The above link shows the irreppresible Ken Miller in action. I want to mention that up-front, because I am deeply indebted to Dr. Miller on a number of levels. A celebrated advocate for evolution who testified for the plaintiffs in the Dover trial, he is also the author of one of the widely-used high-school textbooks in North America, Prentice-Hall Biology. Dr. Miller has graciously allowed me to use his work on more than one occasion, including in the preparation of this post. Details and acknowledgments below.*

In the previous post, I claimed that I was going to present a clear example of an independent test of morphological change being the result of evolution, and the sort of change that clearly supports an inference of common descent between two different species. The example I’ve chosen, the alleged descent with modification of modern chimpanzees and humans from a common ancestor, is just such an example. Because of their prior commitments, almost all creationists are going to feel compelled to admit that this case, if true, is a demonstration of ‘macroevolution.’ I can’t imagine any creationist who wouldn’t admit that the gap between chimps and ourselves is anything other than a large-scale event, since they seem to be at pains to deny anything that compromises the privileged status of a certain primate species.**

So this is a good way to test the 'slippery slope' of 'macroevolution', since when you try to pin some creationists down, they'll admit some changes occurs, even speciation events----but they'll shift the playing field, saying that your example, whatever it was, is not really 'macroevolution' but simply variation within the kind. Even better, this example allows us to address the claim that evolutionary theory is not predictive in a very specific way!

But I'll let Dr. Miller summarize the case. He certainly explains it far better than I ever could:

"As most of you know, there is substantial evidence that our species shares a common ancestor with the great apes –– the gorilla, orangutan and chimpanzee. But can we be sure of this? Can we put that evidence to the test? Today, we can indeed. The complete DNA sequence of one of those great apes, the chimpanzee, was published less than a week ago, and it provides us with a remarkable new opportunity to answer a question that has fascinated people of every culture, of every place and time. Where did we come from?

We human beings carry our genetic information on 23 pairs of DNA-containing chromosomes. The great ape species, on the other hand, have 24 pairs. And there’s the mystery. How could we share a common ancestor with them if you and I and even President Simmons are, quite literally, missing a chromosome? Where’d it go?

Well, if one thought that our genome was "designed," as many Americans seem to, it wouldn’t have gone anywhere. If our DNA was the unique product of an intelligent designer, that fellow could simply have arranged our DNA in fewer packages than the apes, and since there is no real relationship between us and them, nothing would be missing.

But if a fellow named Charles Darwin was right, there is a relationship, a link, and the remnants of that missing chromosome have to be somewhere inside us. You couldn’t just throw a whole chromosome away, and therefore evolution makes a testable prediction. When we lay the human and chimpanzee genomes side by side, we’ve got to find a human chromosome constructed by sticking two chromosomes together from that common ancestor. And if we cannot find it, evolution is wrong. Well, guess what? It’’s chromosome #2.

Our second chromosome was produced by the head to head fusion of ape chromosomes 12 and 13, and the new primate and human data show the exact point at which those two chromosomes were pasted together. No doubt about it –– like a criminal at the scene of a crime, evolution left its messy fingerprints all over us –– and we know where we came from. Like everything else on this planet, we evolved.

Whether you find that conclusion depressing or exhilarating, it changes the way we see our world, our existence, and our relationship to every other living thing that inhabits this planet. It’s practical knowledge, to be sure, but like all true knowledge, it has the power to change, enlighten, and transform."

I can't add much more than that, other than a caution. This example powerfully demonstrates macroevolution, and that the application of TENS to a particular problem (such as the question of our relationship to other primates) yields testable predictions. There is a plausible series of natural events which can account for the genetic and morphological differences between human beings. What it does not demonstrate, however, is that in this particular case all of the evolution we see is entirely due to natural selection alone. But (and this bears repeating) contemporary biology makes no such claim, and those who say that we do are putting forth a 'straw man' to justify their skepticism of evolutionary theory in general. If things were as such critics claim, then the textbooks would not include things like genetic drift or endosymbiosis.

Now, I think this observation has some bearing on some issues that Vox has raised in the past few posts as to how some 'evolutionists' have enlisted Darwin to 'attack religious faith', ridicule politicians who fail to say they 'believe in evolution', or attempt to suppress skepticism about TENS as unscientific. I will try to address these in a future post. For now, I will simply tackle his most recent question for me:

"...if many other complex models which backtested better than TENS have proven to be roundly unsuccessful when their future predictions have been subjected to rigorous scientific experimentation, what is the basis of your apparent belief that TENS-based models will prove more successful?"

I'm not sure this is a meaningful question for me, for two reasons: first, because I don't have a commitment one way or the other against any future model; second, because it's the wrong way to conceptualize the matter, that things will either be TENS-based or not. Here's what I would say: evolution and natural selection are both facts, and in particular cases a relationship between these two facts has been demonstrated, while in general cases it is inferred on the basis of multiple lines of evidence. Any future alternative to the present model will have to account for all the facts currently in our possession, and among those facts are evolution, and natural selection.

* The video is an excerpt from a presentation that Dr. Miller gave at Case Western University in February of 2006, less than two months after Judge John Jones III ruled against the Dover school board. It's highly similar to a talk that I saw Dr. Miller give a few months later in Modesto, California. The illustrations in this post are adapted, with Dr. Miller's permission, from the Power Point that he used in both talks, a copy of which is available here both as a presentation and a PDF file from the AAAS. Dr. Miller has also consented to my sharing excerpts from his commencement address to Brown University students in September 2005, which summarizes the findings under discussion in a concise and user-friendly fashion.

** It should not be inferred that the latter is Vox’s position, or that he will either endorse or reject this particular example. I am very much interested, though, in his response.



Vox has, by his own accounts, been trying to fight off illness, so he's rather graciously refrained from posting until I could finish up. (rueful grin) And I intend to finish up, after this post. In the meantime, Vox, hope you have a speedy recovery.

First of all, I’d like to note some points of agreement with Vox, lest any be led astray:

"I have no alternative to offer TENS subscribers at this point in time, nor do I think I am likely to in the future, but Scott's juxtaposition of my position with Kepler's regarding the Ptolemic model----no doubt made with tongue firmly in cheek---is correct in the sense that there is no reason for scientists to abandon TENS at this point in time. It is, as he and others have said, the best model they've got right now, and it's a perfectly reasonable thing to continue to use it to look for ancient bear-whales and fruit flies that can't breed with other fruit flies."

I admire Vox’s candor, and his pluck. In a zero-sum game, this concession could be beat like a drum, constantly reminding him of his failure to provide another model, much less evidence for that model. I’ll pass, in favor of treating his conclusion:

"I don't object to that, but I'm not particularly interested in it either. Let me know when you're ready to test it instead of using it as a historical dowsing device."

Well, I’m ready to test it and I’m going to demonstrate such a test in the next post in this series, but first honesty requires me to acknowledge a conceptual muddle.

At one level, I know that TENS has been tested, and that this is the best scientific explanation for life’s diversity—as Vox conceded. Strictly speaking, TENS is a theory about the dominant role of natural selection in driving evolution. There are factors other than natural selection known to lead to evolution (such as genetic drift), so TENS is not held dogmatically in individual cases in the absence of data; it's simply the hypothesis of first resort. But, happily for us Darwinians, when individual cases are examined, we typically (but not always) find clear evidence that evolution has occurred, even to the point of leading to a new species, and that natural selection of some kind is involved.

The muddle emerges, however, not in the test of nature (which TENS itself passes with flying colors!), but when TENS is taken to serve as the explanatory framework of modern biology, the ‘big idea’ that unites all sorts of observations from different research programs. There is always the possibility that forces or agents other than natural selection could’ve been involved in individual cases, and so if we are going to start inferring that the large-scale changes we see in the fossil record are the sum of countless individual acts of selection which are themselves impossible to verify, we can sympathize with Vox’s skepticism. I’m even willing to give him the benefit of the doubt for his claim that this skepticism predates and is independent of his conversion to Christianity.

Ideally, what we would want is a method of independently confirming that the morphological changes we see in the fossil record are actually the result of changes in the genetic makeup of the population, and clear evidence that these changes support an inference of common descent between different species. Happily, with the emerging science of genomics, we can do just that with many large-scale events. In my next post, I’m going to choose precisely such an example, one that creationists will feel compelled to admit that, if true, must be one of the large-scale events, and an illustration of the ‘macroevolution’ so many of them are so keen to deny.

As a sneak preview, consider the magazine cover above.


Thanks to the efforts of many dedicated people, Central Valley Cafe Scientifique will begin in October.

What's Cafe Scientifique? A wonderful opportunity for the community to interact with real scientists in a non-academic setting. You can learn more about it here. Our first speaker will be Dr. Paul Crosbie, an ecologist and parasitologist, and he has a fascinating topic that is sure to be a real eye-opener.

The first meeting of CVCS will occur on:

Monday, October 1, 2007
6:30-8:30 PM
Lenny’s Bistro Deli
River Park Shopping Center Fresno
A Google map and driving directions can be found here.
In a happy convergence, I am scheduled to be profiled in the Fresno Bee sometime soon as one of their regular letter writers and I'm going to use this occasion to plug Central Valley Cafe Scientifique.



Abiogenesis, the question of how life began, is distinct from the domain of TENS (the Theory of Evolution by Natural Selection). The latter is interested in the question of how life diversified after it got started, and quite a few sincere laymen have been non-plussed to learn that they are not only kicking a dead horse----they're kicking the wrong dead horse. This confusion has led more than a few of them to conclude (incorrectly, but understandably) that those of us who defend evolution education are performing some kind of 'bait-and-switch'.

At any rate, abiogenesis is not only not a distinct question, it differs in status from TENS. As its full name suggests, TENS is a theory: it is a widely-accepted, well-tested model that has significant predictive and explanatory power, feeding a number of different productive research programs.

Abiogenesis scenarios, meanwhile, do not rise to that status. At best abiogenesis is a hypothesis, which as a premise is consonant with, but not essential to, TENS. In the popular mind it is forever associated with a fifty-year old research program (the Urey-Miller experiments) that, skillful creationists argue, is invalidated by the revelation that this program often relied upon simulations of Earth's early atmosphere that are now known to be inaccurate.

Robert Shapiro argues, therefore, that it is time for a new paradigm. Whether he is right or not, this is a good demonstration that science as practiced is a pretty brutal competition of ideas, not an exercise in 'Aristotle says...'. Please note that both models Shapiro discusses are entirely natural---and consistent with TENS. And yet, no doubt, some quote-miner will descend upon the SciAm article as offering support for creationism.


My previous post hasn't addressed every point that Vox raised over at his site, but I do have more on that, I promise. But (whew) my daily 'hits' on my site went from less than 400 per day a week ago to nearly 8,000 in the last 24 hours, with a significant increase in private emails. So I need a little time to digest all that feedback.

As I'm typing this on my 37-minute lunch break at my school site, I am reminded that I have a lot to do to get my classes ready after the school day is over, and then I have a choir rehearsal this evening. So I won't get home until past 10.

With all of that, I don't intend to post any comments over at Vox's site for awhile and I hope that Vox will hold off with another broadside until I've had a chance to respond to the rest of his last post. Thanks to all of you who've visited, left comments or sent me emails!




Vox now offers us a variation of his favorite line of reasoning, which is to compare the predictive performance of economic models and evolutionary theory. He writes:

Now, I admit that it is theoretically possible that the tremendous problems faced by macroeconomists and financial analysts, whose models are very, very different, will not be experienced by scientists basing their predictive models on TENS. However, given the superior precision of the backtesting of the economic and financial models and the unsuccessful nature of so many TENS backdated "predictions", the logical conclusion based on the current data is that the TENS model is far less likely to prove functional when tested for its future performance in a scientific manner than the inadequate models from other scientific disciplines.

I have to say I’m unimpressed: Do economic models, when backtested, show superior precision to those models based upon TENS? You can only answer ‘yes’ if you ignore questions of scale. Economic models typically model decades, or at best centuries of data: those of us who are used to thinking in terms of ‘deep time’ (millions of years, or more) are likely to be puzzled that any one would think this comparison is valid. Of course models based exclusively on the fossil record are less precise, Vox: they operate on a time scale that is several orders of magnitude greater than any yet attempted in the field of economics. Talk about apples and oranges!


So, let’s try to level the playing field, shall we? As I see it, we have two ways we can proceed:

#1) We can compare the predictions of evolutionary theory with that of economists over the same recent scale of time, say the last 30 years or so. For example, given known parameters of a population, we could predict the likely frequency of a gene under selection in that population over that period of time. We could then compare it with the predictions of economic theory for some particular item, such as changes in the value of a given commodity over the same period of time. I would predict that the former would approach the latter in precision, and perhaps even exceed it due to some of the difficulties that Vox alluded to above.

#2) Conversely, let’s see the economists make predictions over the sort of time scale we Darwinians take for granted. How, for example, would an economist go about predicting the value of a commodity 1,000 years from now? Hmmm....let’s see, in order to do that, they’d have to know supply and demand, I suppose....but wait, demand is a function of population size...aw, gee, populations are biological objects....so...in order to model the value, we’ll need to be able to model any....changes in the population’s demographic. Uhhm...hem....haw.....

You see the problem? Any attempt at building an economic model on even a fraction* of the ‘deep time’ scale used by paleontologists involves modeling biological processes, which in the cases of changes in that population’s demographic involves its evolution! So, Vox, I have to ask: why would a smart feller like you have greater confidence in such an economic model than upon the biology on which it would it would have to be constructed? Human populations, other living things and the physical environment they share (and shape) are all evolving still. Let me suggest that economics, like medicine and agriculture before it, will in the future increasingly rely upon scientific research into how and when populations undergo genetic change—or, as some of like to say, evolve.

* (1,000 years is almost nothing to a paleontologist)


Very few people outside of my circle even know who this guy is, but there are even less people who have done more to defend quality science education in the last decade than this guy. This article from NCSE, if anything, understates Nick's contributions. I am a proud member of NCSE and wish I could afford the pay cut that working for them would almost certainly entail, because I totally believe in the importance of the work they do.

(Update: the link, which was busted, has been fixed)



Somehow this seemed appropriate, given the fireworks the last few days. I want to thank all those who've been visiting and I look forward to your comments.

And yes, this weird, wonderful band is a favorite of mine. These are the Mael brothers, otherwise known as Sparks. Subversive, and often very funny. They were too ahead of their time to be called 'new wave', and they weren't serious enough to be punk, and were more popular in the UK than over here. Love 'em.


Vox has replied, and his response is substantive. I have to admit that I am surprised to the degree that our thinking is convergent on certain points. I will reply at length to the new observations he makes, but for right now I want to focus on the points of agreement, to make sure that there is no misunderstanding.

(sigh) Hopefully, no one will accuse me of equivocating, but we'll see. Vox writes:

"...(2) Scott's genetic definition of evolution differs from the conventional definition based on fossil-based speciation which one commonly encounters in discussions with pro-evolution laymen. (3) I am not attempting to make a proactive case for an alternate theory of speciation or genetic evolution, I am simply defending my position as an evolutionary skeptic.

I agree with (2), though I note that there is greater cross-talk between those who study genetic evolution and the fossil record than ever before, and that 'molecular clocks' and phylogenetic trees derived from the former tend to accord with the latter within an order of magnitude. Those cases that don't aren't being shoved under the rug, either: they are active areas of research.

I also agree with (3) in the paragraph: Vox's skepticism is entirely a negative argument against the prevailing model, not an attempt to foist an alternative model on the rest of us. What I and some others would like to know is where Vox stands on the the question of whether any account presuming natural causes could prove sufficient. How about it, Vox? Is your skepticism on this point confined to TENS (the Theory of Evolution by Natural Selection) alone, or does it extend to any model which confines itself to natural causes?

Anyway, more Vox:

Second, I wish to note a few points that Scott has graciously conceded. (1) There is no clear evidence of speciation in the fossil record. (2) One cannot claim that the Theory of Evolution by Natural Selection (TENS) is the truth and speak as a scientist. (3) Those who attempt to enlist TENS as proof for things which cannot be tested have left the domain of science."

Gulp! I'm going to offer a caveat for (1), since it could easily be misinterpreted.

I don't think any paleontologist would claim that any particular sequence (A-> B-> C) of transitional forms actually unequivocally documents an episode of speciation. We can't know if A is actually an ancestor of B, or if B is actually an ancestor of C. We have to keep in mind that in individual cases other possible explanations for the apparent transition in question might exist. The population represented by A might've co-existed with B, for example, but flourished in greater numbers earlier in the history of life than B (thus leaving more fossils of greater antiquity), and vice-versa, given the impression that population A was ancestral to B when in fact both shared another common ancestor.

So, yes, no clear-cut case of speciation can be demonstrated in any individual fossil sequence. To put it another way, organisms fossilize, but the moment their populations diverge from others (the speciation event) does not. But the inference that speciation occurs doesn't rely upon individual cases, but upon the entire fossil record, and obviously I am persuaded that the inference as a whole is correct. I suspect Vox does, too! So while in a sense I agree with (1), keep in mind my language lacked the necessary precision the topic deserves, and it should not be taken as evidence that I think the fossil record doesn't support the evolution of species, because I do.

More Vox:

(2) One cannot claim that the Theory of Evolution by Natural Selection (TENS) is the truth and speak as a scientist.

This is true, if one is speaking of 'truth' in a non-tentative, dogmatic way, 'Truth' with a capital 'T', the kind of truth the Nazarene says will set you free. Like I said, I'm not in the truth business. The models we build in science are always tentative, always held provisionally. Individual scientists know better than to suggest otherwise, but (especially in popularizations) they often forget that their enthusiasm for this or that proposition comes across as dogmatic, especially when they are being read by someone who defines his or her self in terms of a belief system. Small wonder we scientists are often accused of peddling our own belief system! Most of the time, Vox, I honestly believe that scientists are innocent of this charge. But, you know, I tend to be hyper-optimistic, as PZ observed.

More Vox:

(3) Those who attempt to enlist TENS as proof for things which cannot be tested have left the domain of science."

I agree, obviously. That doesn't make them right or wrong, of course. It just means that such declarations are not science. It's difficult for pro-evolution advocates to steer a middle course here, given the tendency of creationists to insist that their untestable source of Truth trumps our difficult (but not impossible)-to-test model. Unabashed advocacy is a good political strategy, but doesn't necessarily lead to the best science. I can say with authority that scientists tend to speak far more conservatively in our formal pronouncements---that's just the way science is done. Where we often stumble is in popularizations, and (especially) in public debate with the unscrupulous.

Well, that's enough for now. A future post will address Vox's new claims and some points of disagreement. Many have expressed doubts that anything positive can come from such exchanges. I've certainly been frustrated by some of the commenters at Vox's place, but I also have to tip my hat to Starwind (a VD regular), who has demonstrated more genuine intellectual curiousity on the comments section of this blog than many partisans on both sides ever do---and that's refreshing.