31 March 2008

Probability, miracles, and baseball

It's Opening Day, and it mustn't pass without mention here at QoD, especially since probability, randomness and the supernatural are such central topics around here.
Manny connects, game 2 in Japan. Image from Boston Globe online.

I've already confessed that Stephen Jay Gould is one of my favorite authors, and some of his essays I mark for repeat visits. ("The Most Unkindest Cut of All", in Dinosaur in a Haystack, is worth a trip to the library right now.) Gould was an avid baseball fan, and though he was happy to be a minion of the Evil Empire, his reflections on the National Pastime were always memorable.

Well, Gould's favorite ballplayer was Joe DiMaggio, who holds one of the most extraordinary records in all of sports. Gould wrote about this record in a 1988 book review, reprinted as an essay in Bully for Brontosaurus.
In 1941, as I gestated in my mother's womb, Joe DiMaggio got at least one hit in each of fifty-six successive games. Most records are only incrementally superior to runners-up; Roger Maris hit sixty-one homers in 1961, but Babe Ruth hit sixty in 1927 and fifty-nine in 1921, while Hank Greenberg (1938) and Jimmy Foxx (1932) both hit fifty-eight. But DiMaggio's fifty-six-game hitting streak is ridiculously and almost unreachably far from all challengers (Wee Willie Keeler and Peter Rose, both with forty-four, come second). Among sabremetricians — a contentious lot not known for agreement about anything — we find virtual consensus that DiMaggio's fifty-six–game hitting streak is the greatest accomplishment in the history of baseball, if not all modern sport.
So how should we understand this almost unbelievable feat? Gould claims that the streak is "both the greatest factual achievement in the history of baseball and a principal icon of American mythology." A great achievement because, unlike hitting a lot of home runs, or even hitting for a high average, the streak requires "unfailing consistency every day":
...a streak must be absolutely exceptionless; you are not allowed a single day of subpar play, or even bad luck. You bat only four or five times in an average game. Sometimes two or three of these efforts yield walks, and you get only one or two shots at a hit. Moreover, as tension mounts and notice increases, your life becomes unbearable. Reporters dog your every step; fans are even more intrusive than usual (one stole DiMaggio's favorite bat right in the middle of his streak). You cannot make a single mistake.
Okay, so that's why it's a great achievement; but what about the whole 'mythology' thing? Gould goes on to demonstrate the silliness of believing that DiMaggio's achievement was "better" than other (much shorter) streaks, that DiMaggio's streak was longer because of his greatness. Gould claims that we make this mistake because we just aren't wired to understand randomness and 'clumping' in random patterns.
We believe that long streaks and slumps must have direct causes internal to the sequence itself, and we have no feel for the frequency and length of sequences in random data. Thus, while we understand that DiMaggio's hitting streak was the longest ever, we don't appreciate its truly special character because we view all the others as equally patterned by cause, only a little shorter. We distinguish DiMaggio's feat merely by quantity along a continuum of courage; we should, instead, view his fifty-six-game hitting streak as a unique assault upon the otherwise unblemished record of Dame Probability.
Now, it seems to me that Gould is saying that DiMaggio's streak was well-nigh miraculous, meaning that it is so improbable that it really shouldn't have happened. Consider his (now bittersweet) coda:
DiMaggio's hitting streak is the finest of legitimate legends because it embodies the essence of the battle that truly defines our lives. DiMaggio activated the greatest and most unattainable dream of all humanity, the hope and chimera of all sages and shamans: he cheated death, at least for a while.
That's romantic stuff. And just as we're wiping the tears from our eyes, a couple of smart-ass mathematicians walk up and say, "Pull it together, dreamboat."

Yesterday's New York Times, presumably in celebration of Opening Day in the doomed House That Ruth Built, included a fascinating reexamination of the streak, in true Gouldian fashion. Meaning that the authors ran the kind of thought experiment that Gould made famous – they "replayed the tape," not of evolution but of baseball, and examined the likely outcomes. They re-created virtual baseball worlds, using the actual statistics from the history of baseball. Specifically, they created "parallel baseball universes" – 10,000 of them – and looked to see how improbable a super-streak really is.

And the answer is: not very improbable at all. Here's their punch line:

More than half the time, or in 5,295 baseball universes, the record for the longest hitting streak exceeded 53 games. Two-thirds of the time, the best streak was between 50 and 64 games.

In other words, streaks of 56 games or longer are not at all an unusual occurrence. Forty-two percent of the simulated baseball histories have a streak of DiMaggio’s length or longer. You shouldn’t be too surprised that someone, at some time in the history of the game, accomplished what DiMaggio did.

If you find this outcome disappointing, or if you feel I've robbed baseball of one of its supernatural episodes, take heart: the authors did uncover some eerie facts. First, 1941 was an exceedingly unlikely year for such a streak to occur. The vast majority of virtual streaks occurred in the decades before 1940. And there's this:

And Joe DiMaggio is nowhere near the likeliest player to hold the record for longest hitting streak in baseball history. He is No. 56 on the list. (Fifty-six? Cue “The Twilight Zone” music.)
Now, do you suppose the Discovery Institute fellows have read any of this stuff? For their sakes, I hope they like baseball. Their team, unlike their challenge to evolutionary theory, has a reasonable likelihood of success.

28 March 2008

Weekly sampler 12

Shall we play a game? Recall Hugh Ross' fictional tale about the "team of physicists" that remade molecular genetics. Ross claimed, falsely, that:
They noticed that the quantity of "junk" in a species' genome was proportional to that species' degree of advancement.
The biological truth is the opposite: amount of DNA, "junk" or otherwise, is so uncorrelated with other aspects of biology that the situation was termed a paradox when it was first uncovered. Well...let's see the paradox in living color. In the next few Weekly samplers, I'll present you with some organisms (all animals) and we'll see how well you can guess their relative amounts of DNA (per genome) based on their "degree of advancement." Good luck! (Hint: use a quarter; it's easier to catch, and easier to find on the floor if you drop it.)

Which organism has the larger genome?

This one? Or this one?

Answers are here. Explanation can be found on the superb blog of one of the world's leading experts on genome size.

1. This story is 6 years old, but I never heard it till this week. A 52-year-old woman gets DNA testing to determine whether she can serve as an organ donor for her son. The tests reveal that she is apparently not the mother of two of her children. But...she is the mother of all of her children. How can this be?

She's a tetragametic chimera, meaning simply that her body is composed of cells descended from two genetically distinct embryos which evidently fused very early in development. Her ovaries are descended from one of those embryos, but her blood descends from the other. The result: she conceived children with gametes derived from one embryo, but her blood (which was used for the genetic tests) comes from the genetically-distinct other. Each of her cells has just one "parent", but as a whole she is derived from two distinct embryos, each of which arose from two distinct sperm/egg pairs; thus she, as a whole, is derived from four gametes instead of the typical two. Wild! And lots of fun for certain friends of mine who (like me) enjoy reflecting on human personhood and personal identity.

2. The newest issue of The Economist has an interesting piece on a large new European scientific collaboration.
“Explaining Religion”, as the project is known, is the largest-ever scientific study of the subject. It began last September, will run for three years, and involves scholars from 14 universities and a range of disciplines from psychology to economics. And it is merely the latest manifestation of a growing tendency for science to poke its nose into the God business.
Bring it on!

3. This View of Life is a nice-looking site that aims to be "a beginner's guide to a science-based understanding of evolution." I'd love to hear some feedback from anyone who's checked it out. (Via the ASA listserv.)

4. Read Ryan Gregory on the much-abused concept of Just-So Stories.

5. Earlier this week, I heard an interesting story on MarketPlace about "video games that are good for you." I think I'll ditch Text Twist and try this instead. The games "reduce stress and boost self-confidence." Do they have any that add time to the day?

6. At the Howard Hughes Medical Institute (HHMI), a site called BioInteractive is crawling with "free resources for science teachers & students." Lectures, animations, "virtual labs." It's a mixed bag, but very much worth a stroll. (Via Panda's Thumb.)

In high praise of Howard Van Till

Howard Van Till is one of my heroes. It's been a month and a half since his address to the Grand Dialogue, and I still think about it, even though the ideas were all familiar to me. I think this is due partly to the fact that the excellent talk displayed Howard's disarming warmth and generosity, and partly to the fact that he was already one of my heroes. Here I'll discuss some of the main points of the talk, and in the process I hope you'll discover why I hold Howard Van Till in such high esteem.

Howard is professor emeritus of physics and astronomy at Calvin College, where I teach and work. The publication of his 1986 book The Fourth Day – and the ensuing controversy at the college and especially in the Christian Reformed Church (CRC) – had an enormous impact on both. Some commentators suggest that the disputes over evolution that were spawned by the book are largely responsible for the existence of an entire denomination, the United Reformed Church, which represents one of the major secessions from the CRC in the last two decades of the 20th century. The book actually did not tackle biological evolution so much as it described cosmic evolution, the ancient universe, and the tragedy of "scientific creationism." It contains immense wisdom on the nature of science, and many of my colleagues still give it pride of place on their bookshelves.

The controversy exacted a toll, though, and I know just enough of the story to know that it is a sordid and disgraceful tale. I suspect that Howard is hundreds of times more gracious than I would be. And some of his recent public remarks give me the impression that the scandalous (if not blasphemous) behavior of our community led Howard to move away from traditional Reformed Christianity. Howard's theological pilgrimage is not my subject here, but this aspect of Howard's journey is something of a backdrop for my own life as a Reformed Christian scientist, if only because I couldn't do what I do at Calvin if it weren't for Howard and his contemporaries.

Howard's talk was entitled "IS THE COSMOS ALL THERE IS? The quest for answers to big cosmological questions." There are plans to post video at the Grand Dialogue site, but in the meantime you can download the extensive outline that Howard provided from my personal website.

Here are Howard's main questions, with comments that don't already appear on the outline, and then some comments on the question & answer period that followed the lecture.

1. Why is there something rather than nothing?

Howard says this is a "hard question," and I guess we have to agree with him there. This was one of my favorite sections of the lecture, so here it is approximately verbatim, in quasi-dramatic form.

Religion. Because God made something.
Howard. Sorry, that's the answer to a different question. You still have to explain why there's a god vs. no god.
Religion. But it's impossible for God not to exist. He necessarily exists.
Howard. Sorry, that's just too easy. Not all assertions are true, even if offered by brilliant philosophers or theologians.
(Steve. Touché.)
P.W. Atkins & Co. It just happened. From nothing.
Howard. Sorry, that doesn't work either.
I'll just interject here that one reason I look up to Howard Van Till is that he seems to share my discomfort with being identified with a "side."
Howard. What about: "we don't actually know." What we have here is a profound mystery that should inspire profound awe and humility.
At that point, Howard referred to a folk singer named Iris DeMent, and quoted this lyric:
Everybody's wonderin' what and where they they all came from
everybody's worryin' 'bout where they're gonna go
when the whole thing's done
but no one knows for certain
and so it's all the same to me
I think I'll just let the mystery be
The song is "Let the Mystery Be" from the Infamous Angel album.

2. What is the universe like?

Howard identified this as an "easier" question, but he tackled one not-so-easy question when addressing the nature of the universe.

As you can read on the outline, Howard described the universe as "big and old, nearly empty and mostly cold," but emphasized the fact that the universe has "a formational history that is readable by natural sciences," including a formational history of life on earth. Then he outlined what he calls the "Right Stuff Universe Principle" (RSUP), which posits that the universe ("amazingly") has the Right Stuff (resources, potentialities, and capabilities) to actualize everything we see, naturally. (Call it "fine tuning" if you want; same thing as near as I can tell.)

As you might guess, 'naturally' means 'without the need for supernatural filling-in', and 'supernatural action' means specifically coercive divine action; I learned that this latter phrase is the language of process theology. Howard's summary: "The principle is a statement about the adequacy of natural causes to accomplish all the formational histories in question."

If you've read Howard on "robust formational economy" then much of the preceding should sound pretty familiar. But then Howard addressed this question, which I find tiresomely familiar: how did science come to adopt the assumption of the "adequacy of natural causes to accomplish all the formational histories in question"? Quoting Howard:
Some religious critics object to science unfairly excluding supernatural causation. Sorry…that’s a serious and mischievous misrepresentation of the history of science’s consideration of assumptions. [...] The “hybrid” approaches were discontinued because they were inadequate to explain formational histories. The “right stuff” principle was adopted because it worked.
The ellipses indicate parts I didn't write down, but I think it's clear what Howard is getting at. And I think he's completely right. Can you see why this man is one of my role models? The RSUP, in Howard's eyes, is more than just "fine tuning," more than just "getting a bunch of numbers right." It is a truly astounding fact of the natural world. And it raises an obvious and difficult question.

3. How can something as remarkable as the RSUP be true?

Howard proposed several possible answers, found on the outline, including three religious answers worth expanding here (roughly quoting Howard in all cases):

  • In the spirit of St. Augustine, assert that the cosmos is a creation, a manifestation of the Creator's creativity and generosity. God was both able and willing to give it that rich a being. Howard: this is the solution I used to recommend, and still recommend to those embracing “traditional Christian theism.”
  • In the spirit of process theology, postulate that the very natures of God, the world and the God/world relationship are such that supernatural intervention is excluded and so the RSUP has to be true.
  • In the spirit of the ID movement, cancel the question. Deny that the universe has the Right Stuff.
I'm waiting for someone to explain process theology to me. I did buy a brand new book at the conference, which contains lots of process theology (or so I'm told). I'm interested, but my commitment to "traditional Christian theism" is non-negotiable, so I guess I'll just browse.

Howard dismissed the "Cosmic Casino Hypothesis" (the RSUP is the result of dumb luck) as "not very helpful" and he seemed cool to the multiverse. I suspect he favors this last option, quoting as best I can:
And then there's agnosticism, or humility. We'll just say that we don’t really know. Let the mystery be.

4. Does the universe need a creator, and if so what does a creator do?

In this part of the talk, the main idea I found notable was the question of whether there has always been a universe. If I got Howard right here, he said:
I was taught that the answer is clearly “no.” But I’m inclined to disagree now.
I'm not sure what he meant on that one.

5. How would anyone know what a creator is like?

Howard introduced this final section by noting that this question was likely to be the most "disturbing and thought-provoking" of the lecture, stating with disarming good humor but unapologetic bluntness that "I want you to go home with new questions." His focus was on scientific explanations for religious belief, and the outline provides significant detail.

And it was interesting, and it was thought-provoking, but it was hardly disturbing to me, probably because I don't understand why explaining something – whether it's religious belief or photosynthesis or genetic recombination or zits – reduces its religious significance, its majesty, or even its mystery. I've heard about Pascal Boyer's work, and Justin Barrett's, and it's cool stuff, and I just don't get all freaked out about it. Explanation is no alternative to belief.

Howard emphasized the idea (after Justin Barrett) that belief in the supernatural could have emerged through the action of our so-called hyperactive agency detection device (HADD), which is basically the high-sensitivity aspect of our consciousness that jumps at the sound of a twig snapping in the forest. After exploring these interesting ideas, Howard concluded that "having religious beliefs is as natural as natural can be." Then he closed with comments that I jotted down as follows:
But then…how can this brain be trusted to give us true answers [to the big questions above]? One suggestion that is worth testing: perhaps we should deal with these intuitive beliefs the same way we would deal with a ‘snap’ sound in the jungle. We should begin with our intuition, but then turn the question over to our slower, more rational evaluation and see if it holds up. (I place a very high value on rational, as many are quick to point out...) Run the belief through some basic tests, and dare to honor the score. Don’t believe something because it's “emotionally reassuring” or because “tribal orthodoxy” holds it to be true.
"Dare to honor the score." That's a dramatic challenge, and I think Christians should be unafraid to accept it. We have nothing to fear from a sober examination of God's world.

Aftermath and concluding comments

After the lecture, there were responses from two local physicists, including my friend and colleague Deb Haarsma, then there were questions from the audience.

Watching Howard handle questions was, for me, impressive and humbling, and it was this experience that caused me to conclude that Howard was not just a hero but a true role model. Somehow, he's able to combine generous openness with blunt (even fierce) criticism. Some examples:
  • In his response to a rambling comment from an audience member, Howard concluded: "I don't know as much as I used to." The audience answered with its biggest applause of the day.
  • His response in full to a sickeningly self-indulgent sermon riddled with Christianese platitudes and proof texts: "You've given your testimony and we should just leave it at that."
  • One perceptive questioner wondered whether the evolutionary explanation of belief (HADD) would cast the same doubt on scientific understanding as it would on religious belief. Howard identified this as "a classic question and a good one," and agreed that both science and religion "deserve equal criticism." But then this: "When I look at how traditional beliefs are handled in religion vs. science, I think science is doing a superior job with respect to examining its 'traditional beliefs'."
That last comment is the kind of fearless confession that makes me admire Howard so much. It's just not fashionable, especially among Christians, to say that science is better at self-criticism and error correction than is Christianity. But it's true, and maybe someday I'll learn, from Howard, how to be brutally frank without being brutal.

One last thing. I don't know whether Howard Van Till self-identifies as a Christian. And I don't intend to walk away from my faith (or, more specifically, from what I believe to be revelation) under the influence of scientific explanation. But when the subject is science and explanation, I agree with Howard a lot more often that I do with most of the Christians I know, and he has a passion for truthtelling that would completely transform the so-called faith-science dialogue, if even a few more people followed his lead.

25 March 2008

Who speaks for science? Or, why loud atheists are NOT the problem

Last Friday I mentioned a dispute surrounding the comments of some of the advocates of "framing" in science communications. The claim was that the engagement of pseudoscience – or what I would call folk science – is unwise, at least because the attention "enables" the purveyors of such swill. That's an interesting topic of discussion, but the debate has morphed, and the heat turned up on both sides, because the focus in now on the deliciously ironic expulsion of PZ Myers (but not his chum, the occupant of the Charles Simonyi Chair in the Public Understanding of Science at the University of Oxford) from the screening of a propaganda film. I think the discussion is now about something a lot bigger than just "enabling" pseudoscience.

In the unlikely event that you haven't heard about the PZ Myers-Dawkins-Expelled "fiasco," I refer you to Greg Laden's links and/or to the New York Times (no joke).

I'll skip the whole "framing" thing for now, except to note that it involves controversial proposals regarding effective means of communicating science to the public. Here is what Matt Nisbet, a blogger at ScienceBlogs (and a well-known advocate of "framing") wrote about the prominent roles played recently by PZ Myers and Richard Dawkins in the response to some new ID propaganda:

The simplistic and unscientific claim that more knowledge leads to less religion might be the particular delusion of Dawkins, Myers, and many others, but it is by no means the official position of science, though they often implicitly claim to speak for science. Nor does it stand up to mounds of empirical evidence about the complex relationship between science literacy and public perceptions.

Unfortunately, you couldn't focus group a better message for the pro-creationist crowd. And this message is already reaching well beyond the theaters, on display most recently with the PZ Myers Affair chronicled at the NY Times.

As long as Dawkins and PZ continue to be the representative voices from the pro-science side in this debate, it is really bad for those of us who care about promoting public trust in science and science education. Dawkins and PZ need to lay low as Expelled hits theaters. Let others play the role of communicator, most importantly the National Center for Science Education, AAAS, the National Academies or scientists such as Francis Ayala or Ken Miller. When called up by reporters or asked to comment, Dawkins and PZ should refer journalists to these organizations and individuals.

The call for PZ and Dawkins to shut up has drawn significant ire in the blogosphere; I would recommend Orac at Respectful Insolence and Brian at Laelaps as sources of principled resistance on that count, and I share their indignation at the call for self-censorship.

But there's been relatively little emphasis on why Nisbet wants PZ and Dawkins to shut up. I think it's pretty clear that Nisbet is saying this: PZ and Dawkins are outspoken atheists, and ruthless critics of religion, who make controversial and/or erroneous statements, and therefore ought not be speaking for science, at least because their anti-religious fervor can hurt the credibility of science in the public eye. And he's right on every count. But he's wrong to suggest, then, that PZ and Dawkins ought to be silenced. (That he seeks voluntary muzzling is, to me, completely irrelevant.)

I maintain that if we have an "outspoken atheists" problem, the way to solve it is not to silence the voices with which we disagree, but to engage them, debate them, even refute them. Here are some thoughts on how to do that.

1. Put Myers and Dawkins into a more complete context. They're both science writers of renown, because they're both brilliant thinkers and wordsmiths. But neither is a scientist of any significant distinction. Dawkins hasn't published in the professional literature in more than three decades, and Myers' last notable contribution to a science journal was in 1993. It's not an insult to either of these guys to simply note that neither is active in serious scientific research. (Sorry, but some of us who are still working our asses off in the lab get a little testy about how the title 'scientist' gets used.) It's hard to exaggerate the difference between the scholarly achievements of Francisco Ayala and Richard Dawkins; the exalted title of the latter surely contributes to a spectacularly inflated perception of his professional achievements. The exaltation of Richard Dawkins (as a scientist) is not unlike the hilarious fawning over the unremarkable accomplishments of a certain biochemist at Lehigh University, whose CV actually dwarfs that of the estimable atheist ayatollah.

Look, I like PZ, and I like Dawkins. I like reading their work, and everyone can learn from their writing. But let's help the world understand that PZ is a science blogger and college teacher, and that Dawkins is a science writer and not much more. If I were Allen Orr or Sean Carroll, I'd be just a little annoyed that the New York Times referred to PZ as an 'evolutionary biologist', and it wouldn't matter that I happen to agree with much of what he says.

2. Add voices, don't remove them. If science is as diverse as it claims to be, there are surely scientists (maybe even real scientists) who can repudiate the religious claims of the New Atheists. Perhaps whole societies and organizations (such as those cited by Nisbet) will add their voices, not just to the condemnation of ID propaganda, but also to the rejection of anti-religious vendettas launched in the name of science.

We don't need to silence Myers and Dawkins; we need to refute them if and when they claim to speak for science against belief. And we need to speak as scientists, in defense of the integrity of our profession and in defense of our fellow scientists who are being marginalized by atheological fervor, not as slick spinmeisters who know that our grant success rates depend on our silencing of a subset of our colleagues.

And if that doesn't convince you, just try to imagine what it looks like to outsiders when a community tries to shush one of its embarrassingly obnoxious members. It seems to me that this is easily seen (perhaps accurately) as outright dishonesty. Are there some scientists who are skeptics, and who are hostile to religious belief? Of course there are. So?

3. Hold the scientific community accountable for how it responds to misuse of its name. Instead of blaming Myers and Dawkins for doing what they do best, exert moral pressure on the rest of science to be clearer about what is and isn't a legitimate invocation of the authority of science. Christians, after all, are rightly suspected of moral failure when/if they fail to condemn outrages perpetrated in their name. Why should this not be expected of scientists? And while no human can find the time to answer every summons to repudiate the idiocy of fellow travelers, the world has a right to ponder whether relative silence signals tacit approval.

We have some loud atheists who like to pretend that it is science, and not unbelief, that is in conflict with belief. Shall we silence them? OF COURSE NOT. We should thank them for getting some important questions into the public square, then we should make it quite clear that their efforts have little to do with science, and everything to do with their perfectly legitimate but completely religious convictions.

21 March 2008

Weekly sampler 11

First day of spring, 2008.

1. PZ Myers blogged about this interesting new report: examination of the genes for yolk proteins and milk proteins reveals a clear story of the evolution of proteins that nourish embryos and young in vertebrate animals. Pseudogenes figure prominently, and the explanation makes no sense without them. The article (in PLoS Biology) was accompanied by a nice lay summary, but PZ's post is very good too.

Speaking of PZ, if you haven't heard about his hilarious expulsion from a screening of a propaganda film that I won't name, check out his description of the event, or Greg Laden's Blog for bunches of links.

If your kids ever ask you to explain the concept of irony, tell them that Alanis is very confused, then tell them about how PZ was expelled from a movie with a curious title.

2. Are you a former physicist who is feeling ignorant of basic principles of biology? Feeling silly about some of the things you've written about biology, that you now know are complete nonsense? Want to learn a little about biology? Just ask a biologist. They might misspell 'color' and 'honor', but they'll surely know plenty about genetics and evolution, and a quick consult might save you from the humiliation of being thought an arrogant ignoramus. Try it!

3. I've mentioned before that our little state of Michigan, with the worst economy in the U.S. and without any hope of affecting the Democratic presidential nomination, is a hotbed of world-class evolutionary biology. The walking whale Rodhocetus kasrani? In a free museum on the University of Michigan campus. The famous ongoing experiment on selection and evolution in bacteria? In a lab in East Lansing. I could go on. Here's this week's sample: the Digital Evolution Lab at Michigan State. Their simulation program is Avida, and they used it in a prominent study published in Nature in 2003. Lately, with NSF funding, they've been adapting Avida for educational use. I haven't tried it yet, but I'm very interested in the possibility of using it in the classroom.

4. Is it a waste of time – or even counterproductive – to engage folk science and/or pseudoscience? Brian at Laelaps and Abbie Smith at ERV are two of my favorite science bloggers, and they both took the bait when a blogger at ScienceBlogs suggested that responding to anti-science propaganda "enables" it. I assume you already know where I stand: with Brian and Abbie. Via Pharyngula.

5. Dr. Hunter O'Reilly, BioArtist. Very cool.

6. I just looked over an article called "Spending money on others promotes happiness." Reader's Digest? Joel Osteen? The Living Bible? Mr. Rogers? Give up? Here's a hint: the same issue of the same magazine includes an article on a proposal to let scientists edit GenBank, the massive genomic database, in essence turning it into a wiki. (Sounds smart to me.) The magazine is Science, and here's the abstract of that article on "promoting happiness":
Although much research has examined the effect of income on happiness, we suggest that how people spend their money may be at least as important as how much money they earn. Specifically, we hypothesized that spending money on other people may have a more positive impact on happiness than spending money on oneself. Providing converging evidence for this hypothesis, we found that spending more of one's income on others predicted greater happiness both cross-sectionally (in a nationally representative survey study) and longitudinally (in a field study of windfall spending). Finally, participants who were randomly assigned to spend money on others experienced greater happiness than those assigned to spend money on themselves.
I wonder if there's a pseudogene involved somewhere...

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.

13 March 2008

Weekly sampler 10

The sun came out this week and the temperature soared to almost 50. In Phoenix, such a temperature is called 'cold'; here, it inspired us to have a cookout, though it didn't happen because the snow and ice on the deck precluded access to the blessed Weber kettle. But tomorrow, we're there.

And I've been back on my bike this week, dodging cell-phone-wielding buffoons driving alone in SUVs. I wear one of these iridescent yellow-green visible-from-space bike jackets, but I know it's just a matter of time before something terrible happens and I use the F-word on Lake Drive. FOOL!

1. Check out the National Evolutionary Synthesis Center. They sponsor lots of integrative research, and host fellows under various arrangements. (A sabbatical there sounds like a blast.) The Education & Outreach section is pretty meager, but I assume that it will continue to grow, and the Center is a co-sponsor of the new journal Evolution: Education and Outreach.

2. There's a very interesting (and large) collection of pieces on Richard Dawkins at the Times (London).

3. The RATE project is an attempt by young-earth creationists to provide a credible response to the overwhelming evidence for the great age of the earth. The project took several years, and millions of dollars, and generated a two-volume report.

As I always say, it's one thing to believe that the earth must be young, and it's quite another to assert that science backs such a claim. The RATE project, of course, takes the latter route. It's inevitable that the outcome of such an effort will involve the production of comforting folk science, cherry-picked and massaged with care. But does it have to include outright duplicity?

I'm pleased to report that the ASA has undertaken a major response to RATE, and the extent of the discussion exceeded the capacity of the ASA's journal, Perspectives on Science and Christian Faith. So the ASA has put together a web site containing the complete set of reports and articles, which includes responses from RATE and responses thereto. Related: Randy Isaac is the Executive Director of the ASA, and he has a series of articles on scientific integrity on his ASA blog.

4. Scott Carson has some interesting thoughts on miracles and explanation.

5. Every now and then I get questions about whether I'm on thin ice as a Calvin College professor who openly affirms common descent and evolutionary explanations, even for humans. Some people know that my denomination, the church that owns and operates the college, has made statements that seem hostile to common ancestry of humans and other animals. I recently commented on this over at An Evangelical Dialogue on Evolution. While you're there, check out Steve's new post on the Darwin exhibit, now in Toronto. We missed it when it was at the Field Museum in Chicago, but that's okay: we'll try to catch it in London. :-)

6. Today's issue of Nature includes an interesting book review. The book is Creationism and its Critics in Antiquity, in which the author details debates surrounding the argument from design, played out not in Victorian England or 21st-century Pennsylvania, but in ancient Greece. Here's an excerpt from the review:
The brilliance of this book is that Sedley lets the Greeks talk to us and, surprisingly, we can understand what they’re saying. Listen to Empedocles describing a time when the world was filled with a diversity of creatures with improbable combinations of features, most of which were then winnowed out, and you hear the late Stephen Jay Gould illuminating the body plans of the Burgess Shale fossils. Listen to Aristotle heaping scorn on Democritus for supposing that living things self-assemble from accidental combinations of atoms, and you hear Fred Hoyle’s gambit that “a tornado sweeping through a junkyard might assemble a Boeing 747 from the materials therein”. Truly it has been, as Darwin said, just “one long argument”.
7. Watch this weekend for a fun quiz regarding DNA content in different organisms, and my long-promised commentary on Howard Van Till's recent address to the Grand Dialogue.

08 March 2008

Weekly sampler 9

Sorry I'm late; busy week of grant-writing and deadline-beating, then sleep-compensating and dust-clearing. And I did get the Reasons To Believe posts done.

1. Allan Harvey is a chemical engineer (Ph.D.) who regularly posts to the ASA listserv, and he has prepared some highly recommended materials on "Science and Nature in Christian Perspective" that he has used in adult education in his church in Boulder, Colorado. For some reason, I can only open the Executive Summary, but if it's representative of the rest of the series, then the series is a very good, basic overview of the questions of the day. His description of the six meanings of the word 'evolution' is frequently cited on the ASA listserv, and it's very helpful.

2. Neurons are the coolest cells in the cosmos, for sure, but it never occurred to me that they might one day give Build-a-Bear some commercial competition. If you're still confused about the difference between axons and dendrites, or if you don't know what birthday gift to get for that Christian developmental neurobiology blogger in your life, then here's a big hint. (Via Retrospectacle, which has since morphed into Of Two Minds at ScienceBlogs.)

3. Nimravid is an interesting new evolution-centered blog.

4. Brain imaging is getting better; new data demonstrate how a brain scan can accomplish basic mind-reading. Worried about this? Check out this interview of Michael Gazzaniga by Carl Zimmer, delving into related questions. Bonus: you'll learn how to pronounce his name. (Via Neurophilosophy.)

5. Ever heard of The Digital Cuttlefish? It's the nom de plume of a poet and scientifically-inclined skeptic. The work is brilliant, not just because the, um, ink is often aimed at creationists. One delicious poem, "Much Ado About...The Brain?" was featured in Open Lab 2007. But one of my recent favorites is buried in the comments on a post at Pharyngula on Ken Ham's new book.

6. And finally, we all need to stop claiming that the ID movement doesn't do any research. Why, they have a whole institute devoted to scientific research. And that institute has a website. You'll think it's a hacker joke. And maybe it is... (Aw, darn, they removed the hilarious "Welcome to WordPress...start blogging now!" message from their main page.)

07 March 2008

Hugh Ross' shocking fairy tale

“I was to some degree trusting that the vetting process of a reputable book publisher was going to catch this level of duplicity.” But, he added: “Do I wish in retrospect that we had called L.A. child services and tried to run down the history of this person? I certainly do.”
That's Tom de Kay, editor of the Home & Garden section of the New York Times. Last week Thursday, that section ran a story, "A Refugee from Gangland," describing the life of Margaret B. Jones, the author of a just-released "heart-wrenching memoir" set in gangland L.A. The Times piece is fascinating, and the memoir probably is too. One little problem: the memoir has just been revealed to be a fraud. It was wholly fabricated.

In the aftermath, editors and publishers and even journalists are asking hard questions, and the book is being recalled.

It's surprising, jarring, in many ways incomprehensible, and it's just the most recent example of a "gritty memoir" that turned out to be a slick work of fiction.

Some folk science is truly fiction, but it's not that often that one uncovers a cynically fabricated bit of history. And maybe I'm too much of a moral relativist, but I do see a difference between, say, selective citation of the scientific literature in support of a weak or false proposition and, say, completely inventing a story of scientific discovery that paints one's opponents as fools and one's colleagues as brilliant heroes. Let's see if you agree.

IMPORTANT NOTE: this post, seeking to be harshly critical of Hugh Ross, refers to some of his statements as "lies." Please read the rest of this post in conjunction with a more recent post, "On folk science and lies: back to the basics." There I respond to some very important criticism, and agree that "lie" is not a useful or appropriate term here.

In Creation as Science (NavPress, 2006, pages 168-168), Hugh Ross relates a story of scientific discovery that is nothing other than a slick work of fiction. Here's how it begins:
The assumption that the non-protein-coding part of the genome served no purpose caused researchers to abandon study of its features for nearly three decades. Then a team of physicists made an observation that revived interest. They noticed that the quantity of "junk" in a species' genome was proportional to that species' degree of advancement.
You already know that the first sentence is a common falsehood. But here's an interesting new twist: a "team of physicists" somehow "revived interest" in the study of non-coding DNA. Ross claims that they "noticed" a proportional relationship between "junk DNA" and "degree of advancement."

The research to which Ross refers is reported in this brief paper: R.N. Mantegna et al., "Linguistic Features of Noncoding DNA Sequences," Physical Review Letters 73:3169-3172, 1994.

First, the authors of the article in question represent two departments: the physics department at Boston University, and the cardiovascular division of Beth Israel Hospital and Harvard Medical School. The group is truly interdisciplinary, evenly split between the two departments, but Ross elects to refer to it as a "team of physicists," and I think that says a lot about what might explain his egregiously error-filled forays into biology. In fact, one of the coauthors (Ary L. Goldberger) is quite well-known as a cardiologist and the director of the Margret & H. A. Rey Institute for Nonlinear Dynamics in Medicine at Beth Israel Deaconess and Harvard Medical School.

We'll soon see how the claim that this paper "revived interest" in "junk DNA" is an outrageous lie, but what about the proportional relationship between non-coding DNA and "advancement" that Ross associates with the authors of the 1994 paper? Well, it's a very short paper, but here's the only sentence that Ross could possibly have in mind:
An intriguing puzzle is related to the fact that in higher organisms, only a small fraction of the DNA sequence is used for coding proteins; the possible function – if any – of the noncoding regions remains unclear [5].
(The reference there, by the way, is to a review article on "Introns as Mobile Genetic Elements." It's a 37-page survey of one particular class of non-coding DNA, published more than a year before the "team of physicists" was able to "revive interest" in the "study of its features." This should make you laugh, but it's really not that funny.)

Note that the authors of the 1994 paper did not claim that the "quantity of 'junk' in a species' genome was proportional to that species' degree of advancement." Only an ignoramus would have written that, because it's not true; indeed, it's so far from the truth that precisely the opposite is actually the case.

"Degree of advancement" is not a phrase a biologist would use, but let's assume Ross means "complexity," in the way that a giraffe is more "advanced" than a worm, which is more "advanced" than an onion, which is more "advanced" than a mushroom, which is more "advanced" than a bacterium. For decades, biologists have known that the amount of DNA in an organism is utterly unrelated to its complexity. In fact, the very notion of "junk DNA" (referring specifically to pseudogenes, at the time) was invented as a hypothesis to account for the surprising lack of any correlation at all between an organims's DNA content and its size or complexity (or, for that matter, its phylogenetic position relative to other organisms). This observation was so surprising in its time that it was termed a paradox: the C-value paradox.

In other words, Hugh Ross begins his little story with a statement, falsely attributed to an interdisciplinary research group that he inaccurately calls a "team of physicists," that is so stunningly far from the truth that it is incomprehensible as anything other than an outright fabrication. I don't see how it could be a mistake, but perhaps when Reasons To Believe starts issuing retractions and apologies for its myriad falsehoods, Ross will attempt an explanation. (For the record, I'd settle for a correction, an apology, and a pledge to uphold at least minimal standards of academic integrity.)

Believe it or not, it gets worse. Here's the rest of Ross' fabricated fable:
The physicists decided to perform a computer analysis, and in 1994 they published their results. They found that what had long been labeled junk DNA carries the same complex patterns of communication found in human speech. In fact, they found that the junk DNA had an even higher linguistic complexity than did the protein-coding DNA. This breakthrough discovery drew teams of geneticists worldwide into a veritable frenzy to uncover the hidden designs and functions of the portion of DNA once thought useless.

This flurry of research has revealed five kinds of noncoding (for proteins) DNA, and each kind plays an important role in the vitality and function of the organisms in which they reside...
"Breakthrough discovery?" Well, according to Google Scholar, that paper has been cited 187 times, and when I examined this using Scopus, I found that about half of the paper's citations are from biology journals. Most of the remaining citations are from journals focused on physics, computation, and information theory, and most of those are mainly interested in the computational aspects of the 1994 study, not in its implications for genomics or genetics. According to Ryan Gregory, an actual expert in the area of genomic evolution and genome size, the report had no discernible impact on the study of genomes:
It would seem that other computer and physics types were interested, but few mainstream genetics authors picked up on it. Some people challenged it as being an artifact (Bonhoeffer et al. 1996a,b), but mostly I think people dismissed it as wishful thinking, if they even heard of it.
– Prof. T. Ryan Gregory, interviewed by email
And in case you're wondering whether 187 citations since 1994 is a lot, consider that my most cited paper, a 2001 article on p190RhoGAP on which I am co-first author with Madeleine Brouns, has been cited 108 times since then, all by biology journals. It's a very good paper, and it reported some very important results, but I don't think any of my colleagues would call the findings "breakthrough discoveries." What would a 1993-4 "breakthrough discovery" look like? Well, remember microsatellites? They comprise just one interesting class of non-coding DNA that was being intensively studied during the 30 years that Ross claims were lost to science. In 1993, a group from the Mayo Clinic in Minnesota reported that changes in microsatellite DNA are a frequent occurrence in colon cancer. Their paper has been cited almost 1500 times since then. And that review article on introns, which is cited by the "team of physicists" above? It's been cited 324 times since then.

It wasn't a breakthrough; it wasn't even an important or particularly useful result. But the most shocking and disturbing aspect of Ross' fairy tale is the full-blown lie at the end. Hugh Ross claims, falsely, that this insignificant little article launched a "veritable frenzy" of research "worldwide" on the functions of non-coding DNA. A quick look at the trajectory of research in any area of genomics or molecular genetics reveals this to be laughably untrue, but the final proof that Hugh Ross needs to re-examine his basic integrity is that last sentence. He actually claims, in print, that the "veritable frenzy" of research unleashed by the "team of physicists" led to the discovery of the various classes of non-coding DNA:
This flurry of research has revealed five kinds of noncoding (for proteins) DNA, and each kind plays an important role in the vitality and function of the organisms in which they reside...
Now, Ross' list is (you guessed it) not accurate; he doesn't even mention introns, for example. But the jaw-dropping lie, of course, is the claim that the imaginary impact of the "team of physicists" led to research that "revealed" these non-coding DNA elements. I'll leave you with a list of Ross' five classes of non-coding DNA, and references to the reports of their discovery.

Endogenous retroviruses

All of those non-coding elements were discovered more than 10 years before the little paper by the "team of physicists." (UPDATE: Ryan Gregory informs me that some of my dates are too generous: pseudogenes were known by 1977, and Alu elements (SINEs) were described by 1979.)

It's sad but true: you can't believe Reasons To Believe.

And if you work there, and you're reading this blog right now, please do something about this – for Christ's sake, if not for that of your own dignity.

03 March 2008

Talking trash about "junk DNA": lies about "function" (part II)

The creator goes off on one wild, specific tangent after another, or millions simultaneously, with an exuberance that would seem to be unwarranted, and with an abandoned energy sprung from an unfathomable font. What is going on here? The point of the dragonfly's terrible lip, the giant water bug, birdsong, or the beautiful dazzle and flash of sunlighted minnows, is not that it all fits together like clockwork – for it doesn't, particularly, not even inside the goldfish bowl – but that it all flows so freely wild, like the creek, that it surges in such a free, fringed tangle. Freedom is the world's water and weather, the world's nourishment freely given, its soil and sap: and the creator loves pizzazz.
– from Pilgrim at Tinker Creek by Annie Dillard. Harper & Row (1974), p. 137.
Questions about the designs of the panda's thumb, the human appendix and tailbone, and male nipples should caution scientists against jumping too quickly to an evolutionary conclusion whenever some aspect of anatomy seems superfluous. The RTB creation model anticipates that future research into the anatomy of complex animal structures will reveal increasing, rather than decreasing, evidence for exquisite design and functionality.
– from Creation as Science by Hugh Ross, NavPress (2006), p. 170.
Can you tell which of the authors quoted above won a Pulitzer? Heh.

Back to the big lie about "junk DNA" as told by anti-evolution propagandists. The first theme in this cesspool of creationist folk science, as I described in the first installment of this series on "junk DNA", is this: that "junk DNA" is functional and therefore that evolutionary claims regarding its origin are mistaken. Two previous posts have tackled the first half of that howler, describing how creationist portrayals of "functions" for "junk DNA" are scandalously inaccurate. (The most disturbing installment, in which Hugh Ross is shown to have fabricated a bogus history of the study of "junk DNA," with physicists hilariously portrayed as heroes, will be posted separately this week.)

Now to the second half of this folk science fable. These deliberately misleading accounts of "function" for "junk DNA" are used by creationists in two ways.
  1. After falsely claiming that "Darwinian" biologists left non-coding DNA unstudied for decades, they assert that scientists using design-based approaches would never have made this mistake. This claim is irrelevant, at least because the premise is untrue, if not because design proponents would have left the entire bloody genome unstudied while giving lectures and writing books on the impossibility of evolution.
  2. After falsely claiming that non-coding DNA is "functional" despite "Darwinist" claims to the contrary, they assert that this evident "functionality" is evidence against common descent. This is a pretty ludicrous line of reasoning, but let's be clear on why it's wrong, because it's central to the folk science of "junk DNA."
Here's Fuz Rana of Reasons To Believe, summarizing an entire section of his discussion of "junk DNA" in Who Was Adam?
Evolutionary biologists maintain that the pseudogenes, SINEs, LINEs, and endogenous retroviruses shared among humans and the great apes provide persuasive evidence that these primates arose from a common lineage. The crux of this argument rests on the supposition that these classes of noncoding DNA lack function and arose through random biochemical events.
– From Who Was Adam? by Fazale Rana with Hugh Ross, NavPress (2005), p. 235.
That paragraph is excerpted from chapter 14, which is called "What About "Junk DNA"?" And Rana's claim throughout that chapter, as well as on the RTB website, is that a "supposition" of non-function is central to the explanation of common descent with regard to non-coding DNA.

I'm at a loss as to how to characterize Rana's misconduct here. As before, when I've confronted folk science on this blog, I'm struggling to understand how a Christian with even mediocre integrity would consider writing something like that. It can't be that he's stupid or ignorant enough to actually believe it. This is folk science, and it's bad.

To be brief: biologists make neither of those suppositions when they use non-coding DNA elements to establish common ancestry and particular evolutionary relationships. Whether or not a certain DNA element is "functional" doesn't make it any less an indication of common descent, nor have biologists ever assumed universal non-function of non-coding DNA in the first place. (The details of the reasoning actually employed by real scientists in this area will be the topic of the next post in this series.) Rana's continuous assertion that non-function is the "crux" of the phylogenetic argument is subtly disingenuous. (I think the subtlety of the ploy will be clearer as I continue the series and discuss specific types of non-coding DNA and what is known about them.)

Pseudogenes and mobile elements constitute overwhelming evidence for common ancestry, not because of "presumptions" regarding their function, but because they exhibit patterns of inheritance and location (within the genome) that are best explained by common descent. Even if a particular mobile genetic element has been put to work by the genome in which it is embedded, its conserved location in particular lineages (and not in others) presents an observation that is readily explained by common ancestry. In other words, even when it's true that a particular piece of non-coding DNA has a biological function, it's not true that this falsifies the basic explanation of common descent.

The fact that many non-coding DNA elements are known to be non-functional only makes Rana's position more laughable. Consider, for example, the GULO gene, which is necessary for the synthesis of vitamin C. You may be surprised to learn that, among mammals, only humans and their primate cousins, plus guinea pigs, require vitamin C in their diets. All mammals have a gene called GULO in the same general location in their genomes. But in primates, that gene has been mutated in a specific way, rendering it unable to make a functional protein. And in guinea pigs, the gene has been mutated differently. I'll present more examples in the final post in this series, but here's the point of including one in this post: primate species with the same dietary oddity (need for vitamin C) all display the same genetic oddity (mutation of a gene known to be essential for the manufacturing of vitamin C) in the same place in the genome. Think about it: that the outcome of the oddity is "non-function" of the gene is not actually central to the reasoning that identifies common descent as the only rational explanation. If the outcome had been the resurrection of a previously-dead pseudogene, the reasoning would have been the same, and it would be equally compelling.

Finally, the claim that the behavior of non-coding DNA elements such as LINEs or Alu elements (which are known to be mobile elements with sophisticated means of translocation) is due to "random biochemical events" is similarly dishonest. While the landing sites of many of these mobile elements are thought to be largely random (with some interesting and subtle exceptions), the process itself is non-random and fairly well understood. In fact, the combination of these two characteristics (largely known modes of mobility plus largely random or unpredictable landing sites) is exactly what establishes common descent as the only rational explanation for many remarkable genomic patterns.

In summary, creationist claims that non-coding DNA is largely functional are ludicrous, and the notion that a presumption of non-function underlies evolutionary explanations of genomic structure is very misleading. Other creationists are fond of this sort of argument, but at RTB they seem to be banking on it. Such misconduct is immeasurably corrosive to RTB's scientific and intellectual integrity, to say nothing of its witness as a public apologetics "ministry." I don't know what else to say.

01 March 2008

When it's not just a disagreement

Now this is interesting. I can think of plenty of interesting Shakespearean scenes involving conflict and disputation. [Takes a bow] But I couldn't recall the word 'disagree' anywhere in, say, Hamlet or Romeo and Juliet, or even Macbeth. So to a quick search of the Oxford Shakespeare, which unearthed exactly one use of the word, in King Henry VI, Part I:
King Henry. Henceforth I charge you, as you love our favour,
Quite to forget this quarrel and the cause.
And you, my lords, remember where we are;
In France, amongst a fickle wav’ring nation.
If they perceive dissension in our looks,
And that within ourselves we disagree,
How will their grudging stomachs be provok’d
To wilful disobedience, and rebel!
King Henry VI, Part I, Act IV, Scene I, The Oxford Shakespeare
Interesting scene, and reminiscent of the kind of talk one might hear in any community that is facing opposition: we mustn't disagree, or at least reveal our disagreement, because it will signal weakness (real or not) to our enemies. Christians often talk like this. So do Democrats, and Republicans, and sports teams, and I'm sure we could find examples in much odder places than those.

There is much that I could say about this aspect of dissent and disagreement in Christian communities, but I have a different goal here. I want to distinguish mere disagreement from more substantive forms of conflict, because the deliberate smearing of these moral distinctions is a tactic oft employed by propagandists and their defenders.

First off, it should be obvious by now that I have significant and substantive disagreements with most creationists. We disagree about the meaning of large sections of the Old Testament. We probably disagree about the concept of biblical inerrancy, and we probably disagree on the proper role of scripture itself. We almost certainly disagree about the importance of natural vs. supernatural causation, and we surely disagree on the meaning and roles of Christian apologetics. Perhaps we further disagree on various questions regarding human nature, and I'm sure we would disagree on several topics related to the Christian life.

Those are significant disagreements. They're important topics, every one. Some have come up on this blog before, and they'll come up again. But this post isn't about disagreement. It's about confronting dishonesty.

I've already written about folk science and dishonesty; what I want to do here is to close what looks like a loophole. It's the "we just disagree" loophole. (Some think that my substitution of 'folk science' for 'recklessly dishonest propaganda' is loophole enough, and I agree.)

At Reasons To Believe (RTB), Hugh Ross and Fuz Rana believe that all of the species that have ever lived have been separately and miraculously created de novo, and thus they reject the notion of common ancestry. They further propose that the purpose of 3+ billion years of life preceding the advent of humans was largely to create fossil fuels and other raw materials needed for human civilization. (No, I'm not joking.) (I said NO, I'm not joking.) Now, those proposals are completely preposterous, and I'm embarrassed for Ross and Rana, and for their organization and its supporters. But while I think that theologians can probably identify outright errors in their scriptural analyses, I nevertheless view our differences as disagreements. It's an outrage to assert with any theological confidence that God made dinosaurs to provide us with petroleum, but it's not necessarily dishonest to say that. Besides, and this is important: the omnipotent God we both worship could have miraculously created species without common ancestry. So, at least on the surface, RTB and I are merely disagreeing.

Ditto for young-earth creationists, who believe that Genesis commits them to a cosmos created less than 10,000 years ago. I'm certain that they're wrong, and our disagreement is profound, but it's a disagreement. Could the scripture be telling a yet-unintelligible history of a very young universe in the Old Testament? Yes, I think it could. We just disagree on whether it does.

What about the ID folks? Again, lots of disagreement, on most of the same questions as above. (Because the ID movement is, of course, a creationist movement.)

The point is this: yes, of course, I disagree with RTB, and with Answers in Genesis, and with the Discovery Institute. But my most serious criticism of these outfits will be questions about their integrity. At least in principle, you can disagree with me on the historicity of Genesis without lying. But you can't claim that "junk DNA" was ignored by scientists for 30 years without disseminating falsehood. You can disagree with me on the importance of supernatural explanation without even a hint of dishonesty. But you can't claim that biologists have never observed "a measurable change within a species" without lying. You can dislike evolutionary theory as much as you want, and refuse to accept it as an explanation, all without engendering any accusation from me. But you can't talk about a "lack of transitional fossils" without revealing yourself to be either ignorant or duplicitous.

Here's a specific example. At RTB, Fuz Rana seems to be reasonable and thoughtful most of the time. His writing on biology is far more accurate than Hugh Ross' (which is scandalously irresponsible), and he seems to be steering clear of many of Ross' most idiotic notions. Sadly, though, Rana engages in some truly inexplicable behavior that looks for all the world like full-blown dishonesty. I've already mentioned Rana's sickeningly inaccurate portrayal of evolutionary theory on the comment-free RTB "blog." I think this indicates that Rana is willing to write things he knows to be false in defense of his peculiar natural theology. But there's more.

When writing about the interesting topic of convergent evolution, Rana confirms that truth-telling is a secondary priority at RTB. Convergent evolution, or convergence, is the phenomenon in which two apparently unrelated lineages of organisms develop very similar characteristics. On the PBS Evolution site, for example, you can see the extraordinary comparison of ant-eating animals from around the world, all of which independently developed long snouts and other adaptations. Such convergent evolution is not uncommon, and evolutionary theory must of course seek to explain it.

Fuz Rana thinks that convergence is a problem for evolutionary theory. He claims that "the evolutionary paradigm cannot accommodate 'repeatable' evolution." Now, no evolutionary biologist would agree with him, but if all he claimed was that he found convergence to be inadequately explained, or that he was certain that evolutionary theory would never explain convergence to his own satisfaction, I might think he's ignorant, but I wouldn't be justified in saying that he's dishonest. I'd just say, "We disagree." But here's what Rana actually wrote, in a 2000 article found on the RTB website:

The evolutionary paradigm cannot accommodate “repeatable” evolution. When evolutionists observe a tree frog ideally suited for its environment, they assert that natural selection––environmental, predatory, and competitive pressures repeatedly operating on random inheritable variations for long periods of time––has led to this relationship. Chance governs the evolutionary process at its most fundamental level. Because of this, it is expected that repeated evolutionary events will result in dramatically different outcomes.
Rana correctly identifies this idea with Stephen Jay Gould and his 1989 book Wonderful Life. In that book, Gould discusses this famous thought experiment: let's replay life's tape. We'll go back to, say, the Precambrian, and run the whole simulation again. What would we see? Rana continues:

Gould’s metaphor of “replaying life’s tape” asserts that if one were to push the rewind button, erase life’s history, and let the tape run again, the results would be completely different. The very essence of the evolutionary process renders evolutionary outcomes as nonreproducible (or nonrepeatable). Therefore, “repeatable” evolution is inconsistent with the mechanism available to bring about biological change.

This paragraph is perniciously dishonest. Rana moves smoothly from Gould's assertion (about the 'tape of life' and historical contingency) to a characterization of "the very essence of the evolutionary process." And in the previous quote, Rana carefully asserts that "it is expected that repeated evolutionary events will result in dramatically different outcomes." The question he's hoping you won't ask him is this: "'Expected'? By whom, Fuz?"

Gould's ideas on contingency, in fact, have always been hotly disputed. Simon Conway Morris, for example, has written entire books repudiating Gould on this subject. (Conway Morris once held to the contingency view, then changed his mind.) And most prominently, Gould's position has always been utterly rejected by strict adaptationists – those who postulate that natural selection is the predominant force acting in evolution. When adaptationists – such as Richard Dawkins or Daniel Dennett – see convergent evolution, they see strong evidence for the power of natural selection. And they wholly contradict Gould on the "tape of life" experiment, expecting that because organisms adapt to their environments in roughly predictable ways, the trajectory of evolution should be roughly predictable. (Go to Laelaps for an excellent account of these controversies.)

Fuz Rana knows this. But when he sat down to construct another rancid piece of folk science, he apparently elected to deliberately mislead his readers about the real status of contingency ideas in evolutionary theory. He constructed a fictional world in which evolutionary theory is somehow committed to thoroughgoing historical contingency, then proceeded to knock over that pitiful strawman by pointing to examples of convergence.

When Fuz Rana claims to doubt common descent, all I can say is that I disagree. But when he claims...
If life is exclusively the result of evolutionary processes, then biologists should expect to see few, if any, cases in which evolution has “repeated” itself.
...then I can say that's a dishonest claim made by a purveyor of folk science who ought to know better. It's not just a disagreement.