How to evolve a new protein in (about) 8 easy steps

If you have only read the more superficial descriptions of intelligent design theory, and specifically the descriptions of irreducible complexity, you might (reasonably) conclude that Michael Behe and other devotees of ID have claimed that any precise interaction between two biological components (two parts of a flagellum, two enzymes in the blood clotting cascade, or a hormone and its receptor) cannot arise through standard Darwinian evolution. (If you don't know anything about the term 'irreducible complexity' you should probably read a little about it before proceeding.) In other words, you may be under the impression that Behe doesn't think that such a system could arise through a stepwise process of mutation and selection. You may even be under the impression that Behe has demonstrated the near impossibility of such a system coming to be through naturalistic means.

This article was UPDATED on 1 November 2007, incorporating some corrections and clarifications provided by the senior author of the studies described. In other words, this post was peer reviewed, and this is the final version.

You would be mistaken, albeit (in my opinion) understandably so. Behe has not claimed this -- though he's often come pretty close -- and recently he has made it clear that this is not his position. Unfortunately, many of the critiques of irreducible complexity contain significant errors, including the claim that Behe rejects all stepwise accounts of molecular evolution, and you have to look pretty hard to find well-reasoned examinations of the problems with Behe's interesting but fruitless challenge to evolutionary theory.

My purpose in the preamble above is to make it clear that this Journal Club is not intended to refute Behe's claims regarding the ability of Darwinian mechanisms to generate irreducibly complex structures. (In my view, his claims are wholly mistaken, and Christian enthusiasm for his natural theology is a disastrous mistake. But that's for another time.) Rather, it is to discuss a superb recent example of the kind of experimental molecular analysis of evolution that can be done in this postgenomic era. Experiments like this are revealing how evolutionary adaptation actually comes about at the molecular level, thereby addressing the very questions raised by ID thinkers. ID apologists are, in a sense, wise to attack the work described here, because these experiments are the first fruits of the types of analysis that will usher ID into permanent scientific ignominy.

So, to our two papers.

How, exactly, does a protein acquire a new function during evolution? This is one of those "big questions" in evolutionary biology. Broad concepts such as gene duplication are quite helpful in formulating explanations, but the specific question raised is focused on the details -- the actual steps -- that must occur during the step-by-step modification of a protein such that it performs a different job than the proteins from which it has descended. The constraints on the process of change are significant, and the issues are similar to those I discussed when describing the concept of fitness landscapes in morphospace. The problem, basically, is this: how can you change a protein without wrecking it in the process? In other words, can you get from function A to function B, step by step, without passing through an intermediate form, call it protein C, which is worthless (or even harmful)?

These are precisely the questions addressed in an elegant set of experiments reported in two reports over the last year or so. The second article, by Ortlund et al., was reported in the 14 September issue of Science, and built on work reported in Science in April 2006. Their studies focused on two closely-related proteins that are receptors for steroid hormones. In this case, the steroids of interest are corticosteroids (the kind often used to treat inflammation; Ortlund et al. studied receptors for cortisol, which is of course quite similar to cortisone) and a mineralocorticoid (a less well-known hormone, aldosterone, that regulates fluid and salt intake). The hormones are structurally similar (being steroids).

Joseph Thornton, at the University of Oregon, has been studying the origins of these receptors for about 10 years, and has assembled an interesting (and detailed) account of their history. The basic outline is as follows: the original steroid receptor was an estrogen receptor, and is extremely ancient, apparently arising "before the origin of bilaterally symmetric animals" (Thornton et al., Science 2003). (That's seriously ancient, sometime in the Cambrian or earlier.) The progesterone receptor seems to have arisen next, followed by the androgen (i.e., testosterone) receptor. (Now that's intriguing.) Fairly late in this game, the two receptors of interest to us here, the corticosteroid receptor and the mineralocorticoid receptor, were added to the vertebrate repertoire. The two modern receptors are thought to descend from an ancestral corticosteroid receptor, which underwent a gene duplication. Hereafter, I'll refer to the receptors as the corticosteroid receptor and the aldosterone receptor, hoping that all the jargon won't obscure the message.

In a widely-discussed paper published in Science a year ago (Bridgham et al., Science 2006), Thornton's group determined the most likely DNA sequence of this ancestral gene, then "resurrected" it, meaning simply that they created that very DNA sequence in the lab. (Determining the ancestral sequence was a nifty piece of work; actually making the DNA is quite straightforward, especially if you have a little dough.)

Their experiments showed that the ancestral receptor could bind to a hormone that didn't exist yet (aldosterone) while it was functioning as a receptor for corticosteroids. In other words, the receptor was available for activation by aldosterone long before aldosterone was around. (All jawed vertebrates make corticosteroids, but only tetrapods make and use aldosterone, an innovation that occurred at least 50 million years later.) The modern corticosteroid receptor has since lost its ability to interact with aldosterone, and Bridgham et al. chart the most likely evolutionary path, at the molecular level, by which we and other tetrapods came to have a corticosteroid receptor that won't bind to aldosterone. The surprising result, however, is the fact that the ancient receptor was able to bind aldosterone, millions of years before aldosterone is thought to have been present.

The 2006 paper is, I think, more notable as an illustration of an important evolutionary principle ("molecular exploitation" is the authors' term) than as a set of observations; Michael Behe's trashing of the group's work is disgusting, but it's true that the findings are limited in scope. It's worth having a look at the whole paper, though (and I believe it's freely available with free registration), because the authors very clearly explain the rationale for their continuing work, which is to begin to address one of the major "gaps in evolutionary knowledge": the mechanisms underlying stepwise evolution of "complex systems that depend on specific interactions among the parts."

If you're well-read on ID thought, that last sentence should sound pretty familiar. So let's note that prominent papers in science's premier journals are acknowledging that the evolutionary mechanisms that generate complex structures -- including "irreducibly complex" systems -- are as yet poorly understood. And let's give ID credit for asking a good question. (Not a new one...but a good one.)

The 2006 paper did not, as advertised, utterly destroy ID arguments, and again Behe is right to criticize the near-hysteria surrounding that work. But I find Behe's bravado otherwise unconvincing. Because that paper did set up the most recent work, and the whole story illustrates rather clearly how ID's question will (soon) be answered.

The most recent paper adds significantly to the picture, and introduces some genetic concepts that Behe's fans should pray he understands. The authors (Ortlund et al.) took their analysis to a far more detailed level, by extending their previous observations to include much more of the receptor family tree. In the 2006 work, they had assembled a detailed family tree for the receptors, by looking at DNA sequences from living species known to represent various branches on the tree of life. In other words, they chose organisms such as lampreys, bony fish, amphibians and mammals, and examined their DNA codes (for the receptors) to find the changes that occurred in each branch of the lineage. Now, please stop and think about this, because it's really cool. What the authors did was mine existing databases of DNA sequence data, pulling out the sequences of the steroid receptors from 29 different vertebrate species. You could repeat this part of the experiment right now, by referring to their list of organisms in Supplemental Table S5, which provides the ID codes needed to locate the DNA sequences in the Entrez Gene database. Then they charted the changes in the DNA sequence in the context of the tree of life as sketched out in the fossil record. The tree they assembled includes all the steroid receptors, and I've annotated it a little if you want to have a look. They used this tree to guide their further experiments, as I'll explain below. What the most recent paper added to the story was an analysis of the 3-D structure of the various postulated intermediates in the evolutionary pathway. The authors accomplished this by making proteins from the "resurrected" genes, then crystallizing them and using X-ray diffraction techniques to determine their precise structures.

Examination of their receptor family tree revealed something interesting. Most vertebrates have highly specific receptors: the corticosteroid receptor isn't strongly stimulated by aldosterone, and vice versa. But some living vertebrates (skates, in particular) show a different pattern: the corticosteroid receptor isn't all that specific for cortisol. Because the ancestral receptor also lacked specificity (as shown in the 2006 paper), the authors concluded that the receptor acquired its discriminating taste at some point between the branching-off of skates (and their kin) and the separation of fish from tetrapods. Their Figure 1 is a little crowded, but it illustrates this nicely:

To follow the evolutionary narrative in this graph, start at the blue circle, which represents the ancestral receptor that was "resurrected" in the 2006 paper and that happily binds to both corticosteroids and aldosterone. (The graphs on the right side of the figure demonstrate the specificity, or lack thereof, of the receptors at different times in history.) There's a branch leading up and to the left, to the various GRs (corticosteroid receptors), and one leading up and to the right, to the MRs (aldosterone receptors). At the green circle, another branching event occurred, 440 million years ago, at which point certain groups of fishes (skates among them) branched off, up and to the right. The receptor at that point is an ancestral corticosteroid receptor, and it still isn't specific for corticosteroids. But the receptor at the yellow circle, in the common ancestor of tetrapods and bony fishes, is specific. The authors conclude that specificity arose between those two points, between 420 and 440 million years ago. With some (deliberate?) irony, they indicate that process with a black box.

The rest of the paper explores the pathway by which the receptor might have been successively altered so as to install specificity for cortisol. During those 20 million years of evolution, at least 36 different changes were introduced in the makeup of the receptors. By looking at the 3-D structures of the ancestral forms, the authors were able to discern the specific functional ramifications of these various changes, and they found that the alterations fell into three groups:

• Group 'X' alterations included the changes reported in the 2006 article. These are the biggies, that account for much of the functional 'switch' between GRs and MRs. These alterations don't account for the specificity change that occurred inside the black box in Figure 1.
• Group 'Y' alterations are all strongly conserved (meaning that they were permanent changes), and occurred during the black box time period. Moreover, this group of changes is always seen together: modern receptors have all of these alterations, while ancestral receptors have none of them.
  
• Group 'Z' alterations are also conserved changes, but they don't always occur together like group 'Y'.

The authors set about the work of examining the function of "resurrected" receptors bearing these groups of changes. When they introduced group 'X' changes into the ancestral receptor, they got a receptor that was almost modern (i.e., specifically tuned to cortisol) but not quite; this was what the previous work had indicated. Then they hypothesized that the group 'Y' changes, because they were so highly conserved and because they all occurred together, would make the transition complete. But no: instead, the group 'Y' alterations made the receptor worthless, unable to bind any hormone at all. Surprise! Looking at their 3-D structures, they figured out what this meant. The group 'Y' changes were somehow important, but they could only have a beneficial influence in the presence of another set of alterations, group 'Z', which had to occur in advance. The biophysical details don't concern us, but the basic idea is that the group 'Z' changes created a permissive environment for the group 'Y' changes, which are the alterations that complete the development of the modern specific form of the receptor for cortisol.

In genetics, we have a word for this type of interaction between genetic influences: epistasis. The fascinating history of steroid receptor evolution includes examples of what the authors call "conformational epistasis," meaning that some alterations in 3-D structure are required in advance for other alterations to ever get off the ground. Specifically, some alterations are evolutionary dead ends, because they yield worthless proteins, unless those alterations follow another set of changes that generated a different -- and more fruitful -- environment.

The authors then construct a map of what they call "restricted evolutionary paths through sequence space," showing how you can get there from here, without traversing an evolutionary no-man's-land of non-function. The path includes changes that don't apparently improve the receptor, but that yielded the right environment for the changes that did improve function. Their map is in Figure 3:


The idea is that you want to get from the lower left corner of the cube (the ancestral receptor) to the upper right corner (the modern receptor) without hitting a stop sign (a worthless receptor). The green arrows indicate a change in function of some kind, the white arrows no change. Yes, you can get there from here.

The authors note that their data "shed light on long-standing issues in evolutionary genetics," firstly the question of whether adaptation proceeds through "large-effect" changes (mutations), or through baby steps. Their conclusion:

Our findings are consistent with a model of adaptation in which large-effect mutations move a protein from one sequence optimum to the region of a different function, which smaller-effect substitutions then fine-tune; permissive substitutions of small intermediate effect, however, precede this process.

They note that the large-effect changes are inherently easier to identify (of course), and that the painstaking work of "resurrecting" the ancestral proteins and studying their function is the only way to identify the critical small-effect alterations that made the "big jump" work.

The authors also comment on the big "contingency" debate. I'll write more on the whole "rewinding the tape of life" question some other time; for now, we'll just consider the authors' words:

A second contentious issue is whether epistasis makes evolutionary histories contingent on chance events. We found several examples of strong epistasis, where substitutions that have very weak effects in isolation are required for the protein to tolerate subsequent mutations that yield a new function. Such permissive mutations create “ridges” connecting functional sequence combinations and narrow the range of selectively accessible pathways, making evolution more predictable.

If you have read my summary of the wormholes in morphospace story, this metaphor of "ridges" should make a little sense. The authors here are describing the same concept: an evolutionary exploration of a design space, with paths meandering through a map of the possibilities. But:

Whether a ridge is followed, however, may not be a deterministic outcome. If there are few potentially permissive substitutions and these are nearly neutral, then whether they will occur is largely a matter of chance. If the historical “tape of life” could be played again, the required permissive changes might not happen, and a ridge leading to a new function could become an evolutionary road not taken.

The history of the steroid hormone receptor, then, appears to include several different aspects of evolutionary biology combined: "chance" creating opportunity, leading (via epistasis) to selection for improvement, all done step by step, with some steps generating more apparently dramatic change than others.

Amazingly, Michael Behe is pretending that this analysis is utterly unimportant, with no implications at all for ID proposals, because the receptor-hormone system isn't "irreducibly complex." Some critics of ID claim that the goalposts are being regularly moved, and I'm inclined to agree. But let's just grant Behe the difference between protein-hormone interactions and protein-protein interactions. Does anyone really believe that Joseph Thornton's work doesn't show us exactly how the "irreducible complexity" challenge is going to fare in the near future?

More required reading

As a Christian biologist (and now Christian biologist blogger), one of my goals is to help Christians understand biology. And right now, that means I need to focus on helping Christians see the worthlessness of most of the ideas in the Intelligent Design movement, and especially to help Christians see how embracing ID is both theologically and intellectually unwise.

Well, John Farrell is a an ally, and he's a great read. Check out his blog, at Farrellmedia, which he describes as "reports and commentary on the news, science, and creative ends of the media." Among other things, Farrell seems to be particularly interested in (and annoyed by) the enthusiasm of conservative publications like The American Spectator and National Review for the ideas of ID. (I don't follow those publications closely at all anymore, but I have noticed with alarm the fondness for ID that is displayed at Books and Culture.) I've added one of his books, The Day Without Yesterday, to my must-read list. (Just what I need. I haven't even finished The Sonnets.) Last month, a post on John's blog spawned a long discussion at Touchstone. Enlightening, in various ways.

I've also added The Fire and the Rose to my blog list. It's the blog of one D.W. Congdon, a seminary student at Princeton. There you'll find some interesting discussion of theology, science, and, most notably for me, concepts of the soul and the Imago Dei. One of my favorite posts: "Can we still speak of the soul?" My best friend is mentioned in that article.

Finally, I recommend Gordon Glover's blog, based on his book Beyond the Firmament. I haven't read the book (Steve Martin reviews and recommends it over at Evangelical Dialogue on Evolution), but Gordon's comments here and his work on the blog make it clear that he and I have a very similar approach to science and faith.

Now before I get back to work on my slowly-gestating article on evolution of new proteins, I thought I should explain why my articles don't come out every three hours: I'm actually a working scientist -- currently on sabbatical in the lab of a friend and collaborator -- and, well, doing experiments is just as fun as writing about them.

Take that, PZ.

"The gift is not like the trespass"

Our family embraced the Reformed tradition (of evangelical Christianity) while we were a part of Park Street Church in Boston. We have many fond memories of our time at Park Street; I first picked up a copy of Del Ratzsch's excellent Science and Its Limits from the church library there, and it was at Park Street where we first learned about Calvin College. But right now, I'm remembering the many times when I heard a particularly excellent sermon, the kind of sermon that makes you feel as if you're hearing simple and well-known truths for the first time. If you're a Christian, perhaps you know what I'm talking about. This past Sunday, I had one of those experiences. The text was Romans 5:12-21, and when my friend Rev. David Kromminga was finished, I had that weird feeling like I'd never read Romans 5 in my life. It's worth sharing here, because the text is one that surfaces amid creationist objections to evolutionary theory.

If there is any problem at all between evolution and Christian belief, it arises in the context of the historical narrative of redemptive history. (The notion that evolutionary theory, as a natural explanation, is hostile to Christian belief is, in my opinion, preposterous. Hence my low regard for ID.) Specifically, the historical nature of the Fall, in which sin and death entered the world due to the actions of two particular people, is difficult to fit into the narrative of common ancestry.

In my view, the problem is simply historical (the stories don't seem to fit well together), but many Christians see a more serious conflict, because they believe that the existence of a single historical Adam is central in the redemption narrative. In fact, I'm sure that the vast majority of evangelicals would take this position. And Romans 5 would be a big reason why.

The standard proof text is this one: "Therefore, just as sin entered the world through one man, and death through sin, and in this way death came to all people, because all sinned..." (Romans 5:12, TNIV). The basic claim, that sin entered through Adam, is repeated three more times in the passage. Moroever, the passage clearly sets up Adam and Christ as types to be compared. No list of "dangers of theistic evolution" would be complete without reference to Romans 5.

I think this is sad, because it seems to me that Paul is trying to say something much bigger than "Adam brought death, Christ brings life." The problem with that summary is that it strongly intimates a kind of equality between the two types, as though Adam's sin was "cancelled out" by Christ's redemptive work. What Paul is saying, I think, is something like this: "don't think for a moment that one of those is equal to the other." Verse 12: "The gift is not like the trespass." Or, as David put it on Sunday: "the rot does not equal the redemption." Read the whole passage; Paul's repetition suggests that he is determined to make sure we get that message.

I agree that the "historical Adam" question is a tough one. But I'm not sure it's enormously important. Adam was the "dirt man." Jesus is the God man. The gift is not like the trespass. Let's not compare the God man to the dirt man, as though they're two sides of the same coin. And let's not forget that Jesus is the author and finisher, the beginning and the end. Even if we never figure out how that whole dirt-man thing actually went, we'll know everything we need to know if we know the God man.

Sympathy for the Devil's Chaplain (Part II)

Long before Richard Dawkins topped the charts with his recent entry into the folk-religion genre, he was reviled by Christian culture warriors as a Public Enemy, an ayatollah of atheism, the embodiment of the evil that ensnares all who embrace Darwin's Dangerous Idea^TM. His revivalistic fervor, combined with his, um, expertise in handling the media, makes him a near-perfect spokesperson for unbelief, and consequently he is credited with some now-famous pronouncements on subjects related to faith and science.

Now to be sure, some of Dawkins' more colorful and/or controversial statements are indefensible, and his fellow atheists at least occasionally point this out. (I do think that unbelievers should be more willing to disavow some of his truly sickening behavior, but if atheists asked me for quid pro quo, I'd need to blog 10 hours a day just on the subject of evangelical Christian misconduct.)

But this is the second of two articles in which I do penance for referring to the Devil's Chaplain as an 'idiot.' So I'm not going to catalog his misdeeds/misstatements. Instead, I'll to pick a few of his more famous sentences and explain why every Christian's favorite materialist mullah is often just being brutally frank.

First, let's acknowledge that sometimes Dawkins is misunderstood and/or misrepresented. The first few chapters of The Extended Phenotype, as I explained in my previous post, involve Dawkins' careful exposition of the ways in which his ideas had been misconstrued, sometimes wildly so. For a more recent example, consider the whole "brights" episode. In the summer of 2003, Dawkins and fellow atheist apostle Daniel Dennett launched a campaign (in the UK and USA) to get atheists more respect. They called on fellow unbelievers to adopt the label "bright," analogous to the label "gay" successfully adopted by homosexuals. Many Christians I know found this to be arrogant and offensive, mostly because they connected the dots and interpreted "bright" to be the opposite of "dumb" or "dim." Dennett has specifically disclaimed this intention (see also page 21 of Breaking the Spell), and I'm taking his word for it. So, let's not waste our time demonizing Dawkins for offhand comments that may not reflect what he really believes.

Here, then, are some of Dawkins' better-known remarks, and my comments.

1. "Undisguised clarity" or arrogance?

It is absolutely safe to say that if you meet somebody who claims not to believe in evolution, that person is ignorant, stupid or insane (or wicked, but I'd rather not consider that).

--from a review of Blueprints: Solving the Mystery of Evolution, in the New York Times, 9 April 1989

Ah yes, this is, I think, The Mother of All Richard Dawkins Quotes. It's provided fodder for Christian critics of all stripes, essentially all of whom express indignation and outrage. I see two types of responses. One response is universal: everyone who attacks the statement says that it is arrogant or bullying. The other is specific to anti-evolution critics: they say (of course) that it is wrong. In this latter camp, we find young-earth creationists denouncing Dawkins with typical vitriol, but also "skeptics" like Alvin Plantinga, who insist that there can be reasoned doubt about evolutionary explanations.

On the first count, while I agree (as do other atheists) that Dawkins can be abrasive and insensitive, I am generally uninterested in controversies surrounding etiquette. There are, of course, appropriate and inappropriate ways to tell someone that they don't have a bloody clue what they're talking about, but I know just how hard it can be to remain patient while being regaled (for the umpteenth time) with all the stock objections to evolution. (My most recent little piece of hate mail came from a man who shamelessly confessed to having first learned all the biology he needed to know from a local weatherman. I AM NOT MAKING THIS UP.) Yes, there is probably a nice way to say "you're wrong about that," but (perhaps owing to my Scottish ancestry) I'd rather be clearly corrected than have to sit through all the fawning disclaimers.

I think Dawkins was trying to say "evolution is beyond a reasonable doubt" in a dramatic and attention-getting way. And he succeeded. Now, was he displaying arrogance or intolerance? I'm quite sensitive to this charge; it has been thrown at me by at least one evolution-bashing colleague. I do worry about being arrogant, at least because I'm not (usually) trying to be obnoxious. But, as Dawkins noted in a subsequent reflection on criticism of the quote in question: "undisguised clarity is easily mistaken for arrogance." Was he being over-the-top obnoxious? Intolerant? Insensitive? Well, let's have a look at a little of the context of the quote:

We are not talking about Darwin's particular theory of natural selection. It is still (just) possible for a biologist to doubt its importance, and a few claim to. No, we are here talking about the fact of evolution itself, a fact that is proved utterly beyond reasonable doubt. To claim equal time for creation science in biology classes is about as sensible as to claim equal time for the flat-earth theory in astronomy classes. Or, as someone has pointed out, you might as well claim equal time in sex education classes for the stork theory. It is absolutely safe to say that if you meet somebody who claims not to believe in evolution, that person is ignorant, stupid or insane (or wicked, but I'd rather not consider that).

If that gives you offense, I'm sorry. You are probably not stupid, insane or wicked; and ignorance is no crime in a country with strong local traditions of interference in the freedom of biology educators to teach the central theorem of their subject. I recently toured East Coast radio stations, doing phone-ins. I came away optimistic. I had expected hostile barracking from creationists with closed minds. Instead, what I found was genuine curiosity and honest interest. I got sincere questions from intelligent people who really wanted to know because they had literally no education in evolution.

--from a review of Blueprints: Solving the Mystery of Evolution, in the New York Times, 9 April 1989

When the quip is put back into its native habitat, I find it to be provocative but not inappropriate. It can be paraphrased, in my opinion, as follows: "If you claim to doubt evolution, then I'm quite sure this is because you don't know much about it. I can think of a few other reasons, but they're not nearly as likely, and some of them wouldn't reflect well on you." And I do think that the context makes clear that Dawkins is specifically addressing common descent.

Which brings us to the second response to the quote: that it is wrong, because there is plenty of room for reasonable doubt regarding common descent. In my view, common descent is indeed beyond a reasonable doubt. (If I felt like dealing with the different meanings of the word 'evolution,' I would have typed them here.) And so, like Dawkins, I think there are relatively few means by which one would arrive at rejection of common descent. Ignorance is by far the most commonly-traveled path. Stupidity sure isn't going to help. Insanity is not worth discussing. Wickedness...well, some people do seem to, um, prevaricate about evolutionary science, but come on: that's not what Dawkins was saying. He was saying this: if you doubt common descent, you either don't understand it, or you are refusing to understand it. And to Dawkins, this refusal to understand, this willful ignorance if you will, is insane, stupid, even wicked.

Now, it's important to note that Dawkins was referring to common ancestry in his comments. Many Christian critics imply that Dawkins was denouncing any and all skepticism of evolutionary theory. I think the fuller context of his remarks makes clear that this criticism is invalid.

But is ignorance really the only reason why a reasonably intelligent person might reject common ancestry? In his follow-up, Dawkins allows that his analysis may have been incomplete:

There is perhaps a fifth category, which may belong under 'insane' but which can be more sympathetically characterised by a word like tormented, bullied or brainwashed. Sincere people who are not ignorant, not stupid and not wicked, can be cruelly torn, almost in two, between the massive evidence of science on the one hand, and their understanding (or misunderstanding) of what their holy book tells them on the other. I think this is one of the truly bad things religion can do to a human mind. There is wickedness here, but it is the wickedness of the institution and what it does to a believing victim, not wickedness on the part of the victim himself.

It is here that I part with Dawkins, at least a little. I know people who doubt common descent (more specifically, universal common descent), not because they are ignorant of the data or of the explanation, but because they have an additional data set that needs to be taken into account. These folks understand the Bible to be making certain factual claims about the age of the earth or of the nature of the Fall. They know, full well, why scientists accept common descent as a scientific explanation, but are searching for a rival explanation that also enfolds the "biblical data." As I've written before, I think these people are mistaken about the "biblical data," but they are not torn, tormented, bullied, brainwashed. You can probably tell that I respect the ideas and work of these young-earth creationist theorists vastly more than those of the Intelligent Design movement. Similarly, I find Alvin Plantinga's (now dated) criticisms of evolutionary science to be embarrassingly weak (even in their time), but when he expresses doubts based on possible points of factual conflict with Christian belief (i.e., the assertion that humans were created "specially"), then his skepticism cannot be dismissed using Dawkins' rubric.

2. Darwin made me an atheist.

Darwin made it possible to be an intellectually fulfilled atheist.

-- from The Blind Watchmaker (1996 Edition), page 6

Plenty of Christians are convinced that evolution is a particularly sharp implement in the Devil's toolbox; some creationists seem convinced that the theory is at the root of every known evil. (Adam must be relieved.) Certainly many are quite sure that accepting evolution is a big step toward unbelief.

And that's what Richard Dawkins thinks, right? Well, maybe, but here's that quote in its complete context:

...what Hume did was criticize the logic of using apparent design in nature as positive evidence for the existence of a God. He did not offer any alternative explanation for apparent design, but left the question open. An atheist before Darwin could have said, following Hume: 'I have no explanation for complex biological design. All I know is that God isn't a good explanation, so we must wait and hope that somebody comes up with a better one.' I can't help feeling that such a position, though logically sound, would have left one feeling pretty unsatisfied, and that although atheism might have been logically tenable before Darwin, Darwin made it possible to be an intellectually fulfilled atheist.

-- from The Blind Watchmaker (1996 Edition), page 6 (italics in original)

In other words, Darwin provided a natural explanation for a previously-unexplained set of observations -- granted, a vast and overwhelmingly impressive set of observations -- namely, "endless forms most beautiful" in living creations. But really, that's all Darwin did, and I think that's all Dawkins is saying here. This matters to atheists, I presume, because unexplained stuff (of any kind) makes them uncomfortable. Providing a natural explanation for anything -- comets, hurricanes, pleasure, pain, neuronal development -- makes the world a little more comfy for an atheist. And that makes sense to me. As Alvin Plantinga puts it: "...evolution serves to answer what would otherwise be a crushing objection to naturalism."

I think Dawkins is surely right about all this, but I think it's a mistake for Christians to overemphasize his otherwise indisputable assertion. First of all, while scientific explanations might make it easier for an atheist to sleep, they ought not affect the slumber of a believer, unless that believer, like Dawkins, has anchored her/his belief in natural phenomena that can't be explained. I reject the notion of God as an Explanation, and I'm distressed by the impression that so many of my fellow Christians feel so compelled to find unexplained phenomena, so as to label them "God's work." Second of all, I think it's a dangerous thing to suggest that people become atheists because of a scientific theory. Maybe that's because, as a Reformed Christian, I don't think it's nearly that easy to separate someone from the love of Christ. And finally, I am uncomfortable with the notion, upon which whole ministries seem to be based, that scientific explanations (or lack thereof) are strongly linked to belief. Doesn't Hebrews 11:3 say something different?

3. Believing without evidence?

Richard Dawkins, the scientist's scientist, actually confessed that he has religious belief -- in evolution. He said that he would believe it even if it were unsupported by evidence. No, really:

Even if there were no actual evidence in favour of the Darwinian theory (there is, of course) we should still be justified in preferring it over all rival theories.

Even if the evidence did not favour it [evolution], it would still be the best theory available!

-- from The Blind Watchmaker (1996 Edition), pages 287 & 317 (italics in original)

Oh, the fun that ID people have had with these. Outside the intended context, it does look like Dawkins is advocating "blind faith" in evolutionary theory, as though he embraces the theory only to escape the clutches of a loathed rival. Whether or not Dawkins sees evolution that way, the quotes above are not what they seem, and in fact they are assertions with which I handily agree.

Let's take the second quote and put it back into the paragraph from which it was excerpted:

The theory of evolution by cumulative natural selection is the only theory we know of that is in principle capable of explaining the existence of organized complexity. Even if the evidence did not favour it, it would still be the best theory available! In fact the evidence does favour it. But that is another story.

-- from The Blind Watchmaker (1996 Edition), page 317 (italics in original)

Here Dawkins is doing something that I tried to do in my first post on this blog: he is separating the evidence for evolution from the explanatory power of evolutionary theory. Notice that he didn't write, "Even if the evidence contradicted it..." In fact, Dawkins loves to relate the response of J.B.S. Haldane to the question of whether and how evolution could be falsified: "fossil rabbits in the Precambrian." It's really not reasonable at all to suggest that Dawkins is claiming that one ought to accept evolution in spite of the evidence, and the rest of the chapter ("Doomed rivals") from which the quotes are taken makes this quite clear.

What Dawkins is saying, I think, can be paraphrased like so: "We ought to prefer evolutionary theory over its rivals, whether or not there is more evidence in favor of evolution, because the theory is the only one that provides a compelling natural explanation for biological complexity." You don't need to be an atheist, or a "Darwinian fundamentalist," or wicked or insane, to agree. You need only be a person who prefers natural explanations for the natural world, a person who thinks that the formation of the wonders of God's biological creation can be understood by some of those very wonders.

Okay, I'm done with my penance. Back to the Journal Clubs; I have a backlog of articles worthy of our attention.

It's October in Boston...and in Phoenix

I did promise to make baseball a part of this blog, and so far it's been all sorts of serious stuff about science and faith. And now it's October! We all know what that means. In fact, it's going to an excellent fall in the Matheson household, for we are fans of two major league teams: first and foremost, the Boston Red Sox, and second, the Arizona Diamondbacks. (I'm from Phoenix and my wife Susan is from Tucson; 3 of our 4 children were born in Tucson; the fourth in metro Boston.) Those two teams own the best regular-season records in their respective leagues. Woo hoo! The Sox won tonight, and the D-backs are playing some hapless Midwestern team as I write this.

Well, if you are not yet excited about postseason baseball, but would like to be, I offer the following exercise. It involves neither of our favorite teams, but is based instead on one of the most outstanding plays in postseason baseball history. Now if you will, please work through the steps in order.

1. Make sure your computer's sound is on, loud.
2. Listen to this broadcast excerpt. Just listen to the whole thing. If you don't know exactly what is happening, you can come back after you've completed the exercise.
3. Watch the video of the event. You'll see a link called "350K" next to a description of the achievement.
4. Watch this video at YouTube. Listen for the desperate plea while the ball is in flight. (The same person is screaming a few seconds later.)

If that doesn't help you get ready for the MLB postseason, then you're probably a soccer fan, and that means we should get back to science and faith, in hopes that we have some common ground...

Go Sox!

(For those readers who are unhappy, perhaps because they loathe the Mets or any team from Gotham, try this out. It's from 2004.)

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.