Showing posts with label Introduction. Show all posts
Showing posts with label Introduction. Show all posts

01 August 2024

The essence of Quintessence of Dust: welcome to Blaugust 2024

Today begins Blaugust 2024, an annual blogging festival that is fun and challenging. Last year I made it halfway through August with a post every day—this year I'm aiming for 20 posts for the month.

The festival aims to create and maintain a community, and so the main theme this year is for everyone to write an "introduction to me and my blog" post. (Actual quote from the organizer: "While I am not going to make you wear nametags to orientation, it would be lovely if you spent some time with that very first blog post to introduce yourself and the kind of content that you create.")

About me:

Professionally, I'm a biologist and a writer, with deep experience as an editor (the curating kind). I like to work in intense scientific environments, alongside people doing the kind of research that intends to change the world. I haven't worked in a lab for more than 10 years but I sometimes daydream about going back somehow.

I like to write and think about all aspects of biology, especially about evolution, genetics, and neuroscience.

10 August 2023

What I learned about me when I started reading novels again

A few years ago, I somehow realized that I wanted to read more stories.

My work as a journal editor involved hours of intense scientific reading every day, and my insatiable interest in biology meant that my recreational reading was almost exclusively about science. But I could remember how much I loved stories as a kid: Tom Sawyer, The Black Stallion, all the Roald Dahl things. I read almost no fiction at all as a high schooler, then as a young Christian adult I read The Lord of the Rings trilogy and (urp) the Chronicles of Narnia. As a dad, I read (aloud with the family) all of the Harry Potter books, and that was great memorable fun. Somehow about 15 years ago I decided to read The Poisonwood Bible. (Unforgettable.) But my extensive reading habits were largely focused on science and Shakespeare.

To be sure, I derive both enjoyment and inspiration from science and from Shakespeare, but in retrospect it seems I needed to feed a part of me that finds inspiration in stories. In novels. And so I started collecting novels, specifically from female authors. I put a few on my Christmas list, and my loved ones obliged, and there they were on my shelves. Unread.

Then for some reason, not even two years ago, I decided to do it. I had a trip coming up: my annual journey to New York to co-lead the Scientific Writing Retreat at Cold Spring Harbor Laboratory. We had moved to Arizona, so the journey had evolved from a 4-hour ride on Amtrak to an all-day trip across the continent. I don't remember why, but I picked The Ten Thousand Doors of January by Alix Harrow, and started reading on the plane.

08 August 2023

Rebel scum

This week in the Blaugust 2023 blogging festival, the broad theme is "Introduce yourself." Yesterday I alluded to my bardolatry and its place in the cornerstone of Quintessence of Dust, but that's not really an introduction. So here is a bit more about me: I love the Star Wars universe and I'm into evolution, and both of those things are deeply connected to my main tendency—I'm a rebel.

That might sound romantic and all, but I'm actually being somewhat precise and referring to some useful counsel I got in the past few years as I considered Gretchen Rubin's Four Tendencies. The Rebel tendency describes me all too well. I hate being told what to do. I hate being controlled. I hate even suspecting that I'm being controlled. Here's how Rubin captures much of my life: "Telling a Rebel what to do makes them less likely to do it, even if it’s something they want to do."

There are advantages to being a Rebel but big weaknesses as well. Another tagline of the Rebel tendency is this LOLsob-inducing truism: "You can’t make me, and neither can I." So, the perhaps obvious disadvantage is that it can be extra difficult to get tasks done whenever there is a sense that someone or something is ordering it to be done. I'm not lazy; in fact, I work too much. But whenever I sense that someone is telling me what to do, I have to work around my natural instinct to resist their brazen attempt to control me. (Heh.) Otherwise, I'll find ways to not do the task (or meet the obligation, or whatever).

What are the advantages of that tendency? Are there any?

03 August 2023

An extrovert's response to the nightmare of remote work

March of 2020 seems a very long time ago. The coronavirus pandemic was roaring to life in the US, and it had arrived in Cambridge, Massachusetts where I lived and worked. I was leading an international team of editors, half of whom worked in the Cell Press office in Cambridge near the MIT campus. That month, the goal was to flatten the curve, so that our great hospitals and their heroic staffs would not be overwhelmed by COVID patients. There were no vaccines, and we were still wiping down grocery bags because we knew so little about the transmission of the virus. What we knew was that if we stayed away from each other, we would give the virus fewer opportunities to spread. So, early that month, I asked the team to start working from home. About a week later, the whole company moved to working from home.

My bike at Deer Island in Boston

Long before March 2020, I knew I was something of a unicorn in the world of professional editorial work. My colleagues were (and are) generous and committed and brilliant. I think we all had those things in common. But one thing I didn't share with them was my extroversion. I'm a true extrovert, and as near as I can tell I am one of less than a dozen extroverts in the world who work as a journal editor. I'm joking, but I'm serious when I say that when I became a journal editor more than 10 years ago, I stood out immediately among scores of serious introverts. (True story: our open-concept office had "zones" based on noise level, and I was banned from the quiet area. Not just discouraged. Banned.) And so in March 2020, when there were cute jokes going around about how we could be "heroes" by working from the sofa (Google "couch potatriotism"), I was unamused. Working from home meant that I lost my daily bike ride through Cambridge to a bustling workplace full of my friends and colleagues.

02 August 2023

Change is hard. Evolution is Easy. Episode 1 of many.

Miranda on a beach in a storm, looking out to sea
ARIEL: Full fathom five thy father lies.
Of his bones are coral made.
Those are pearls that were his eyes.
Nothing of him that doth fade
But doth suffer a sea change
Into something rich and strange.
The Tempest, Act 1, Scene 2

I do apologize for this dull cliche, but I know I'm right about this: change is hard. I don't mean that it's hard to adapt after someone or something forces a change on you. That's true too, but it's not my topic here. I'm talking about this: you want to change, or you need to change, or both. You know what the change has to be. Maybe you know what the first step has to be. It's change, and it's hard.

Call it personal growth or self-improvement, or maybe it's habit-breaking or demon-wrestling. Whole libraries could be stocked with materials on how to change. Even when we know we're loved, and believe we're okay, we can see opportunities and challenges that require us to change.

I won't claim to have deep knowledge of the technical literature on how people manage to change. But I do have several decades of experience in the practice of personal growth and change. I have repeatedly faced my need to change, and one of the first lessons I had to learn was the fact that effecting change is a lot harder than it sounds. It's not that easy to face one's need to change but it's vastly more difficult to make it happen. Change is hard.

But evolution is easy.

14 January 2023

Quintessence of Dust 2023 restart: the what

So, Quintessence of Dust is back in business. (A few days ago, I wrote about why.) Yay! Here are some soon-coming attractions. A couple are book-length projects at various stages of embryogenesis, but the rest are posts and series that represent ideas to dissect/develop and thoughts to get out in the world.

1. My main book project is yet untitled but is well defined enough (barely) to warrant some posts in which I can try out the ideas. The book is about the so-called animal toolkit and the related theme of deep homology. I'll explore those topics then suggest that they tell us something important about the design and evolution of animals. I aim to cause some trouble. And yes, I wrote 'design'.

2. Another less well-developed book idea is tentatively titled "Evolution Is Easy" and that's all you get for now.

3. I just finished The Day Without Yesterday by my friend John Farrell, about the not-well-enough-known cosmologist and priest, Georges Lemaître. I'll write about my impressions of the book and of Lemaître, and I'll try to get John to join in. Maybe an interview of some kind?

4. Other books I've read recently and would like to write about: The Gene's-Eye View of Evolution by J. Arvid Ågren; From Darwin to Derrida by David Haig; and two novels by my current favorite author, Alix Harrow. I just bought (with some hesitation) the new book by Simon Conway Morris, From Extraterrestrials to Animal Minds: Six Myths of Evolution. If the book doesn't piss me off too much,  I'll write about it.

08 January 2023

Quintessence of Dust 2023 restart: the why

It's early January 2023, a little before sunset in Tucson. Live image below, showing the glorious Santa Catalina mountains (the snow on the upper reaches is more apparent earlier in the day) and my dinner preparations (shrimp and veggies on the grill).

I've decided to start writing here at Quintessence of Dust, after another long hiatus. Here are some of my reasons.

1. I like to write, and I have things to say, and I self-identify as an author. For eight years, I have co-organized and taught in the Scientific Writing Retreat at Cold Spring Harbor Laboratory. I'm a writer and I need to write, if only for myself.

2. I have an idea for a book, along with some introductory work (but no sample chapters yet) and writing here will help me develop those thoughts. The idea is over twelve years old and has never faded away, which I take to mean that I need to get it out of my system somehow.

3. I have other ideas kicking around in my head and most of them are worth writing about. I have one new intellectual passion that is totally worth writing about: the Sky Islands that nearly surround us here in Tucson.

4. I have an exciting new job with great new people at an organization that's all in for open science. I recently turned over the tens digit on my age-o-meter. My kids will very soon be all out of college. (One is about to start a postdoc!) All of this led, predictably, to a spasm of reflection on projects and vision. One clear result is that I'm feeling more inspired.

12 August 2008

First blogiversary for Quintessence of Dust

Actually, my first post went up 3 August 2007, a little more than a year ago, but my first real article wasn't posted till 19 August, so I guess today is as good a day as any to celebrate. It's been a fun year, coinciding with my sabbatical, which ends [sniff] in 3 weeks. Once I'm back in my professor routine, I expect that my posting will be less erratic, especially since I requested a new office that's a bit removed from the beaten track. We'll see.

Thanks to all for reading and commenting. (I think I'll do better at responding to comments when my schedule calms down.) I'm especially thankful to Steve Martin at An Evangelical Dialogue on Evolution for being the first to find me and welcome me to the blogosphere. John Farrell was an early encouragement, and Panda's Thumb linked to one of my first journal club articles. The high point was the teosinte article, which was linked at ERV, Pharyngula and PT and which was honored with a place in The Open Laboratory 2007. The blog has about 240 subscribers and gets roughly 100 hits a day. Room to grow, but it's nice to have enthusiastic readers.

To Mike Beidler: thanks for the compliment; it's my favorite link in the one-year life of the project. To Gordon Glover: keep up the fantastic work; your book is a precious gift.

Here's to Year 2 of Quintessence of Dust. More journal clubs, more developmental biology, a little less bitching about lame creationist claptrap. Or your money back.

18 March 2008

On folk science and lies: Back to the basics

Months ago, I was worrying about how to characterize creationist statements that are untrue or misleading. The claims in question are not merely false (mistakes of various kinds can generate falsehood) and are not statements of opinion with which I disagree. They are claims that are demonstrably false but have been asserted by people who are certain (or likely) to know this. In other words, they bear the marks of duplicity. I said:

As a Christian, I am scandalized and sickened by nearly all creationist commentary on evolution. But I'm not a misanthrope, and so I find it hard to believe that so many people could be so overtly dishonest.

So I proposed the term 'folk science' as a way to refer to belief-supporting statements that sound scientific but do not seek to communicate scientific truth. I have two goals in my practice of using this phrase: 1) I recognize folk science as a particular type of argumentation, and I want to be able to accurately identify it as such; and 2) I want to create space within which I can identify falsehood, and especially falsehood that seeks to mislead, without making unwarranted accusations.

Not everyone was all that excited by this. One example I used, in which Fuz Rana presents a completely inaccurate  and wholly misleading summary of evolutionary theory, led one commenter (Henry Neufeld) to reflect as follows:
But I'm still having a hard time wrapping my brain around the idea that someone with any sort of education in biology could manage to say some of the things creationists say. For example, in the blog post you cited from RTB, there are huge areas of evidence for common descent (everything related to the genome, for example) that are simply omitted. It would seem to me that even a person who had read only the popular literature would at least be aware of such evidence.

I can understand those poorly educated in science falling for folk science it's easier and it makes you feel better! But I have a hard time understanding how a biologist could do so.

And Steve Martin of An Evangelical Dialogue on Evolution, had this to say:

I think there is a different level of accountability for those in leadership. We all need to take seriously the words in James 3:1. (And I’m speaking for myself here too  even if my own role is virtually insignificant in the larger debate). For those in leadership that ignore data that contradicts their teaching, I’m not sure the appeal to “folk science” cuts it. Integrity is just way too important.

Some people noted that the moral and intellectual milieu within which folk science is generated is not amenable to simplistic moral analysis. But I surmise that many of my respondents back then were concerned about going soft on crime, as I put it.

Lately, as I've been describing the folk science of "junk DNA," I have run across examples of falsehood that stretch the limits of the term 'folk science,' in that they resemble what many people would refer to as 'lies.' And I started to describe these disheartening and regrettable falsehoods as 'lies,' even as 'outrageous lies.' These are descriptors that I had deliberately avoided in my earlier posts, and I'm sorry to say that I drifted into this habit rather than making a specific decision to use this more serious language.

My friend and colleague Kevin Corcoran is urging me to reconsider this practice in a St. Patrick's Day post on his blog, Holy Skin and Bone. Now would be a good time to read his post, and the intense discussion that it generated. Come on back here when you're done.

Now, I don't buy Kevin's argument about the implications of the word 'lie'; he asserts that to call a statement a 'lie' is to call the speaker a liar, and I disagree. I don't see any problem with separating the statement from the speaker, and I think many English speakers would agree. If you read that the Holocaust never happened, you're reading a lie, no matter how you end up characterizing the motivations or competence of the writer. How else could we refer to the sinful practice of "repeating lies?" Moreover, I think a lie can evolve, such that it can come to be through careless repetition (with modification), subtly transformed into a perniciously misleading statement when full-grown. In other words, I believe that a lie can exist without being traceable to a specific liar. In fact, I think it's likely that Hugh Ross' sickening fable about the "team of physicists" arose through some sort of evolutionary process, and not through a spasm of malicious dishonesty at a keyboard in Glendora, CA.

But what's the difference between a lie and a falsehood? Unlike Kevin, I label a statement a 'lie' after making a judgment regarding intentionality. If a statement is being used to deceive, or was conceived to deceive, then I will judge it to be a lie, whether or not the person who most recently uttered it – or who forwarded the email in which it was found or whatever  meant to deceive. In this vein, I regularly deem the behavior of some people to be the repeating or spreading of lies, without necessarily assuming that those people are dishonest in any way.

The problem, though, is that some people (Kevin, at the least) don't see things this way at all. And if, as I suspect, Kevin speaks for others as well, then some of my readers have reached the conclusion that I believe Hugh Ross to be a malicious liar. This is not the case, and I have explicitly stated as much in previous posts on this subject. But it just won't do to have confusion regarding character judgments. I will henceforth commit myself to complete avoidance of the word 'lie' in describing folk science. If I think something is really an actual lie, I'll show it to Kevin before I write anything about it. (Seriously.)

Now let me be clear: I will continue to refer to certain examples of RTB's behavior as misconduct, and I will not hesitate to identify the promulgation of falsehood by Ross and Rana as irresponsible, indefensible, and even dishonest. I will not hesitate to question Hugh Ross' intellectual integrity, and I think he should not be considered trustworthy as long as he persists in the reckless dissemination of fabricated nonsense that serves only to direct Christians away from basic facts of biology. The fabricated fable about the "team of physicists" is deeply troubling to me, and it should be troubling to anyone who claims the name of Christ. If I knew Hugh Ross, I would urge him to do whatever is necessary to change course, and I would encourage RTB to invest in mechanisms designed to establish and maintain basic integrity. But I won't call him a liar, or refer to his falsehoods as lies, and I won't assume that he seeks only to mislead or misinform Christians.

Please provide me with some feedback, and feel free to be as critical as you can.

01 January 2008

De-bunking, not debunking

I'll soon post the first in a series of articles that will explain why I believe that Christians are unwise to turn to Reasons To Believe (RTB) or to other proponents of "intelligent design" for competent Christian commentary on evolutionary biology. I think it's important for Christians to reject folk science and the lack of integrity its presence implies, and my goal in creating Quintessence of Dust is to help Christians understand biology.

But in response to my introductory post on RTB's repeated misuse of the concept of "junk DNA," a commenter, dbecke, raised a very serious concern regarding this quest of mine:
I'm still looking for a philosophical and theological position here that isn't "folk" philosophy or theology. As I mentioned earlier, I'm not sure it does a great service to those of us in the evangelical community who want to confront this honestly to merely debunk popular creationist organizations. We need serious evangelical theological input on how all this relates to the doctrines of scripture, man, and the fall. Are there theologians at Calvin, for example, who will accept and contextualize your position? Otherwise it seems to me that there's a danger of debunking people's faith along with the folk science. [italics are mine]
My comment in response mentions some resources that dbecke and others might consult in search of evangelical "contextualization" of common descent, and I try to reveal why it is that I'm not as agitated by the theological issues as are some of my friends and colleagues. But that is insignificant compared to the risk of "debunking people's faith," which is my subject here.

I think the thrust of dbecke's point is that the exposure of deficient creationist folk science by itself is not helpful, because thinking evangelicals also need a theological framework within which to consider natural history and causation. In a very basic sense, I agree, because I affirm that all Christians need a theological framework within which to consider all of creation. And even more generally, I think that dbecke is right to call on evangelical scholars to carefully consider the ancient earth and common ancestry in the context of historic confessions of Christian faith and traditional commitments of evangelical Protestantism.

But I have two big problems with the way the challenge is presented. Addressing these concerns gives me the opportunity to be clear about my theological perspective, and about the risks I see in most creationist apologetics. My intent, then, is not to contradict or correct dbecke as much as it is to explain exactly why I strive to discredit creationist folk science (and lies).

My two objections to this challenge involve my rejection of these two proposals:
  1. It is assumed that the faith of a Christian can be undermined ("debunked") by rhetoric or argumentation; and
  2. It is asserted that, given the aforementioned assumption, the debunking (by a fellow Christian) of bogus apologetic claims entails unacceptable risk to the faith of those who embraced those claims.
In short, I don't buy the premise and I disagree even more vehemently with the conclusion.

Those who know what it means to be Reformed might already understand my rejection of the premise. I hold faith to be a function of God's grace, so that people come to faith by virtue of the work of God, who alone brings the dead to life. I'm a good enough Calvinist to believe that no one can be snatched out of God's hand. Therefore, I don't believe that people are won to faith by reason, and conversely I don't believe that people can be separated from Christ by argumentation. (How all this actually works is another topic.) So if I seem to be unmoved by warnings about "debunking" people's faith, chalk it up to my Calvinism (and roll your eyes if it helps).

But I'm even more concerned about the suggestion that debunking folk science can lead to the "debunking" of someone's faith. For the sake of argument, let's grant that someone could be talked out of their belief. Now let's imagine someone who has based some measure of his belief on false claims regarding the natural world. For example, let's consider someone who has come to faith after reading Creation as Science by Hugh Ross. (We'll call this person Sam.) Now let's assume that Sam actually believes that "biologists have yet to observe any significant evolutionary change, other than extinctions" (p. 142) and that Sam concludes (with Ross) that this factoid (among others concocted by RTB) points to the reliability of Genesis 1. Sam's faith is contaminated by folk science, and in this case the folk science is bogus and easily refuted.

Sam's faith, then, is vulnerable to whatever extent it is dependent on folk science. And there are three possible outcomes here. Maybe Sam will sail through life without ever confronting the most basic facts about evolution. Or maybe Sam will live in blissful ignorance until the fateful day that s/he meets, say, Sam Harris. Or maybe Sam will meet fellow Christians who will help decontaminate his or her faith and, if all goes well, leave her or him strengthened and encouraged by the knowledge that the foundation of our faith is not to be found in our understanding of eukaryotic genetics.

If you want to worry about Christians being exposed to the "debunking" of their faith, you should worry most about that second possibility. (See Ronald Numbers' testimony at the beginning of The Creationists for an example.) If you want to help, then think about ways to encourage Christians in their faith as defined by your favorite creed, focused on the only one with the power to save. And if you want to express anger, vent it at those who are peddling shabby folk science labeled as 'apologetics'.

One of my aims is to help people de-bunk their faith. Bunk is worthless at best, dangerous at worst, and a disgrace to the name of Christ in any case.

I'll sign off with this little fable I composed (in consultation with a budding novelist to whom I've been married for 23 years and 3 days). I hope it crystallizes my ideas and intentions so that I don't need to express them again soon.
The New Bicycles

Once there was a town in which there were many large highways that converged around a prominent hill. Atop that hill sat the town's only library. In order to get to the library, citizens of the town had to traverse the highways, which were frequented by speeding trucks and vehicles driven by reckless and malicious punks. The highway system was occasionally expanded, and there were frequent if not always confirmed reports of grisly deaths on the highways. Citizens had always found various ways to get to the library in safety, but many never attempted the trip, and folks were always looking for safer and more convenient routes to the top of the hill.

One day there was a commotion in the town square, which was situated about a mile from the library. A tall, wise-looking man in a suit was advertising a new and highly effective means of getting to the library. He was selling bicycles, and his claims were extraordinary. "This bicycle," he announced, "will get you safely to the library every time, and it will be faster and easier than any other means you can imagine. This bicycle has been compared to every other conveyance ever designed, and it has been found to be utterly superior to all of them."

Some people were a little skeptical, and asked some obvious questions. How do you know so much about bicycles? "I worked for ten years as a car salesman." Who designed the bike? "I did, with some help from my assistant, who has done detailing on motorcycles." How does it work? "Simple. Just read the manual. You ride, really fast, straight up this road till you get to the library." Wait, is it really that easy? "It sure is. I explain it all in my books." But what about the dangerous highway crossings? "No problem at all. The bike sails right through. Works every time."

He sold a lot of bikes, and people seemed happy with the product. Some ecstatic customers returned and reported that they had reached the library without so much as a scratch. Some had even seen the murderous punks on the road, but reported no problems. (Those that didn't return...well, no one heard from them, so I guess everyone thought they were okay.)

But one day a new person showed up in the town square. She rode up on a Kona Dr Dew (you know, the all-weather twelve-speed with fenders and disc brakes) wearing bike shorts and a super cool jersey. Her helmet had a sun visor, and her backpack clanked with tools. She was quite curious about the bikes that the man was selling, but he didn't seem interested in discussing them with her.

She looked the bikes over, then she started talking to his customers. "I wouldn't buy that bike if I were you." Why not? "It's quite poorly made. For one thing, it doesn't have any brakes." How would you know it doesn't have brakes? "Well, I'm a cyclist and a bicycle repair specialist." So? The man who sold me this is a famous bike salesman. He once sold cars, you know. "Yes, I know, but I think it's pretty clear he doesn't know very much about bikes. This bike is dangerous. It will get you to the library quickly and easily, but it's not safe. You're in danger when crossing the roads." Someone else scoffed. Oh, nonsense. I've ridden mine to the library, and I'm fine. I brought back this book about how to go really fast across the highway on my bike. It's written by the salesman.

The cyclist continued inspecting the bikes, discovering numerous flaws in their design and learning that the customers rode the bikes through some particularly dangerous intersections. As she urged people not to buy or ride the salesman's bikes, she found that some were confused about their options. Are you saying there are bikes that are better than this one? "Oh, yes, definitely. You can get a bike with brakes and with gears and with mirrors. But you don't need a bike at all. You can walk. There are stoplights and crosswalks at some of the intersections elsewhere in town. You can get to the library without so much risk, and you can enjoy the view of the town on the way. It takes longer, and it's more effort, but it's fun and interesting, and you can use the money you would have spent on the bike to buy good walking shoes. Or books."

Then the cyclist was approached by an earnest young man. Why are you telling people to get off the bikes? Some of them might not get to the library. "I'm not telling them to skip the library. I'm not even telling them they have to walk. I'm just trying to get them off those dangerous bikes." But the bikes get them there quickly and easily, and some people depend on the bikes for their access to books. "Y'know, kid, I'm certain that there are other ways to get to the library -- walking, for instance. But even if some people need a bike, there are other bikes that are much better made. Sometimes they're even a lot cheaper. I mean, that guy at Macbeth Cyclery is pretty much giving them away. And I repeat: these bikes here are dangerous. Some of the punks on that road are trying to hurt people who are on the way to the library. Crossing the highway with a defective bike is foolish, don't you think?" The young man shook his head. I don't know. Are you sure that people won't get hurt on the way to the library? "No, I'm not sure of that, and I'm not saying that walking removes all risk. But I'm sure that people are not better off when they're riding across a freeway on a bike with no brakes that was designed by a car salesman."

30 December 2007

More peer review of my blog articles

I've gotten some more feedback on one of my Journal Club posts, from Sean Carroll and Chris Hittinger, the authors of the Nature paper on gene duplication that was the focus of one of my recent reviews of an article from the recent scientific literature. Chris identified some minor imperfections, and I've revised the original post in response to his comments.

This got me thinking. Most of my Journal Club posts are constructed according the BPR3 guidelines, and are indicated as such by the "Blogging on Peer-Reviewed Research" icon. The icon, and my participation in the BPR3 organization, are meant to direct readers to blogging that adheres to the kinds of academic and scientific standards that characterize real scholarship.

But some of my posts have actually been reviewed, by the authors of the scientific articles about which I've written. That is, some of my articles have been peer reviewed, and this means that I'm particularly confident in the completeness and accuracy of that work. So I designed a new icon, to indicate a post of mine that has been peer reviewed, by at least one of the coauthors of the research under discussion. Three of my posts now display the new icon. I've also instituted a new topic label, "Peer-reviewed blog post," which will only be attached to articles that have undergone this type of review.

So look for my "This post was peer reviewed" icon on certain Journal Club posts, indicating that:
  • the post was read by at least one of the authors of the scientific article discussed in the post; and
  • the post was revised to address any corrections or clarifications offered by the reviewer(s).
And don't thank me -- thank the busy and hard-working scientists who take the time to read the blog entries and provide thoughtful feedback as well as encouragement. These folks are typically quite pleased to know that Christians want to read and understand their work. So, thanks to them, and thanks to you for reading.

23 December 2007

Why I like the "New Atheists"

Recently I made a few comments on Greg Laden's Blog over at ScienceBlogs, in which I expressed some, um, concern regarding an aroma of ugly anti-Christian thuggery. The context was a silly (and banal) article on the "War on Christmas," which is some idiotic dustup in the so-called Culture Wars.

I've bashed Richard Dawkins' The God Delusion repeatedly on this blog. I'll probably do it again. And I dissed another crappy blog at ScienceBlogs because it consists of far more "atheist chest-beating" than science or scientific commentary.

All this might give the impression that I don't like atheists, or that I object when they get loud and feisty, or that a prominent aim of this blog is the debunking of atheist claims or the engagement of atheist polemics. Let me be clear: none of the above is true.

My primary audience  the group of people for whom I intend to write  is Christian, and especially evangelical. This doesn't mean that I assume that only Christians will read or appreciate the blog, but it does mean that I nearly always write with thinking Christians in mind. I am working to discredit the anti-evolution folk science of Reasons To Believe because I want evangelicals to abandon apologetics that damage the reputation of Christ and the church, and so I'm writing about their elementary errors for the sake of Christian integrity. Debunking nonsense and disarming attacks of various kinds are major goals of mine, but the targets aren't atheists  they're Christians.

But still, you might wonder what I think of the New Atheists. In short: I think they're a welcome addition to the public square. Here are a few of my reasons.

1. Christianity (perhaps I should say Christendom) needs opposition.

For one thing, such opposition is a bit like peer review. The New Atheists aren't merely announcing their unbelief. They're saying, "we think your belief is idiotic." And they're saying, "we think your belief is harmful." I say we think of those challenges as negative comments from a manuscript reviewer. In science, when you get a nasty review of a manuscript, you either revise the manuscript or you explain to the editor why the reviewer is mistaken. (Or both. Usually both.) Even if the reviewer is a butthead, her/his critique must be effectively dealt with if the editor is to be convinced that the paper is worthy of publication. As I've mentioned before, peer review often makes the original article much better.

Moreover, active opposition can expose weaknesses that the church is otherwise unable to see or unwilling to acknowledge. These flaws might be noted by the critics, or they might be revealed in the ways Christians respond to the attack.

2. Unbelievers should be represented in the public square, in the same way that various faiths are (or ought to be).

The Christian Right has its culture warriors, other faiths have their well-known organizations and representatives. Right-wing Christians can applaud James Dobson, and thereby contribute to the cultural conversation; others of us can oppose him, and similarly stake a claim. How can it be unhealthy or inappropriate for atheist voices to speak similarly on behalf of like-minded persons?

3. The New Atheists are providing atheists an opportunity to clarify their various cultural positions, individually and collectively.

I suspect that many atheists don't care to be identified with an "atheist community" at all, but to whatever extent they do, they can use the New Atheists as a starting point for identifying areas of specific interest in public discourse. The New Atheists are speaking loudly in the public square, and some of them have staked out positions that may not represent anything remotely resembling a generalized "atheist" position.

I am eager to know, for example, whether most atheists would find Francis Collins' description of his conversion to represent a religious attack on science. Sam Harris apparently does. Is this a typical position for an atheist? For an atheist scientist? I would prefer to work with unbelievers who reject such warmongering, just as I would prefer to work with Christians who denounce and disavow just about everything Pat Robertson has ever said. The New Atheists, if nothing else, have created new topics for discussion, and given everyone new opportunities to weigh in on those questions.

4. The attack of the New Atheists has encouraged me as a Christian.

Wait...huh? I'm dead serious. I've read most of Dennett's Breaking the Spell, as well as his Darwin's Dangerous Idea and much of Consciousness Explained. (I really enjoy his writing and his arguments.) I haven't read any of Sam Harris other than that sickening letter to Nature, nor have I read Hitchens (outside my ravenous consumption of everything he writes in the Atlantic Monthly). But I've read almost everything Dawkins has ever written, including The God Delusion, and I've seen the hilariously sycophantic pleading on his behalf by Dennett and Michael Shermer. And this is my response:
That's it?! That's all you got?!
Now don't get me wrong. I don't think the New Atheists are stupid for doubting, or even for considering Christianity to be rubbish. I just don't find anything in their writing that is a threat to my belief.

So...here's to the New Atheists. May God richly bless them.

17 November 2007

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.

29 October 2007

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.

30 September 2007

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.

19 August 2007

Introducing me: on common descent and explanation

What is the evidence for common descent?

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

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

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

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

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

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

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

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

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

05 August 2007

Why "Quintessence of Dust?"

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

Hamlet, Act II, Scene II (Arden Shakespeare)


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

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

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

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


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

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

03 August 2007

Kicking off my blog

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

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

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

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

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

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