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Thursday, September 16, 2010

What the Pope Said

 
The current edition of the leader of the Roman Catholic Church is visiting Britain. It's a state visit, for reasons that aren't clear.

The Pope delivered a speech when he arrived [Pope's Holyroodhouse Speech Transcript]. Here's part of what he said ...
Even in our own lifetime, we can recall how Britain and her leaders stood against a Nazi tyranny that wished to eradicate God from society and denied our common humanity to many, especially the Jews, who were thought unfit to live. I also recall the regime’s attitude to Christian pastors and religious who spoke the truth in love, opposed the Nazis and paid for that opposition with their lives. As we reflect on the sobering lessons of the atheist extremism of the twentieth century, let us never forget how the exclusion of God, religion and virtue from public life leads ultimately to a truncated vision of man and of society and thus to a "reductive vision of the person and his destiny" (Caritas in Veritate, 29).

...

Today, the United Kingdom strives to be a modern and multicultural society. In this challenging enterprise, may it always maintain its respect for those traditional values and cultural expressions that more aggressive forms of secularism no longer value or even tolerate. Let it not obscure the Christian foundation that underpins its freedoms; and may that patrimony, which has always served the nation well, constantly inform the example your Government and people set before the two billion members of the Commonwealth and the great family of English-speaking nations throughout the world.
Accommodationists take note. The Pope has just told us that "extreme atheism" and Nazis can be lumped together in the same paragraph. He has just announced that "aggressive forms of secularism" don't respect or tolerate the cultural values of most Britons.

I expect the same criticism of the Pope that I see from accommodationists when they think "New Atheists" have stepped over the line.

Waiting ......

Meanwhile, the British Humanist Society responds [BHA Reacts to Pope's first remarks on state visit].
The notion that it was the atheism of Nazis that led to their extremist and hateful views or that somehow fuels intolerance in Britain today is a terrible libel against those who do not believe in god. The notion that it is non-religious people in the UK today who want to force their views on others, coming from a man whose organisation exerts itself internationally to impose its narrow and exclusive form of morality and undermine the human rights of women, children, gay people and many others, is surreal.


Wednesday, September 15, 2010

I Can't Believe He Actually Said That!

 
GilDodgen is an Intelligent Design Creationist who sometimes posts at Uncommon Descent. Here are links to some examples of his "work."

Why Do We Call Them IDiots?

IDiot Logic on Display at Uncommon Descent

Resistance to Science

A State of Extreme Cognitive Dissonance

IDiot "Irony"

Poor IDiots, Wrong Again

Last week he posted an article that I ignored—as did everyone else with anything better to do (like watching reruns of Hogan's Heros) [see, Why Secular and Theistic Darwinists Fear ID]. That article generated a lot of comments on Uncommon Descent and this made GilDodgen very excited. It prompted him to post again today [My Proclivity for Inspiring Long UD Threads] in order to offer this explanation.
My thesis is that people like me, a former materialist atheist, who have been influenced by logic, reason, and evidence (i.e., the ID movement) represent the greatest threat to the reigning nihilistic and anti-intellectual Darwinian orthodoxy.
Yep, I'm sure that's the answer.


Monday, September 13, 2010

Science, Religion, Politics, and American Law

 
Here's part of an interview with Richard Dawkins on the Salon website [The flying spaghetti monster]. I stand solidly with Dawkins on this particular issue. He is absolutely correct that the war between rationalism and superstition trumps the local fight with American creationists.
I have to ask you about a letter that I've come across from the intelligent design advocate William Dembski. He thanked you for your outspoken atheism. His letter to you said, "I want to thank you for being such a wonderful foil for theism and for intelligent design more generally. In fact, I regularly tell my colleagues that you and your work are one of God's greatest gifts to the intelligent design movement. So, please, keep at it!" What do you make of that?

Yeah, I get that quite a lot. It is a very difficult political dilemma that we face. In the United States of America at the moment, there's a big battle going on, educationally, over teaching evolution in public schools. Science is definitely under attack. And evolution is in the front-line trench of that battle. So a science defense lobby has sprung up, which in practice largely means an evolution defense lobby. Now, it is true that if you want to win a court case in the United States where it's specifically on the narrow issue of should evolution be taught in the public schools, if somebody like me is called as a witness and the lawyer for the other side says, "Professor Dawkins, is it true that you were led to atheism through the study of Darwinian evolution?" I would have to answer, "Yes." That of course plays into their hands because any jury is likely to have been brought up to believe that atheists are the devil incarnate. And therefore, if Darwin leads to atheism, then obviously we've got to throw out Darwinism. Well, that is exactly what Dembski is getting at. He claims to like the things that I say because I am playing into his hands by allowing people like him to make the equation between Darwinism and atheism.

But it's not just Dembski. I've heard this from various scientists -- hardcore evolutionists -- who wish you would tone down your rhetoric, quite frankly.

That is absolutely true.

They say this hurts the cause of teaching evolution. It just gives fire to the creationists.

Exactly right. And they could be right, in a political sense. It depends on whether you think the real war is over the teaching of evolution, as they do, or whether, as I do, think the real war is between supernaturalism and naturalism, between science and religion. If you think the war is between supernaturalism and naturalism, then the war over the teaching of evolution is just one skirmish, just one battle, in the war. So what the scientists you've been talking to are asking me to do is to shut my mouth. Because for the sake of what I see as the war, I'm in danger of losing this particular battle. And that's a worthwhile political point for them to make.

Well, I think a lot of these scientists really do accept Stephen Jay Gould's idea of non-overlapping magisteria. These are hardcore evolutionists, but they say religion is an entirely different realm. So you, with your inflammatory rhetoric, just muddy the waters and make life more difficult for them.

That is exactly what they say. And I believe that actually is the political reason for Steve Gould to put forward the non-overlapping magisteria in the first place. I think it's nonsense. And I'll continue to say that I think it's nonsense. But I can easily see, politically, why he said that and why other scientists follow it. The politics is very straightforward. The science lobby, which is very important in the United States, wants those sensible religious people -- the theologians, the bishops, the clergymen who believe in evolution -- on their side. And the way to get those sensible religious people on your side is to say there is no conflict between science and religion. We all believe in evolution, whether we're religious or not. Therefore, because we need to get the mainstream orthodox religious people on our side, we've got to concede to them their fundamental belief in God, thereby -- in my view -- losing the war in order to win the battle for evolution. If you're prepared to compromise the war for the sake of the battle, then it's a sensible political strategy.

Throughout the ages, one has resorted to that kind of political compromise. And maybe it would be a good thing for me to do as well. But as it happens, I think the war is more important. I actually do care about the existence of a supreme being. And therefore, I don't think I should say something which I believe to be false, which is that the question of whether God exists is a non-scientific question, and science and religion have no contact with each other, so we can all get along cozily and keep out those lunatic creationists.


Sunday, September 12, 2010

Right On!

 
sandwalk.blogspot.com is probably written by a male somewhere between 66-100 years old. The writing style is academic and happy most of the time.
Except that I'm only 64. See UrlAi.com.


I was so impressed by the accuracy of this analysis that I decided to check out some other blogs. Here's the result for Post-Darwinist.
post-darwinist.blogspot.com is probably written by a male somewhere between 26-35 years old. The writing style is academic and upset most of the time.
I don't think Denyse O'Leary is going to be happy about this! Three of the four conclusions are wrong. The only one they got right is that she is upset most of the time.

On the other hand, John Wilkins will probably be pleased with,
evolvingthoughts.net is probably written by a male somewhere between 66-100 years old. The writing style is academic and upset most of the time.
It's always flattering to come across as being older and wiser than you really are!


Hat Tip: Friendly Atheist: This is Why You Can’t Trust Blog-Analyzing Websites

Wednesday, September 08, 2010

Mutations and Complex Adaptations

Michael Lynch is one of those rare scientists who not only think outside the box but successfully stimulate others to do so. I read all of his papers and I'm always very impressed, even though I don't always agree with everything he says.

I recently attended the 18th Annual Meeting of the Society for Molecular Biology and Evolution in Lyons, France, where I met Michael Lynch for the first time. He gave a talk on Evolution of Mutation Rates, a topic many of us treat with a large degree of skepticism—until we're confronted by Michael Lynch. He makes a convincing case for variable rates of mutation in different species and he challenged us (me) to defend the idea that there was a linkage between DNA replication rates and mutation rates. That's a linkage I've always assumed would constrain mutation rates to a narrow range. Now I'm not so sure.

I've been putting off posts about the many exciting things I heard in Lyon because I'm busy with the 5th edition of my textbook but SteveF provoked me into saying something about Michael Lynch by posting a comment on my blog [Larry, you might find this shiny new paper by Michael Lynch in PNAS interesting]. Damn you, SteveF, and thanks.

We had been discussing how the IDiots view mutation and I mentioned that Michael Behe was mostly, but not entirely, correct when he said that if two mutations are required for a complex adaptation then it is very unlikely to happen [Bated Breath].

In a paper just published in PNAS, Michael Lynch explains why it's "not entirely correct" (Lynch, 2010).
The development of theory in this area is rendered difficult by the multidimensional nature of the problem. One strategy has been to ignore all deleterious mutations and to assume that selection is strong enough and mutation weak enough relative to the power of random genetic drift and recombination that evolution always proceeds by the sequential fixation of single mutations (e.g., refs. 6–11). Such an approach provides a useful entree into the evolutionary dynamics of rare adaptive mutations with large effects. Under these conditions, the expectations are clear—with larger numbers of mutational targets and a reduced power of random genetic drift, the rate of adaptation will increase with population size, although more slowly than expected under the assumption of sequential fixation (12, 13). The motivation for these models, which are specifically focused on total organismal fitness, derives from case studies of adaptations with apparently simple genetic bases, e.g., some aspects of insecticide resistance (14), skin pigmentation (15), and skeletal morphology in vertebrates (16).

Nevertheless, a broad subset of adaptations cannot be accommodated by the sequential model, most notably those in which multiple mutations must be acquired to confer a benefit. Such traits, here referred to as complex adaptations, include the origin of new protein functions involving multiresidue interactions, the emergence of multimeric enzymes, the assembly of molecular machines, the colonization and refinement of introns, and the establishment of interactions between transcription factors and their binding sites, etc. The routes by which such evolutionary novelties can be procured include sojourns through one or more deleterious intermediate states. Because such intermediate haplotypes are expected to be kept at low frequencies by selection, evolutionary progress would be impeded in large populations were sequential fixation the only path to adaptation. However, in all but very small populations, complex adaptations appear to be achieved by the fortuitous appearance of combinations of mutations within single individuals before fixation of any intermediate steps at the population level (e.g., refs. 17–26).
Read the paper. You'll find an interesting discussion of recombination—a discussion that does not assume most of the standard myths about recombination. Lynch points out that when it comes to fixing two independent mutation the effect of recombination is just as likely to break up linkage as enhance it. Recombination cannot make much of a contribution to the fixation of two mutations that are required for a complex adaptation unless the mutations are closely linked (e.g. same gene).

However, there are some circumstances where large population sizes can overcome the problem of fixing multiple mutations even if there's a negative correlation between mutation rate and population size. This is the "scaling" parameter mentioned in the title of Lynch's paper.

This is not unlike what Behe's says in The Edge of Evolution where he points out that in malaria parasites (e.g. Plasmodium falciparum) the probability of a double mutation is significant because there are trillions of organisms. In large mammals, however, the probability is much lower because the population size in much smaller.
Changing multiple amino acids of a protein at the same time requires a population size of an enormous number of organisms. In the case of the malaria parasite, these numbers are available. In the case of larger creatures, they aren't.
Behe concludes that this is the "edge" of evolution. Since these kinds of mutations are required for complex adaptations, it follows that evolution can't account for complex adaptations. You'll have to read Behe's book to find out who can design such complex adaptations.

So far, this is pretty much standard orthodoxy. Given that multiple, independent, mutations might be required simultaneously it's very unlikely that evolution will ever see them in some species. It's one of the reasons why Behe's book is so unexciting. There are other ways to account for the adaptive value of multiple mutations, including the fact that many of the individual mutations may be slightly deletersious but, nevertheless, fixed by random genetic drift.

What Lynch's paper shows is that the standard orthodoxy might be wrong! His models suggest that fixation of multiple mutations in small population may be well within the range of probability required for evolution of complex adaptations.
In summary, the preceding results suggest that some general scaling properties may exist for the rapidity with which various types of adaptations can be assimilated in different populationgenetic contexts. In particular, prokaryotes appear to be much more efficient than eukaryotes at promoting simple to moderately complex molecular adaptations, and substantially so for those involving joint changes at different genetic loci. In contrast, adaptations requiring three or more novel mutations may arise more frequently in small populations, regardless of the level of recombination between selected sites. In the absence of comprehensive information on the molecular basis of adaptation in multiple lineages (i.e., the typical number of sites involved and their degree of epistatic interactions), these general predictions are currently difficult to test. Nevertheless, the ideas presented herein are likely to bear significantly on a number of ongoing controversies regarding the nature of adaptation, including the barriers imposed by adaptive valleys in a fitness landscape (22, 40), the role of compensatory mutation in evolution (41), and the relative rates of incorporation of adaptive and nonadaptive mutations in various lineages (42–44).(my emphasis-LAM)


Lynch, M. (2010) Scaling expectations for the time to establishment of complex adaptations. Proc. Natl. Acad. Sci. (USA) publishe online, Sept. 7, 2010 [doi: 10.1073/pnas.1010836107]

World University Rankings

The World University Rankings 2010 are out. The rankings are based on factual information, such as number of papers published, but also on personal opinions. 40% of the score is determined by a survey of academics that asks about "academic reputation." Another major component is based on a survey of employers who are asked to evaluate the quality of undergraduates they hire.

All types of university are including in the ranking but certain adjustments are made for size—for example, the faculty at smaller universities publish fewer papers. The various categories are identified in the list.


I don't agree with these rankings. It's going to be extremely difficult to complete against the Ivy League schools in the USA and Oxbridge in the UK because of their enormous reputations from the past. Who knows whether these schools are as good as they think they are? You aren't going to find out by giving such a high score to reputation surveys.

Having said that, there are a few things we can learn from the World University Rankings. Here's the top ten.
  1. University of Cambridge UK (L,VH,FC)
  2. Harvard University USA (L,VH,FC)
  3. Yale University USA (M,VH,FC)
  4. University College London UK (L,VH,FC)
  5. Massachusetts Institute of Technology USA (M,VH,CO)
  6. University of Oxford UK (L,VH,FC)
  7. Imperial College London UK (L,VH,FC)
  8. University of Chicago USA (M,VH,FC)
  9. California Institute of Technology USA (S,VH,CO)
  10. Princeton University USA (M,VH,CO)
Four of the top ten universities in the world are in the United Kingdom. No matter what you might think of the way these schools are ranked, it's time we stopped propagating the myth that American universities are by far the best in the world. The UK has about 62 million people or about one-fifth the population of the United States. By any reasonable criterion, it is the country that's created and maintained the best universities in the world. If you won't go that far, at least you'll have to concede that America is not the slam-dunk winner, as so often assumed (mostly by Americans).

The top Canadian university is McGill University at number 19. The University of Toronto comes in at 29th, just behind the University of California, Berkeley. Toronto and UC Berkeley are both XL, VH, FC. The only other Very Large university ahead of them is the University of Michigan at number 15.


Monday, September 06, 2010

Julian Baggini on Science vs. Religion

 
Here's a free-lance philosopher I agree with, sometimes [Julian Baggini]. He's writing for The Independent about Stephen Hawking's new book [Julian Baggini: If science has not actually killed God, it has rendered Him unrecognisable].
This reflects an inconvenient truth about science that religion would prefer to ignore. For although it is true that science doesn't rule out a role for religion in providing meaning, or a God who kick-started the whole universe off in the first place, it does leave presumed dead in the water anything like the God most people over history have believed in: one who is closely involved in his creation, who intervenes in our lives, and with whom we can have a personal relationship. In short, there is no room in the universe of Hawking or most other scientists for the activist God of the Bible. That's why so few leading scientists are religious in any traditional sense.

This point is often overlooked by apologists who grasp at any straw science will hold out for them. Such desperate clinging happened, disgracefully, in the last years of the philosopher Antony Flew's life. A famous atheist, Flew was said to have changed his mind, persuaded that the best explanation for the "fine-tuning"of the universe – very precise way that its conditions make life possible – was some kind of intentional design. But what was glossed over was that he was very clear that this designer was nothing like the traditional God of the Abrahamic faiths. It was, he clearly said, rather the Deist God, or the God of Aristotle, one who might set the ball rolling but then did no more than watch it trundle off over the horizon. This is no mere quibble. The deist God does not occupy some halfway house between atheism and theism. Replace Yaweh with the deist God and the Bible would make less sense than if you'd substituted Brian for Jesus.

So it is not true that science challenges only the most primitive, literal forms of religion. It is probably going too far to say that science makes the God of Christianity, Judaism and Islam impossible, but it certainly makes him very unlikely indeed.
The last sentence is technically correct in the same sense that this sentence is technically correct: "It is impossible to prove that the tooth fairy doesn't exist but science makes her existence very unlikely indeed."

Julian Baggini might be right about this but he's dead wrong about some other things. For example, in The New Atheist Movement is destructive, he writes,
“What do you think about the four horsemen?” It's a question I often get asked, quite understandably, since I wrote the Very Short Introduction to atheism. That book provides no answer, because it came out before Richard Dawkins, Daniel Dennett, Sam Harris and Christopher Hitchens unleashed their apocalypse. But surely I must have an opinion on the biggest phenomenon in popular atheism since Bertrand Russell?

Well I do, but it comes with one huge caveat: I have not read any of their books. That does not, however, disqualify me from having an opinion about them. Let me defend both apparently intellectually disreputable confessions.
I'm sorry but the fact that he hasn't read the books does, indeed, disqualify him from having an "informed" opinion about them. He may have another kind of opinion but why should I listen to it?

Baggini also says,
For me, atheism’s roots are in a sober and modest assessment of where reason and evidence lead us. That means the real enemy is not religion as such, but any kind of system of belief that does not respect these limits on our thinking. For that reason, I want to engage with thoughtful, intelligent believers, and isolate extremists. But if we demonise all religion, such coalitions of the reasonable are not possible. Instead, we are likely to see moderate religious believers join ranks with fundamentalists, the enemies of their enemy, to resist what they see as an attempt to wipe out all forms of religious belief.
Well, he's just said that science makes the Judeo-Christian-Islamic god "highly unlikely indeed." That doesn't leave very many "thoughtful, intelligent believers" to accommodate, does it? Having just demonized Judaism, Christianity, and Islam, what moderate religions does he think atheists should form coalitions with? Are there any deists out there?


Sunday, September 05, 2010

Mutation and Intelligent Design Creationism

 
One of the long-standing criticisms of Intelligent Design Creationists is their continuing effort to confuse the general public about modern evolutionary theory. Here's the latest effort by "johnnyb," just posted on Uncommon Descent [Responding to Merlin Part I – How Merlin’s Paper Validates Several Claims of the ID Movement].

The article discusses a recent paper by Francesca Merlin1 from the Department of Philosophy, University of Montréal, Québec, Canada [Evolutionary Chance Mutation: A Defense Of the Modern Synthesis’ Consensus View]. Note the title. She is defending the "Modern Synthesis' Consensus View." (The paper was published in an online, open access, journal called Philosophy & Theory in Biology. The link to the paper isn't working.)

Here's what johnnyb says,
Many people claim that ID’ers have made up the word “Darwinism” as a straw man which we can easily knock down. Nothing could be further from the truth. ID’ers use the word Darwinism, because it identifies, with technical specificity, what we are objecting to. Darwinism specifically means that the mutations which are selected are happenstance – they are not determined by the needs of the organism. This is specifically labelled as the “Darwinian” view by Merlin (see pg 3 of her paper).

This is important because many ID’ers support many parts of evolutionary theory – myself included. However, most ID’ers think that one particular part of evolutionary theory is fundamentally flawed – the Darwinian view of mutations. Many ID’ers are basically neo-Lamarckians, believing that mutations (at least the biologically beneficial ones) tend to be goal-oriented rather than haphazard.

So it is important to note that the controversies spoken of by IDers which are happening in biology are real controversies. Merlin didn’t write this paper as a critique of a scientist to a non-scientist, but rather a controversy among scientists as to whether or not the Darwinian conception of mutations are valid. Therefore, from this we can conclude that (a) there is nothing wrong with Darwinism as a term for a specific type of evolution, (b) ID’ers use the term Darwinism in its correct, technical sense (in contrast to Lamarckianism), and (c) there is a genuine conflict happening among biologists. I have no doubt that Wright, Jablonka, and Lamb are in the minority. That neither invalidates their work nor the significance of the controversy.
First, let's address the "Darwinism" strawman. We know exactly why the IDiots use the term "Darwinism" instead of "modern evolutionary theory." It's because "Darwinism" harkens back to the ideas of Charles Darwin in 1859. The IDiots want everyone to think that modern scientists are slaves to the ideas of a Victorian from the 1800's. They've tarred Charles Darwin with repeated attacks on his "racist" and "immoral" views and they want to stick most modern evolutionary biologists to that tar baby. Furthermore, they know full well that "social Darwinism" is evil—by using "Darwinism" to describe modern science they conjure up an association with that non-scientific viewpoint.

Most IDiots don't understand modern evolutionary theory so they don't know the difference between it and "Darwinism." Some IDiots do know the difference, but they lie about it and continue to use "Darwinism" for its rhetorical value.

Enough of that. I'm more interested in the new version of Intelligent Design Creationism that johnnyb is describing. It seems to be very similar to what Ken Miller describes in his book Finding Darwin's God and it may not be very far from what Francis Collins writes in The Language of God. Does johnnyb have any scientific evidence that mutations are "goal-oriented" or is his version just the same-old, same-old, criticism of modern evolutionary theory? Does johnnyb have an explanation for how such "goal oriented" mutations arise? After all, that's the essence of a proper scientific theory. It's not sufficient to just criticize the consensus scientific view, you also have to provide a better explanation that accounts for the facts. How about it? Are there any IDiots out there who want to take a shot at explaining how "goal-oriented" mutations arise?

Incidentally, if you want to read what a real scientist has to say about mutations then go look at the series of postings by Arlin Stoltzfus on Mutationism. You can see the last posting at: The Mutationism Myth, VI: Back to the Future. It has links to all the others. Arlin explains what Darwin really meant when he talked about variation—Darwin didn't know about mutations or modern genetics.


1. Currently at L'Institut d'Histoire et de Philosophie des Sciences et des Techniques at the Université de Paris.

How Darwinism Ruined America

 

John G. West is a senior fellow at Disco and associate director of the Center for Science and Culture. He has written a book titled Darwin Day in America: How our politics and culture have been dehumanized in the name of science.

I haven't read it yet but I intend to. I subscribe to the old-fashioned, quaint, notion of "know your enemy."1 Here's a short summary posted on the website.
Darwin Day in America tells the disturbing story of scientific expertise run amuck, exposing how an ideological interpretation of Darwinian biology and reductionist science have been used to degrade American culture over the past century through their impact on criminal justice, welfare, business, education, and bioethics.

At the dawn of the last century, leading scientists and politicians giddily predicted that science—especially Darwinian biology— would supply solutions to all the intractable problems of American society, from crime to poverty to sexual maladjustment.

Instead, politics and culture were dehumanized as scientific experts in thrall to the assumptions of philosophical materialism began treating human beings as little more than animals or machines. In criminal justice, these experts denied the existence of free will and proposed replacing punishment with invasive “cures” such as the lobotomy. In welfare, they proposed eliminating the poor by sterilizing those deemed biologically unfit. In business, they urged the selection of workers based on racist theories of human evolution and the development of advertising methods to more effectively manipulate consumer behavior. In sex education, they advocated creating a new sexual morality based on “normal mammalian behavior” without regard to longstanding ethical and religious imperatives.

Based on extensive research with primary sources and archival materials, John G. West’s captivating Darwin Day in America tells the story of how American politics and culture have been corrupted by scientistic ideology. Marshaling fascinating anecdotes and damning quotations, West’s narrative explores the far-reaching consequences for society when scientists and politicians deny the essential differences between human beings and the rest of nature. It also exposes the disastrous results that ensue when experts claiming to speak for science turn out to be wrong. West concludes with a plea for the restoration of democratic accountability in an age of experts.
This is really confusing. I've been told that America is a Christian nation and it certainly looks that way from the outside. Christianity seems to dominate American culture and all the polls indicate that Americans are among the most religious nations in the industrialized world. All the politicians promote god thinking and the Bible at every opportunity. At times it seems like half the radio stations are preaching Christian virtues.

In the face of all this religion and godliness, how did a few evil, misguided, scientists2 manage to subvert an entire country? I guess I'll have to read the book to find out.

1. So it is said that if you know your enemies and know yourself, you can win a hundred battles without a single loss.
If you only know yourself, but not your opponent, you may win or may lose.
If you know neither yourself nor your enemy, you will always endanger yourself. Sun Tzu: The Art of War.

2. For the record, I oppose social Darwinism and all its implications. So do 99.99% of scientists.

Tuesday, August 31, 2010

Is Glenn Beck an IDiot?

 
Watch this video right to the end and hear Glenn Beck say, "Charles Darwin, the father of modern day racism." That's the standard creationist line—one that's especially prominent on the IDiot blogs. Beck's statement is factually incorrect. It's actually the Christian God of the old testament who's the father of modern day racism.




The Mutationism Myth, VI: Back to the Future

This is the eighth in a series of postings by guest blogger, Arlin Stoltzfus. You can read the introduction to the series at: Introduction to "The Curious Disconnect". The first part is at: The "Mutationism" Myth I. The Monk's Lost Code and the Great Confusion. The second installment is: Theory vs Theory. The third part is: The Mutationism Myth, II. Revolution. The fourth installment is: The Mutationism Myth: III Foundations of Evolutionary Genetics. Part five is The Mutationism Myth, IV: Mendelian Heterodoxies. The sixth installment was The Mutationism Myth, V: The response to Mendelian heterodoxies.

This is Arlin's last contribution. The entire series has been an excellent introduction to the history of evolutionary theory and the concept of mutationism. There are many ways in which the so-called "Modern" Synthesis has to be revised and extended. One of them is to reinstate the concept of mutationism which was purged from evolutionary theory in the 1940s. If you want to understand why this is important then these articles are the place to start.



The Curious Disconnect

Today on The Curious Disconnect (credits), we wrap up our 6-part series on the Mutationism Myth, and set the stage for the future by locating the primary weakness of the 20th century neo-Darwinian consensus in its theory of variation.

I'd like to thank Larry Moran for hosting this series of posts on Sandwalk. If it still seems like a good idea later in the year, I will continue the Curious Disconnect on my own blog site (to be announced).

The Mutationism Myth, part 6. Back to the Future

The Mutationism Myth, a story about how the discovery of genetics affected evolutionary thought, continues to be part of modern neo-Darwinism's monologue with itself (e.g., Charlesworth and Charlesworth, 2009), being used even by leading thinkers calling for an "Extended" Synthesis (e.g., Pigliucci, 2010 1). Since April, we've been deconstructing the Mutationism Myth by exploring what the early Mendelians actually thought, and how their view was replaced by the Modern Synthesis (MS).

Today we'll take the opportunity to review what we've learned and start unpacking its relevance for the future of evolutionary biology.

Review

In the Mutationism Myth (see part 1 for examples), the founders of genetics misinterpret their discovery, concluding that evolution takes place by large mutational jumps, without selection. The false gospel of these "mutationists" brings on a dark period of confusion and error that lasts until the 1930s, when theoretical population geneticists (Fisher, Haldane and Wright) prove that Mendelian genetics is not only compatible with selection, but provides the missing link that completes Darwin's theory and unites all the biological disciplines. The "Modern Synthesis" combining genetics and selection becomes the foundation for all subsequent evolutionary thought.

As we discovered, the Mutationism Myth isn't very accurate. Heredity is not missing from Darwin's theory; selection is not missing from the Mendelian view. Darwin had a theory of heredity both in the sense of a set of phenomenological laws, and in the sense of a mechanism to account for them (part 2). Both were wrong. The Mendelians synthesized genetics and selection, rejecting Darwin's "Natural Selection" theory due to its dependence on fluctuations or "indefinite variability" (defined by Darwin as the subtle variations that arise anew each generation in response to conditions of life). As we know today, such enrivonment-induced fluctuations are non-heritable.

In part 3, we found that the Mendelians laid the conceptual foundations of evolutionary genetics (later formalized mathematically), while part 4 addressed how their view diverged from Darwinian orthodoxy. The Mendelians assumed that new hereditary variants arise rarely and discretely, by mutations whose effects may be large or small. Each new mutation is likely to be rejected, but it may be accepted by chance, especially if it improves fitness. Because, in this view, change depends on discrete events of mutation, the Mendelians (part 4) considered the process of mutation to be a source of initiative, discontinuity, creativity and direction in evolution (Stoltzfus, 2006). This view expanded the role of variation well beyond the subordinate role of raw materials that Darwin had imagined.

The Mendelians were unable to convince naturalists (the majority of their biologist peers) to accept their new view of evolution, nor even a new view of inheritance. Many naturalists remained wedded to Lamarckian and Darwinian views of "soft inheritance".

As we found out in part 5, the "Modern Synthesis" (modern neo-Darwinism) claimed to reconcile Darwin's own view with genetics, though it quietly ignored Darwin's errors while depicting the Mendelians as foolish "saltationists", dismissing their "lucky mutant" view and their ideas about the role of mutation in evolution. In the MS view, each species has a "gene pool" that automatically soaks up and "maintains" hereditary variation, providing abundant "raw materials" for adaptation. The key innovations of this view were to define "evolution" as "shifting gene frequencies" in the "gene pool", to erase the link between "Darwinism" and Darwin's own theory of soft inheritance, and to develop a theory of causation in terms of population-genetic "forces", in which continuous shifts in allele frequencies are the common currency of causation. The new theory put mutation in a subordinate position of supplying infinitesimal "raw materials" for selection. As a result, the MS created a consensus where the Mendelians had failed: naturalists such as Ernst Mayr found that they could accept Mendelian genetics without giving up adaptationist preconceptions.

A bright line

The backdrop for this whole discussion (in case you missed it) is that the MS is strikingly wrong in its neo-Darwinian departures from the Mendelian view. I've implied this several times, and perhaps I've waved my hands and pointed vaguely to mountains of molecular evidence contradicting the MS, but I haven't made this point perfectly clear.

In a moment, I will do that, but first I want to make clear what is at stake.

The Mendelians allowed that evolutionary change could be initiated by an event of mutation, and they interpreted this to mean that mutation was (to an unknown degree) a source of initiative, discontinuity, creativity and direction in evolution. The MS represents a very deliberate rejection of this view, and proposes instead that evolution is a complex sorting out of available variation to achieve a new multi-locus equilibrium, literally by "shifting gene frequencies" in the "gene pool". The rate of evolution, in this view, does not depend on mutation, which merely supplies the "gene pool" with variation; evolution is not shaped by mutation, which is the "ultimate" source of variation, but not the proximate source.

When I made this distinction at a 2007 symposium in honor of W. Ford Doolittle, Joe Felsenstein was in the audience and pointed out that, while Fisher may have looked at things in this way, Wright's stochastic view took into account random events, like new mutations. It's true that Wright's "shifting balance" model assigns a prominent role to random genetic drift, while Fisher's view was deterministic. However, these are just two different flavors of the same "shifting gene frequencies" paradigm: neither view incorporates new mutations. The absence of new mutations from Wright's shifting balance process is apparent from the fact that Patrick Phillips (1996) extended it to include a new starting phase ("phase 0") of "waiting for a compensatory mutation".

The fact that contemporary evolutionary biologists, for the most part, don't understand this aspect of their intellectual heritage is not evidence of a cover-up. Scientists don't get much chance to learn history. The history that they absorb is mainly from stories that appear in scientific writings, like the Mutationism Myth and the Essentialism Story, stories that represent Synthesis Historiography (Amundsen, 2005), the discipline of telling history in ways that make things turn out right for the Modern Synthesis. Synthesis Historiography teaches us that "saltationism" (Mayr's pejorative term for the Mendelian view) and other alternatives to neo-Darwinism are nonsensical, "doomed rivals", supported only by "typologists", creationists, vitalists and other crazies. That is, Synthesis Historiography teaches the TINA doctrine: There Is No Alternative.

As contemporary research drifts away from the "gene pool" theory and the Darwinian doctrines of the MS, each evolutionary biologist remains confident that, due to the TINA doctrine, his own view must be "neo-Darwinian". In reality, alternatives are being explored with increasing vigor in molecular evolution, evo-devo, and evolutionary genetics.

A few folks today are in the reverse situation of being familiar with MS orthodoxy, but not with recent research. Dawkins (2007) stakes his critique of a book by "intelligent design" creationist Michael Behe entirely on his faith in the gene pool theory. Behe claims, in effect, that there was not sufficient time for all the mutations needed to account for evolution. Dawkins responds by attacking the premise that evolutionary rates depend on mutation rates:

"If correct, Behe's calculations would at a stroke confound generations of mathematical geneticists, who have repeatedly shown that evolutionary rates are not limited by mutation. Single-handedly, Behe is taking on Ronald Fisher, Sewall Wright, J.B.S. Haldane, Theodosius Dobzhansky, Richard Lewontin, John Maynard Smith and hundreds of their talented co-workers and intellectual descendants. Notwithstanding the inconvenient existence of dogs, cabbages and pouter pigeons, the entire corpus of mathematical genetics, from 1930 to today, is flat wrong. Michael Behe, the disowned biochemist of Lehigh University, is the only one who has done his sums right. You think? The best way to find out is for Behe to submit a mathematical paper to The Journal of Theoretical Biology, say, or The American Naturalist, whose editors would send it to qualified referees."

With his signature over-the-top rhetoric, Dawkins insists that "mathematical genetics" has proven that evolutionary rates are not limited by mutation. Allowing for some exaggeration, this is an accurate representation of MS orthodoxy ca. 1959, the approximate vintage of Dawkins's views. If Mayr had been alive, he might have said the same thing.

Meanwhile, no one who has been active in evolutionary genetics research in the past 15 years would represent the current state of knowledge in this way. If you want to know what a contemporary researcher would say, take a look at the most recent issue of Evolution in which the article by Douglas Futuyma (famous for his evolution textbook) gives many examples of how evolutionists (including himself) repeated the doctrine that mutation does not "limit" evolution, but argues that we are no longer making this dubious assumption. Another example would be the piece by Ronny Woodruff and James Thompson (1998) that introduces their symposium volume on Mutation and Evolution.2

Yet the MS and its "gene pool" theory have left their mark on evolutionary biology, even if the MS itself has largely disappeared from the collective memory of researchers. One indelible mark is what Gillespie calls "The Great Obsession" of population genetics to understand the "maintenance of variation", but that's a story for another day.

Another indelible mark is the long absence of mutationist models of "adaptation", a topic that has blossomed just in the last dozen years. Allen Orr has achieved well deserved fame for his innovations in this area, and we'll discuss his work briefly in the next section. For now, let us note how other researchers have pointed out the absence of such models:

"Almost every theoretical model in population genetics can be classified into one of two major types. In one type of model, mutations with stipulated selective effects are assumed to be present in the population as an initial condition . . . The second major type of models does allow mutations to occur at random intervals of time, but the mutations are assumed to be selectively neutral or nearly neutral." (Hartl & Taubes, 1998)

"The process of adaptation occurs on two timescales. In the short term, natural selection merely sorts the variation already present in a population, whereas in the longer term genotypes quite different from any that were initially present evolve through the cumulation of new mutations. The first process is described by the mathematical theory of population genetics. However, this theory begins by defining a fixed set of genotypes and cannot provide a satisfactory analysis of the second process because it does not permit any genuinely new type to arise. " (Yedid and Bell, 2002)

These authors are not trying to make a point about history or about the Modern Synthesis: they are simply claiming the novelty of their own models of adaptation that incorporate new mutations. And what they are saying is that the paradigm of 20th-century population genetics is "shifting gene frequencies": overwhelmingly, it's a body of theory about what happens to the variation that is present in a population as an initial condition, not about a larger-scale process in which there are new beneficial mutations.3

One small step for a phage, one giant leap for evolutionary biology

The actual role of mutation in evolution is not what is theorized in the MS. Many arguments could be made to support this contention, but I'm going to make just one argument drawing on one source, namely Rokyta, et al., 2005. I choose this argument because it is particularly compelling and concise. My argument addresses the lucky mutant view of initiative or (to put it another way) dynamics.

Rokyta, et al. is a study of parallel evolution in an experimental population of the bacteriophage phiX174, published in Nature Genetics. It was hailed as "the first empirical test of an evolutionary theory" (Bull & Otto, 2005), where the theory in question is Orr's (2002) ingenious extension of Gillespie's (1984) "mutational landscape" model to take into account predictions of extreme value theory.4

In spite of the fancy name, the "mutational landscape" model of sequence evolution is simple. Rather than considering all conceivable evolutionary changes from a starting sequence, we simplify the problem by considering only changes that occur via 1-bp mutations. That set of possibilities, by definition, is the "mutational landscape" or (my preferred term) the "evolutionary horizon". Each change will shift the evolutionary horizon, but it's easy to recompute the horizon, because it's easy to enumerate (theoretically) all the alternative sequences.

We are going to make this a model of beneficial changes ("adaptation"). A beneficial mutation is introduced into the population of N individuals at some total rate Nu, and faces acceptance with a probability of 2s, based on the classic formula p = 2s for the probability of fixation of a new beneficial mutation.5 For beneficial substitution i with selection coefficient si, the probability6 is just Nu*2si. If we divide an individual Nu*2si by the sum of all such values on the horizon, we get a normalized probability: the probability that the next step in our evolving system is step i. The factor Nu*2 is the same for every step, so it cancels out: only the si values matter. To evolve our sequence, we just sample from this probability distribution of possible steps, then recompute the new evolutionary horizon in preparation for the next step. Easy! 7

From past experiments, Rokyta, et al. know which steps on the horizon are beneficial, and they even know the selection coefficients. They know that sometimes, the same evolutionary steps happen in parallel, in replicate phage populations. They can compare the observed pattern of parallel evolution with the pattern predicted from theory.

Now, the preceding description suggests something fascinating: the cutting edge of evolutionary genetics today, with papers that get published in Nature Genetics with commentaries, uses experimental systems to explore the "lucky mutant" view of parallel evolution.

But the story gets even better. Rokyta, et al actually reject Orr's model, in its original version. They find more parallel evolution than expected. Why? Because the model treats all mutation rates equally. Note above that we canceled out mutation rates on the grounds that they are all the same. But that's not realistic. Some mutations are more likely than others, and this will affect the rate at which they are introduced into the population and subjected to acceptance or rejection. The more heterogeneity in rates of mutation, the more parallel evolution. Rokyta, et al. found that if they revised the model to take into account transition:transversion bias (I think it's about 5-or 6-fold under the experimental conditions), then the predicted amount of parallelism matched the observed amount.

Just let that soak in for a moment. We have an experimental study and a precise model. Evolution in this model is characterized by origin-fixation dynamics, dependent on the rate of mutational introduction of new alleles, and on their probability of fixation. Both factors affect the outcome of evolution; both factors affect the chance of parallelism. The experimental study eliminates (statistically) a model that lacks mutational bias in the introduction of new alleles. Thus the study clearly illustrates the dual causation of evolutionary change, in regard to its dynamics.

Back to the future

The MS is wrong, and not in a small way: it's wrong because reality just looks too much like the antithesis of the MS, i.e., the mutationist view. For instance, as we found out in part 4, Vavilov (1922; see Stoltzfus, 2006) understood the dual causation of parallel evolution, including the role of parallel variation. By contrast, Mayr famously said that the search for homologous genes or homologous mutations was foolish.

This mistaken prediction is repeated ad nauseam in the evo-devo literature. If you have been following along, you now understand why Mayr would make such a prediction. The MS makes substantive claims about evolution, among which are the claim that, while mutation is ultimately necessary to keep the "gene pool" from drying up, selection doesn't need to wait for a new mutation, but draws together a multi-locus optimum from the abundance of raw materials in the gene pool; "evolution" is so far removed from the process of mutation, with so many complex dynamic processes interceding, that the outcome of evolution does not depend on specific events of mutation. If evolution really were like that, parallel mutation would be unimportant. That is, Mayr's prediction accurately reflects the logic of the MS. But as the Rokyta, et al study (and many others) show, the prediction is not fulfilled.

According to Dawkins, "the entire corpus of mathematical genetics" from 1930 to "today" (i.e., about 1959, for Dawkins) would be "flat wrong" if one accepts the premise that evolution depends on new mutations, or that it is limited by the mutation rate. While this view is not often defended, that isn't because it's Dawkins's own personal opinion. Dawkins is accurately characterizing a theory that makes substantive claims about the world, a theory that most of us have forgotten. One of these claims is that "evolution" can be represented mathematically as a process of shifting the frequencies of alleles already present in an initial population, without new mutation; sometimes this doctrine is invoked by saying that "macroevolution" can be extrapolated from "microevolution".

If evolution actually worked like this, then evolutionary change would not exhibit a dependence on the rate of mutation, and Dawkins would be right in his criticism of Behe. But this is wrong. In fact, the dependence is so sensitive that effects of only a few-fold are noticeable, as the Rokyta, et al study (and many others) shows.

I'm not going to mince words. The MS is wrong, and not in a small way: reality looks too much like the mutationist view that we (the scientific community) rejected when we bought into the MS. We need another theory1, perhaps several others.

The road less traveled

What's wrong about the MS, and what its replacement(s) must replace, is its theory of the role of variation in evolution. In future posts on the Curious Disconnect, I intend to focus on this issue. The Mutationism Myth suggests a lesson about how to develop (or rather, how not to develop) a theory of variation.

Darwin knew that hereditary variation played a vital role in evolution. He studied the subject intensely. He found that organisms vary in many different ways, and on many scales, but the evidence on heredity was bewildering and inconclusive. Lacking the means to derive a mechanism of evolution by reasoning upward from genetics, Darwin reasoned downwards from his premises that 1) organisms are exquisitely and pervasively adapted to their niches, 2) selection must have played some role in this, and 3) Mother Nature never makes a jump. Gould argues that Darwin's willingness to posit precise restrictions on variation was a stroke of genius.8 Darwin knew that discrete "sports" (mutants) could be heritable, but he discounted them: they could not make his theory work as desired. Instead, he staked his "natural selection" theory on the heritability of fluctuations, because they were infinitesimal, indefinite (unbiased), and "everywhere present", being induced in abundance whenever organisms encountered altered "conditions of life". Inferring the heritability of fluctuations completed his theory and made it work.

But it was wrong: the fluctuations that made Darwin's theory work are non-heritable, as the Mendelians discovered.

The architects of the MS tried again, with advantages unavailable to Darwin. Not only did they know genetics, they had some mathematical tools to work out unforeseeable implications of genetic concepts. However, they didn't have the knowledge to distinguish among different, genetically consistent modes of evolution. They had to fill in this gap somehow. Their downwards Darwinian reasoning and their upwards Mendelian reasoning met in the middle with the "gene pool": a theory of population genetics that would supply abundant, infinitesimal, "random" variations, in order to rationalize their commitment to the same premises Darwin accepted. That was the genius of the MS.

But again, it was wrong.

If we look at Darwinism in Popperian terms, as a theory1 that takes risks and generates potentially falsifiable claims, then (counterintuitively) it is largely a theory of the role of variation in evolution. The claims that selection is "important", and that it has some inalienable role in adaptation, carry little risk and have been widely accepted for 150 years. By contrast, the restrictions that Darwinism places on variation, in order to make it a subordinate factor that supplies "raw material" to selection, are risky and controversial, e.g., the claim that variation is random with respect to the direction of evolution, or that the rate of evolution does not depend on the rate of mutation, or the "gradualist" claim that variation is not a source of discontinuity. The architects of the MS invested the "gene pool" with nearly magical properties in order to improve the prospects for adaptation. Problematic claims about the role of variation are, and have been for 150 years, the overwhelming basis for scientific criticism of Darwinism.

And this problematic view of variation is based on reasoning from the premise that organisms are exquisitely and pervasively adapted to their niches, to the conclusion that variation must play just the right role of supplying abundant raw materials to make this possible. I believe that there is something fundamentally wrong with this mode of reasoning. Perhaps it betrays a kind of subconscious Panglossian agenda. Every time I give a lecture on mutation-biased evolution, someone suggests that perhaps the mutation biases themselves are adaptive, as though this inference could restore one's faith that everything turns out for the best, and that "the ultimate source of explanation in biology is the principle of natural selection" (Ayala, 1970). Remarkably, the evo-devo-inspired view that seems destined for inclusion in the emerging "Extended Synthesis" is headed down much the same path, with a focus on the idea that the process of variation has been jiggered to make things turn out right for adaptation. What's revealing about this new view is how little attention its proponents have paid to understanding precisely, in terms of population-genetic causation, how the process of variation shapes evolution, before jumping ahead to the shadowy inference that the process of variation itself was shaped by selection for this very role.

We are not going to go down that same road here on the Curious Disconnect, which should make things all the more interesting.

References

Ayala, F. J. 1970. Teleological Explanations in Evolutionary Biology. Philosophy of Science 37:1-15.

Bull, J. J., and S. P. Otto. 2005. The first steps in adaptive evolution. Nat Genet 37:342-343.

Charlesworth, B., and D. Charlesworth. 2009. Darwin and genetics. Genetics 183:757-766.

Dawkins, R. 2007. Review: The Edge of Evolution. Pp. 2. International Herald Tribune, Paris.

Gould, S. J. 2002. The Structure of Evolutionary Theory. Harvard University Press, Cambridge, Massachusetts.

Hartl, D. L., and C. H. Taubes. 1998. Towards a theory of evolutionary adaptation. Genetica 103:525-533.

Medawar, P. B. 1967. The Art of the Soluble. Methuen and Co., London.

Nei, M. 2007. The new mutation theory of phenotypic evolution. Proc Natl Acad Sci U S A 104:12235-12242.

Orr, H. A. 2002. The population genetics of adaptation: the adaptation of DNA sequences. Evolution Int J Org Evolution 56:1317-1330.

Phillips, P.C. 1996. Waiting for a compensatory mutation: phase zero of the shifting-balance process. Genetical Research, Cambridge 67:271-283.

Rokyta, D. R., P. Joyce, S. B. Caudle, and H. A. Wichman. 2005. An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus. Nat Genet 37:441-444.

Woodruff, R. C., and J. D. Thompson. 1998. Preface in R. C. Woodruff, and J. D. Thompson, eds. Mutation and Evolution. Kluwer, Dordrecht, The Netherlands.

Yedid, G., and G. Bell. 2002. Macroevolution simulated with autonomously replicating computer programs. Nature 420:810-812.


Notes

1 Pigliucci, along with Gerd Muller, edited a book on "the extended Synthesis" with papers from a select group of thinkers who were invited in July, 2008 to a special meeting in Altenberg, Austria. The book is now available in paperback: http://www.amazon.com/Evolution-Extended-Synthesis-Massimo-Pigliucci/dp/0262513676

2 from p. 1 "Although mutation is a key parameter in the genetics of populations, the role of mutation as an evolutionary factor has been debated since the time of Darwin. Early geneticists, who held to the 'classical' view of the genome as being homogeneous with occasional mutant alleles, saw new mutation as a major determining force in adaptive change. When the classical view was replaced with the 'balance' view of the genome, i.e., highly heterogeneous, pre-existing variation became more important as the resource on which selection would act. Many, therefore, began to disregard new mutation as a significant force in evolution, since the level of genetic diversity is already so high that new mutants would generally be expected to add little to that resource . . . Mechanisms responsible for maintaining levels of genetic diversity became the focus of attention, and mutation pressure is now thought by many to have only minor significance, especially when compared to selection, recombination, gene flow, and similar factors. We think this position, like the classical view, is too extreme. While there can be little doubt that mutation per se is not the principle driving force it was once believed to be for phenotypic evolution, we see growing evidence that its role is under-appreciated in important situations. The rate and pattern of mutation can be influenctial variables in adaptive responses, and the role of mutation in evolution deserves to be reexamined."

3 Orr (2002) notes the absence of such models by making a far more sweeping claim that population genetics has ignored, not just new-mutations models of adaptation, but all models of adaptation, and instead has focused on neutral and deleterious alleles. That is an odd thing to say, given that the quantitative genetics of adaptation have been a topic for a long time. In any case, here is what Orr says: "Evolutionary biologists are nearly unanimous in thinking that adaptation by natural selection explains most phenotypic evolution within species as well as most morphological, physiological, and behavioral differences between species. But until recently, the mathematical theory of population genetics has had suprisingly little to say about adaptation. Instead, population genetics has, for both historical and technical resasons, focussed on the fates of neutral and deleterious alleles. The result is a curious disconnect between the verbal theory that sits at the heart of neo-Darwinism and the mathematical content of most evolutionary genetics. "

4 Also known as the theory of records—"record" in the sense of "pinnacle of achievement". Given a series of records, such as the world record in the long-jump, what's the interval of time to the next record, and by how much will it break the previous record? The theory of records addresses such questions. Can you see how this would be useful to make a predictive theory of adaptation?

5 Rokyta, et al. used a different formula for the probability of fixation, because the classic approximation only works for s << 1, whereas the phiX174 populations experience very large s, sometimes s > 1.

6 Formally Nu*2si is not a probability but a steady-state rate (e.g., for an infinite-alleles model). If we treat it as an instantaneous rate, and then compare it to all other instantaneous rates, this makes it a relative probability of choosing step i over a short interval.

7 For our present purposes, we don't need to explain Orr's addition to this model, which was a theory of the distribution of the favorable s values under generalized assumptions (oddly, the commentators on Rokyta, et al. did not mention that Orr's theory wasn't really needed, and that the study really was a test of the mutational landscape model itself).

8 Gould (2002, p. 140) is not endorsing Darwin's error about fluctuation. Darwin's followers think of that mistake as a trivial detail. Instead Gould is endorsing a more general inference. Here is what he writes. "Darwin reasoned that natural selection can only play such a role [as exclusive source of creativity and direction] if evolution obeys two crucial conditions: (1) if nothing about the provision of raw materials—that is, the sources of variation—imparts direction to evolutionary change; and (2) if change occurs by a long and insensible series of intermediary steps, each superintended by natural selection—so that "creativity" or "direction" can arise by the summation of increments.


Under these provisos, variation becomes raw material only—an isotropic sphere of potential about the modal form of a species. Natural selection, by superintending the differential preservation of a biased region from this sphere in each generation, and by summing up (over countless repetitions) the tiny changes thus produced in each episode, can manufacture substantial, directional change. What else but natural selection could be called 'creative,' or direction-giving, in such a process? As long as variation only supplies raw material; as long as change accretes in an insensibly gradual manner; and as long as the reproductive advantages of certain individuals provide the statistical source of change; then natural selection must be construed as the directional cause of evolutionary modification.


These conditions are stringent; and they cannot be construed as vague, unconstraining, or too far in the distance to matter. In fact, I would argue that the single most brilliant (and daring) stroke in Darwin's entire theory lay in his willingness to assert a set of precise and stringent requirements for variation—all in complete ignorance of the mechanics of heredity. Darwin understood that if any of these claims failed, natural selection could not be a creative force, and the theory of natural selection would collapse. "



Credits: The Curious Disconnect is the blog of evolutionary biologist Arlin Stoltzfus, available at www.molevol.org/cdblog. An updated version of the post below will be maintained at www.molevol.org/cdblog/mutationism_myth6 (Arlin Stoltzfus, ©2010)


Sunday, August 29, 2010

Center for Inquiry Doublespeak

 
On August 27th, the Center for Inquiry USA issued a statement on the controversy surrounding the renovation of the Islamic Cultural Center in New York City [CFI Releases Statement in Response to the Proposed Islamic Religious Center in Lower Manhattan]. Here's the last paragraph.
CFI maintains that a mosque near Ground Zero, in and of itself, is no worse than a church, temple, or synagogue. It is undeniable that the 9/11 terrorists were inspired by their understanding of Islam, and that currently there are far more Islamic terrorists in the world than terrorists of other faiths, but the deeper threat confronting humanity is not confined to Islam. To the contrary, it is presented by all religions. Religious morality is based on faith and authority, with the authority often being a sacred text cobbled together long ago that readily lends itself to contradictory interpretations. The Bible and the Koran have been used to justify almost everything, from mass slaughter of those with other beliefs, to slavery, to oppression of women and gays and lesbians, to the throttling of scientific research—as evidenced by the recent halt to stem-cell research. Faith will continue to harm and kill, whether it is in Oklahoma City or New York City, until people stop basing their conduct on imaginary divine commands and accept their responsibility to reason together. To honor those killed by faith fanatics, Ground Zero and its immediate vicinity should be kept free of any newly constructed house of worship — of any religion.
This statement triggered a storm of controversy in the blogosphere. The main objection was that CFI is adopting an anti-religious stance that sounds intolerant. I agree.

I'm a proud member of the Centre for Inquiry Canada but I'm less than pleased with the American version. The people speaking and writing for CFI USA don't speak for me. This included Paul Kurtz, founder of CFI, before he was ousted.

CFI USA soon realized they had goofed. Today they sent out a revised statement [CFI Releases a Clarification and Revision of Statement on Ground Zero Controversy]. Here's the last paragraph of today's (August 29th) statement.
CFI’s unequivocal support for the legal right of Muslims to place a community center near Ground Zero does not imply that CFI views the new center as an event to be celebrated. To the contrary, CFI is committed to the position that reason and science, not faith, are needed to address and resolve humanity’s problems. All religions share a fundamental flaw: they reflect a mistaken understanding of reality. On balance, CFI does not consider houses of worship to be beneficial to humanity, whether they are built at Ground Zero or elsewhere.
Yeah, right. It's better but it's still silly. I look forward to a time when nobody wants to built houses of worship but until that time they are free to build them wherever they want, as far as I'm concerned. The "revised" (i.e. backpedeling) statement is better but it still sounds like CFI USA is against building of houses of worship when they should be advocating rationality and skepticism.

I wish there was a way to give up my membership in the international organization but retain my membership in the Centre for Inquiry Canada.


Saturday, August 28, 2010

The Scientific Method

 
Over at Respectful Insolence, Orac picked up on a comment by Dr. R.W. and said [Some excellent questions for medical reporters] ....
An excellent idea, and Dr. R.W. has a list of some things that every medical journalist should know. My favorites? These:
  • Outline the scientific method. (I'm betting there are a lot of journalists out there reporting on medicine who can't outline the scientific method.)
  • Explain why consideration of biologic plausibility is important in the evaluation of health claims and why evidence based medicine often fails when biologic plausibility is not taken into account. (This one is hard, but knowing the answer would eliminate a lot of truly ignorant articles like the one Parker-Pope wrote yesterday.)
I was surprised that Orac picked teaching the scientific method as one of his favorites. I don't think there's any such thing as a "scientifc method" that garners majority support among scientists and/or philosophers. This led to a discussion in the comments section of his post.

What do you think? Is there a "scientific method"? If so, what is it?


Wednesday, August 25, 2010

Bated Breath

 
Jonathan Wells made an announcement that sets my heart all aflutter. I just can't wait for his new book to appear Zombie Genes?.
Richard Dawkins, Douglas Futuyma, Michael Shermer, Philip Kitcher, Kenneth Miller, Jerry Coyne and John Avise have also written recent books in which they argue that much of the human genome consists of "junk DNA" that provides evidence for Darwinian evolution--and evidence against intelligent design.

But the notion of "junk DNA" owes more to the historical contortions of neo-Darwinian theory than to biological evidence. In fact, there is now a large and growing body of evidence that Collins, Dawkins, Futuyma, Shermer, Kitcher, Miller, Coyne and Avise are dead wrong on this point--as I will show in my forthcoming book, The Myth of Junk DNA.
I teach a course that analyzes the "science" behind Intelligent Design Creationism and the book we use is Icons of Evolution. Problem is, the students have already written over 100 essays on this book and there's little more they can say. The book has been thoroughly trashed.

Next year we'll have an entirely new Jonathan Wells book to kick around. Yeah!


[Photo Credit: Jonathan Wells from Conservapedia]

Tell Me Something I Don't Know

 
Chad Orzel is bored so he asked his readers to Tell him something he doesn't know. It's lot's of fun reading the comments on his blog so I though I'd ask for more.

Can you tell me something I don't know? I can assure you that there's plenty of opportunities.