28 June 2008

Uncommon Descent conversation, part 5

Below is my fifth contribution to the discussion at Uncommon Descent, in the thread called "Theistic Evolutionists...we can help you." My previous post, addressed to "jerry," has not gone up on UD, for reasons unknown. Perhaps readers can spot the problem (e.g., a dirty word hidden in some scientific jargon) and UD visitors can pass that information to the UD magistrates.

Interestingly, yesterday I discovered that my comments were posted immediately, without moderation. But the contribution below is now reporting that it "awaits moderation," so I'm back in purgatory for some reason, probably related to the unexplained rejection of the response to "jerry." Anyway, here it is, and we'll see if it also appears (with the previous post) on UD.

Thomas @70:

First a note to all: I attempted to post a response to jerry here last night, but it hasn't gone up and I don't know why. You can read it at my blog, but I hope we'll get it up here soon.

I think I will let this be my last word on the topic of randomness and how various TEs handle it, and I'll try to keep it brief. But if there's something specific you'd like me to address, by all means point it out.

You have made it quite clear, I think, what you want "TEs" to do. But you have failed to convince me that this is anything but completely trivial, and I have judged your complaint to be unimportant. To summarize my own position: Darwin's "mechanism" was natural selection acting on random variation. Darwin, without any scientific or metaphysical support, added non-teleology to his mechanism, and the result is something that you and I seem to agree to call "Darwinism." Christians, we seem to agree, can't embrace that thing we're calling "Darwinism." (Non-Christians, even non-theists, might choose to reject "Darwinism" for the same reasons, namely that it incorporates unjustified metaphysical pronouncements that don't add explanatory force.) But since Darwin added his metaphysical proviso without justification, and since the proviso does no explanatory work, it can (and should) be removed as unceremoniously as it was added. The consequences of this move are of course not trivial, but the move itself is completely trivial.

Again, I don't speak for any of those other folks, but I surmise that one reason they don't provide the disclaimers you desire is that they, like me, are concerned that they will be misunderstood. The term "Darwinism" is, in my opinion, very often deliberately meant to confuse. In our conversation here, it's gone well, but only because I made it very clear, right from the beginning, what I meant by "Darwinism." This distinction is rarely made clear, but it's hugely important. Without it, a person reading your post, referring to our agreement "that the Darwinian mechanism is at least partly wrong," might reasonably conclude that I am unconvinced of the explanatory power of natural selection acting on random variation. Perhaps because I'm a scientist, I can barely imagine interpreting "the Darwinian mechanism" in any other way. But that's what you and I have done here. The potential for misunderstanding is significant, and I haven't even factored in the ID movement's fondness for martial rhetoric and propaganda.

And Thomas, I do not take seriously your comments about people like Francis Collins "poisoning the public discourse in the country." It's not that I think Ken Miller is right about everything (hardly), or that I think Collins hasn't missed some pitches. No, the basic problem is that your movement has no moral credibility with me. You are speaking from within a blog that represents everything I loathe about the movement. You are whining about "hostility" in a blog that revels in the belligerent taunting of my colleagues and that breezily describes people like me as "spineless appeasers," "Neville Chamberlains," or "dhimmis" while asserting that we have entered a "pact with the Devil." Your movement's contempt for evolutionary creation has been communicated all too clearly, and if I were you I'd be much more focused on building and maintaining scholarly relationships with those who are willing to be responsible critics, or even on forcefully disclaiming your movement’s many abuses of science and scientists, than I would be on feigning victimhood.

I am committed to working hard at maintaining collegiality in discussions with folks like you and StephenB and jerry, in my role as "friendly critic." But if you want me to be a friend, you'll have to change your approach significantly. At the very least, you should re-examine my original post, regarding some very important problems I have with your movement, and consider whether the conversation is going in the right direction.

But lest you think I'm not listening: yes, you can count on me to criticize bogus or unfair arguments by TEs, and yes, I think there are times when interesting discussions of design and God's action are lost in the fog of culture war.

27 June 2008

Uncommon Descent conversation, part 4

A few interesting responses on the Theistic Evolutionists...We Can Help You thread at Uncommon Descent, one from a poster named jerry who asked a few straightforward questions. My response is below as usual.

To Jerry @68:

Thanks for the words of welcome. I need to be relatively brief now, especially on Behe's work, but I'm happy to discuss biology and evolution with anyone anytime, and I welcome questions, the more specific the better. I hope you and the others here will be patient with me: I work full time in the lab, run a blog of my own, and juggle several additional writing projects among my time with my wife and four kids. When/if there's a question you really want me to address, make it clear.

First, re banning on this site, I've heard from too many decent people on this topic to believe that the policy here is a good one. And the claim that people are banned due to "ad hominems" is laughable, as anyone who reads this blog knows all too well. I've been warmly welcomed, and that's all that matters in this conversation, but please don't ask me to defend your venue. It is what it is, and I happen to think it's a mess -- let's leave it at that.

"I think design is the question, and you think it's the answer." Here, basically, is what I mean. In your first paragraph, you note that you and others here "do not believe there is any naturalistic mechanism that can explain macro evolution or the origin of life," and so you "opt for design events as the only answer." Design, for you, is the answer, and the question was how did these biological systems come about? In between, we find your conclusion that the phenomena in question cannot be explained naturalistically.

I start with the same question: how did these biological systems come about? At the same time, I notice design, "purposeful arrangement of parts," even "prodigies of nature." As I already mentioned in my first post here, I'm quite happy discussing design, and completely reject the suggestion that design has no place in science. Baloney! Design is what we're trying to understand. Design is the question. Here is this biosphere, filled with mind-blowing nanomachines and indescribably intricate processes. Do we need a mathematically-inclined philosopher to coax the specter of "design" out of modern probabilistic theories? Do we need an underinformed biochemist to locate "design" through analysis of mutation rates in Plasmodium falciparum? Good heavens, no. It's right there; it's everywhere. Detecting design, for me, is almost effortless, natural, automatic. (Consider the vocabulary of cell biology, which we can further discuss later.) And so I identify "design" as the very thing I'm trying to understand. My question becomes how did all of this design come about?

I think, then, that we can identify at least two crucial ways in which our thinking diverges. First, design for you is the stuff you use to fill explanatory gaps -- it's the answer. For me, it's the thing we seek to understand -- it's the question. Second, you are convinced that "naturalistic" explanation of natural history is not possible. I'm not at all convinced of this, and in fact I expect God's world to be largely amenable to natural explanation. In other words, I expect that naturalistic mechanisms can account for biological evolution, just as I expect that they can account for embryonic development and for, say, autism. Did that answer your question?

And what about Behe's The Edge of Evolution? Writing carefully about his errors is not easy; evolutionary genetics is challenging under the best of conditions, and laypersons are understandably poorly-equipped to grasp the necessary details. I have been planning a series on my blog, and this conversation might get that project moved up on the to-do list. I've explained some of the most dramatic errors on my blog, and I'll add three further comments here.

1. In TEoE and elsewhere, Behe presents a highly simplified vision of adaptation and microevolution, in which only beneficial mutations are maintained in populations. He gives the impression that a population would only harbor a given mutation or polymorphism if that change had been specifically favored by selection. This is a substantial mischaracterization of evolutionary genetics, overlooking some very important aspects of eukaryotic genetics. There are several mechanisms, well-known to geneticists but almost universally neglected in popular discussions of evolution and inheritance, that can lead to the maintenance of a non-adaptive or "non-beneficial" allele in a population, especially in a sexually-reproducing diploid population (like, say, Plasmodium falciparum). Moreover, during evolutionary and/or environmental change, the beneficial-ness of a particular allele can change completely. Beware of simple evolutionary stories in which adaptation can only proceed in happy little steps from good to better to best. Genetics is more complicated (and interesting) than that.

2. The book's central argument is based fundamentally on population genetics, but ignores the work of the world's most prominent and accomplished geneticists. Allen Orr, for example, is precisely the kind of expert whose work should be the focus of Behe's analysis, but Behe's references to Orr's work are minimal. He leaves untouched the entire field of evolutionary genetics, merely cherry-picking two of Orr's papers. The point is this: a serious consideration of evolutionary genetics -- never mind a complete rewriting of the entire field -- should show marks of serious engagement with existing ideas. TEoE doesn't even try to do this. And most tellingly, Behe hasn't been able to get population geneticists to endorse his book, or to follow up on his assertions. Did he even ask Allen Orr to read the manuscript before going to press? Has he asked Allen Orr to critically review the book, the way any real scientist would seek critical feedback before (or after) advancing a big new idea?

3. If Behe's claims in TEoE are correct, he will soon be the most celebrated biologist since Watson and Crick, and perhaps of all time, for he will have shown conclusively that essentially everything in the biosphere has arisen through mechanisms unknown to science. It is impossible to exaggerate the magnitude of the impact of such discoveries, and I assure you that if I thought there was anything there at all, I would hasten to follow up on Behe's skeletal introduction, devising bioinformatic analyses to bolster his hypothesis and working hard to establish myself as a part of this historic sea change in science. I would achieve scientific "immortality" for myself, worldwide acclaim for Calvin College, and maybe enough of a raise to retire my student loan debt while paying for Christian school education for my kids. Guys, if Allen Orr or Michael Lynch or Sean Carroll or Francis Collins or Craig Venter thought there was anything even remotely plausible about Behe's analysis, they would marshal resources of every kind to pursue the question, and some of them would gather investors and start an institute, bearing the name of some benefactor eager to have his/her name associated with the most momentous discovery of the 20th century and with the Nobel Laureate who made it happen.

Wake up, people. There's nothing there.

26 June 2008

Survivor:UD -- when will they vote Matheson off?

Okay, that'll probably be the last UD moderation joke, because my irresistible charm has had its predictable (non-random) effect. I have a nice discussion going with two regulars at Uncommon Descent, StephenB and the original poster, Thomas Cudworth. I'll post my contribution below as usual, and you can read the rest of the conversation in the growing thread at Uncommon Descent.

Before you go there, have a look at this nice (older) post on randomness in the Bible, at Martin LaBar's blog, Sun and Shield. Martin is a regular commenter here, and his blog is a joy to read.

Please jump in here if you wish; I don't moderate comments and will welcome any and all.

I'll respond to both Thomas and StephenB here. First, to the moderator: thanks for posting my comments. The discussion has been profitable, and I take it that Thomas and StephenB would agree. Please note that I am mirroring my own contributions on my blog, Quintessence of Dust, and will continue to do that, at least so that others can participate in the conversation. (I don't moderate comments.) In answering both Thomas and StephenB, this post got pretty long, and I would understand if you asked us to move it elsewhere. Just let me know.

To Thomas @61:

I do think that your statements appear to bracket God's power, but you didn't mean to say that, and I think I see why we're struggling to understand each other here. You discuss "pure Darwinism" and "strict Darwinism" and "the naked Darwinian mechanism." Here you are referring, I gather, to random mutation and natural selection with a further stipulation: that no divine guidance of any kind is involved. (We could substitute 'design' or 'teleology' here and my point would be the same.) And you are, I think, correct in identifying that -ism with Mr. Darwin, as Prof. Hodge so ably demonstrated. Hodge was right: "Darwinism," so defined, is atheism. This may mean that I'm not a Darwinist, but a Grayist. (I would be most pleased to bear that name if I thought anyone else would get the allusion.) The point, though, is this: your criticism of Christians who embrace "Darwinism" only makes sense if those Christians embraced the Darwinism that Hodge railed against, which he correctly identified as atheism. And that means your criticism reduces to this: Christians shouldn't be atheists. I'm struggling to understand why you think so many Christians are that stupid, which we'd have to be in order to embrace the "Darwinism" that you condemn. With all due respect, you should reconsider a line of argument that can only imply abject stupidity (or perhaps evil) on the part of the Christians that you name. For my part as a Christian evolutionist, I'll gladly make the statement you call for: Darwin was indeed "partly wrong" about the "mechanism of evolution," because he insisted on ateleology, with neither scientific nor metaphysical justification. Trivial.

So, Thomas, I'm not at all sure who these Christian TEs are who embrace atheistic Darwinism. I'm pretty sure they don't exist. In any case, I'm not one of them, and my intention here at UD is to speak only for myself.

With the understanding that I do not seek to speak for others, I will say that I reject your accusation against three of the four Christian scholars you singled out. Francis Collins contradicts you on page 205 of The Language of God; Ken Miller in chapter 8 of Finding Darwin's God, and especially on pp. 238-9; Denis Lamoureux refers explicitly to evolution as a "teleological natural process ordained by God." I don't know Ayala's work on this subject well enough to know where he stands, but I very much doubt that you have gotten him right. Perhaps I have misunderstood you again, but whether you retract your accusations or not, I can't currently take them seriously.

My point about atheists was meant only to note that the viciousness of the rhetoric on UD constitutes a major deterrent to me with regard to your movement. I would not count myself among Christians who engage in such practices. But that doesn't mean I wouldn't have lunch with you. I'll even buy.

Finally, thanks for making me feel welcome as a "friendly critic." I don't buy your martyr case, and I'm mostly amused by the apocalyptic martial prose, but I also don't doubt that people have been treated unfairly. More importantly, I won't call you a bad scientist or a bad theologian for thinking about design. I may, on the other hand, point to bad science or bad theology (mostly bad science) done in the name of ID, and you and your friends are going to have to do a better job of distinguishing criticism of your ideas (some of which are spectacularly bad) from diabolical attempts to destroy you and anyone who looks like you. (Bill Dembski botched this badly in his fatwa-like rant from two weeks ago; read it carefully and see if you can understand my disgust.)

To StephenB @62:

I'm not sure what to do with most of your comments, except to thank your for taking the time to lay out your thoughts and to do it with a measure of respect. Just a few responses, then I'll answer your question at the end.

1. I do not belong to any particular school regarding God's work in the world. Kenosis is interesting -- that's all I said. Your thoughts parallel mine for the most part. I wouldn't go as far as to say that Psalm 19 and Romans 1 imply that "design in nature is detectable," but that might be because I'm suspicious of the word "design" here. I suspect that your claim regarding those scriptural passages is indicative of some very significant differences in outlook between you and I.

2. Your rebuttals of Stephen Barr are interesting and informed, but my purpose in citing his piece was to highlight Aquinas' very clear pronouncements regarding "chance" and providence. That was all.

3. You write: "God CAN use random events. The problem is, however, TEs insist that God does EVERYTHING that way." Well, StephenB, obviously I'm not a TE. I'm not sure there's any such thing as a Christian TE, by your reckoning, and I'm not sure there's anything more for us to discuss on this particular topic.

4. You asked about the various phenomena I listed as examples of scientific explanations that invoke randomness. Here's a brief overview.

a. Axonal pruning is widespread during vertebrate brain development, and is preceded by the overgrowth of axonal projections into a target field. These projections are guided by various mechanisms into that target field, but once there they find themselves in competition with an excess of other axons. These so-called exuberant axonal projections are postulated to fill the target field randomly, meaning that they display no discernible pattern. Pruning (also termed selection for obvious reasons) occurs following competition, which usually involves electrical activity of the axons. Analagous processes are involved in the elimination of excess synapses, and even excess neurons.

b. Mammalian females have 2 X chromosomes, while males have only one. Since gene dosage seems to be adjusted such that one X chromosome is enough for any given cell (which makes sense given that male cells have only one to start with), one of the two X chromosomes in every cell in a female's body is inactivated. (This occurs during early development, and results in the organism becoming a chimera of areas that express the maternal X chromosome and areas that express the paternal version.) Because the exact chromosome that will be chosen in any given cell cannot be predicted, the process is referred to as "random." Evidence in favor of this view comes from the examination of coat color in cats and mice.

c. Erosion...the Grand Canyon...think fractals. And meteorites...if I say that meteorites are falling "randomly" onto the earth's surface, would you think I was making an atheistic metaphysical claim? Or would you understand me to be saying that there seems to be no discernible pattern?

d. Random (meaning unbiased) fertilization is the basis of Mendelian genetic analysis. If I ask you about the probability of your getting cystic fibrosis based on your parents' known status as carriers, I'm assuming random fertilization. And when geneticists see non-Mendelian inheritance patterns, they don't think "design."

e. The genes that encode antibodies (in mammals, at least) are generated by a frenzy of genetic shuffling during embryonic development. The shuffling involves some non-random processes combined with an error-prone process that randomly generates vast combinations of antibody structures.

Apparently random processes are ubiquitous in biological systems, especially during development, and I'm a developmental biologist. Is it clear why I'm completely turned off by all the nonsense about random vs. God's work?

25 June 2008

Day 2 on Uncommon Descent: waiting for the axe to fall

My comment on Uncommon Descent yielded a single response, from one StephenB, who had two things to say. He was curious about my side note regarding "some pretty clear statements about chance and God's providence in Scripture" and then he reiterated what we all know very well: that he and other ID proponents see "Darwinian evolution" as a "an unintended, unconscious, chance process with no plan."

He left without comment my reasons for avoiding contact with his movement. I guess I was not misunderstood, which is good.

Here's my comment in response. Feel free to lay odds on its inclusion at UD.

To StephenB @57:
Thanks for the response. It seems there are just two issues to tackle here.

1. You asked about my view of chance in Scripture. I note that God's people commonly used the casting of lots to make decisions (choosing the scapegoat, selecting Judas' replacement, choosing Saul as king) and Proverbs 16:33 seems pretty clear to me: "The lot is cast into the lap, but its every decision is from the Lord." My claim is not that "design by chance is a Scriptural concept." My claim is much more basic: the notion that "random" processes, including Darwinian evolution, are "out of God's control" is indefensible. Thomas Aquinas, I gather, would agree.

StephenB, I can't even imagine why a Christian would want to make that assertion about God's action in the world, even if that person had never read about the deliberate use of random devices in the Bible and God's claim to control those devices. A Christian who talks like that is one who views God and the world very differently than I do.

2. The rest of your response, it seems to me, can be summarized in this phrase: "The problem is that some want to impose on God a Darwinian process, which is, by definition, a non-control process, and then try to make it fit in with a picture of God under control." As I noted in my first comment, this claim (that Darwinian evolution is necessarily a "non-control" process) is nonsense. The best you can do is label it true "by definition" and then haul out quote-mined proof texts from confused atheists. (I'm not saying that you've quote-mined; I'm only saying that the only support such an assertion can possibly muster is the existence of those who agree.) What you most certainly cannot (honestly) do is demonstrate that God does not (or cannot) work through events or processes that we label "random."

Now again, let me point to the common ground here. Neither of us believes that the marvels of creation came about by "accident" or through a process that God "can't control." I'm pretty flexible on questions of what God knows and when, and I'm interested in kenosis and other models of God's interaction with creation that make room for creaturely freedom. But like you, I reject the notion that creation unfolds outside of God's control. And that means that some of what your movement claims to value is also valuable to me.

But one last thing. Do you feel compelled to reject and/or oppose scientific models of axonal pruning or synapse elimination or X chromosome inactivation or erosion or fertilization or meteorite impacts or generation of antibodies that invoke the concept of randomness? Can you see why I (as a developmental biologist) would hesitate to follow you down this road?

24 June 2008

War declared on "spineless appeasers"

I very seldom read Uncommon Descent, for lots of reasons, two of the most prominent being that I am angered and sickened by culture-war rhetoric and I am uninterested in "design" as an explanation. But when Bill Dembski declared (culture) war on "theistic evolutionists" (see my post at Clashing Culture for links and discussion) I took notice (via the ASA listserv, populated by some who actually do read UD). And when the brilliant and decent Ted Davis posted a long comment on UD trying to explain to DaveScot (who refers to "theistic evolutionists" as "spineless appeasers") why many Christian evolutionists won't have anything to do with his movement, I thought I should try a comment, to see if there is a possibility of occasional dialogue.

I registered at UD a week ago, but didn't visit the site or comment till today, when I saw a piece at The Panda's Thumb pointing to a new post at UD by a new poster, one Thomas Cudworth. The author points to "incoherence" in the thinking of "theistic evolutionists" and it seemed like a good place to toss in some comments. In case my maiden voyage hits the iceberg of "comment moderation" at UD, or for those of you who just won't go to UD, here is the response I posted there this evening.

Just a few responses to Thomas' original post. I will respond as though the post was directed at me, but please don't assume that I speak for other evolutionary creationists. My focus is on why I can't "join" you in the ID movement.

1. I embrace evolutionary explanations because they have explanatory power. For the same reason, I embrace naturalistic explanations for the development of the human brain, and for the causation of cancer, and for the formation of the Grand Canyon. All of these explanations involve mechanisms that are referred to as "random." In fact, randomness and chance are interesting topics for Christians of all kinds and in nearly every aspect of scientific inquiry (if not all of life). In my view, to focus on these issues exclusively in the context of biological evolution is a huge mistake. If I thought the ID movement were really about wrestling with the notions of chance, providence and design in the analysis of God's world, I'd be happy to join the conversation. It's not, and I'm not.

2. I'm astonished by the casual claim that "Darwinian evolution" is "out of God's control" because of the role of "chance." Leaving aside some pretty clear statements about chance and God's providence in Scripture, I find the statement to be either a tautology ("Darwinian evolution is out of God's control because Darwin/Dawkins said it was") or a pronouncement regarding God's sovereignty that is anathema to me as a Christian (and especially as a Reformed Christian). In grumpier moods, or after reading some of the more obnoxious comments on this blog, I would suggest that such talk approaches blasphemy, but in any case I would not count myself among Christians who talk that way about God's world and his work. It's one thing to say you don't buy the Darwinian explanation, or to say that you're confused about the working of God's purposes in the midst of seemingly random events; it's another to declare that there are processes that God can't "control."

3. Regarding design, I don't have any desire at all to "ban the notion of design from science." In fact, I'm quite comfortable discussing design and wondering about the ways it can come about. I find most of the ID movement's claims about "complexity" and whatnot to be unconvincing (and Behe's work in TEoE is disastrously flawed), but I don't think the question is either silly or inherently unscientific. (Perhaps this means I'm not the kind of "TE" you have in mind.) On questions of design, my main difference with your movement is probably summarized aptly as follows: I think design is the question, and you think it's the answer. But this means I'm just not that interested in your movement's goals.

4. Unlike many on this blog, I don't harbor hatred for atheists, not even "unsavory" atheists, and I actively seek opportunities to interact with skeptics. I have many friends and very close collaborators who are atheists, and I just joined a collaborative blog that seeks to create constructive conversations among believers and skeptics, on scientific topics. Even if we agreed on everything else, your movement (or at least the corner of the movement represented by this blog) would be something I would carefully avoid, not only because I despise the culture-war rhetoric, but because the people you hate are many of the people I love.

Now, please let me sign off by saying that while I'll never join your movement, I do want to be counted as a "friendly critic" who is willing and able to identify areas of common ground between us. You approached some of that common ground in your post, and I thought it was worth a try responding in my first comment at UD. Sorry about the length...

19 June 2008

Wait...did you say "eldritch?"

It's exciting to live in the era of evolutionary genomics, when new genomes are being published approximately once a week, and the light of genomic analysis is being trained on more and more branches of the tree of life. This week sees the unveiling of the genome of Amphioxus, a primitive vertebrate that has long been known to be a key piece of the puzzle of animal evolution, and the results are sharpening our hypotheses about the genesis of major animal groups.

First a little about the results published in this week's Nature. Amphioxus is the fancy name for lancelets, which are small and simple sea-going creatures that represent a very interesting branch on the tree of life: they constitute a group called the cephalochordates, which is one of the three living groups of chordates. (Remember "kingdom, phylum, class, order, family, genus, species"? Humans are vertebrates, and vertebrates are a subdivision of the chordates.) Vertebrates and tunicates (sea squirts) are the other two groups. Because the lancelets are similar in structure to vertebrates, more so than are the tunicates, they were long thought to be more closely related to vertebrates, and so it was postulated that tunicates were more "basal" on the evolutionary tree. But two years ago, new analyses strongly suggested that it is the lancelets that are the most basal group. And so the lancelets became even more interesting: understanding their genomic structure would surely provide clues to the nature of the original chordate genome.

The examination of the lancelet genome (well, it's the genome of one lancelet of one species) provides substantial new insight into vertebrate evolution. For some solid overviews, check out Nobel Intent at Ars Technica, and the press release from UC Berkeley. Here are just a few tidbits that got my attention:
  • The findings strongly support the hypothesis that the vertebrate gene set was diversified through two ancient whole-genome duplications. This phenomenon and its role in the generation of new gene functions have been discussed here before.
  • The lancelet genome contains roughly the same number of genes as the human genome.
  • Comparison of the various chordate genomes reveals that there are very few chordate-specific genes. Specifically, the authors described 239 "chordate gene novelties" out of 22,000 genes in the lancelet. The nature and function of these genes is intensely interesting, and indeed the authors devote a separate report to issues related to this. But think about it: only 1% of the genes in chordates (vertebrates and all their relatives) are "novel" among genes from all other organisms.
  • So if the toolbox isn't all that different between lancelets and lions, despite divergence at least 550 million years ago, then what is different? Anything? As John Timmer notes on Nobel Intent, the authors could find relatively few examples of regulatory DNA sequences that are conserved between lancelets and vertebrates, pointing to the likelihood that changes in regulation of a (mostly) common genetic toolkit is a major factor in evolution of form. (Okay, so that was just a plug for evo-devo. It's my blog.)
But one more thing. Why the bizarre title for this blog entry? Well, Henry Gee at Nature wrote a very nice News & Views summary of the genome report, and here are a few not-so-randomly-selected excerpts:
The age of genomics has rescued the amphioxus from chthonic obscurity, as new data — now including Putnam and colleagues’ paper and three companion reports in Genome Research — have reinvigorated the study of the origin of the vertebrates.
Is there a typo in there?
The 520-megabase genome of B. floridae would, therefore, be nothing much more than a curiosity without the comparative context offered by the increasing number of completed or draft animal genomes from humans to sea anemones... Such studies reveal the amphioxus genome to be, in fact, of preternatural importance.
But with Putnam and colleagues’ publication on page 1064 of the draft genome sequence of Branchiostoma floridae, one of the 25 or so recognized species of amphioxus, this eldritch organism is set to re-enter public life.
Eldritch? Eldritch?? What the heck?!

'Preternatural' I can handle, barely, but 'eldritch' and 'chthonic'... Yes, there's a story here, and it's very funny. Enjoy, and have fun in your next Scrabble game.

12 June 2008

Weekly sampler 20

Wow, lots going on lately.

1. So, what is a species? The concept is much abused by creationists, so that an already-challenging topic is turned into an abyss of confusion and obfuscation. John Wilkins is a philosopher of science who runs a superb blog over at ScienceBlogs, Evolving Thoughts. He's an expert on this whole species thing, and he recently provided a fascinating commentary on the issue and on a Scientific American essay on the topic by the dashing Carl Zimmer. Warning: spoiler ahead!
So my answer to the question Carl proposes: what is a species? is that a species is something one sees when one realises that two organisms are in the same one. They are natural objects, not mere conveniences, but they are not derived from explanations, but rather they call for them...
2. Oh, speaking of Carl Zimmer, check out this deliciously disturbing story of manipulation in nature, starring some of the creatures that drove Charles Darwin to agnostic distraction: parasitic wasps. Don't read this one at night.

3. Okay, so I've been a little hard on Jim Watson around here. He was "forced out" of his position at Cold Spring Harbor after he was reported to have made some plainly racist statements. Richard Dawkins was indignant, probably because Watson is a fellow atheist who Dawkins fawns over in The God Delusion. I had mixed feelings. On one hand, I was outraged by Watson's nakedly disgusting racist remarks; on the other, I was concerned about the likelihood that his comments on evolution and cognition would be ignored (or worse, rejected) in the uproar.

Well, Watson was recently interviewed by Henry Louis Gates, Jr., at an interesting site called The Root. Watson says that he is "mortified" by "those three sentences in the Sunday Times article." I'm pretty sure all three sentences appear in this paragraph:
He says that he is “inherently gloomy about the prospect of Africa” because “all our social policies are based on the fact that their intelligence is the same as ours – whereas all the testing says not really”, and I know that this “hot potato” is going to be difficult to address. His hope is that everyone is equal, but he counters that “people who have to deal with black employees find this not true”. He says that you should not discriminate on the basis of colour, because “there are many people of colour who are very talented, but don’t promote them when they haven’t succeeded at the lower level”. He writes that “there is no firm reason to anticipate that the intellectual capacities of peoples geographically separated in their evolution should prove to have evolved identically. Our wanting to reserve equal powers of reason as some universal heritage of humanity will not be enough to make it so”.
It seems to me that a discussion of the last two sentences could be quite fruitful; Watson is right about evolution, but wrong about what that must mean about the "equality" of "them."

4. Here's an interesting place to hang out: The Galilean Library. When I first followed a link there, I assumed it was a repository along the lines of Darwin Online. But no: here's how the community is described:
The aim of TGL is to provide a venue for people interested in the sciences and humanities and the possibility of learning more about them in community with others. Its rules are strict, relative to other discussion forums, and standards of expected behaviour are high, but all users need to do is demonstrate a genuine commitment to friendly and respectful dialogue with others in good faith. It consists in a Library of essays, at both introductory and more advanced levels, alongside a Discussion Forum where members of our community meet to converse and debate.
Cool. And yes, they do have stuff by Galileo, including that masterpiece of science-faith dialogue, Letter to the Grand Duchess Christina.

5. Kevin Corcoran unearths ancient secrets of scientific explanation. Now I get it.

6. A slick new Tangled Bank is up at Syaffolee.

7. A recent post in Steve Martin's ongoing series on "Evangelicals, Evolution, and Academics," by Karl Giberson, led to a lengthy and robust discussion there and on the ASA listserv. And a new post in the series, by Gordon Glover, just went up. It has this in-your-face title: "Why Evolution should be taught in Christian schools." Required reading.

8. Hey! My wife and I are looking for scholars (or just friends) in Scotland and/or London who would be willing to help us with our January trip to London and Edinburgh to study Christianity and the Scottish Enlightenment. Doesn't that sound like a great time? Please get in touch if you agree.

9. Reasons To Believe is a morass of misinformation about biology and evolution, but this is a new low: some "guest scholars" have contributed a series on "Evolution as Mythology" which is a rancid concoction of dishonest quote mining and fallacious reasoning that should make any informed Christian seethe. So much for RTB's claim to respect science and scientists; that series is a tour de force of the kind of arrogance-fed ignorance that forms the backbone of the young-earth creationism that RTB claims to eschew. Here's a typically nauseating morsel:
Even though macroevolution seems improbable via the traditional pathway (and regulatory genes are a strong argument for creationism) the myth-like character of neo-Darwinism continues to keep it as the dominant theory. As Behe says, “Most biologists work within a Darwinian framework and simply assume what cannot be demonstrated.”23 Evolutionists even claim regulatory genes make neo-Darwinism more plausible because punctuated equilibrium is more easily explained by regulatory genes, but this only emphasizes how the myth of macroevolution must be protected with religious zeal.
Note to RTB: your intellectual integrity is mediocre at best, and your failures are magnified, not hidden, by your attempts to claim moral high ground in "debates" involving science and faith. Your organization desperately needs reform.

05 June 2008

Clashing Culture: an interesting new conversation

I would bet that many of you have explored Thomas Robey's excellent blog, Hope for Pandora, focused on medicine, science and religion. Apparently bored by the routine of learning (and assisting in) life-saving medical procedures and reflecting on how such events are tied to moral and social debates in this country, Thomas has launched a new blogging community, Clashing Culture (subtitled "Conversations About Science and Faith"), and invited me to be a member. I foolishly agreed. (Foolish because I'm behind on other writing projects, while finally getting active lentiviral vectors in my lab experiments, and still haven't paid off my student loans.)

Thomas describes the endeavor as:
a blogging project where scientists and laymen, Christians and atheists can hold conversations about topics where science and religion converge... My goal is to develop a venue where the authors respect one another but are comfortable laying out their full arguments and critiques.
A worthy goal for sure, and the wonderful Mike from Tangled Up in Blue Guy is already on board, so I agreed to crosspost relevant rants articles from here. Check it out, leave comments, and offer feedback.

04 June 2008

Evolution and creation at Calvin College

Go to An Evangelical Dialogue on Evolution to see a two-part series I contributed, on evolution and creation at Calvin. The first part, posted on Monday, describes the intense controversy of the 1980's and 1990's at Calvin (and in the Christian Reformed Church). The second part went up today, and contains my musings on the current climate.

The larger series, on Evangelicals, Evolution, and Academics, is interesting and valuable, and some very important voices are yet to come.

01 June 2008

Weekly sampler 19

A few interesting and/or important tidbits for Monday.

1. Brian at Laelaps provides a list of some very useful books available electronically for free. Authors include slouches like Cuvier, Lyell and Huxley.

2. PZ Myers has an excellent new column up at SEED Magazine, discussing the pufferfish genome and referring to Ryan Gregory's excellent work. (Larry Moran adds commentary, and is talking about a poll.) If you need a refresher on "junk DNA" and the worthless creationist arguments it has spawned, note that I've added a Junk DNA tag to my topics list.

3. Steve Martin at An Evangelical Dialogue on Evolution is in the midst of an important and informative series of guest posts on "Evangelicals, Evolution, and Academics." Last week, Richard Colling provided some thoughtful reflections on the delicate art of communicating evolution to believers. (Some of my readers will be glad to know that I read Colling's words carefully.) One early line that caught my eye: "Indeed, an ungodly and consuming fear of evolution has engulfed the Christian community." Up this week: yours truly, on the topic of evolution at Calvin College. I wonder if I should update my CV...

4. James Kidder describes himself thus: "I am a Christian, librarian, palaeoanthropologist, evolutionary biologist and web page designer with an all-consuming interest in apologetics and controversies in science and religion." His blog is called "Science and Religion: A View from an Evolutionary Creationist" and I recommend it very highly.

5. If you can't make it to the Field Museum in Chicago to see the Evolving Planet exhibition...well, first try harder. But if you really can't get there, check out this incredible animation of the Cambrian ocean. Wonderful Life, indeed.

6. Baseball meets intelligent design! On the ASA listserv last week, Randy Isaac posted a link to a video, and asked:
How would we apply the explanatory filter to this video? Can we determine by probabilities whether it was edited? Or designed?
You can read about the explanatory filter elsewhere if you must, but what I really want you to do is to simply watch the video with Randy's questions in mind, and see what you think. Then maybe leave a comment here.

7. Read Ken Miller on Expelled, and why he wasn't interviewed, in the Boston Globe.

8. Monkeys can control robotic arms with "just their thoughts." Whereas my non-robotic limbs are wired directly to my motor cortex, and I seem to have far less control of them than these monkeys do...

The brain of S.S. Korsakov (alt. Korsakoff), a dead Russian genius. From Vein and Maat-Schieman, Brain 131: 583-590, 2008.

Oh, and while we're on the subject of brains, you have to check out this post on brains of dead Russian geniuses. (Where are the brains of dead Russian morons?)

9. Ten optical illusions in two minutes. AWESOME video; don't miss it!