Belief, evolution, evil, and me

My recent post on the so-called problem of evil has generated some interesting comments that are worth addressing in a separate post. The comments raise questions of a somewhat personal nature, but because I write as a Christian, I think the issues are fair game.

One commenter, Ron, addresses the "compatibility" of God and suffering, and reads Scott Carson to be claiming that we must either blame humans for the whole mess, or dismiss suffering as unimportant since "the body is just a physical shell." I think Scott's answer is bigger than that, and would point Ron to some of Scott's more recent articles, but Ron's remarks do raise the question of what I think of suffering and the "problem of evil."

And Paul wonders why I believe any of Christianity, after correctly noting that I don't think that evolution or the problem of evil poses "a threat to Christians."

First evolution (i.e., common descent, and specifically shared ancestry between humans and other creatures). In my view, evolution as a scientific explanation is no more a threat to Christian belief than any other scientific explanation. (My favorite comparisons would involve embryonic development, where natural explanation is ubiquitous, largely uncontroversial, and contradicted by certain readings of certain biblical passages.) If evolution is a special problem for Christians, the problem is not in the explanation, but in the historical narrative. I don't consider that a "threat" to Christian belief, but I do think it's a problem worth working on. Perhaps by the end of this post it will be clear why I'm not threatened by the historical narrative issue.

Let me explain a little more about why I think evolutionary theory is no different from other science in its potential to undermine belief. Science, to me, is the rational exploration of God's creation. This ongoing exploration has enabled humans to assemble reliable explanations for innumerable phenomena of interest: sunrise and sunset, moonlight, weather, growth and development of plants and animals, causation of various diseases. Some of these are phenomena for which biblical writers offered "explanations" that are either incorrect (on a plain reading) or are not natural explanations at all. In my view, various "scientific" accounts in the Bible are easily seen to be folk science or, more generously, what John Calvin called "accommodation." This fact about scripture was known to many Christians long before anyone even dreamed of an ancient earth or common descent. Evolution came very late to that game, and it seems to me that those who claim to reject faith upon reading in Genesis about the "two great lights" in "the vault of the sky" are on better footing than those who reject Christianity because evolution falsifies "each according to its kind."

Furthermore, in case this isn't already obvious, I reject any implication that natural explanation even addresses divine action or agency. Psalms 104 and 139 famously deal with biological phenomena of great interest to biologists, including predation and human embryonic development, and assign causation to God using some of the same Hebrew words used in more fantastic contexts in Genesis. More to the point, Paul in Colossians 1 seems to identify Christ as the source of essentially all natural causation: "For in him all things were created: things in heaven and on earth, visible and invisible, whether thrones or powers or rulers or authorities; all things have been created through him and for him. He is before all things, and in him all things hold together." And so I find distinctions between natural and supernatural causation to be pedantic at best, dangerous at worst. God works in the world. I'm curious about how he does it, and I happen to believe that much of this work can be understood.

The problem with evolution, as I've noted before, is that the history of human sin (i.e., the fall) does not fit clearly as a historical narrative. And while I concede that this is a problem, I don't see how it's a deal-breaker for Christian belief (or for my belief, anyway). Before I explain why, let me turn to the problem of evil.

It seems to me that the problem of evil, as typically presented, reduces to something like this: "If I were God, I would do X. God doesn't do X. This is a problem."

Don't like that paraphrase? How about this one: "God must be good. If he's good, he should do good things. And he should stop bad things. I have determined that he doesn't always do good things and/or stop bad things. This is a problem."

I haven't written the problem in those ways so that I can convince unbelievers that the problem is silly or that they are stupid for wrestling with it. I wrote it like that to illustrate how I, as a believer, see the "problem." My faith doesn't start with moral reasoning or other judgments and end with God, like this: "I have determined that God does good things, therefore I will believe in Him." Indeed, that kind of talk is antithetical to my Reformed perspective. I start with my belief. I start with an act of grace, leading to belief. I start with God: "completely wise, just, and good" as the Belgic Confession puts it. And, noting that biblical authors -- and Jesus himself -- did not seem to fret about the "problem of evil," I conclude that the existence of suffering is, in fact, "compatible" with God's character and existence. The alternative, that I would judge God's actions, is an absurdity to me as a believer.

And this leads me to Paul's question: why do I believe? He offers me these choices: "Do you believe it because you are convinced by some reasoning or does it just resonate with you?" It's not the former, so I guess it's the "resonate" thing. I can't really say why I believe; I attribute my faith to an act of God himself, in good Calvinist fashion. But I can offer this additional observation regarding "what makes me tick": I see my faith and my reading of scripture as radiating out from the life of Jesus. His incarnation, life, death, and ascension are The Story. I don't start at the beginning, with the ancient Near Eastern cosmology, then work my way through till I get to Pentecost. I really do focus on Jesus, the Alpha and the Omega.

As I explained before, my emphasis on Christ's preeminence makes the academic issue of Adam's actual home address a mere curiosity. And natural evil? Well, among other things, his incarnation accomplished this: he didn't make our suffering go away; he entered into it with us. That might not be what I "want," or what I would do, but it's so very different from the sterile Hobson's choice that standard "problem of evil" formulations present.

All right, sorry that went on so long. My intent was to be open about my belief, and the perspectives that underlie my thoughts on this blog. Now back to some hard science.

Peer review of my blog...let's see Behe try this.

Like every other scientist I know, I'm a big believer in peer review. The self-checking mechanism that peer review represents is surely one big reason for the success of science. Accountability, error checking, "wisdom in many counselors," and enforcement of community standards -- those are some ways of expressing the benefits of peer review. Some scientists, upon publishing their research, will thank the reviewers for making their article better. In his scathing review of Michael Behe's The Edge of Evolution in the New York Times, Richard Dawkins saved his most devastating criticism for last, by noting that Behe has

bypassed the peer-review procedure altogether, gone over the heads of the scientists he once aspired to number among his peers, and appealed directly to a public that — as he and his publisher know — is not qualified to rumble him.

--"Inferior Design," The New York Times, 1 July 2007

(Your irony meter should be pegged: Dawkins has famously done the same thing in The God Delusion. But that's another topic.) Peer review is a foundational principle in the scientific community, and those who eschew it are expressing outright contempt for the scientific enterprise.

Peer review isn't perfect, of course, and in fact it's only as good as the people who do it. It's not uncommon for us to get reviews that are wrong, even laughably so, or that have been written by "peers" who evidently didn't understand the work at all. And, on the flip side, the process isn't as blind or unbiased as it is often portrayed; scientists know how to slant their writing toward likely reviewers, and how to cherry-pick journals and potential reviewers in hopes of getting a better outcome. Yes, peer review is a human endeavor, with all the weaknesses of the humans doing it. But only a fool (or a demagogue) would consider doing science without it.

Well, here I am writing about science on a blog. One thing I really want is some peer review, at least to reduce the dangerously-high likelihood that I'll embarrass myself by posting something goofy. And so, I've been asking other scientists to read my articles. Specifically, after reviewing articles from the recent literature, I've contacted the authors and asked them to read the blog and provide comments. I've done four Journal Clubs so far, and the authors of two of them have graciously provided me with feedback. Now, these are top-flight scientists publishing in Science and Nature, and I was pleasantly surprised at their willingness to share some time with me. One of them is Joe Thornton, senior author of the two articles on steroid hormone receptor evolution that I recently summarized. With Joe's permission, I here present a summary of his review of my work.

One thing Joe didn't like at all was my gentle treatment of Michael Behe:

I think your description of Behe's argument is too generous. As you state, he doesn't argue that nothing can evolve in stepwise fashion, because selection can drive the evolution of such systems if each step increases fitness. But Behe does argue that integrated systems, in which the function of any part depends on the existence of the other parts, cannot evolve in such a fashion because selection cannot favor the origin, maintenance, or optimization of the parts until the entire whole is present. This argument is incorrect, because -- as we have shown -- such systems can be assembled by recruiting old molecules that previously had different functions to participate in new interactions, thus generating a new, integrated complex.

Joe's right about Behe's argument (with respect to irreducible complexity), and it's a lousy argument. But it is frequently misunderstood and oversimplified, and worse, right now, it is being erroneously conflated with the argument in The Edge of Evolution, which is actually different. My purpose in my seemingly too-polite comments about Behe's challenge was to direct readers to more serious engagement (and refutation) of Behe's claims and errors. Specifically, I wanted to draw attention to Larry Moran's work on Sandwalk, where he notes that some of the recent reviews of The Edge of Evolution have been grossly bungled, giving free shots to Behe and his attendant propaganda network. Dawkins, for example, in the NY Times review, is clearly aware of the mistake that Behe is making, but I think his piece is easily misunderstood (or twisted) to suggest that Behe doesn't believe in "microevolution." We can blame Behe for being unclear, even obfuscatory, and we'd be right, but that won't help us explain his damaging errors to non-scientists. For now, I'll risk seeming "too generous" to Michael Behe in order to ensure that I deal accurately and effectively with his carefully-packaged misinformation mistakes.

Joe did find some mistakes in my article, which I've now fixed:

1. I claimed that his most recent work assembled a detailed family tree for the various steroid receptors. In fact, the 2006 paper presented and discussed that same tree.


2. I claimed that the family tree was constructed from sequences of the two types of receptors, from 30 vertebrates. In fact, 29 species were involved, and the number of receptors known in each species ranged from just one to more than the two I was discussing. This was an error of simplification, and not very important, but it's been corrected.

And Joe noted, as I did, an oversimplification in the article:

It's an oversimplification to refer to the "corticosteroid receptor" and the "aldosterone receptor." For one thing, aldosterone is a corticosteroid. For another, the so-called aldosterone receptor exists in species that don't make aldosterone; in those species, it's generally a deoxycorticosterone (DOC) receptor -- another corticosteroid. DOC appears to be the oldest of the hormones and was probably the ligand for the ancestral receptor, before aldosterone itself evolved.

In this case, I've left the oversimplification as is, and encourage those who are irritated by it to read Joe's papers for the complete experience.

So there. My blog's been peer reviewed, to whatever extent Joe Thornton and I are "peers." :-) (I've made the cut on The Panda's Thumb twice, but unlike Joe, I've never been honored by the President of the United States for my work.)

But again with his permission, I'd like to share some of Joe's thoughts on the relationship between the "challenge" of ID and the work of real scientists like Joe (and me).

I'd like to be clear that, although the language we use to describe the question about the evolution of complexity may indeed be familiar to ID proponents, our work was in no way motivated by their arguments. This "puzzle" has motivated me since I began studying receptors, before Behe wrote his first book and before I had ever heard of ID. I continue to study the evolution of hormone-receptor evolution because it provides a superb system for unraveling the evolution of molecular complexity and for reconstructing the mechanisms by which gene functions evolved. The relevance of our findings to the social debate about ID didn't escape my notice, of course, and I didn't shy away from them; nevertheless, our research directions are motivated by evolutionary questions, not a desire to respond to ID.

This, I think, is one big risk entailed in the engagement of ID claims: that the magnificent science being done by Joe Thornton and hundreds of his colleagues would be portrayed as a "response" to ID. Good scientists, in my experience, tap into reserves composed mostly of intense curiosity, intellectual audacity (I consider that a compliment), and personal ambition. I'm horrified by the fact that ID's errors are linked to Christianity, and I'm willing to work on discrediting the movement, but I also know that this motivation could never fuel the kind of effort that generates science like Joe's or Chris Organ's or Abbie Smith's. My own work on cytoskeletal signalling systems in neurons could certainly be applied to ID claims in some way, but I'm not motivated by this at any discernible level. I just want to know how neurons work, and I want to be published more, and I want a renewal of my grant.

And finally, Joe noted the inverted perspective of ID with regard to explanation. When I talk to audiences about ID, I try to get them to consider this inversion by asking: "If 'intelligent design' is the answer, what was the question?" Design, it seems to me, is the thing we're trying to explain. It's not the explanation. Well, here's what Joe wrote in response to my blog entry:

You say, "And let's give ID credit for asking a good question." On one hand, I agree. Behe did, in parallel to us, identify the modern molecular version of the evolutionary puzzle of complexity: how can complex integrated systems, in which the function of any one part seems to depend on its interactions with the others, evolve under the influence of selection? Darwin was well aware of this puzzle, and the evolutionary geneticist H. Muller addressed it in a 1939 paper, explaining how complex systems that are historically assembled come to look "irreducible" as they evolve to be ever more functionally integrated. There have been many exemplars documenting the evolution of complexity at the morphological and physiological levels. But in recent decades, with the rise of molecular biology, innumerable systems comprised of tight functional interactions among molecules have been revealed. And few clear case studies were available to explain how complex systems evolve at the molecular level. So this is an important question indeed. But I am not convinced the ID proponents have ever really asked it. We reacted to this puzzle and knowledge gap as a question which stimulated a research program; after years of work, we now have some answers. The ID proponents, in contrast, put forth the issue of complexity as an answer, as an intrinsically unresolvable paradox that somehow gives the lie to Darwinian evolution. They do not ask, "How could complex systems evolve?" Rather, they argue, "Such systems cannot evolve by Darwinian mechanisms." And whenever scientists generate knowledge that begins to answer the question, the ID proponents bend over backwards to dismiss it. It appears this is a question to which they do not want an answer. That is a very big difference in the response to the apparent puzzle of complexity.

Very well said, don't you think?

So, there are some results of peer review of my blog. This week or next, I'll present the results of peer review in my blog. A couple of years ago, to much fanfare, Jonathan Wells published a paper on a topic I happen to know quite well. So I'll do some peer reviewing of my own, and we'll see whether ID really has produced something of scientific substance.

You should get college credit for reading this blog.

By way of the blessed Sandwalk, I present evidence that my blog is challenging (or that I should write shorter sentences containing less jargon):

Oh look. It's the problem of evil.

There are some really superb blogs over at Science Blogs, and some of the best ones are required reading here. It's hard to stomach PZ's religious blatherings, but he's a gifted science writer and a skilled commentator on developmental issues in evolution. Laelaps is a treasure trove, and Shelley Batts should have won that scholarship; her neuroscience blog, Retrospectacle, is varied and always sharp. And I'm sure that undiscovered treasures are buried in the many blogs I've never visited.

But there are some blogs over there that are little more than the diaries of atheists. Not that there's anything wrong with that (i.e., godlessness): Larry Moran's Sandwalk is one of my must-reads, as is Abbie Smith's ERV, and like many well-informed bloggers who are evolutionists, both are skeptics. Their blogs are important because they're full of serious science, the kind of analysis that is actually more dangerous to creationism and ID than the newsletter fodder that gets pinned up on the walls of the blogs of less thoughtful commentators. If the bosses at Science Blogs haven't already tried, they should beg Larry Moran to move Sandwalk to Science Blogs. And if they're starting to consider a no-growth policy, then they should let Sandwalk take the place of the surprisingly shallow EvolutionBlog of Jason Rosenhouse.

Early on here at QoD, I had EvolutionBlog on my Blogs of Note list, simply because a prominent blog (as evidenced by its presence at Science Blogs) on "the endless dispute between evolution and creationism" seemed apropos. But it's sadly short on science, and long on anti-faith chest-beating. Ooh, but here's something new: the problem of evil.

There are at least two things that I find odd about much of what passes for atheist commentary on the problem of evil. First, folks like Rosenhouse seem to think that every instance of suffering (by humans or giraffes or echidnas or moths) represents a new instance of the problem of evil, as though the problem is magnified with each new meal by a carnivore. Heaping more dead salmon on the pile, it seems to me, doesn't change the basic problem of suffering in God's world. Second, I'm fascinated by the nearly-ubiquitous implication that the problem of evil is somehow linked to common descent. Huh? Humans, including Christians, were quite well acquainted with suffering and natural evil -- on an apocalyptic scale -- long before Darwin scooped Wallace. The problem of evil, if it's a problem for Christianity, isn't linked in any unique way to evolutionary theory.

But there's not much more for me to say, because Scott Carson does it so much better. I've removed the worthless EvolutionBlog from my blogroll, and replaced it with Carson's An Examined Life. (Thanks to John Farrell for the tips.) His latest post, Notes from the Scorecard Department, is the kind of blog article that should make textbook publishers nervous. If you're a Christian, be warned: you may find harsher words there for yourself than for blissfully ignorant bloggers like Jason Rosenhouse. And if you think the question of suffering is a big deal, start with Carson's claim that the Problem of Evil isn't a problem at all. No matter how you come down on the question, take note of the difference in depth of thought and analysis. Rosenhouse:Philosophy :: Behe:Genetics.

What happens in my brain when I imagine that people actually read my blog?

Lady Macbeth [to Macbeth]: Great Glamis! worthy Cawdor!
Greater than both, by the all-hail hereafter!
Thy letters have transported me beyond
This ignorant present, and I feel now
The future in the instant.

--Macbeth, Act I, Scene V. (The Oxford Shakespeare)

Obsessions with self-preservation
Faded when I threw my fear away
It's not a thing you can imagine
You either lose your fear
Or spend your life with one foot in the grave
Is God the last romantic?

--"Spark" by Over The Rhine (Drunkard's Prayer, 2005)

Optimism or delusions of grandeur? Bullish or blinkered? Looking on the bright side, or gazing through rose-colored glasses? Am I a romantic, or am I just in denial?

I do consider myself a romantic, and this blog is a testament to a particular form of optimism that I just can't shake off: I'm ever hopeful that people (like me) can learn new things and change their minds. But sometimes I worry: is my optimism (on this subject, and hundreds of others) unreasonable? Or worse...is my optimism unreasonable but also adaptive, a pitiful delusion without which I can't otherwise get by?

[Waits for jeers of skeptics to die down] Actually, being (overly) optimistic is apparently a universally human trait. I may be a romantic, but...I'm not the only one. (Imagine!)

Consider these opening sentences in a research article ("Neural mechanisms mediating optimism bias," Sharot et al., Nature 450:102-105) published in Nature this week:

Humans expect positive events in the future even when there is no evidence to support such expectations. For example, people expect to live longer and be healthier than average, they underestimate their likelihood of getting a divorce, and overestimate their prospects for success on the job market.

Lord, what fools these mortals be! Yes indeed; but how does this happen? The study by Sharot et al. set out to identify mechanisms in the brain that might account for what they call "pervasive optimism bias." First the authors note that this "optimism bias" is considered to be a mark of good mental health, and exhibits apparent adaptive value; excessive pessimism correlates with symptoms of depression, and of course excessive optimism can lead to recklessness. A "normal" dose of optimism, they note, "can motivate adaptive behaviour in the present towards a future goal." Nevertheless, the authors describe this normal (wild-type?) human stance as "a moderate optimistic illusion." Yikes! We're all deluded.

Okay, so how does this work? Previous work has shown that, when imagining the future, people use the same brain systems that they employ when recalling the past, suggesting that the construction of an imagined future involves the rearrangement of pictures and stories from the remembered past. So we might expect to see these systems somehow involved in the expression of optimism.

The authors used functional MRI (fMRI) to look at brain activity while subjects were thinking about events in their lives that centered on a "life episode" like "winning an award" or "the end of a romantic relationship." They correlated the brain imaging with the participants' ratings of their experience of these episodes, which were either past or future events (i.e., recollections or imagined scenarios). And they used a psychological test (the Life Orientation Test-Revised, or LOT-R) to measure "trait optimism" and thereby estimate the relative optimism or pessimism of individual experimental subjects.

The behavioral data alone reveal some interesting things about people and their optimism. Amazingly, future positive episodes were judged to be more positive than past positive events, and were felt to be closer in time than any other experience, past or future. And there's more:

Negative future events were experienced with a weaker subjective sense of pre-experiencing, and were more likely to be imagined from an outsider viewing in, than positive future events and all past events (Fig. 1b). The more optimistic participants were, as indicated by the LOT-R scores, the more likely they were to expect positive events to happen closer in the future than negative events, and to experience them with a greater sense of pre-experiencing (Fig. 1c, d).

So, humans in general seem to think (or feel) that the future looks better than the past, and optimistic people seem to be able to better connect with the positive illusion of the future that they create.

Combining the various techniques enabled the authors to identify some brain regions of interest (ROIs) with regard to optimism. Some of these areas are The Usual Suspects: the rostral anterior cingulate cortex (rACC), the posterior cingulate cortex, and the dorsal medial prefrontal cortex, all areas that were previously implicated in autobiographical memory recall and in the construction of imagined future scenarios. Activation of these regions accompanies optimism, presumably because optimism requires a vision of the future. That's all interesting and informative, but it's not what makes this paper so intriguing. I think the paper's real impact arises from the fact that the imaging analysis implicated a fourth brain area in optimism bias: the amygdala. This region of the limbic system is famously involved in emotional processing, and the authors suggest that the amygdala's role in optimism is to add emotional impact to the imagined future events. They demonstrate "strong functional connectivity" between the amygdala and the rACC during the process of imagining future positive events, and not while imagining negative scenarios. And, importantly, they document a correlation between the strength of activation of the rACC and the overall optimism of the person, as measured by the LOT-R. I find this graph compelling:
Two aspects of their discussion are worth noting. First, not surprisingly, the authors highlight the relevance of their findings to the understanding of depression. Perhaps depression causes -- or arises from -- malfunctioning of the systems that Sharot et al. have implicated in optimism. Second, the authors make an important distinction between remembering and imagining in the interpretation of their results. Namely, there are two potentially relevant differences between remembering and imagining: the temporal difference (past versus future) and the reality difference (real versus imaginary). The authors speculate that the optimism bias functions when constructing imaginary scenarios, and that the past versus future distinction is only relevant because the past is real and the future is imaginary.

In any case, the article provides another glimpse into the workings of the hunk of meat in our skulls, a messy wet organ that somehow creates memories and imagination, and in the process conjures various carrots, hanging out there in front of us, urging us to ignore our (reasonable) fears and plunge into an unknown future, eyes on an illusion concocted by...functional crosstalk between the amygdala and the rostral anterior cingulate cortex.

That last part didn't sound quite right. But I think that's the way it is. And I think Christians should get used to learning how various aspects of humanness are explainable on the basis of the workings of the brain.

Now I'll imagine a future where my blog article, on the brain systems that fill us with optimism, is being read by scores of people, all picturing their own private versions of the grail beacon.

Article(s) discussed in this post: Sharot, T., Riccardi, A.M., Raio, C.M. and Phelps, E.A. (2007) Neural mechanisms mediating optimism bias. Nature 450:102-105.

PZ's mutating meme

About a week and a half ago, I was infected with an evolving blog meme, and I think the only way to get better is to pass it on. Brian over at Laelaps tagged me; maybe he's annoyed about my suggestion to his profs that they assign him more homework, or maybe he's indignant at my mention of the RU Screw. I know he wants to be a transitional fossil, but I doubt he wants to be an evolutionary dead-end, so I'll help him out just this once.

The meme started over at Pharyngula, where you can read about its origins. Here are the rules:

There are a set of questions below that are all of the form, "The best [subgenre] [medium] in [genre] is...". Copy the questions, and before answering them, you may modify them in a limited way, carrying out no more than two of these operations:
* You can leave them exactly as is.
* You can delete any one question.
* You can mutate either the genre, medium, or subgenre of any one question. For instance, you could change "The best time travel novel in SF/Fantasy is..." to "The best time travel novel in Westerns is...", or "The best time travel movie in SF/Fantasy is...", or "The best romance novel in SF/Fantasy is...".
* You can add a completely new question of your choice to the end of the list, as long as it is still in the form "The best [subgenre] [medium] in [genre] is...".
* You must have at least one question in your set, or you've gone extinct, and you must be able to answer it yourself, or you're not viable.
Then answer your possibly mutant set of questions. Please do include a link back to the blog you got them from, to simplify tracing the ancestry, and include these instructions.
Finally, pass it along to any number of your fellow bloggers. Remember, though, your success as a Darwinian replicator is going to be measured by the propagation of your variants, which is
going to be a function of both the interest your well-honed questions generate and the number of successful attempts at reproducing them.

First, my phylogeny:
My great-great-great-grandparent is Metamagician and the Hellfire Club.
My great-great-grandparent is Flying Trilobite
My great-grandparent is A Blog Around the Clock
My grandparent is The Anterior Commissure
My parent is Laelaps

And my contributions to the meme pool:

The best scary movie in sociopolitical dystopias is:
Children of Men

The best sexy song in pop rock is:
"With or Without You" by U2.

The best scary story in romantic short stories is:
"The Cask of Amontillado" by Edgar Allan Poe

The best B-movie in 1980's horror films is:
Alligator
I'm leaving this one in, but I've never seen this fine piece of cinematic art, or any other B-movie in the horror genre, and I've already used up my two mutations. I think this is a blow to my viability, but we'll let God PZ decide.

Now I get to infect some other bloggers. I'd like to infect ERV, but she's already been kissed, and she's a busy grad student, so I'm going to target Christians for infection. I tag:
Siris
John Farrell
Steve Martin at An Evangelical Dialogue on Evolution
The Fire and the Rose

Now we'll see whether this expansion into a new niche will result in an adaptive radiation or a mass extinction.

Blogging on peer-reviewed research

One of my main goals in this blog is to help non-scientists (Christian readers in particular) understand science and God's world, by reviewing and explaining recently-published scientific research. I've been calling these posts "Journal Clubs" in honor of the kind of small-group discussion of the literature that formed the backbone of my scientific education (past and present).

It takes a lot more effort to prepare one of those articles than it does to post a link to the latest gaffe by a creationist or a racist Nobel laureate, and I've often wished I could make my Journal Club entries stand out more. It turns out, not surprisingly, that plenty of other science bloggers (and/or blogging scientists) have had the same desire. Happily, some of them actually did something about it, resulting in the creation of Bloggers for Peer-Reviewed Research Reporting, now incarnated at BPR3.org.

You can read all about it on Cognitive Daily over at ScienceBlogs; one of the bloggers there, Dave Munger, is spearheading the BPR3 effort.

So, I'm joining this excellent movement. From now on, I'll mark my Journal Clubs with the official icon. This will enable readers to identify the serious science, and the posts will find their way into a collection at BPR3 through an aggregator. Just as importantly, I think, the icon commits me to a set of standards, which includes:

1. The post should offer a complete formal citation of the work(s) being discussed.
2. The post author should have read and understood the entire work cited.
3. The blog post should report accurately and thoughtfully on the research it presents.
4. Where possible, the post should link to the original source and / or provide a DOI or other universal reference number.
5. The post should contain original work by the post author -- while some quoting of others is acceptable, the majority of the post should be the author's own work.

And this is cool and important: abuse can be reported, and repeated misconduct gets your work kicked out of the aggregator. Nice.

So look for the just-unveiled icon of BPR3 on my Journal Club articles henceforth, and thanks for shopping at Quintessence of Dust.

An example of purely naturalistic explanation

2004 might have been a miracle, but...

They selected teosinte...and got corn. Excellent!

Evolutionary science is so much bigger, so much deeper, so much more interesting than its opponents (understandably) will admit. It's more complicated than Michael Behe or Bill Dembski let on, and yet it's not that hard to follow, for those who are willing to try. The best papers by evolutionary biologists are endlessly fascinating and scientifically superb, and reading them is stimulating and fun.

Yet, as an experimental developmental biologist reading work in evolutionary biology, I often find myself yearning for what we call "the definitive experiment." Molecular biology, for example, can point to a few definitive experiments -- elegant and often simple -- that provided answers to big questions. Sometimes, while examining an excellent evolutionary explanation, I think, "Wouldn't it be great if they could do the experiment?"

Now of course, plenty of evolutionary biology is experimental, and I've reviewed some very good examples of experimental evolutionary science on this blog. But when it comes to selection and the evolution of new structures and functions, the analysis often seems to beg for an experiment, one that is simple to conceive but, typically, impossible to actually pull off -- there's not enough time. The previous Journal Club looked at one way around this limitation: bring the past back to life. Even better, though, would be to find an example of evolutionary change in which the new and old forms are still living, so that one could do the before-and-after comparison. It would look something like this: take a species, subject it to evolutionary influences of some kind until the descendants look significantly different from the ancestors, then compare the genomes (or developmental processes) of the descendant and the ancestor, in hopes of discovering the types of changes at the genetic or developmental level that gave rise to the differences in appearance or function of the organisms. That would be a cool experiment.

In fact, that kind of experiment has been done, more than once. The best example, in my opinion, involves an organism far less sexy than a dinosaur or a finch or a whale: Zea mays, better known as corn (or maize).

Corn is a grass, but a grass that's been so extensively modified genetically that it's barely recognizable (to non-specialists like me) as a member of that family. Wait...genetically modified? Yes, and I'm not talking about the really modern tricks that gave us Bt corn or Roundup Ready corn. In fact, the wonderful stuff they grow in Iowa is quite different from the plants that humans first started to harvest and domesticate in Central America a few millenia ago. Corn as we know it is the result of a major evolutionary transformation, driven by selection at the hands of humans. (I don't find the natural/artificial selection distinction at all useful, since there's no explanatory difference, but you can refer to the selection under consideration here as 'artificial' if it makes you feel better.) The story has been a major topic in evolutionary genetics for decades, but it's largely absent from popular discussions, probably because the Discovery Institute has wisely avoided it. I hope it will soon be clear why you won't find the word 'teosinte' anywhere at discovery.org.

For many years, the origin of corn was a mystery. Like most known crops, it was domesticated 6000-10,000 years ago. But unlike other crops, its wild ancestor was unknown until relatively recently. Why this odd gap in our knowledge? Well, it turns out that corn is shockingly different -- in form, or morphology -- from its closest wild relative, which is a grass called teosinte, still native to southwestern Mexico. In fact, corn and teosinte are so different in appearance that biologists initially considered teosinte to be more closely related to rice than to corn, and even when evidence began to suggest a genetic and evolutionary relationship, the idea was hard to accept. As John Doebley, University of Wisconsin geneticist and expert on corn genetics and evolution, puts it: "The stunning morphological differences between the ears of maize and teosinte seemed to exclude the possibility that teosinte could be the progenitor of maize." (From 2004 Annual Review article, available on the lab website and cited below.)

But it is now clear that teosinte (Balsas teosinte, to be specific) is the direct ancestor of corn. In addition to archaeological evidence, consider:

• The chromosomes of corn and teosinte are nearly indistinguishable at very fine levels of structural detail.
• Analysis using microsatellite DNA (repetitive DNA elements found in most genomes) identified teosinte as the immediate ancestor of corn, and indicated that the divergence occurred 9000 years ago, in agreement with archaeological findings.
• Most importantly, a cross between corn and teosinte yields healthy, fertile offspring. So, amazingly, despite being so different in appearance that biologists initially considered them unrelated, corn and teosinte are clearly members of the same species.

The basic idea, then, is that corn is a domesticated form of teosinte, exhibiting a strikingly distinct form as a result of selection by human farmers. And that means that we have a perfect opportunity to examine the genetic and developmental changes that underlie these "stunning morphological differences." We can do the experiment.

First, have a look at an example of one of the evolutionary changes in teosinte under human selection.

The small ear of corn on the left is a "primitive" ear; the brown thing on the right is an ear from pure teosinte. (Both are about 5 cm long.) The "primitive" ear is similar to archaeological specimens representing the earliest known corn. Image from John Doebley, "The genetics of maize evolution," Annual Review of Genetics 38:37-59, 2004. Article downloaded from Doebley lab website.

The thing on the far left is a teosinte "ear," the far right is our friend corn, and the middle is what you get in a hybrid between the two. Photo by John Doebley; image from Doebley lab website.

The pattern of branching of the overall plant is also strikingly different between corn and teosinte, and you can read much more on the Doebley lab website and in their publications.

When I first heard about this work at the 2006 Annual Meeting of the Society for Developmental Biology, I was astonished at the amount of basic evolutionary biology that was exposed to experimental analysis in this great ongoing experiment. Here are two key examples of the insights and discoveries generated in recent studies of corn evolution.

1. Does the evolution of new features require new, rare, mutations in major genes?

Perhaps this seems like a stupid question to you. Anti-evolution propagandists are eager to create the impression that evolutionary change only occurs when small numbers of wildly improbable mutations somehow manage to help and not hurt a species. And in fact, experimental biology has produced good examples of just such phenomena. But there is at least one other genetic model that has been put forth to explain the evolution of new forms. This view postulates that many major features exhibited by organisms are "threshold" traits, meaning that they are determined by many converging influences which add together and -- once the level of influence exceeds a threshold -- generate the trait. The model predicts that certain invariant (i.e., never-changing) traits would nevertheless exhibit significant genetic variation, since evolutionary selection is acting on the overall trait and not on the individual genetic influences that are added together. Hence the implication that...

...populations contain substantial cryptic genetic variation, which, if reconfigured, could produce a discrete shift in morphology and thereby a novel phenotype. Thus, evolution would not be dependent on rare mutations, but on standing, albeit cryptic, genetic variation.

--from Nick Lauter and John Doebley, "Genetic Variation for Phenotypically Invariant Traits Detected in Teosinte: Implications for the Evolution of Novel Forms," Genetics 160:333-342, 2002.

In that paper, the authors show that several invariant traits (e.g., number of branches at the flower) in teosinte display significant genetic variation. In other words, the traits are the same in every plant, but the genes that generate the traits vary. The variation is 'cryptic' because it's not apparent in basic genetic crosses. But it's there. The authors ask: "How can cryptic genetic variation such as we have detected in teosinte contribute to the evolution of discrete traits?" Two ways: 1) the variation is available to modify or stabilize the effects of large-effect mutations; and 2) variation in multiple genes can be reconfigured such that it adds up to a new threshold effect. Note that the first scenario is clearly applicable to the kind of evolutionary trajectory outlined by Joe Thornton's group and discussed in a previous post. The second scenario is particularly interesting, however, since it addresses an important question about the role of selection. Consider the authors' discussion of this issue:

At first glance, cryptic variation would seem inaccessible to the force of selection since it has no effect on the phenotype. However, if discrete traits are threshold traits, then one can imagine ... that variation ... could be reconfigured such that an individual or population would rise above the threshold and thereby switch the trajectory of development so that a discrete adult phenotype is produced. We find this an attractive model since evolution would not be constrained to “wait” for new major mutations to arise in populations. (Italics are mine; ellipses denote deletion of technical jargon, with apologies to the authors.)

In fact, in a 2004 review article, Doebley is bluntly critical of the assumption that new mutations were required during the evolution of corn, and seems to suggest that this view led researchers significantly astray:

There is an underlying assumption in much of the literature on maize evolution that new mutations were central to the morphological evolution of maize. The word "mutation" is used repeatedly to describe the gene changes involved, and Beadle led an expedition ("mutation hunt") to find these rare alleles. The opposing view, that naturally occurring standing variation in teosinte populations could provide sufficient raw material for maize evolution, was stated clearly for the first time by Iltis in 1983. Although new mutation is likely to have made a contribution, anyone who has worked with teosinte would agree that teosinte populations possess abundant genetic variation. [...] Allowing for cryptic variants and novel phenotypes from new epistatic combinations to arise during domestication, it is easy to imagine that maize was domesticated from teosinte.

--John Doebley, "The genetics of maize evolution." Annual Review of Genetics 38:37-59, 2004.

Compare that discussion, and others like it in the paper I'm quoting, with the yapping about mutations that passes for anti-evolution criticism of evolutionary genetics. I can find no evidence that Michael Behe or any other ID theorist has even attempted to seriously address the importance of genetic variation in populations. I haven't read The Edge of Evolution yet, but I have it right here, and the index suggests that Behe hasn't tried to engage genetics beyond the high school level. There's a good reason why Behe is an object of scorn in evolutionary biology. He wants you to think it's because his critics are mean. No; it's much worse than that.

2. Does evolutionary change ever result from a "gain of information," or does Darwinian evolution merely prune things out?

It would be easy to get the impression from various creationists and ID proponents that mutation and selection can only remove things from a genome. Young-earth creationist commentary on "microevolution" (a yucky term for the now-undeniable fact of genetic change over time) always adds that this kind of change involves NO NEW INFORMATION. (The caps are important, apparently, since caps and/or italics are de rigueur in creationist denialism on this topic.)

Similarly, Michael Behe wants you to think that beneficial (or adaptive) mutations are some kind of near impossibility, and that when they do happen it's almost always because something's been deleted or damaged, with a beneficial outcome.

Studies of evolution in corn and teosinte (and other domesticated plants), not to mention findings like the HIV story on Abbie Smith's now-famous blog, tell a different -- and, of course, more wonderfully interesting -- story. In a minireview on the genetics of crop plant evolution in Science last June, John Doebley notes that most of the mutations that led to major evolutionary innovations occurred in transcription factors, which are proteins that turn other genes on and off. Then this:

Another remarkable feature of this list is that the domesticated alleles of all six genes are functional. If domestication involved the crippling of precisely tuned wild species, one might have expected domestication genes to have null or loss-of-function alleles. Rather, domestication has involved a mix of changes in protein function and gene expression.

In other words, the new genes are not dead or damaged; they're genes that are making proteins with new functions. ('Allele' is just the term for a particular version of a particular gene, and 'null', as you might have guessed, is a version that is utterly functionless, as though the gene were deleted entirely.) Now, if you've even flipped through The Origin of Species, you might not be surprised by Doebley's conclusion:

Given that the cultivated allele of not one of these six domestication genes is a null, a more appropriate model than "crippling" seems to be adaptation to a novel ecological niche -- the cultivated field. Tinkering and not disassembling is the order of the day in domestication as in natural evolution, and Darwin's use of domestication as a proxy for evolution under natural selection was, not surprisingly, right on the mark.

The change from teosinte to corn happened in about a thousand years. That's fast evolution. Apply selection to a varying population, and you get new functions, new proteins, new genes, completely new organisms. Fast.

So in summary, we can do the experiment. And we've done the experiment. ('We' being John Doebley and his many able colleagues.) And we've learned a lot about evolution and development. Now if we can just get people to read it. Then they'll know more about evolution, and about God's world, and about the trustworthiness of the anti-evolution propaganda machines that are exploiting the credulity of evangelical Christians.

Pop quiz! Put your browsers away.

UPDATE: answers posted at the end.

Which of these plant specimens doesn't belong? (Images will be properly credited in a forthcoming article which will explain why they're so interesting.)

The images are all the same magnification, but have been colorized so that the color won't give you any clues. Focus on the structure of each specimen, and pick one that doesn't belong with the others. (Insert Sesame Street reference here.)

1	2	3	4

Want a hint? One word: teosinte (tay-oh-SIN-tay).

ANSWER: Picture number 1 is wheat. The rest are Zea mays. See next post.