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Tuesday, March 23, 2010

National Accommodationists Host Templeton Prize Announcement

Richard Dawkins gets it right: Shame on the National Academy.

The American National Academy of Science has agreed to serve as the host for the Templeton Foundation as they give out a prize to the best person who speaks in favor of science and religion. (Francis Collins is the odds-on favorite to win.) This is despicable behavior for a "scientific" organization. Why can't they be neutral when it comes to the potential compatibility science and religion?

How many of you think the National Academy would host an award for the best atheist scientist?

Previous Templeton Prize winners include: Mother Theresa, Billy Graham, Aleksandr Solzhenitsyn, Chuck Colson and Freeman Dyson. Only one of these was eligible for membership in the National Academy of Science.


Sunday, March 21, 2010

Benefits of Chiropractic Care?

 
As most of you know, chiropractors in the UK are coming under the gun for making false, unscientific claims. This backlash was prompted by a suit launched by the British Chiropractic Association against Simon Singh. Singh's "crime"?—he suggested in an newspaper article that many claims by chiropractors were bogus.

If you want to support Simon Singh and support attempts to fix British libel laws go to the Sense About Science website: National Petition for Libel Law Reform.

The regulations governing chiropractors in North America are much more lax than those in the UK. Canadian and American chiropractors can make all sorts of claims about their treatment—claims that have no scientific evidence to support them—without incurring any penalties. Whereas British chiropractor websites have been take down for fear of prosecution, those in North America are still going strong.

I was reminded of this today when a chiropractor posted a comment on Canada's New Minister of State (Science and Technology) Is a Chiropractor. "Dr."1 Ross Carter included a link to his website, which advertises his private practice, so I had to delete the comment and replace it with a modified version.

Just for fun, here's some of the clams that are posted on GentleDR.com. According to Ross Carter, chiropractic care can help with a lot of problems such as ...
  • For pregnant women, they are able to deliver much easier.
  • For babies, they have improved developmental abilities and prevent the possibility of acquiring scoliosis.
  • For kids, it helps prevent asthma, ear infection, bedwetting, among other things.
  • For adults, they are able to generate more energy and increase productivity.
  • For senior individuals, they attain better balance and prevent injury caused by falling off.
I don't think any of these claims would be allowed in the UK.


1. British chiropractors are not allowed to imply that they are medical doctors.

Saturday, March 20, 2010

Michael Ruse: Confused Accommodationist, and Proud of It!

 
Michael Ruse has published some articles on The BioLogos Foundation website. Recall that this foundation was set up by Francis Collins and its mission is very clear.
The BioLogos Foundation is a group of Christians, many of whom are professional scientists, biblical scholars, philosophers, theologians, pastors, and educators, who are concerned about the long history of disharmony between the findings of science and large sectors of the Christian faith. We believe that the Bible is the inspired Word of God. We also believe that evolution, properly understood, best describes God’s work of creation. Founded by Dr. Francis Collins, BioLogos addresses the escalating culture war between science and faith, promoting dialog and exploring the harmony between the two. We are committed to helping the church – and students, in particular – develop worldviews that embrace both of these complex belief structures, and that allow science and faith to co-exist peacefully.

BioLogos represents the harmony of science and faith. It addresses the central themes of science and religion and emphasizes the compatibility of Christian faith with scientific discoveries about the origins of the universe and life. To communicate this message to the general public and add to the ongoing dialog, The BioLogos Foundation created BioLogos.org.
Got it? This is a group of people who think that science and religion (e.g. evangelical Christianity, Roman Catholicism) are compatible with science.

Michael Ruse's essay fits right in to this theme [Accommodationist and Proud of It, Part I] Problem is, Ruse doesn't understand why he's an accommodationist.
And yet, I am excoriated at every turn. Why? Simply, because I am an “Accommodationist.” I think that some kind of intellectual meeting is possible with religious believers, including Christian religious believers. As it happens, I believe that in America it is tremendously important politically to bring evolutionists together with people of religious commitment, but I absolutely and completely would not argue for a position that I thought wrong because it was politically expedient to do so. I would not say that emotion plays no role in my position. It does indeed. That helps me to take a stand that I think right against folk with whom I would much rather be a friend than a scorned enemy. But I think one can make a sound case for the position I have taken and still accept strongly today. In this essay, I try to explain what I believe and why I believe it. Why I am an “Accommodationist,” whatever that might mean, and proud of it.

Please understand: this piece I am writing now is not so much a response as a reaction. What I mean by this is that I don’t want to whine about being mistreated or misunderstood or whatever. As I have already intimated, in a way to respond in such a way would be almost hypocritical, because I rather like the fact that I stir people up so much that they want to strike out as they do. But I think there is some value in trying to see where I have come from, what I believe at the moment, and why I have fallen out (or raised the ire of, because frankly it was not I who started the quarrel) of people who in most respects you would think would be my natural allies. I am going to write this in a rather personal way because above all it is rather personal. I think, however, even those of you who think writers should never reveal anything of themselves will be able to strain through the personal and see the arguments underneath.
Oh dear! Ruse is terribly confused.

The accommodationist term was made up to describe atheists who go out of their way to defend religious beliefs as being compatible with science.1 They claim that religion is a way of knowing separate from science. They claim that science can't investigate the important claim of religion so it's perfectly okay to be a scientist and, at the same time, believe in life after death, miracles, and humans who are the son of God. They are accommodationsts because they pretend there's no conflict between science and many religious beliefs.

Accommodationists are NOT defined as people who have Christian friends and who are willing to ally with their friends on common causes like keeping creationism out of the schools. Those are traits shared by those of us who believe that science and religion are incompatible. Believe it or not, I have friends who believe in God and so does PZ Myers and Richard Dawkins. (I suspect Jerry Coyne probably has such friends as well.) Bringing that up only confuses the issue.

I can't believe that Ruse is ignorant of this distinction because he's written many articles about the compatibility of science and religion. Is he being deliberately misleading on the BioLogos website?

Perhaps he'll clarify this point and demonstrate that he understands the difference between being an accommodationist and being a friend and ally of people who believe in the supernatural. There are going to be more essays, but you can skip Part II [Accommodationist and Proud of It, Part II: A Christian Childhood]. There's nothing worth reading there.

P.S. Michael Ruse complains a lot about being misunderstood. The remedy is not to blame his opponents—although we are rarely blameless—but to try and write more clearly.


[HatTip: Jerry Coyne - Weekend Accommodationism]

1. They were originally called Neville Chamberlain Evolutionists, as Ruse points out in his article. That term has been dropped but you get the idea. Accommodationists describe otherwise intelligent atheists/evolutionists who compromise their principles when it comes to dealing with the beliefs of some (but not all) believers. They do this in order to maintain the peace.

Friday, March 19, 2010

I'm Not an Expert but I Sometimes Play One on TV

 


In Ziyology, Ziya finds the answer the question you've been asking for years...why do men have nipples?
[Daily Planet].



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.


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.




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

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.

Wednesday, March 17, 2010

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.





Ryan Gregory Visits Toronto

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


Starts: Friday, March 19th 2010 at 7:00 pm
Ends: Friday, March 19th 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



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."





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


Monday, March 15, 2010

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.


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?


Thursday, March 11, 2010

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.


Wednesday, March 10, 2010

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.


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.


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.