Wednesday, April 29, 2009

The Evolution of Protein Folding: Is a Crisis Brewing for Darwin?

Historically speaking, there is a distinction to bear in mind between puzzles that prove a challenge to a scientific theory and puzzles that turn into a crisis. The Michelson-Morley experiment in the late 19th century proved to be a crisis for classical physics. So did black-body radiation. The former led to Einstein's special theory of relativity. The latter to quantum mechanics. Both involved radically new ways of visualizing space and time that could not be avoided if --in the case of Einstein-- symmetry was to be reached between classical mechanics and Maxwell's electrodynamics, and--in the case of Planck-- sense was going to be made of all the observational data on radiation. On the other hand, up to the end of the 19th century, Newtonian physics had weathered many puzzles that required some refinement of the theory only.

Darwin's theory has also faced its share of puzzles (and continues to). Before the advent of genetics in the early 20th century, for example, natural selection was looking like something far worse than a puzzle for evolution. Then population genetics grew as a field and the work of specialists such as Simpson, Dobzhansky (to name just a few) established firmer grounds for natural selection.

Still, a crisis is what many skeptics of evolution thirst for, and as often happens what you'd like to see can blind you to what is actually there (or not there). Proponents of Intelligent Design think it's the complexity of the bacterial flagellum that cannot be explained in terms of genetic variation and natural selection.

I was struck by a comment made a while back related to proteins. It all started with Francis Beckwith's post at What's Wrong with the World on the incompatibility between Aquinas and Intelligent Design.

WWWTW blog is self-consciously modeled on Chesterton's classic essay collection of the same name (and in fact I have a first edition American, 1910, soon approaching it's 100th birthday and in very good condition). And while it is encouraging that Aquinas and Intelligent Design don't fit--it remains odd to me that the hostility many academics of Catholic, mainline protestant and Orthodox traditions have for evolution is subtler but not fundamentally different from that of, well, fundamentalists and the more overt intelligent design proponents. Which is to say: an always negative tendency to attack scientists for what they don't know yet. For all the adherence to Aquinas and his arguments from secondary causes, it seems many can't resist falling into the God of the Gaps reasoning implied by the natural theology of Protestant William Paley. (Whatever happened to checking in with Cardinal Newman?)

For example, apropos of a quip by Lydia McGrew dismissing the use of computer models for evolution ("Just amazing what you can do when "seeing" computer programs "evolve" rather than dealing with actual biological entities. If that counts as "scientists have shown" I have several bridges to sell them."), fellow What's Wrong With the World blogger (and, I'm green with envy to say, instrument-rated private pilot) Zippy followed up:
This is an important point. The computer models that computational biologists use bear (or at least bore, a few years back when I was studying this at the graduate level, and still bear every time I do the due diligence) very little resemblance to what is actually going on in physical reality. I've mentioned this before, but here it is again: as far as we know random polypeptide chains of any significant length don't fold into stable native states under physiological conditions at all, let alone fold into nontoxic stable native states, let alone fold into stable native states which perform a useful function which can provide fodder for natural selection, let alone do all that and result in wholly new kinds of proteins, cell types, tissues, organs, or species. And all-atom computer models of hundred-residue chains don't even exist: they are well beyond the compute power available to present day researchers. Computerized protein structure predictions are based on lookup-table statistical analysis of homologes (I know, I had to do some in order to pass a bioinformatics course), not on any kind of at all even remotely workable model of what is actually taking place at the molecular level.

The victory party is still very, very, very premature; but if the neo-Darwinists don't keep holding it, someone might get the idea that they've been doing nothing but blowing smoke for a century or two for reasons that don't have much to do with a dispassionate search for the truth. And we can't have that.

By this reasoning, evolution is apparently worse than an empty suit, prematurely being celebrated by scientists doing nothing. The assertion here seems to be that no actual progress is being made on what amounts to a major problem for evolutionary biology.

Is a crisis in the offing? As we'll see, the answer is no. But it is a challenge, and a fascinating one that, to this layman's eye, looks bound to lead to more fruitful discoveries.

So, let's start with the computer models. Mark Pallen, professor of Microbial Genetics at University of Birmingham, and author of the Rough Guide to Evolution, tells me, "Computer models are obviously simpler than reality and one could not establish from first principles by computer modeling the evolutionary pathways that led to the first proteins, nor model every possible structure in sequence space."

"But," he adds, "this is a bit like saying you can never understand the architecture of a church without an atomic resolution model of all the materials and components that make it up. Or that because we cannot model every atom in the atmosphere, we have no understanding of the weather and cannot make useful weather forecasts. While we may not be able to predict the folded structure of a protein from its sequence, let alone of every 100 amino acid protein in protein sequence space, that does not mean we cannot perform experiments or make observations that inform our understanding of early protein evolution."

According to Nick Matzke, a researcher at the Huelsenbeck Lab, Center for Evolutionary Genomics at U.C. Berkeley, "the processes that we think produce new genes/proteins etc. are not equivalent to random-assembly-all-at-once-from-scratch... We have duplication, modification, selection, rearrangement, etc. "

"Even the very first polypeptides were pretty certainly not assembled all-at-once-from-scratch from a pool of 20+ kinds of amino acids in even proportions, in D- and L-form, as creationists and various beknighted physicists blithely assume. Probably the first time a proto-tRNA grabbed an amino acid and made a short chain, the chain was composed of glycine and few common hydrophobic amino acids and was quite short. Cavalier-Smith (2001) suggests that the original function may have just been a hydrophobic tail for association with a membrane. All of the improbability statistics are irrelevant in this sort of scenario, chirality isn't an issue, etc. "

This is in line with the current research, for example, of Professor Andrei N. Lupas, director of the Department of Protein Evolution at the Max-Planck-Institute for Developmental Biology in Tübingen.

Accrording to Prof. Lupas, "The problem arises from the fact that random polypeptide chains indeed essentially do not fold (I would estimate the proportion to about 1:1020 for polypeptides in the range between 70 to 120 residues). Clearly abiotic systems cannot produce the starting material for a random exploration of folding space (never mind the problem of passing on the information on anything useful you encountered) and it beggars belief that biotic systems could emerge that produce 99.99999999999999999% trash for an initially barely selectable benefit. "

But this is hardly a reason to toss out the principles of evolutionary biology. According to Prof. Lupas: "The solution obviously is to propose that an initial RNA world used peptides for other purposes, in which folding was not an issue, but that it selected for peptides that could become structured upon encountering an RNA scaffold (there is ample evidence that there is a natural affinity between peptides and nucleic acids and that random peptides have a tendency to bind into the grooves, becoming structured through the exclusion of water). The issue then becomes to explain how a set of (non-folding) peptides could yield (folding) polypeptides under natural selection.

"In my department at the MPI in Tübingen, we explore the hypothesis that folded proteins indeed arose from this preselected pool of peptides, through amplification, fusion and recombination. By being written into one chain, these peptides preselected for the ability to form secondary structures would have found that in many cases they could now exclude water between each other, without the need for an RNA scaffold. Folding would thus be an emergent property resulting from the increased length and complexity of peptides. If this is true, then we think we should be able to reconstruct this vocabulary of peptides in the same way in which ancient languages such as indo-European have been reconstructed through the comparison of modern languages."

Two of Lupas' recent papers are here:
On the evolution of protein folds: are similar motifs in different protein folds the result of convergence, insertion, or relics of an ancient peptide world?
Lupas AN, Ponting CP, Russell RB.J Struct Biol. 2001 May-Jun;134(2-3):191-203.

More than the sum of their parts: on the evolution of proteins from peptides.
Söding J, Lupas AN. Bioessays. 2003 Sep;25(9):837-46.

Professor Lupas also contributed a chapter to Computational Structural Biology, published last September, which is devoted to the evolution of protein folds. Here's a snippet worth quoting at length from the end of the chapter:
Proteins may have originated by the repetition of short peptides, a process that efficiently yields fibrous proteins such as coiled coils and β-helices.39,40 Repetitive sequences appear to have a higher chance of folding and also more favorable structural properties than nonrepetitive sequences.41,42 The problem of passing on the sequence information, however, remains unsolved. Also, domains seen today do not have fibrous elements at their core; there is a discontinuity in fold complexity between fibers and all other folded domains and fibers are structural, not catalytic elements, whereas the primary role of proteins is catalysis.

We favor a scenario for the origin of proteins by fusion and recombination from an ancestral set of peptides, which emerged in the context of RNA-dependent replication and catalysis (the “RNA world”).15 These peptides, originally short chains of abiotic origin, would have been selected as co-factors of ribozymes, broadening their catalytic spectrum and improving their stability and folding efficiency. As the abiotic pool became depleted, ribozyme-based organisms developed an evolutionary incentive to ligate peptides catalytically, and later also to establish a primitive code so as to increase the yield of useful peptides. The need for improved specificity provided the evolutionary pressure for the emergence of peptides capable of assuming secondary structure on an RNA scaffold. The assembly of longer polypeptide chains from these pre-optimized peptides led to folding as an emergent property, when peptides found that they could now exclude water between themselves (“hydrophobic collapse”) in the absence of an RNA scaffold. The dominant role of recurrent supersecondary structures in the architecture of modern folds43 may be the result of this process.

Whatever the mechanism, it appears to have ceased a long time ago, since the basic complement of proteins in living beings has not been enriched by new folds for hundreds of millions of years and has probably been essentially stable since the time of the last common ancestor. Why is that? Did nature find most islands of stability available to the 20 natural alpha-amino acids in one burst around 3.8–3.5 billion years ago? Or is it that, once a set of folded and functional proteins was in place, no new exemplars could emerge across the complexity boundary imposed by the twin constraints of structure and function, without being eliminated immediately by established competitors? The issues resemble the questions surrounding animal bodyplans. These also emerged in a comparatively short time (the “Cambrian explosion”) and only a very limited number became established. Even though new opportunities arose periodically through large-scale extinction events, none led to the emergence of new body-plans; rather, the openings were filled by survivors with the same or similar body plans as the extinct species.
From the other side of the world, Ian Musgrave, professor at the University of Adelaide in Australia writes, "as others have already said, proteins probably didn't arise from random assembly of 100+ amino acids in one go in the first place. " But they didn't need to. He cites, among others, these two papers:

Keefe AD, Szostak JW. Functional proteins from a random-sequence library. Nature. 2001 Apr 5;410(6829):715-8. Link here.

J Mol Evol. 2003 Feb;56(2):162-8.Can an arbitrary sequence evolve towards acquiring a biological function? Hayashi Y, Sakata H, Makino Y, Urabe I, Yomo T. (Musgrave: "The answer is yes.")

Keefe and Szostak are optimistic about their progress:
Our isolation of new functional proteins shows that it should be possible to obtain an unbiased view of the inherent diversity of all possible protein structures, and to determine whether biological proteins represent only a small subset of this diversity. Comparing the sequences of our newly evolved ATP-binding proteins with biological ATP-binding proteins has not revealed any significant similarity; structural data will also be required to reveal whether these proteins, especially the Zn2+ metalloprotein, are similar to those of any biological proteins.

In conclusion, we suggest that functional proteins are sufficiently common in protein sequence space (roughly 1 in 1011 that they may be discovered by entirely stochastic means, such as presumably operated when proteins were first used by living organisms. However, this frequency is still low enough to emphasize the magnitude of the problem faced by those attempting de novo protein design.

According to Musgrave, "a modest fraction [of random polypeptides] (somewhere between 1 in 108 and 1 in 1012) have some sort of selectable function."

These are just a few scientists with whom I raised the question. There are many more making the evolution of protein folding the center of their attention. Far from being a black box embarrassment to evolutionary biology, the evolution of protein folding turns out to be a challenge worthwhile to quite a few specialists.

So where does that leave the assertion of crisis at the state of protein evolution? To me it seems no different than the discredited irreducible complexity arguments of the ID movement. Because protein folding cannot be fully explained now by the principles of evolutionary biology (i.e, descent with modification by the mechanisms of genetic variation and natural selection), the thinking goes, it must therefore call into question the entire theory.

As I mentioned earlier, I understand why this kind of argument is irresistible to fundamentalist evangelicals. But it still surprises me that academics with a clear tradition of appreciation for Aquinas and secondary causes flirt with it.

Tuesday, April 28, 2009

A good post by Massimo Pigliucci:
Scott — who is an atheist — has repeatedly said that one cannot claim that science requires atheism because atheism is a philosophical position, not a scientific one. She leverages the standard distinction between philosophical and methodological naturalism: if you are a scientist you have to be a methodological naturalist (i.e., assume for operative purposes that nature and natural laws are all that there is); but this doesn’t commit you to the stronger position of philosophical naturalism (i.e., to the claim that there really isn’t anything outside of nature and its laws). Years ago, when I first met Genie Scott, I had a Dawkins-like problem with this. I saw the distinction as sophistic hair splitting, and told her so (she was my guest for one of the annual Darwin Day events at the University of Tennessee). Then I started taking philosophy courses, understood what she was saying, and found it irrefutable. I sent her an email apologizing for my earlier obtusity.

That said, both Genie and I do recognize that science is one of the strongest arguments for philosophical naturalism, and I suspect that in her case, as in mine, a pretty big reason for why we are atheists is because of our understanding of science. Still, the philosophical/methodological distinction is both philosophically valid and pragmatically useful, since it doesn’t serve the purposes of either science or education to fuel an antagonism between a small minority of atheistic scientists and 90% of the world's population (those taxpayers, on whose good will the existence of science and the stipends of most of said scientists depend).

Monday, April 27, 2009

I've got bad news for Christopher Hitchens
It's long been known by booksellers and publishers that the New York Times weekly 'list' has never really been a very accurate tally of what indeed is selling in the U.S. I recommend every once in a while taking a look at USA Today's more accurate listing. It's not encouraging.

For the last week on record (4/19/2009), for example, we can note that there is not one science book on the list. Out of 150. On the other hand, it looks like books for Young Readers are pretty much dominating sales everywhere, so we know the younger generation likes to read. (This would be even more encouraging if there were fewer vampire novels--but on the other hand, who am I to complain? I started out sucking down every Star Trek adaptation in print in the 1970s.)

That said, I think the world can do without the cynical new craze of Jane Austen novels being re-fitted to accommodate zombies. (I did enjoy the Zombie Survival Guide. That kind of parody I think is completely legit.)

Christopher Hitchens may want to rethink boasting about his place on the current New York Times bestseller list. On USA Today, God is Not Great doesn't even rate.

Which may be a sign that even 'new' atheism is getting old.

Friday, April 24, 2009

Hitch:

On the question of Turkey's accession, I used to be able to make either case. Admitting the Turks could lead to the modernization of the country, whereas exclusion could breed resentment and instability and even a renewal of pseudo-Ataturkist military rule. On the other hand, admission would put the frontiers of Europe up against Iran and Iraq and the volatile Caucasus, so that instead of being a "bridge" between East and West (to use the unvarying cliché), Turkey would become a tunnel.

The Strasbourg crisis clarifies the entire picture and should make us grateful to have been warned in such a timely fashion. Turkey wants all the privileges of NATO and EU membership but also wishes to continue occupying Cyprus, denying Kurdish rights, and lying about the Armenian genocide. On top of this, it now desires to act as a proxy for Islamization and dares to waste the time of a defensive alliance in trying to censor the press of another member state! Kouchner was quite right to speak out as he did, and the Turkish authorities will now be able to blame the failure of their membership scheme not on the unsleeping plots of their enemies, but on the belated awakening of their former friends.

Complete article.

Tuesday, April 21, 2009

Brendan O'Neill is ready to stick a spoon down his throat over Susan Boyle.
Of course, everyone loves a good show tune. And everyone loves an underdog. But Boylemania has become about so much more than an underdog singing a good show tune. Rather, Ms Boyle has been turned into an SIE (Shared International Experience) whose angelic voice and against-the-odds international fame apparently reveal that feminism is alive and well, beauty is overrated, the recession ain’t that bad, cynicism is dying, and God still loves us. You think I’m exaggerating? Consider the 10 craziest things that have been said over this past week-and-a-half of global Boylebarminess.

Monday, April 20, 2009

The Drowned Giant
British writer J.G. Ballard has passed away at age 78. Mostly known for his novels Crash and Empire of the Sun, both made into mediocre Hollywood films, he was to my mind a better short story writer.

His collection The Terminal Beach includes two of my favorite short stories, The Drowned Giant and The Lost Leonardo. The former was about the reaction of a seaport city to the appearance of a dead giant, washed up on the beach one morning.

Friday, April 17, 2009

It being National Poetry Month, there are a couple of things you shouldn't miss:

One is that Siris, in addition to being a philosopher for the working day, is an excellent poet. As demonstrated by samples here and here. And that's just the tip of the iceberg. He posts verse often, so if you haven't subscribed to his blog, add him to your blogroll.

The other is this site, which I understand from the cracker-jack producers behind it, is still in development phase but promises to build a fairly impressive media library within the next few years.

Tuesday, April 14, 2009

My short story, A Circle of Cypresses, has just been published in the new issue of Dappled Things.

Friday, April 10, 2009


Good Friday
We're so used to just repeating texts from the Gospels this time every year, we can forget how much more startling art can be. Imagine what a satellite might have snapped about 1,979 years ago. I've always found this tech art (by the Glue Society), haunting.

Thursday, April 09, 2009

Stanley Jaki, physicist, priest, author and teacher: 1924 - 2009
One of my favorite historians of science, Fr. Jaki, has passed away, at age 84. After lecturing last week in Rome he went to Spain for further meetings and succumbed to a heart attack.

Jaki was a Gifford Lecturer at the University of Edinburgh, 1974-75 and 1975-76, the prestigious, century-old academic appointment in the disciplines of philosophy and theology, which has included as past lecturers Hannah Arendt, John Dewey, William James and Albert Schweitzer.

He was deeply committed to the conjunction between faith and reason, arguing that the flourishing of science in Europe was intrinsically related to the Christian understanding of creation and the Incarnation.

I have about 20 of his published books, and I reread chunks of them (and highlight them to death) whenever I can. I had the good fortune to hear him lecture at MIT and elsewhere in Cambridge about 15 years ago. He had a marvelous (sometimes biting) sense of humor, and even in the course of just a few lectures I could tell he was not the kind of man to suffer fools gladly.

His books are invaluable resources, just for the reference material and bibliographies alone. And no one seriously studying the rise of science in the West can ignore his work, even if (as I would say) the 'mainstream' of history of science scholars does not agree with his views.

More here.

Reality Check
I want to follow up on Siris' post about the problem with blogging, especially the danger of blogging too much about just one subject (i.e., politics, religion, one branch of science). I think his points are well taken. It goes without saying, of course, that losing a sense of perspective can include losing your sense of humor.

I realized this when one of my readers, pretty new to the blogging world, sampled the thread below about Brooks' and the End of Philosophy. Here's what he wrote:

I read through two threads today until my brain was full: Siris > PZ (excellent) > David Brooks aka "The Missing Link". Also read enough of Larry Moran's "Sandwalk" to make me want to take a crap. Evidently, if you disagree with a Moran, you're an idiot.... [But, Stephen Gould wrote ... and you're clearly not a scientist ... evolution is a fact ...idiot...] (Pardon me while I flush!)

I did however enjoy some of the banter in the comments: facts vs. theory etc. - especially those posted by Bryan Goodrich. Although I can't claim to understand all he's saying (regarding statistics), I think he makes some good arguments and "... to avoid looking stupid in the future", I'd much rather listen to him than Moran. Now, that's a fact.

As for the PZ comments, I particularly enjoyed Michael X. (comment#14 ) replacing "awe, transcendence [and] joy [etc] with "bacon, bacon, and bacon." Awesome! Now I'm hungry! Thanks a lot Michael! As much as I'm enjoying the rest of the thread turn into a hockey fight over the meaning of Star Trek episodes, all this talk of food is making me hungry. :)

I see what Siris meant about the risks of apologetics and blogging. But, like at any good hockey game, every now and then it feels good to lean over the boards and yell "F*%$ you!" at the opposition.

So, without further ado, as Socrates might if he were alive today, I'm going to "look" through my refrigerator, "find" a "just" steak, and "apply" it to my grill. David Brooks' assertions not withstanding.
Yes, there is a real world out there, indepedent of the blogosphere. And that's a happy thought for a Holy Thursday.

Wednesday, April 08, 2009

Oh, boy. I'm with Brandon on this one. El PZoid hits the nail on the head:

Feelings of transcendence exist, and no one denies it. Those feelings seem to be rather easily triggered by a whole host of phenomena, from a focal seizure to a morning in ritual to a beautiful sunset. We don't neglect the phenomenon, but it does seem to be a poor mechanism for achieving an understanding of physics. There is more to the universe than morality and feelings, you see, and what I would argue is not that emotions like those listed don't exist or are unimportant, but that they have a place, and it is not as sufficient evidence for how the world works.

As for this strange idea that the evolutionary approach says nothing about individual responsibility…I have no idea what the man is talking about, other than that he is blithering ignorantly. I strongly urge that Mr Brooks try using his cerebral cortex in addition to his brain stem and hypothalamus when writing — that's another of those areas where emotional prejudices need to be supplemented with reason and knowledge.

Tip of the hat to Deuce for alerting me to Brooks' piece.

Bart Ehrman's Book, Interrupted
Ben Witherington, in the first of a two-part review of Ehrman's new book:
Now it is always a danger to over generalize when we are dealing with as important a matter as the ‘truth about the Bible’. And frankly it is simply untrue to say that most scholars or the majority of Bible scholars or the majority of serious critical scholars would agree with Bart Ehrman in his conclusions about this or that NT matter. NT scholarship is a many splintered thing, and Ehrman’s position certainly does not represent a majority view, or the critical consensus about such matters. At best, one has to say yes and no repeatedly to what Bart takes as the critical consensus about such matters. Bart Ehrman, like the more radical members of the Jesus Seminar (e.g. Robert Funk cf. Robert Price) represents a minority position which has indeed been very vocal in proselytizing for their point of view. So this book should have come with a caveat emptor--- “Buyer Beware: Hyperbolic claims about what most or the majority of critical scholars of the NT think will be frequent in this tome”. The appeal to authority or expertise in any case does not really settle much. The issue is—what is the evidence and why should we draw this or that conclusion? The other issue is--- why mislead the general public about what “the majority of serious critical scholars” have been saying? Perhaps an end run has been done from the outset--- you define a small circle of scholars as the serious ones, the critical ones, the real scholarly thinkers, the real historians, and then having defined your own group narrowly enough, you then say—“the majority of such people think…” Evangelicals are sometimes just as guilty of this ploy as others, but in any case, it does not help when one misrepresents the actual state of play of things among scholars to the general public.

Bart reminds us early on that the method of studying the Bible taught in most mainline seminaries is “the historical critical method”. It is also, in fact perhaps the main method of teaching the Bible in evangelical seminaries today as well. And two of the major things one is taught, quite correctly in the study of this method are: 1) ancient historical texts must be studied in their original historical contexts to be properly understood; and 2) modern post-Enlightenment historiography is at odds with the historiography of most ancients, particularly when it comes to the issue of God’s involvement in human history.

There is a further corollary—in order to understand the Gospels or Acts, or Paul’s letters, or Revelation, one needs to understand the features and characteristics of such ancient literature—in short their respective genres. The Gospels are written like ancient biographies, not modern ones, or in the case of Luke-Acts like an ancient work of Hellenistic (and Septuagintal) historiography. Unless one knows the conventions and limitations that apply to such literature, one is in no position at all to evaluate whether there are “inconsistencies” “errors” or other problematic features of such literature. Error can only be assessed on the basis of what an author is attempting to do and what literary conventions he is following. Let us take an example Bart uses from p. 7 of his book—the fact that in John the cleansing of the temple comes early in the Gospel account, whereas in the Synoptics it is found in the Passion narrative. He is right of course that some modern conservative Christians have attempted to reconcile these differences by suggesting Jesus did the deed twice--- once at the beginning and once at the end of the ministry. The problem is, that this conclusion is just as anachronistic (and genre ignoring) as the conclusion that the Gospels contradict each other on this point. What do I mean?

If you actually bother to read ancient biographies (see e.g. Tacitus’s Life of Agricola, or Plutarch’s famous parallel lives) you will discover that the ancients were not pedants when it comes to the issue of strict chronology as we are today. The ancient biographical or historiographical work operated with the freedom to arrange there material in several different ways, including topically, geographically, chronologically, to mention but three. Yes they had a secondary interest in chronology in broad strokes, but only a secondary interest in that.
If one studies the Fourth Gospel in detail and closely in the Greek, comparing it to other ancient biographies what one learns is that it is a highly schematized and edited product, and the sign narratives are arranged theologically not primarily chronologically. And whilst this might cause a modern person some consternation, it is not a reason to say that John contradicts the Synoptics on this Temple cleansing matter. The Fourth Gospel begins by showing that Jesus replaces the institutions of Judaism with himself—a theological message (he is the Passover lamb, he is the Temple where God’s presence dwells etc.). The Synoptic writers are likely presenting a more chronologically apt picture of when this event actually happened. But strict chronology was not the major purpose of the Fourth Evangelist, we should not fault him for not giving us information we might want to have, or for focusing on the theological import of the event, rather than its timing. Such was the freedom, within limits, of ancient biographies and histories. I must disagree with the conclusion then when Bart says “Historically speaking, then, the accounts are not reconcilable.” (p. 7). False. This is only so if one insists on a flat modern anachronistic reading of the text which pays no attention to what the authors are attempting.
Anachronistic reading is Ehrman's specialty, and it sure seems to sell.

Saturday, April 04, 2009

Siris has a very thoughtful--and I think quite accurate--post about the risks of apologetics and blogging.

Thursday, April 02, 2009

Critical Thinking in the Classroom *
I recently got acquainted with a young instructor who teaches science to seventh-graders at an evangelical school. He's a graduate of Wheaton College and a recent convert to Catholicism. This affords him an interesting perspective on how evangelicals handle science in the classroom, in particular how the whole 'teach the controversy' approach trumpeted by Bible science types plays out in practice.

The text the school in question ordered for this young teacher's class is Exploring Creation with General Science. The author, Jay L. Wile, is a young earth Biblical literalist with a Ph.D. in nuclear chemistry. In terms of suggested experiments for kids, my teacher friend tells me that generally the book has a lot to recommend it: great ideas for simple experiments and so forth, and apparently it's a favorite with homeschoolers. So far, so good.

But...inevitably the age of the earth has to be discussed. That is,
catastrophism: the view of literalists that the earth is only a few thousand years old and much of what geologists have uncovered suggesting otherwise can be explained as the result of a series of cataclysmic events that happened over a very short time, to fit with a literal interpretation of the Book of Genesis. Modern geologists take a uniformitarian view of the earth, and see the layer upon layer of different strata in the Earth's mantle as evidence of the planet's changes being gradual over billions of years.

According to my teacher friend, "Wile pushes catastrophism while 'teaching the controversy.'" He writes, "I talked to the principal about my annoyance with the whole thing and he, being the cool guy that he is, is fine with my particular take on it (Old Earth/Evolution), but still thinks the controversy ought to be taught.

"So I've been doing research on uniformitarianism [and] catastrophism and realizing that the idea of putting these two theories in front of seventh graders and,
A. expecting them to understand what is going on, much less B. make a real judgment between them, is just beyond absurd.

"Until seventh graders have a grounding of basic knowledge about standard geology, there's no point in asking them to determine anything based on classroom presentations of 'evidence' culled from one simplistic textbook and a teacher who knows little about geology."

[I'm trying to imagine a similar seventh grade class where the textbook gives an overview of
A. The Copenhagen Interpretation of Quantum Mechanics and B. Bohm's Non-local Hidden Variable Model --and expect seventh graders to be able to 'weigh the evidence' and make a judgment about it. Only Earth Science and evolution seem to bother literalists. But I digress.]

My correspondent adds, "As soon as I start looking at the various arguments, I realize that creation science, flood geology, Intelligent Design - all of that - makes
no real attempt to engage with mainstream science. But, if they're doing science at all, they need to be able to beat the scientists at their own game or there's no point. So in other words, they're not really arguing with scientists. They're arguing with other Christians and using 'science' to bolster their argument: that the Bible requires a particular theology and hermeneutic. Which just means that Christians on the other side, if we want this debate to not be completely won by the loudmouths, have to come up with a compelling hermeneutic and theology."

Not surprisingly, the problem makes his approach to class challenging.

"We're making a timeline of the ages of the earth in class. I've been looking for a comparable catastrophist timeline explaining the same evidence (as uniformitarianism) and ... not finding it."

There are no shortage of Biblical videos to view for the kids as well. "The worst," he writes, "is watching ... and realizing that the guy could be arguing that 'Hitler was bad' and the non-sequiturs and equivocations would make you begin to question his case.

"The biggest issue here is how Wile sets up his science book - and, by the way, his attitude strikes me as completely ingenuous the entire time - so as to make it seem like he is presenting a fair case to be judged on the evidence."

For example, Wile does a unit in which he attempts to establish, scientifically, the material historical integrity of part of the Bible.

"[He] assumes that that same integrity applies to all the different books and literature in the Bible," writes the instructor, "and thus treats Genesis 1-11 as a legitimate historical source with evidence to be weighed in the balance together with radiometric dating, stratigraphy, index fossils, contintental drift, etc. Then he presents uniformitarianism and catastrophism, followed by a list of potential 'problems' with either side.

"At the end of which he concludes,
'both uniformitarianism and catastrophism have difficulties. Regardless of which view you take, you will run into what seem to be unsolvable problems' (Wile 209, emphasis author's)."

"If I didn't tend to trust these people since I grew up among them and know their basic sincerity, I would swear they were being actively disingenuous."

Not surprisingly, evolution is considered a weakness of the uniformitarian view:
"So, which is it? Is there independent evidence for the process of evolution or not? Well, the short answer to this question is 'no.' You will learn more about evolution when you take biology. For right now, however, let's look at what should be the main line of data that relates to evolution." (Wile p. 210, emphasis author's).

I did a little googling on the texbook author, Jay Wile, and it seems, like so many proponents of Biblical literalism, he peddles bad faith arguments against evolution. This, for example, comes from a sample lecture promo.

In this seminar, Dr. Jay L. Wile, a nuclear chemist, explores the complicated Creation Versus Evolution debate. He discusses Christian attempts to make the Genesis account compatible with the theory of evolution and shows how these attempts fail. The conclusion is that a literal interpretation of Genesis is completely incompatible with the theory of evolution. He then proceeds to show that this is not at all a problem for someone who is both a Christian and a scientist. He presents strong scientific evidence that supports a literal interpretation of Genesis and equally strong scientific evidence that discounts the theory of evolution. He discusses evolutionists' attempts to explain away this data and how such attempts fail. Perhaps the most intriguing part of this seminar comes when Dr. Wile details some of the fantastic life forms on this planet whose existence can never be explained using the theory of evolution. Regardless of how science-oriented you are, this seminar will strengthen your faith and give you an even deeper appreciation for the marvelous Creation that God has given us.

Those evil evolutionists... again. What's funny is this lecture is immediately preceded by one dedicated to 'Critical thinking'.

One of the biggest failures of our public and private school systems is that they do not teach students how to think critically. In this seminar, Dr. Wile gives you specific suggestions as to how you can teach your child to think critically, regardless of the subject matter that the student is learning. You will learn how to help your student evaluate statements, look for hidden assumptions, find political/social agendas, and discover faulty logic. Although Dr. Wile's area of interest is science, he will show you how critical thinking applies to all academic areas, as well as all facets of your life.

This narrow, defensive approach to science may seem fine at the grade school level and even high school level for home schoolers. But what happens when the kids who show a real aptitude for science and interest in pursuing a career... get to college-- and they have to confront not just professors with working labs but fellow students-- and the weak foundations of their Bible 'science' simply don't stand up to scrutiny? How many of these kids will then turn on their faith and consider it all a pack of lies (as Einstein did and others) because their particular branch of Christianity has a deeply faulty attitude to the natural order?

* updated to reflect a couple of corrections.

Wednesday, April 01, 2009

Michael Behe has been awarded the Nobel Prize for Biochemistry.