Direct Measurement of Human Mutation Rate

Given what we know about errors in DNA replication, we estimate that every human infant carries 130 new mutations [Mutation Rates].

This number correspond to 75 mutations per haploid genome per generation or a mutation rate of 2.3 × 10^-8 per base pairs in the haploid genome (3.2 × 10⁹) per generation. This value is consistent with a variety of experimental measurements, notably the rate in Y chromosomes [Human Y Chromosome Mutation Rates].

A recent paper in Science attempted a direct measurement of the mutation rate by comparing the complete genome sequences of two offspring and their parents. They estimate that each offspring had 70 new mutations (instead of the predicted 130) for a mutation rate of 1.1 × 10^-8 per haploid genome per generation (Roach et al. 2010).

This value is only half of the rate expected from previous results and John Hawks is pretty concerned about that: A low human mutation rate may throw everything out of whack. If it's true then the time of divergence of humans and chimps would have to be set at 9 Myr and a lot of studies of recent human evolution could be off by a factor of 2.

I don't think there's any cause for concern because the measured rate in these sequenced genomes is not nearly as reliable as you might think. Most people imagine that it's merely a question of adding up all the differences between the genomes of the two offspring and their parents. Problem is, that number came to 49,720 potential mutations and that's certainly wrong. What to do?

The authors checked their data and did a bunch of re-sequencing to confirm the differences. They ended up with 28 confirmed differences in the two genomes. That's too low, so they went back over the data to see if they could find false negatives. After some careful analysis they were able to estimate the false negative rate and adjust the final tally to 70 new mutations in each diploid offspring. (Recall that the calculation based on known DNA replication error rates was 130 mutations per diploid genome per generation.)

This is how they arrived at their final value of a mutation rate. Given the possible sources of error in the genome sequence data, I don't think we should get too excited about this number. After all, it's only a bit lower than previous estimates. We should be celebrating the remarkable consistency of the data and not the variability.

John, you don't need to re-write your grant—at least not for that reason.

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Roach, J.C., Gustavo Glusman, G., Smit, A.F.A., Huff, C.D., Hubley, R., Shannon, P.T., Rowen, L., Pant, K.P., Goodman, N., Bamshad, M., Shendure, J., Drmanac, R., Jorde, L.B., Hood, L., and Galas, D.J. (2010) Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing. Science (Published Online March 10, 2010) [doi: 10.1126/science.1186802]

Introduction to "The Curious Disconnect"

This is the first of a series of postings by a guest blogger, Arlin Stoltzfus. Arlin has some important ideas about modern evolutionary theory and I'm happy to give him a chance to put them on Sandwalk.

Arlin Stoltzfus is a computational biologist with a background in bacterial population genetics and molecular evolution. He is a Research Biologist at the National Institute of Standards and Technology (NIST), and a Fellow of the Center for Advanced Research in Biotechnology. Much of his current work focuses on software and databases for evolutionary analysis, in collaboration with an international group of peers interested in improving interoperability. He also does basic research on evolution, and has contributed to our understanding of the history of introns, the origins of complexity, and the role of mutation in evolution. When he isn't doing science or spending time with family, his favorite diversions are playing the piano, bicycling, and martial arts.

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Introduction to The Curious Disconnect
Arlin Stoltzfus, ©2010
This is a longish introduction to a series of postings that will be released over the next 6 months or so. A version of this document with corrections and updated links will be maintained at http://www.molevol.org/files/cdblog/intro.html.

Striking a chord

The title of this series—The Curious Disconnect—comes from a 2002 article by eminent evolutionary geneticist Allen Orr (Orr 2002), who had broken new ground by developing predictive models of adaptation, and was reflecting on why such models weren't developed long ago, referring to "a curious disconnect between the verbal theory that sits at the heart of neo-Darwinism and the mathematical content of most evolutionary genetics".

That struck a chord with me. Since the 1990s, I had struggled with a "disconnect" that emerged while I was digesting a think-piece by paleontologists Elisabeth Vrba and Niles Eldredge (Vrba and Eldredge 1984). Among other things, Vrba & Eldredge made the startling suggestion that a key theme of "evo-devo" was that "bias in the introduction of phenotypic variation may be more important to directional phenotypic evolution than sorting by selection". By 1999 when Constructive Neutral Evolution appeared (Stoltfus 1999), my thinking had shifted noticeably toward emphasizing 1) the mechanistic distinction between the process of introducing variants and the (separate, subsequent) process of reproductive sorting (selection and drift), and 2) a research program of accounting for non-randomness (in evolution) by invoking both bias in the introduction process, and bias in the sorting process.

This way of thinking suggested that mutational-developmental bias in the introduction of variation was a general cause of evolutionary bias or direction. That contradicted two things I knew about evolutionary thinking. First, I knew that the notion of "internal" variational causes of direction, called "orthogenesis", had been rejected as a heresy. Second, I knew that, among contemporary researchers, mutation bias was not seen as a general bias on the course of evolution, but as a special aspect of neutral evolution, incompatible with selection.

I was confident that Vrba & Eldredge were headed in the right direction, but when I surveyed the theoretical literature, I could not find proof. Instead, Fisher, Haldane and Wright—the canonical founders of theoretical population genetics—all argued against a causal link between mutation and the direction of evolution, on the grounds that "mutation pressure" would be overcome by opposing "selection pressure", as in their mutation-selection balance models. Later, when "neutral" thinking became popular, this "opposing pressures" schema was interpreted to mean that mutation-biased evolution is possible, but only when selection "pressure" is absent. This was the conventional wisdom, but I knew it was wrong.

Thus, a few years later, when Lev Yampolsky and I (2001) used computer simulations to demonstrate that bias (mutational or developmental) in the introduction of variation is a possible cause of direction in neutral or adaptive evolution, we were showing a causal link that is both 1) a basic principle of population genetics, and 2) a heresy at odds with the professed views of the founders of population genetics.

What a "disconnect"! Indeed, the first premise of this blog series is that the "disconnects" in evolutionary biology are not just curiosities, but important challenges.

Deeper into the "disconnect"

Eventually I came to see these two "disconnects" as parts of the same syndrome. The retarded development of what Orr sees as predictive models of "Darwinian adaptation" is due mainly to the fact that the models are not properly Darwinian. These models (like many used in molecular evolution) treat evolutionary change as a recurring origin-fixation process in which new mutant alleles are introduced, and then individually face acceptance or rejection according to a probability function representing the effect of reproductive sorting.¹ Our Darwinian ancestors rejected this kind of "lucky mutant" or "mutationist" framework as anti-Darwinian.

Instead, they were committed to a view in which adaptation takes place at many loci simultaneously on the basis of infinitesimal variation so abundant that the process does not depend on the rate of new mutations. Given such a view, "evolution" can be reduced to shifting the frequencies of alleles already in the "gene pool". When evolution is redefined in this way, the introduction process disappears and its effects become inaccessible. This explains the retarded development of the Yampolsky-Stoltzfus model.

Notice that this is not just a matter of "verbal theory" versus "mathematical content". Vrba & Eldredge had a verbal theory that suggested a way to combine causes, and Yampolsky & Stoltzfus demonstrated its implications formally with computer simulations; Wright, Haldane and Fisher had a verbal theory of combining causes that drew on mathematical treatments of mutation-selection balance. These two conceptions of evolution lead to two different predictions on a major issue.

This suggests that there are different theories about the role of variation in evolution, and indeed, there are.

Having different theories is not a bad thing. In a healthy scientific discipline, one expects different theories to compete with each other for success in prediction and explanation.

The problem is that this healthy sorting-out process isn't happening. The disconnects mentioned above go back generations. The problem is not that we haven't solved them already, but that we are not consciously and openly engaged in solving them. Rather than having a rigorous and decisive debate to resolve these and other troubling issues, we are bogged down in confusion.

The Wrong Turn

How did things get so muddled? I have a possible explanation. I don't expect you to believe my explanation just yet, because it depends on a lot of arguments that I have not presented yet. However, I need to present this historical hypothesis anyway to provide a context.

The main reason, in my opinion, that the process of science has gone so badly off track in evolutionary biology is the success of the Modern Synthesis.The main reason, in my opinion, that the process of science has gone so badly off track in evolutionary biology is the success of the Modern Synthesis. The Modern Synthesis was simultaneously both a reactionary theory of evolution- lets call it "Darwinism 2.0"- and a progressive socio-political campaign to establish Evolutionary Biology as a discipline with a unifying "modernist" narrative (a claim to subsume all relevant phenomena).

As a scientific theory, the Modern Synthesis replaced Darwin's fictional process of "fluctuating variation" with a verbal theory of the "gene pool". Like software engineers trying to re-design a popular application for a new operating system, the architects of the Modern Synthesis re-engineered the mechanistic "back end" of Darwinism to fit Mendelian genetics, but they left the "front end" the same, in order to preserve the familiar "look and feel" of Darwinism 1.0.²

The mechanistic secret to Darwinism 1.0 was variation on demand: "altered conditions of life" automatically turn on the flow of variation, producing abundant infinitesimal hereditary fluctuations precisely when (due to the "altered conditions of life") they would be leveraged by selection to build adaptation. Genetics refuted Darwin's theory of fluctuation (along with Lamarck's theory). The "gene pool" theory in Darwinism 2.0 held that Mendelian populations act as dynamic buffers of genetic diversity, so that abundant infinitesimal Mendelian variation is "soaked up like a sponge" and even "maintained", ensuring its constant availability. Thus, in Darwinism 2.0, the evolutionary engine comes with a tank full of fuel that automagically keeps itself full; in Darwinism 1.0, there is no storage tank, but fluctuating variation supplies fuel on demand, directly to the engine. Either way, the abundance of formless infinitesimal "raw materials" ensures that selection may spring into action to build anything, anywhere, anytime.

Though the "gene pool" idea was ingenious, no such reconciliation of Darwinism and genetics was necessary. A century ago, upon the discovery of genetics, scientists began moving rapidly toward a fresh and credible framework combining Mendelian genetics with reproductive sorting. While Darwin had rejected a role for "sports" or mutants on the grounds that they violated his principle of natura non facit salta (nature does not make leaps), early geneticists had no such doctrinal allegiances. With minor exceptions, they were ready to follow the evidence wherever it seemed to be leading, happily embracing dramatic saltations, and just as happily embracing tiny increments of change, depending on where the evidence seemed to point. They did not need to reconcile genetics with Darwinism, only with evolution.

But that was not enough for some. And that is when we took The Wrong Turn.

Within a generation, the leaders of the new discipline of Evolutionary Biology were all marching under a flag of unification—and there was no turning back. In hitching itself to Darwinism 2.0, the newly minted discipline of Evolutionary Biology had mortgaged its future to purchase the theoretical analog of a baroque castle. The proud new owners of this castle were not about to knock down any walls, much less to sell the place for something brighter and more open.

Science seeks consilience, and gets . . . muck

Science is driven by ingenuity, but its also driven by our aversion to cognitive dissonance. Uncovering and addressing "disconnects" or contradictions or paradoxes results in consilience, e.g., consilience between our intuitive verbal thinking, our mathematical theories, and our experimental results.

Surprises and contradictions invariably emerge in any discipline, and so this process of seeking consilience did not stop just because we underwent a mass conversion to monotheorism. The process continues, not by rejecting inadequate conceptual structures and building new ones, but by treating every challenge as a superficial problem that can be patched up with formless globs of conceptual mud- think of feckless notions like "constraints" or "contingency" or "molecular evolution". "Contingency" is a clumsy attempt to adapt a teleological and deterministic world-view to fit dynamic indeterminism.

The notion of "constraints", likewise, is a kludge to adapt an idealized view in which selection chooses from among all that is possible, to fit more closely to the reality that the process of variation renders some possibilities more likely than others. Ideally, we would have a theory that treats variation not as a static precondition, but as a process with kinetics that impose biases on the process of evolution. What we have instead is a concept of "constraint" that, if interpreted literally, is inadequate to cover all but the most extreme cases of variational effects (which typically are not rigid restrictions, but mere quantitative preferences), and if interpreted vaguely enough, can cover anything. Recasting the role of variation in terms of dynamic processes would require major renovations to the baroque castle, and who has time for that? Rather than developing a new view, we have opted for the vagueness and flexibility of "constraints".

Likewise, under healthier conditions, "molecular evolution" would have brought down the castle. Remarkably, in the 1970's, the same clique of influential thinkers (Mayr, Simpson, Dobzhansky, et al) were both 1) congratulating each other for having unified biology—not just evolution, but all of biology—in the Modern Synthesis (Mayr and Provine 1980), and 2) waging a deliberate campaign to convince biologists that results from molecular comparisons that seemed to fly in the face of this Modern Synthesis were not a direct challenge, because "molecular" and "organismal" represented different "levels" of organization with different metaphysical leverages, one for addressing ultimate "why" questions, and the other for mechanistic "how" questions (Dietrich 1998). Darwinism 2.0 survived due to our willingness to embrace a vapid new catechism: molecular evolution is different (but we still have one theory).

The "curious disconnect" is like a major rift or canyon, but its so full of mud that some pandits survey the state of evolutionary biology, and see only solid ground:

Any criticism of the synthetic theory that turned out to have some substance was subsumed in a modified version of this theory. Instead of being a weakness, this ability to change is one of the chief strengths of the synthetic theory of evolution" (Hull, 2002)

This is the process of reconciliation at work, and as you can see, sometimes the result is a steaming pile of offal.

Thus, the second premise of The Curious Disconnect is that, in the absence of a rigorous reconciliation of "disconnects", what we got instead is just a muddled, non-rigorous reconciliation. As this process continued decade after decade, we got bogged down in the muck.

The last "Synthesis" we'll ever need, or want?

Importantly, when I refer above to The Wrong Turn, I do not mean merely that a weak theory emerged with enthusiastic support. That might have been easy to fix-- by simply discarding the theory later-- had it not been for a more subtle shift by which we came to believe that our discipline required a single formalism to encompass everything we do and to provide all the answers to The Big Questions of evolution. We decided that, in order to be legitimate, we had to have an "ism".

One indication that we feel this way is that every few years, one of my colleagues notices that we've outgrown our ism, leaving some embarrassing bits exposed, and proposes to remedy this by calling for a "Newer" or "Extended" Synthesis, or calling on us to "finish" The Unfinished Synthesis. Not only do these proposals imply that 1) we used to have a comprehensive synthesis, and 2) such a synthesis continues to be possible and desirable, they also tend to suggest 3) the next synthesis really is here already, and just needs to be acknowledged.

I disagree with all of this, for reasons that I'll explain in subsequent posts.

For now, I just want to note that this doctrine of monotheorism is an anchor weighing us down. It sets an unachievable standard. It leads us to be embarrassed about the "disconnects" that we have, and to imagine that one new "synthesis" paper is going to set things right again, as though we already have agreed on a new set of answers and all it takes is for someone to state them out loud.

Contradictions, conflicts and "disconnects" are inevitable. The healthy approach to them is not to pretend that they don't exist, or shouldn't exist, but to confront them, beginning with the process of developing deep awareness.

So, I'm not going to propose another "synthesis". My primary goal is to raise awareness of problems and to achieve intellectual clarity, not to propose solutions. Once we are aware of the problems, we might all agree on the answers, but I doubt that the answers will be so obvious.

Whats ahead

This posting is just an introduction. I've tried to make three points. The first point is that there are deep "disconnects" or problems in the structure of evolutionary thought that have persisted for decades. Some of these diconnects relate to the role of variation in evolution.

The second point is that decades of attempts to rationalize conflicts and rescue decrepit doctrines and prop up the reputations of dead authorities have left us bogged down in confusion. This is not because the scientific issues are necessarily hard (though in some cases they are). Its because of the baggage we are carrying.

The third point is that a key part of this baggage is the belief that at every point in time all our work has to be subsumed by one great theory that is central to our identity as a discipline. I hope to convince you to reject this way of thinking. The realization that there are major problems to be solved ought to be exhilarating, not embarrassing. In my view, we should be starting a dialog, not calling for a resolution as though the problems were known and the answers were obvious.

So, when we wade into the "curious disconnect", we are going to be up our ears in muck that has accumulated for generations. But, we are not going to get bogged down, because we understand the nature of the problem and we aren't going to solve it all at once. We got into this mess primarily by a kind of shallow historical conservatism, preserving old doctrines and old ideas at the expense of conceptual rigor. To get out of this mess, we have to believe that, in science, its better to be clear than to be right. Our rule is going to be "if in doubt, toss it out". For instance, I truly believe that evolutionary theory would be better off if we all stopped invoking "random" and "constraint", immediately, today. "Random" is a constant source of confusion due to evolutionary biologists who are wedded to the doctrine "mutation is random" but who aren't committed to using a standard meaning of "random", and who simply devise a special definition to rescue this doctrine.

If that sort of muck-raking sounds interesting to you, I hope that you will follow The Curious Disconnect as it unfolds. Below is a list of whats coming up (in no particular order, and subject to change):

• In a 4-part series, we'll explore The Mutationism Myth
  
• We'll see how a simple verbal ambiguity can cloud our thinking in theory(I) vs. theory(II)
  
• And we'll go further in this vein in Are there "mathematical" and "verbal" theories?
  
• In Render unto Selection we'll practice some ways to make causal attributions when multiple causes are at work
  
• Creativity and Gradualism will introduce the topic of Big Questions
  
• Then, in The Big Questions, we'll consider the scope and explanatory power of evolutionary theories (and be humbled by the results)
  
• In Mutation and Randomness (and other forms of domness), we'll learn how repeating a phrase will keep it alive even if no one knows what it means
  
• In What's your favorite popgen? we'll compare the 3 frameworks that have dominated theoretical evolutionary genetics
  
• I'll discuss Orr's particular "curious disconnect" in When "Darwinian" Adaptation Isn't
  
• We'll reject linguistic tyranny in Confronting Your Inner Fascist: what you "must" do
  
• You'll learn why I'm not yearning for another "synthesis" in The Last Synthesis We'll Ever Want
  
• We'll study ways to misinterpret evolutionary biology's simplest and most elegant theory in Misunderstanding the Neutral Theory
  
• In 4 Neutral Theories and 1 Big Misunderstanding we'll consider the neutral theories of biogeography, molecular evolution, paleontology and ecology
  
• So, you're saying its all just random? explains Constructive Neutral Evolution, and some curious responses to it
  
• In Scientific Creationism, we'll poke fun at the recurring phenomenon of scientific origin theories that push all the interesting stuff so far back in time that the theory has no useful implications

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1. This origin-fixation framework rose to prominence in the context of "molecular evolution" and the Neutral Theory, but can be traced back to the early work of geneticists such as TH Morgan. 2. For the sake of simplicity, I'm leaving out the theory originally known as "neo-Darwinism", which we could think of as "Darwinism 1.2". This view, championed by Wallace and Weismann, preceded the Modern Synthesis as well as many early discoveries of genetics, and it particularly emphasized the abundance and universality of infinitesimal variation. While Darwin's original view included acquired effects (a la Lamarck) and direct effects (a la Buffon), neo-Darwinism had only the mechanism of infinitesimal variation plus selection, which was the core of Darwin's theory and his most distinctive contribution. Dietrich, M. R. 1998. Paradox and persuasion: negotiating the place of molecular evolution within evolutionary biology. J Hist Biol 31:85-111. Hull, D. L. 2002. History of Evolutionary Thought. Pp. E7-E16 in M. Pagel, ed. Encyclopedia of Evolution. Oxford University Press, New York. Mayr, E., and W. B. Provine. 1980. The Evolutionary Synthesis: Perspectives on the Unification of Biology. Pp. 487. Harvard University Press, Cambridge, Mass. Orr, H. A. 2002. The population genetics of adaptation: the adaptation of DNA sequences. Evolution Int J Org Evolution 56:1317-1330. Stoltzfus, A. 1999. On the possibility of constructive neutral evolution. J Mol Evol 49:169-181. Vrba, E. S., and N. Eldredge. 1984. Individuals, hierarchies and processes: towards a more complete evolutionary theory. Paleobiology 10:146-171. Yampolsky, L. Y., and A. Stoltzfus. 2001. Bias in the introduction of variation as an orienting factor in evolution. Evol Dev 3:73-83.

Canada Did Not Send Troops to Vietnam

 
This won't come as surprise to Canadians. We know that Canada gave Vietnam a pass. But Ann Coulter doesn't know this. (This is from 2006 but if Canadian Cynic can still use it make fun of the right-wing nutbars, then so can I.)

The one good thing about Ann Coulter is that she makes Sarah Palin look smart.

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Ryan Gregory Visits Toronto

 
Evolutionary Imagery: Illustrating (and Distorting)
the History of Life

Starts: Friday, March 19^th 2010 at 7:00 pm
Ends: Friday, March 19^th 2010 at 9:00 pm
Location: Centre for Inquiry Ontario, 216 Beverley St., Toronto ON (just south of College St. at St. George St.)

Visual metaphors have been used to convey evolutionary ideas since Darwin's time. Some of the earliest kinds of images are still in use, even though they may do more to distort than to illustrate actual evolutionary processes. This seminar will explore two major evolutionary icons, the "Tree of Life" and "evolutionary line-ups", as they have been used in the past and how they must be interpreted today. Dr. T. Ryan Gregory completed his B.Sc. (Hons) at McMaster University in 1997 and earned his Ph.D. in evolutionary biology and zoology from the University of Guelph in 2002.

Ryan blogs at Evolver Zone: Genomicron and his main research interests are genome size and evolution.

$5, $4 for students, FREE for members

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Math Challenge

 
Jeffrey Shallit posted the questions for the 2010 Bernoulli Trials at the University of Waterloo (Waterloo, Ontario, Canada). This is a math contest for undergraduates. You have to decide whether each of following questions are true or false.

Professor Shallit liked the questions because one or two made him think for a bit. Bully for him! When I looked at the list I can honestly say that none of them (not a single one) made me think of anything except what is a Bernoulli and why is he doing this to undergraduates?

I wonder if I could made up questions like this for biology students? I don't think so—the choices would have to be "mostly true" and "mostly false."

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Happy Saint Patrick's Day!

 
This is my granddaughter Zoë celebrating her very first St. Patrick's Day.


Some of her Irish genes come from Jane's side of the family via my maternal grandparents. The shortest connection is to the parents of my grandmother. My great-grandfather was Thomas (Keys) Foster, born in County Tyrone on September 5, 1852. He immigrated to Canada in 1876. Thomas married Eliza Ann Job, born in Fintona, County Tyrone on August 18, 1852. She immigrated to Canada in 1877.

Thomas and Eliza settled in Saskatchewan in 1883 and that's where my grandmother was born. Other ancestors in this line came from the adjacent counties of Donegal (surname Foster) and Fermanagh (surnames Keys, Emerson, Moore) and possibly Londonderry (surname Job).



Happy St. Patrick's Day (2009)
Happy St. Patrick's Day (2008)
Happy St. Patrick's Day (2007)
Niall Nóigiallach - Niall of the Nine Hostages

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Predictions of Intelligent Design Creationism

I love it when they make predictions. Here's what Casey Luskin just posted over on Evoluton News & Views (sic) [A Response to Questions from a Biology Teacher: How Do We Test Intelligent Design?]

Regarding testability, ID makes the following testable predictions:

(1) Natural structures will be found that contain many parts arranged in intricate patterns that perform a specific function (e.g. complex and specified information).

Such natural structures exist. They are perfectly compatible with evolution. This prediction does not distinguish between Intelligent Design Creationism and real science.

(2) Forms containing large amounts of novel information will appear in the fossil record suddenly and without similar precursors.

The vast majority of of species with novel information have arisen gradually with plenty of transitional fossils to document their evolution. In a small number of cases (e.g. Cambrian Explosion) the evidence for evolution from known precursors is too sophisticated for creationists to follow. This prediction is not supported; therefore, Intelligent Design Creationism is falsified for all species where we have lots of data.

(3) Convergence will occur routinely. That is, genes and other functional parts will be re-used in different and unrelated organisms.

Convergence is perfectly consistent with evolution. This prediction is meaningless.

(4) Much so-called “junk DNA” will turn out to perform valuable functions.

Most of our genome is junk. The evidence for this is overwhelming. Intelligent Design Creationism has been falsified.

That was easy.

In this regard, ID is falsifiable. When we test these predictions, ID passes those tests.

No it doesn't. Two of the "tests" are consistent with evolution so the "test" is meaningless. Intelligent Design Creationism fails the other two tests.

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What Is This?

 
Some of you might not be regular readers of Panda's Thumb. If you're one of them, shame on you. Check it out to see what kind of an organism is shown in the photo. Is it animal, plant, fungus, protist, or bacterium?

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Accommodationism in Dover

The Kitzmiller v. Dover trial took place in September/October 2005. The issue was whether Intelligent Design Creationism should be presented to Dover high school students as a valid scientific controversy [Kitzmiller v. Dover Area School District. The plaintiffs successfully argued that Intelligent Design was a religious view and as such it should be excluded from the science classroom.

The general thrust of the plaintiff's argument was laid out in the opening remarks of their lawyer (Eric Rothschild). They intended to show that science is restricted to natural causes. It cannot make statements about the supernatural. Since intelligent design refers to God it must be religion, not science, and should not be presented in a science classroom.

At this trial, you will hear the parties use the term "methodological naturalism." Methodological naturalism is the term used to describe science as self-imposed limitation, that it will only consider natural causes for natural phenomena. Science does not consider supernatural explanations because it has no way of observing, measuring, repeating, or testing supernatural events. It doesn't mean that supernatural events, including divine miracles, have not happened, just that science cannot properly make any statements about them.

But intelligent design will not accept the well-established boundaries of science and openly rejects methodological naturalism, the way science has been practiced for centuries. Why? Because it has to. In the end, no matter how many stones intelligent design throws at the theory of evolution, the only alternative it presents for the development and diversity of life, the only explanation for how a bacterial flagellum or the human eye came to be is a miracle, an abrupt appearance, an act of supernatural creation. That, by itself, establishes intelligent design as a religious argument, not a scientific argument, for the creation of biological life that cannot be taught to public school students.

This position is convenient because it defines non-overlapping magisteria. It means that someone can believe in miracles and supernatural beings without violating the principles that govern science. It's a good way of making the claims of intelligent design appear to be outside the bounds of science while, at the same time, allowing moderate religious scientists to live under the big tent of science.

It's a politically and legally effective tactic, but it it correct? I don't think it is. I think science is allowed to investigate claims of miracles and whether there are supernatural beings, just as it's allowed to investigate claims of the paranormal.

Whether or not this is a good description of science, it's clear that in the context of Kitzmiller v Dover the tactic was very successful. The Judge, John E. Jones III, accepted the definition of science and noted in his ruling that science is limited to methodological naturalism [Memorandum Opinion: Kitzmiller et al v. Dover Are School District et al.].

Expert testimony reveals that since the scientific revolution of the 16th and 17th centuries, science has been limited to the search for natural causes to explain natural phenomena. (9:19-22 (Haught); 5:25-29 (Pennock); 1:62 (Miller)). This revolution entailed the rejection of the appeal to authority, and by extension, revelation, in favor of empirical evidence. (5:28 (Pennock)). Since that time period, science has been a discipline in which testability, rather than any ecclesiastical authority or philosophical coherence, has been the measure of a scientific idea’s worth. (9:21-22 (Haught); 1:63 (Miller)). In deliberately omitting theological or “ultimate” explanations for the existence or characteristics of the natural world, science does not consider issues of “meaning” and “purpose” in the world. (9:21 (Haught); 1:64, 87 (Miller)). While supernatural explanations may be important and have merit, they are not part of science. (3:103 (Miller); 9:19-20 (Haught)). This self-imposed convention of science, which limits inquiry to testable, natural explanations about the natural world, is referred to by philosophers as “methodological naturalism” and is sometimes known as the scientific method. (5:23, 29-30 (Pennock)). Methodological naturalism is a “ground rule” of science today which requires scientists to seek explanations in the world around us based upon what we can observe, test, replicate, and verify. (1:59-64, 2:41-43 (Miller); 5:8, 23-30 (Pennock)).

As the National Academy of Sciences (hereinafter “NAS”) was recognized by experts for both parties as the “most prestigious” scientific association in this country, we will accordingly cite to its opinion where appropriate. (1:94, 160-61 (Miller); 14:72 (Alters); 37:31 (Minnich)). NAS is in agreement that science is limited to empirical, observable and ultimately testable data: “Science is a particular way of knowing about the world. In science, explanations are restricted to those that can be inferred from the confirmable data – the results obtained through observations and experiments that can be substantiated by other scientists. Anything that can be observed or measured is amenable to scientific investigation. Explanations that cannot be based upon empirical evidence are not part of science.” (P-649 at 27).

This rigorous attachment to “natural” explanations is an essential attribute to science by definition and by convention. (1:63 (Miller); 5:29-31 (Pennock)). We are in agreement with Plaintiffs’ lead expert Dr. Miller, that from a practical perspective, attributing unsolved problems about nature to causes and forces that lie outside the natural world is a “science stopper.” (3:14-15 (Miller)). As Dr. Miller explained, once you attribute a cause to an untestable supernatural force, a proposition that cannot be disproven, there is no reason to continue seeking natural explanations as we have our answer.

One of the people who testified for the plaintiffs was John Haught, a Roman Catholic Theologian. He was asked to define science and distinguish it from religion. His testimony is a very good example of the accommodationist position so I'm quoting it below in order to illustrate that view. (The transcripts are freely available on the NCSE website, see Kitzmiller Trial Transcripts.)

Q. Focusing on natural science, what is science?
A. Science is a mode of inquiry that looks to understand natural phenomena by looking for their natural causes, efficient and material causes. It does this by first gathering data observationally or empirically. Then it organizes this data into the form of hypotheses or theories. And then, thirdly, it continually tests the authenticity of these hypotheses and theories against new data that might come in and perhaps occasionally bring about the revision of the hypothesis or theory.

Q. You said that science seeks to understand the natural world through natural explanations. Is that important?
A. Yes, that's critical. The science, by definition, limits itself self-consciously, methodologically, to natural explanations. And that means that anything like a supernatural reality or transcendent reality, science is simply not wired to pick up any signals of it, and therefore any reference to the supernatural simply cannot be part of scientific discourse. And this is the way that science carries on to our present day.

Q. Would that mean this is the way modern science is conducted?
A. Modern science we date from roughly the end of the 16th to the 17th Century, in that period of time. And it was at that time that the great figurists of modern science, almost all of whom were deeply religious men themselves, decided self-consciously that this new mode of inquiry would not appeal to anything that's not natural, would not appeal to things like value, importance, divine causation, or even anything like intelligent causation.

These are not scientific categories of explanation. And ever since the 16th and 17th Century, modern science, as it's called, leaves out anything that has to do with theological or ultimate explanation.

....

Q. Does this make science at odds with religion?
A. By no means. Science and religion, as I've written in all of my books, are dealing with two completely different or distinct realms. They can be related, science and religion, but, first of all, they have to be distinguished. The medieval philosopher said, we distinguish in order to relate. And when we have a failure to distinguish science from religion, then confusion will follow.

So science deals with questions relating to natural causes, to efficient and material causes, if you want to use Aristotelian language. Religion and theology deal with questions about ultimate meaning and ultimate purpose. To put it very simply, science deals with causes, religion deals with meanings. Science asks "how" questions, religion asks "why" questions.

And it's because they're doing different things that they cannot logically stand in a competitive relationship with each other any more than, say, a baseball game or a baseball player or a good move in baseball can conflict with a good move in chess. They're different games, if you want to use that analogy, playing by different rules.

Q. You've used another analogy in discussions with me that might be illuminating. This is the boiling water analogy. Could you give us that?
A. Yes. I think most of the issues in science and religion discussions, most of the confusion that occurs happens because we fail to distinguish different levels of explanation. And so what I advocate is layered or -- layered explanation or explanatory pluralism, according to which almost every phenomenon in our experience can be explained at a plurality of levels.

And a simple example would be a teapot. Suppose a teapot is boiling on your stove and someone comes into the room and says, explain to me why that's boiling. Well, one explanation would be it's boiling because the water molecules are moving around excitedly and the liquid state is being transformed into gas.

But at the same time you could just as easily have answered that question by saying, it's boiling because my wife turned the gas on. Or you could also answer that same question by saying it's boiling because I want tea.

All three answers are right, but they don't conflict with each other because they're working at different levels. Science works at one level of investigation, religion at another. And it would be a mistake to say that the teapot is boiling because I turned the gas on rather than because the molecules are moving around. It would be a mistake to say the teapot is boiling because of molecular movement rather than because I want tea. No, you can have a plurality of levels of explanation. But the problems occur when one assumes that there's only one level.

And if I could apply this analogy to the present case, it seems to me that the intelligent design proponents are assuming that there's only one authoritative level of inquiry, namely the scientific, which is, of course, a very authoritative way of looking at things. And they're trying to ram their ultimate kind of explanation, intelligent design, into that level of explanation, which is culturally very authoritative today, namely the scientific.

And for that reason, science, scientists justifiably object because implicitly they're accepting what I'm calling this explanatory pluralism or layered explanation where you don't bring in "I want tea" while you're studying the molecular movement in the kettle. So it's a logical confusion that we have going here.

I think that's a prety good description of the accommodationist position as I understand it.

One of the interesting aspects of the trial is that when John Haught started to testify as an expect on science there was an objection from the defendant's lawyer. He claimed that Haught was a philosopher, not a scientist, and therefore was not an expert witness with respect to defining science. The objection had to be withdrawn when the defendant's lawyer discovered that he had already approved pre-trial documents where Haught discussed science.

Later on there was the following exchange,

Q. Well, according to Gould, the message of Darwinian science is that life has no purpose. Is that a scientific claim?
A. No. And I think if you ask Gould, he would have to admit that, also.

Q. Okay. Daniel Dennett, do you know who he is?
A. Yes.

Q. He's a philosopher. Is that right?
A. He's a philosopher at Tufts University.

Q. Right. And he claims that Darwin is incompatible with religious beliefs?
A. Yes. He's a philosopher, not a scientist. That's a philosophical belief.

Q. Well, what about E. O. Wilson, who is a biologist at Harvard, he puts Darwin's science in direct competition with religion, does he not?
A. Yes, because he is one of these people who unconsciously conflates his very good evolutionary science with a very suspect metaphysical belief system. Not always, but at times.

I'm sorry, but I can't help but snicker at such testimony from a Roman Catholic philosopher. He's testifying as an expert on science but criticizes another philosopher for making statements about science (justifiable, in my opinion, but still hypocritical). Then he criticizes a scientist for mixing up his science with his metaphysical beliefs.

What, exactly are those "very suspect metaphysical belief system" that John Haught avoids but which entraps E.O. Wilson? Why it's the "religion" of materialism.

Q. And by a materialist world-view or belief system, what does that mean?
A. Materialism is a belief system that claims that matter, lifeless and mindless matter, is the ultimate foundation of all reality, and there's nothing more ultimate than that. So it's kind of religious in the first sense of my term, a belief in something of ultimate importance. For the materialist, matter is the ultimate creator, the ultimate source of all being, and therefore it excludes the existence of anything supernatural, certainly the existence of God.

So, materialism isn't something that could just arise by default among those people who don't fall for religion. No siree. It has to be a religious view of its own.

If you think about it, that's very strange. Western Europeans are raising a whole generation of children who will have never been brainwashed by religion. They will be materialists by default because they've never known anything else. But according to Haught (he's not alone) they will be engaging in adopting a form of religious belief system, just like E.O. Wilson. How does that work?

So, what exactly are the limitations of science that we are supposed to adhere to? Earlier I criticized the concept of methodological naturalism because it seemed to rule out investigations of the paranormal as well as investigations of miracles. Robert Pennock, another philosopher, was asked about that during his testimony and he had a ready answer. See if you are convinced.

Q. Isn't it true that as we sit here today scientists are investigating what some people call psychic powers?
A. I know that there are a few scientists who did that I believe. Mack is one name, someone who's done this. So there are a few scientists who have done that, that's right, and what they do in that case is really the same thing. It's often misunderstood to think, to call something paranormal means that it is supernatural. Essentially what's going on in those scientific investigations is to say no, that's not so. We will again treat this purported phenomenon, ESP or telekinesis for example, as though this is a natural, still yet unknown, but ordinary causal process, treating it essentially in the same way we treat other things under the constraints of methodological naturalism, reconceptualizing it as a natural thing rather than a supernatural.

Cool. You can investigate the paranormal because it's not supernatural and you can treat it as a potential natural phenomenon. Presumably you will reach the conclusion that is is not a paranormal event.

But for some reason you can't do that for miracles and the role of God in theistic evolution. That's forbidden science.

Excuse me if I'm confused.

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Just Say "No"

 
The Discovery Institute promotes Intelligent Design Creationism and they are all agog over Stephen Meyer's new book, Signature in the Cell: DNA and the Evidence for Intelligent Design.

Disco is upset with Francisco Ayala, a leading evolutionary biologist who did not have kind things to say about the book. So, what to do?

All they could think of was to challenge Ayala to a debate: Leading Intelligent Design Advocate Challenges Former President of American Association for the Advancement of Science (AAAS) to Debate.

Should Ayala accept? I say no way. Discuss.

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Arabidopsis thaliana

 
Today's Botany Photo of the Day features Arabidopsis thaliana, also known as thale cress.

Arabidopsis is a famous model organism¹ but it's not as familiar to most people as fruit flies or yeast. Check out the photographs to see what this plant looks like.

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1. A "model organism" is an organism that's extensively studied by a large number of research labs. These species usually serve as representatives of larger taxa. In this case, Arabidopsis is a typical flowering plant.

The NCSE Position on Science vs Religion

NCSE is the National Center for Science and Education. This is the main American organization fighting against creationism. I am a member and I urge everyone to support NCSE.

In an earlier posting I said, with respect to accommodationism, "As you know, it's the official position of the National Center for Science Education."

Josh Rosenau is a Public Information Project Director for NCSE and he replied to this claim in a comment on Sandwalk [Josh Comment].

This is simply false. We may not be able to convince one another of theological/scientific matters, but can we have the discussion without manifest inaccuracy?

Here is NCSE's official position:

"What is NCSE's religious position?

"None. The National Center for Science Education is not affiliated with any religious organization or belief. We and our members enthusiastically support the right of every individual to hold, practice, and advocate their beliefs, religious or non-religious. Our members range from devout practitioners of several religions to atheists, with many shades of belief in between. What unites them is a conviction that science and the scientific method, and not any particular religious belief, should determine science curriculum."

At best, this is an affirmation that some religions may be (or may not be) compatible with science. It is not a blanket statement of absolute compatibility, and suggesting that it is simply misleads your readers.

Josh links to the NSCE website as proof that the accommodationist position is not the "official" position of NCSE. The statement he quotes is irrelevant to the discussion so let's look further into the NCSE webpages.

Before doing that, let me agree partly with Josh. It would have been better if I had not used the word "official" since that is a stronger statement than I wished to make. It would be better to say that the public stance of NCSE is to be supportive of the accommodationist position in preference to the idea that science and religion are in conflict and in preference to the position that NCSE should not take a stance on this controversial issue.

Let's look at the part of the NCSE website that deals with Science and Religion. The main page is authored by Peter M. J. Hess, NCSE Faith Project Director.¹

In public discussions of evolution and creationism, we are sometimes told by creationists and opponents of religion alike that we must choose between belief in creation and acceptance of the theory of evolution, between religion and science. Is this a fair demand? Is the choice that stark? Can one believe in God and accept evolution? Can one both accept what science teaches and engage in religious belief and practice?

These are complex issues, and deserve thoughtful consideration before a decision is made. Theologians, clergy, scientists, and others belonging to many religious traditions have concluded that their religious views are compatible with evolution, and are even enhanced by the knowledge of nature that science provides. Just as vigorously, other theologians, clergy, and members of other religious traditions reject evolution as contradictory to and thus incompatible with their faith positions. And some nonbelievers argue that the methodology and findings of science are philosophically incompatible with any meaningful form of faith. Passions often run high on all sides.

This section of our website offers resources for exploring a wide array of religious perspectives on scientific questions, and scientific perspectives on topics of interest to various religious groups. We also provide resources for anyone interested in a general exploration of the relationship between science, especially the evolutionary sciences, and religion. One goal of this section of the website is to make the public aware that the dichotomous view represented by creationists and antireligious atheists leaves out a large range of more moderate religious views. We hope that you find these materials useful in considering these important issues.

It certainly looks to me like NCSE is taking up the issue rather than being neutral as I would prefer. It looks to me like there's a tilt toward getting people to understand that you don't have to choose between the extremes of creationism and "antireligious atheists" but, instead, should opt for the "range of more moderate religious views."

The first article is also by Peter Hess and it addresses the question God and Evolution. He's what appears on the NCSE website ...

Of course, religious claims that are empirically testable can come into conflict with scientific theories. For instance, young-earth creationists argue that the universe was created several thousand years ago, that all the lineages of living creatures on Earth were created in their present form (at least up to the poorly-defined level of "kind") shortly thereafter, and that these claims are supported by empirical evidence, such as the fossil record and observed stellar physics. These fact claims are clearly contradicted by mainstream paleontology, cosmology, geology and biogeography. However, the theological aspect of young-earth creationism—the assertions about the nature of God, and the reasons why that God created the universe and permitted it to develop in a particular way—cannot be addressed by science. By their nature, such claims can only be—and have been—addressed by philosophers and theologians.

The science of evolution does not make claims about God's existence or non-existence, any more than do other scientific theories such as gravitation, atomic structure, or plate tectonics. Just like gravity, the theory of evolution is compatible with theism, atheism, and agnosticism. Can someone accept evolution as the most compelling explanation for biological diversity, and also accept the idea that God works through evolution? Many religious people do.

That certainly has all the earmarks of an accommondationist position as far as I'm concerned. Perhaps Josh can explain why my interpretation is wrong.

Another link is to a part of the NCSE website that deals with the Clergy Letter Project.

The Clergy Letter Project was initiated in 2004 by Michael Zimmerman, now Dean of Butler University in Indiana, as a response to the common misperception that science and religion are inevitably in conflict, especially around the question of evolution. In response to by a series of anti-evolution school board policies in Wisconsin, Dr. Zimmerman worked with Christian clergy throughout Wisconsin to prepare a statement in support of teaching evolution. Within weeks nearly 200 clergy in a wide variety of denominations had signed the statement, and that number has now grown to more than 11,660

I wonder if there's a link to similar petitions from scientists and philosophers who think that science and religion are in conflict? Perhaps Josh can point us to such a webpage that NCSE has put up for balance because otherwise one might get the impression that NCSE actually endorses the statement signed by all these theists.

There's another webpage written by Peter Hess and hosted on the NCSE website. It's about How Do I Read the Bible? Let Me Count the Ways.

Currently, most mainstream Christian and Jewish denominations hold that the Bible was not intended by its authors to teach us about science — a way of knowing which did not exist at the time the Hebrew oral traditions were set in writing as the Book of Genesis. These denominations do not draw from the Bible the literal truths that the earth is flat, or that a global flood once covered Mt. Everest, or that we inhabit a geocentric cosmos, or that the world was created as we now observe it in six solar days, or that species were specially created in their present form and have not changed since the days of creation.

Rather, they read the Bible as a record of a people's developing moral relationship with the God in whom they placed their trust. In a 1981 address to the Pontifical Academy of Sciences, for instance, Pope John Paul II said, "Cosmogony itself speaks to us of the origins of the universe and its makeup, not in order to provide us with a scientific treatise but in order to state the correct relationship of man with God and with the universe. Sacred Scripture wishes simply to declare that the world was created by God, and in order to teach this truth, it expresses itself in the terms of the cosmology in use at the time of the writer." Viewed as such, the Bible enshrines timeless ideals about the integrity of creation and human responsibility within that creation. For these believers, part of that responsibility is using the gift of human rationality to discover the exciting story of how life ― including human life ― has developed on the earth.

I couldn't find the atheist webpages or, for that matter, the Hindu and pagan webpages on the NCSE site. I'd like to alert Josh to the fact that since these balancing points of view are difficult to find (or non-existent, gasp!) one might easily get the impression that NCSE was only supporting Christian accommodationist points of view.

Eugenie Scott has an article entitled, Do Scientists Really Reject God?. The answer is "no."

In a recent issue of RNCSE, Larry Witham reported on research he and historian Edward Larson carried out to investigate the religious beliefs of scientists.They had surveyed a sample of 1000 individuals listed in American Men and Women of Science, (AM&WS), using questions originally asked by the Gallup organization in a series of polls of American religious views.The report, entitled "Many scientists see God's hand in evolution", concluded that although scientists were quite different from other Americans in their views of "extreme" positions— such as young earth creationism and atheism—they were very similar to other Americans in the "middle" or "theistic evolution" position.

In the table below, the full wording of Gallup's question 1 is, "Humans were created pretty much in their present form about 10 000 years ago." The difference between scientists and other Americans is striking. Scientists also respond quite differently to the third question, "Man evolved over millions of years from less developed forms. God had no part in this process." But scientists' responses to Gallup's "theistic evolution" question—"Man evolved over millions of years from less developed forms of life, but God guided the process, including the creation of Man"—directly mirrors that of the general public. The "middle ground" is apparently equally attractive to scientists as it is to the general public.

Correct me if I'm wrong but that doesn't sound like a neutral position on accommodationism and it doesn't sound like support for the idea that science and religion may be in conflict. It sounds like accommodationism.

The 5th link from the "Science and Religion" home page is Resources especially for clergy.

The articles below have been selected especially for clergy from various sections of NCSE's website as entry points into topics of interest.

I don't see an official NCSE webpage called "Resources for Atheists." I wonder why?

Let's look at one other link on the NCSE site. This one is to a speech by Eugenie Scott, the Executive Director of NCSE [Science and Religion, Methodology and Humanism]. It's an old speech but it the content represents the current position of the Executive Director and I've heard her make the case for accommodationism many times.

Her argument goes like this. Science is concerned with methodological naturalism. Many statements about religion cross over some imaginary line into the realm of philosophical naturalism. Science is not concerned with the metaphysical realm of philosophical naturalism but can only stick to methodological naturalism and statements about the natural world. When people say that science and religion are incompatible they are not really speaking about science because there are many supernatural questions that science can't address.

Thus, science and religion occupy separate magisteria and can easily be compatible.

I argue for the separation of methodological from philosophical materialism for logical reasons, and for reasons based on the philosophy of science. It is also possible to argue from a strategic standpoint. Living as we do in a society in which only a small percentage of our fellow citizens are nontheists, we who support the teaching of evolution in the public schools should avoid the creationist's position of forcing a choice between God and Darwin. Creationists are perfectly happy if only 10% of the population (the percentage of nontheists) accepts evolution. I am not. I want people to understand and accept the science of evolution; whether or not someone builds from this science a philosophical system that parallels mine is logically and strategically independent. An ideology drawn from science is not the same as science itself.

Ironically, I find myself being praised and encouraged in my position by conservative Christians and taking flak from some fellow nontheists, including some scientists. I must say, though, that over the last several months I have presented lectures at several universities and two meetings of professional scientists in which I have argued that a clear distinction must be drawn between science as a way of knowing about the natural world and science as a foundation for philosophical views. One should be taught to our children in school, and the other can optionally be taught to our children at home. Once this view is explained, I have found far more support than disagreement among my university colleagues. Even someone who may disagree with my logic or understanding of philosophy of science often understands the strategic reasons for separating methodological from philosophical materialism — if we want more Americans to understand evolution.

Josh, while it may be incorrect to say that accommodationism is the "official" position of NCSE, it seems clear to me that it's the only position that your website supports and it's the only position that your leaders advocate in public.

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1. Does NCSE have an Atheist Project Director?

What Is Knowledge?

John Wilkins said something in the comments on his blog [On the need for grownups [Thoughts from Kansas]] that I'd like to discuss.

I do not think, contrary to some, that science exhausts the realm of knowledge, largely because I have a fairly broad and fallibilistic notion of what it is to know something – you can know that it is wrong to eat fish on a Friday, for example, or that one must not abuse children, neither of which are scientific questions. So I have no truck for those who merely assert that knowledge is all and only scientific – you have to argue for it.

I'm one of those naive scientists who don't understand philosophy so forgive me if I make some silly errors in logic.¹

First, John, I wish you'd stop making false claims about those people you disagree with. I don't know anyone who simply ASSERTS that science is the only way of knowing. On the other hand, I do know people (I am one) who adopt it as a working hypothesis.

I'm looking for evidence of other ways of knowing that might provide valid knowledge. So far I haven't found any so my hypothesis hasn't been falsified.

Now, the problem here falls into the realm of epistemology—defined as "the study of knowledge and justified belief" (Epistemology). As with most philosophical issues, the discussions in that field are far too obtuse for most people to follow. Just look at the article I linked to. I imagine that 99% of people who follow that link will not read past the first section on "What Is Knowledge?"

Here's how I think of "knowledge" in the context of this debate. Knowledge, in my mind, is a form of justified belief that can be affirmed as true by all people. In other words, "knowledge" in this sense is something that applies universally and not just to particular individuals. Your definition of "knowledge" is much broader and that means we are talking past each other. I'm surprised you didn't recognize this.

Here are some examples. I think we should "know" that the Earth revolves around the sun, we should "know" that life evolved from a common ancestor, we should "know" that our species was not almost wiped out by a giant flood in 2500 BCE, we should "know" that some humans believe things that aren't true, and we should "know" that humans have a finite life span. These are all examples of the kind of knowledge that I'm referring to.

Note that there's an immediate problem here since clearly not everyone agrees with my statements of knowledge. In other words, they are not really universally accepted. Does that disqualify them from being examples of true knowledge? Perhaps, but I think we can at least agree that they are good candidates for the kind of knowledge I'm talking about. (We can't realistically demand "universal" acceptance since there will always be some kooks who disagree with even the most obvious examples of knowledge.)

Another potential candidate is, "God exists." The tough part is trying to decide which of these potential candidates for knowledge are true and which ones aren't. The ones we reject don't count as knowledge. I claim that the scientific way of knowing is a tried and true approach to arriving at knowledge of this sort, i.e. things that we can universally agree on. I don't see any other ways of knowing that have achieved the objective.

What about statement such as, "I know that it's wrong to eat fish on Friday" or "It's wrong to abuse children"? I don't think either of those qualify as "knowledge" in the sense that I'm concerned with. You may believe that it's wrong to eat fish on Friday and that belief may be justified by your desire to remain a respected member of your Roman Catholic church, but it hardly qualifies as the kind of knowledge that might be universally accepted as true.

The rule that you shouldn't abuse children isn't "knowledge" at all, in my opinion. It's a rule that our society accepts in order to promote peace and harmony and conform to our concepts of rights and respect for fellow humans.

That rule may be informed by evidence and rationality or it may derive from what your pastor tells you about God's perceived will. But no matter how you come to accept these rules of society they don't count as potential examples of universal knowledge. At best, the rule is secondarily derived from such potential universal knowledge that remains to be proven (Universal Moral Laws).

I'm not sure if this makes sense.

One more thing, when John says, "neither of which are scientific questions" it reveals a different version of science than the one I propose. I'm trying to make the case for science as a way of knowing and, if John accepts my definition, then every question about knowledge is potentially a scientific question. One can't just arbitrarily dismiss something as not being a scientific question without explaining why you can't get an answer by applying rationality, evidence, and skepticism. When John dismisses questions arbitrarily it's called "begging the question."

His logic goes like this:
1: Science can address all questions about knowledge.
2: Some questions are not scientific.
3: Therefore, science can't address all questions.

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1. John Wilkins says, "First of all I have little confidence that scientists and other science-based critics of the philosophical arguments have a good grasp of what those arguments are."

Who's the Grownup in the Science vs Religion Debate?

Joshua Rosenau has fired another shot in the accommodationist war. As usual, he focuses more on rhetoric and mudslinging than on the logical arguments that are presented by both sides. In this case, he demeans all those who disagree with him in On the need for grownups [Updated]. Apparently, there are very few honest people on my side of the argument.

I'm not going to reply to Josh. He's gone beyond the pale as far as I'm concerned and no amount of rational argument is going to convince him that science and religion may not be compatible. His mind is firmly made up and now he's just making sure that his side gives out as many insults—perceived or real—as it receives.

John Wilkins is another matter. He has posted a defense of Josh [On the need for grownups [Thoughts from Kansas]]. I think it might be worthwhile to address his arguments in an attempt to shed some light on the problem and avoid the worst of the name-calling.

So, here goes ....

Josh Rosenau has a sermon on the perils of attacking those who think science and religion can coexist at On the need for grownups [at Thoughts from Kansas]. It’s a pretty damned good sermon. He points out that the claim that science and religion are incompatible is itself an untested, and hence unscientific claim. It’s a point I would like to discuss a bit.

Good, let's discuss. We begin by defining terms. I claim that science is a way of knowing based on rational thought, skepticism, and evidence. I claim that when that way of knowing is applied to religious claims, those claims can be shown to be false or, at the very least, unsupported. Thus, if you are committed to science as a valid way of knowing, it follows that, when you stick to that commitment, the vast majority of religious beliefs are not compatible with science.

Do you have to make the assumption that the scientific way of knowing is a valid way of knowing? No, you don't. If you want to believe in other ways of knowing, such as faith, revelation, and just-so stories, then you are perfectly free to do so. In that case, science is probably not compatible with your worldview and you can believe in the tooth fairy, deny climate change, and refuse to vaccinate your children. No problem. No conflict.

However, if you do adopt the axiom that science is a valid way of knowing then I think most of those beliefs (and more) are not compatible with your choice. John is about to show us why that's bad philosophy.

Back when a philosophy known now as logical positivism was fashionable, the claim was made that whatever was not scientifically verifiable was metaphysical rubbish. This was known as the Verification Principle. Karl Popper, among others, noted that the Verification Principle was not scientifically verifiable and was therefore, on its own account, metaphysical rubbish. That put an end to that version of logical positivism (although no philosophical position ever really dies). It was self-defeating.

So far, so good. I'm not a fan of Karl Popper. (However, I note that John is vastly over-simplifying the views of Popper and conveniently ignoring the reasons why the Verification Principle might be valid.)

What Jerry Coyne and the anti-accommodationists are doing, as Josh points out, is a version of logical positivism (Josh does not use that example – that’s me). They are saying that those who attempt to argue that religion and science are compatible or might coexist are being unscientific, are themselves being unscientific. In fact, the data is that science and religion coexist nearly all the time – most of those who support scientific views are religious. This is because most of everyone is religious, of course, but the fact remains: if one approaches this as a scientific matter, science and religion just are coexistent, that’s the fact of the matter.

Let's dissect this paragraph. First, my anti-accomodationist argument is that once you accept that science is a valid way of knowing, then it follows that most religious claims are not compatible with that approach to knowledge. I have yet to see a valid accommodationist argument that addresses this important point. True, Ken Miller, Francis Collins, and Simon Conway-Morris have made the attempt but in the end their arguments boil down to a rejection of science as the only way of obtaining valid knowledge. In other words, they limit science to just those areas where it can't conflict with religion and then lay claim to other ways of knowing that rule in the religion magisterium. Presumably, John thinks that is a scientific way of reasoning.

Second, John repeats to tired old argument that just because there are people who claim to be good scientists AND are religious, then it follows logically that science and religion are compatible. (Actually, he says that they "coexist," but I assume he means compatible.) This is a very silly argument and I don't understand why John persists in using it. If it were true, then science has to be compatible with every single belief that's ever been held by anyone who claims to be a scientist. In other words, science is compatible with Young Earth Creationism since we know for a fact that there are many scientists who are Young Earth Creationists.

Please, John, for the sake of all of us, drop this argument. It's not going to convince any of us accommodationists and it makes your side look ridiculous since it puts you in the position of defending Young Earth Creationism and other kooky ideas that must be compatible with science if your argument is valid. You know darn well that there are many people who hold on to contradictory ideas. The fact that those people exist is NOT evidence that the ideas are compatible. (There's probably a name for that kind of flawed reasoning.)

What Coyne and others seem to want to argue is that religion and science should not be coherently expressed by a single person. That is a philosophical position one might argue for, philosophically. It is not a fact of science, though, nor, it seems, a fact of logic. So argue for it. Others, as is the way of debates, will argue the contrary, or some other view. As an accommodationist, I think that whether or not science and religion should be treated as compatible, in fact they are, or as compatible as any potentially competing set of beliefs may be, such as the belief that science is the only way to gain justifiable beliefs, which is not, itself, scientifically justifiable.

John, you tacitly admit that science and religion are a "potentially competing set of beliefs." That's the point, isn't it? I argue that if you adopt science as a valid way of gathering knowledge then most everything about religion fails the tests of science. Those who claim to be scientists and still believe that there's a God who answers prayers are expressing two contradictory positions. You can't claim to be thinking like a scientist while holding on to beliefs that have been refuted by science. I claim that almost all claims of religion fall into the set of things that are incompatible with the scientific approach to knowledge (deism is a debateble exception).

I don't understand your position. Perhaps it hinges on the idea that accepting science as a way of knowing is supposed to be a "fact" of science. I have never made that claim and, as far as I know, neither have any other prominent defenders of the incompatiblity of science and religion.

I do assume that science is the only valid way of acquiring knowledge but that's a testable assumption—at least in theory. All one has to do to refute that argument is demonstrate the existence of valid forms of knowledge that cannot possibly be derived from the scientific approach AND ARE COMPATIBLE WITH SCIENCE AS A WAY OF KNOWING. The last part is important. Acquiring knowledge by revelation is another way of knowing and if all of that knowledge was perfectly compatible with science then science and religion would be compatible. If the knowledge acquired by listening to imaginary voices in your head conflicts with the scientific approach then religion and science are not compatible.

You don't have to accept my assumption that science is a valid way of knowing. That's not the point. I agree that that the assumption cannot be justified as "scientific" since that's a circular argument much like to one you used to dismiss Popper. The point is that once you make that assumption and become a scientist, you can't just arbitrarily pick and choose how you are going to apply that way of knowing. You can't say that your scientific approach will help you understand whether the climate is changing but when it comes to deciding whether it's better to pray for your sick child or take her to the hospital then you'll rely on some other way of knowing. You can't be consistent if you say that science helps you understand evolution but you need to shift to another way of knowing when trying to decide whether you have a soul that lives on after you die.

Lot's of people may do that, but they aren't being logical or consistent. They may say they are being logical and consistent (e.g. Ken Miller, Francis Collins) but surely, as a philosopher, you recognize that what people say isn't always the truth.

By the way, feel free to offer up examples of knowledge gained by religion that are fully compatible with the scientific approach but couldn't have been derived from that approach alone. Those would be positive examples in favor of your position on compatibility. It would be a refreshing change to hear an atheist (agnostic) compatibilist give us a few examples instead of just ranting against our position.

This is why I made my snide cheap shot about the split in Dawkins’ website. Dawkins, Coyne, and many others (but not all those who happen to agree with them substantially, I hasten to add) are in the business of building an exclusionary group. Ken Miller and Francis Collins believe in religion? Exclude them from science, and damn them to the outer hell of irrationality. The irony that this is itself an irrational behaviour (or, better understood, is an act of strategic rationality rather than conceptual, to keep allies close and enemies away) escapes them, as our own sins always do.

John, it doesn't help your cause to write things like that. For years people have been claiming that science and religion are perfectly compatible. As you know, it's the official position of the National Center for Science Education. Scientific groups such as the National Academies and AAAS also promote this belief. It's only in the past decade that people like me have been pointing out the flaws in those positions and advocating a reexamination of that widespread assumption.

For decades we've been demonstrating that Young Earth Creationism and Intelligent Design Creationism conflict with science. They are not compatible with science. For decades we've been biting our tongue when softer versions of creationism are touted as "scientific," religious, alternatives to the extreme versions of creationism. The idea being promoted was that there's some arbitrary line separating some religious beliefs from others. If you stay on one side of that line you are scientific but if you step over the line you are not. People like Ken Miller made this argument: he says that he can be a Roman Catholic and all of his Roman Catholic beliefs are perfectly compatible with being a scientist. Michael Behe, on the other hand, is a Roman Catholic whose beliefs are not compatible with science, according to Ken Miller.

Now, along comes a group of people who are fed up with having to bite their tongue in the face of such obvious irrationality. We present counter-arguments to the claim of compatibility. We suggest that the difference between Ken Miller and Michael Behe is quantitative, not qualitative. We suggest that that imaginary line between scientific theists and non-scientific theists is just that: it's imaginary.

Yes, it's true that this argument labels Ken Miller, Francis Collins, and Simon Conway-Morris (among others) as irrational thinkers. It's true that we state quite categorically that they can't claim to be thinking like scientists while, at the same time, falling down before frozen waterfalls as though they were a sign from a supernatural being. Is this "exclusionary"? Well, I suppose it is but it's no more exclusionary that the group you support. You're not trying to include me in your group of accommodationists (or agnostics) are you?

My point is that your argument is illogical and irrelevant. All points of view are exclusionary to some extent. The people who agree with you are included and the people who disagree with you are not. You are being exclusionary. Does that have anything at all to do with whether your argument is valid or not? (Hint: no, it doesn't.) I thought philosophers were supposed to be good at logic and good at understanding false and irrelevant arguments.

You say, "The irony that this is itself an irrational behaviour ..." Why am I being irrational when I argue that religion isn't compatible with a scientific approach to knowledge? And why is it ironic? As far as I'm concerned, the ironic part is that for many decades we bought into the belief that some religious views were incompatible with science but other, equally bizarre, beliefs are perfectly compatible with science. Do you believe that God created the universe 10,000 years ago?—that's not scientific. Do you believe that God performs miracles just about every day?—that's compatible with science. Do you believe that God killed almost everyone on Earth in a giant flood?—that's not scientific. Do you believe that God sent his son to visit Earth then raised him back up into heaven?—that's perfectly compatible with science. Is this an example of rational thinking?

You also claim it's irrational to argue for the incompatibility of science and religion because it is bad politics ("to keep allies close and enemies away) escapes them, as our own sins always do"). Please, drop this argument. You've been following this debate for long enough to know better. In case, you've forgotten the issue, let me state the relevant points one more time.

• This is a discussion about the meaning of science and religion and whether they are compatible. My "allies" in that discussion are those who agree that science and religion are in conflict. My "enemies" are those, like you, who disagree. Please don't continue to made false assumptions about who my allies should be.
• From a political perspective, we argue that major organizations like NCSE should adopt a neutral position on the issue of compatibility. That's not what they have been doing. By allying with, and agreeing with, accommodationists they are excluding potential allies like me. I do not advocate that they officially adopt my position. I argue that they stop excluding me from the conversation by siding 100% with my "enemies." Got it? It's not rocket science. Try and keep up. The people who are being politically unwise are groups like NCSE who insist on adopting a controversial position that brings them into conflict with a great many scientists. We advocate neutrality. Why is that more irrational than taking a position that excludes people like me? Why are we labeled as the ones who are rejecting allies in the fight against creationism? You're not making sense here.
• When it comes to the bigger picture, I'm participating in a debate about rationality and superstition. The evolution/creation debate is a subset of that much larger debate. My allies in that large debate are fellow atheists and skeptics and we are fighting against superstitious beliefs of all kinds. My allies are people like Richard Dawkins, PZ Myers, and Jerry Coyne (among others). Many of the superstitious beliefs are religious. My enemies in that debate are all those people who promote superstition and irrational (IMHO) worldviews. Those "enemies" include Ken Miller, Francis Collins, and Simon Conway Morris as well as Michael Behe, Bill Demski, and Paul Nelson. Please don't try to tell me that Ken Miller should be my ally.¹ He's not on my side in the debate that matters. I'm the one who will decide who are my allies and who are my enemies. It's illogical for you to arbitrarily try and make that decision for me. This has been explained to you many times. Do you not listen or do you have cogent arguments about why my choice of allies is incorrect? (If you have cogent arguments, then why not make them instead of the strawman arguments you obviously prefer?)

For example, Coyne’s term “faithiest” is a term of opprobrium and abuse, just as Josh points out, other racial or sexual epithets are. While one may not identify the exclusion of non-”Caucasians” or LGBT’s in American society with that of accommodationists (or, for that matter of atheists in theist America), they are of the same kind if nowhere near the same degree. Dawkins’ claim that accommodationists “like the idea that someone has faith” or that we “have faith in faith” is a similar act of abuse. But they are rational, of course. No self-defeating behaviour for them, no sir.

If this is the main point you want to make then you could have done it much better—and much less hypocritically—by leaving out everything else. Make up your mind. Are you criticizing the position I take or are you just complaining about the rhetoric that's being used on both sides of the debate?

Anyone reading your posting would conclude that you are belittling the argument that science and religion are in conflict. Then to top it off you complain that in addition to being "unscientific," "irrational," and "exclusionary," your "enemies" are also being mean because they call you names. Don't you see any irony in that?

Look, I don’t care if atheists are aggressive or not. Certainly being excluded themselves, they have the right to be loud and proud. I think they should speak out at every turn. But does that require that they must denigrate and belittle those who don’t entirely agree with them? Must they turn into what they themselves despise? It seems, sadly, this is the human condition. But don’t pretend to be the vanguard of rationality when you are just as irrational and tribal as everyone else. The term for that is not “rational”, but “hypocritical”.

Pot, kettle black.

Anytime you'd like to continue this debate without calling me names, I'm happy to oblige. I'll try and refrain as well, although it does take some of the fun out of the discussion.

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1. I can ally with Ken Miller in the fight against extreme forms of creationism and I'm happy to do so. That doesn't mean I have to agree with him on everything else. He's a grownup—as am I—and he can handle people who disagree with him on some issues but agree with him on others.