explanatory issues are different in that arena. More to come.

Now you know where I stand on evolution. I’m an NCSE Steve, and I think evolutionary theory is fascinating, powerful (as an explanation) and awe-inspiring (as a view of life’s history). Are there problems for Christians? Sure. But they’re not insurmountable, and there’s nothing to fear in exploring God’s world.

Why "Quintessence of Dust?"

What a piece of work is a man, how noble in reason, how infinite in faculties, in form and moving how express and admirable, in action how like an angel, in apprehension how like a god: the beauty of the world, the paragon of animals — and yet, to me, what is this quintessence of dust?

—Hamlet, Act II, Scene II (Arden Shakespeare)

When I consider your heavens, the work of your fingers, the moon and the stars, which you have set in place,

what are mere mortals that you are mindful of them, human beings that you care for them?

You have made them a little lower than the heavenly beings and crowned them with glory and honor.

—Psalm 8:3-5 (Today's New International Version)

Then the Lord God formed a man from the dust of the ground and breathed into his nostrils the breath of life, and the man became a living being.

—Genesis 2:7 (Today's New International Version)

Kicking off my blog

Well, it's August 3, 2007, and I'm setting up my blog. It's called Quintessence of Dust, and it will deal with issues of science and Christian faith, focusing on genetics, development, evolution, neuroscience and topics related. I'll regularly address intelligent design and creationism, among other scientific issues that attract the attention of evangelical Christians. My main theme will be scientific explanation.

Most typically, I will base my comments on a very recent article in the scientific literature. I'm shooting for one of these article-based commentaries ("Journal clubs") per week. Minor entries will be interspersed as I feel inspired.

I anticipate errors and correction, and I'll post corrections prominently.

Theology, philosophy and Shakespeare will also figure semi-prominently. I don't really care about politics, so it won't often contaminate the blog unless and until a politician speaks on a topic of interest. (And, of course, they often do.) Boston Red Sox baseball will always trump politics.

So, here's Hamlet getting the first big quote (ripped unceremoniously out of context):

"...there is something in this more than natural, if philosophy could find it out."
--Hamlet, Act II, Scene II