Four Nails in Darwin's Coffin

 
Charles Darwin died on April 19, 1882 and he was buried in Westminster Abbey on Wednesday, April 26, 1882.

The IDiots have just realized that Darwin is dead. Tonight they will celebrate the event by presenting four discoveries that are not very well explained by Darwin's original theory of natural selection, published in 1859. (That's 151 years ago.) The "four nails" will be revealed at an event being held at Southern Methodist University.

I predict these "nails" are either gross misunderstandings of real science or discoveries that are explained by modern evolutionary theory. I'm pretty confident about this prediction since I know the reputation of the four hammers at the conference. They are ...

Douglas Axe, who thinks that the evolution of new protein folds is impossible.

Richard Sternberg, worries about what a gene is and about the relationship between genotype and phenotype.

Jonathan Wells, who's fond of making up elaborate tales about why evolution is wrong.

Stephen Meyer, who thinks that 2oth¹ century biochemistry and molecular biology disprove evolution.

I wonder if we're going to get any honest reporting on this event or whether journalists will rely entirely on DISCO press releases?

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1. No, this is not a mistake. Meyer hasn't yet made it into this century. Neither have the other IDiots.

On Describing IDiots as Creationists

This is from Satirizing Scientism a blog whose goal is "Mocking Scientism, Evolutionism, and the Arrogance of the Academy." A posting from last month has advice for evolutionists [Presenting: An op-ed piece from Dr. Strangelove].

5. Do not hesitate to mischaracterize ID's motives. Although ID proponents, unlike creationists, are really quite good about sticking to scientific arguments, it is to your advantage to not distinguish between the two. In fact, we recommend that you always append the term "creationism" to ID so that it reads intelligent design creationism.

Since we have succeeded in getting the courts to discredit creationism (thank you, ACLU!), this has the effect of (a) immediately attributing religious motives to ID, (b) implying that that ID has no more scientific basis than creationism, and (c) immediately diverts the discussion away from scientific evidence to fears of Taliban-like imposition of religious dogma. Because scientists are objective and open-minded, dogma should be ours to impose and hopefully that will increasingly be the case.

I'm one of those people who use the term "Intelligent Design Creationism."¹ I think it's quite appropriate to distinguish between various forms of creationism. There's Young Earth Creationism, Old Earth Creationism, and Scientific Creationism, so why not Intelligent Design Creationism? What all three have in common is belief in a creator. Theistic Evolution is another example of creationism.

It's extremely difficult to draw nice neat boundaries around these various kinds of creationism—especially Intelligent Design Creationism and Theistic Evolution Creationism. However, it's quite easy to distinguish between all forms of creationism and real science.

There is another point of view on this issue. Some people, including many theists and some atheists, think that the word "Creationist" should be reserved for Young Earth Creationists who believe in the literal truth of the Bible. By this definition, the other theists who believe in a supernatural designer would not be creationists even though their "designer" is also a creator, and, in fact, the same God that the Young Earth Creationists believe in.

From this perspective, the advocates of Intelligent Design can avoid being called creationists and they can continue to pretend that their beliefs are scientific and have nothing to do with God.

The Theistic Evolutionists also like this tactic. It allows them to avoid the creationist label as well. Accommodationists tend to avoid referring to Theistic Evolution as an example of creationism but they often dump Intelligent Design into the creationist tent. The logic behind this is to steer clear of alienating theistic evolutionists by pointing out that they are creationists. Apparently, theistic evolutionists are insulted when confronted with the truth.

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1. Those who believe in Intelligent Design are characterized as IDiots—this is just a short-hand way of referring to them since "Intelligent Design Creationists" is too hard to type.

Richard Dawkins Has a Few Words to Say About the Pope

 

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[Hat Tip: Pharyngula]

The Accommodationist Position

 
Some people are confused about the accommodationist position. Here's a good example from Janice Taylor published in The Times (London) and reproduced on RichardDawkins.net. The standard accommodationist rhetoric comes from atheists (secularists) who direct a great deal of anger toward the vocal atheists but go out of their way to excuse their religious friends.

I never thought I could utter this sentence, but I agree with the Pope. Like him I feel distaste for “aggressive forms of secularism”, although maybe I’d term it differently. I’d call it macho atheism as preached by unholy warlords.

...

Dawkins, Hawking, Hitchens: these male (always male) demagogues, bashing their anti-Bibles on to bestseller lists, smugly uncloaking the magician to show his act is mere incense smoke and mirrors. As if the rest of us require professors of theoretical physics or evolutionary biology in order to ponder the big questions of human existence, any more than we need a priest.

At least Christopher Hitchens, a US citizen, must maintain his thunderous volume to be heard above the American Tea Party movement’s Creationist tumult. (Although I thought it inconceivable that the mighty Hitch could ever be boring until I read his book, God is Not Great, a monotone, unreadable harangue.) But the other two are here in Britain. How are their crass insults to decent, thinking Catholics adding to a sane and necessary discussion about religion’s place in our public life?

...

Like the majority of British people, I have little religious faith, but the peace I feel in, say, a spartan Suffolk church connects me with my northern chapel-going ancestry. While I may not believe, the peace and quietude, the sense of something transcendent that makes my life on Earth seem at once precious and utterly insignificant, gives me sympathy towards those who do. My devout Catholic neighbour, who worked unpaid delivering babies in an African clinic, the born-again Christians who befriended my lonely aunt, even the Jamaican ladies in church hats who bring me tracts depicting in colourful line drawings the very moment the dead will rise again — they don’t make me long to assert my moral superiority or slap them round the head with Darwin.

And I’d guess the majority of my fellow heathens, those who don’t have iconoclastic non-fiction to flog, would agree. Secularism needs to stand behind the progressive movements within the Catholic Church, already challenging its policies on women, contraception, homophobia and child abuse, not run ahead of them screaming. It might concede that the Pope has a point that secular values have struggled in the past decade when morality was wholly defined by the free market.

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Atheists Must Apologize for Hitler

 
The Catholic League has just posted this on their website [ATHEISTS MUST APOLOGIZE FOR HITLER].

Catholic League president Bill Donohue reacts to the way British atheists are handling Pope Benedict XVI's trip to their homeland:

The pope cited Hitler today, asking everyone to "reflect on the sobering lessons of atheist extremism of the 20th century." Immediately, the British Humanist Association got its back up, accusing the pope of "a terrible libel against those who do not believe in God."

The pope did not go far enough. Radical atheists like the British Humanist Association should apologize for Hitler. But they should not stop there. They also need to issue an apology for the 67 million innocent men, women and children murdered under Stalin, and the 77 million innocent Chinese killed by Mao. Hitler, Stalin and Mao were all driven by a radical atheism, a militant and fundamentally dogmatic brand of secular extremism. It was this anti-religious impulse that allowed them to become mass murderers. By contrast, a grand total of 1,394 were killed during the 250 years of the Inquisition, most all of whom were murdered by secular authorities.

Why should atheists today apologize for the crimes of others? At one level, it makes no sense: apologies should only be given by the guilty. But on the other hand, since the fanatically anti-Catholic secularists in Britain, and elsewhere, demand that the pope—who is entirely innocent of any misconduct—apologize for the sins of others, let the atheists take some of their own medicine and start apologizing for all the crimes committed in their name. It might prove alembic.

The accommodationists are going to be all over this one. They'll rip Bill Donohue to shreds, right?

Waiting ....

Meanwhile, let's follow the logic. Atheists are people who don't believe in god. According to people like Bill Donohue, if you've failed to be convinced by any of the arguments in favor of superstition then you have to take the blame for the actions of everyone else who hasn't fallen for the common delusions of religion. (Including imaginary non-believers like Hitler.¹)

Okay. Where does this sort of logic take us? Bill Donohue and the Pope don't believe in the tooth fairy. Neither did any of the people who flew airplanes into buildings on September 11, 2001. .... Do you see where this is headed?

Donohue's "logic"—using the word in its loosest sense—is based on a false premise. He assumes that atheists (those who haven't accepted religion) share a common moral and ethical position that makes them collectively responsible for the actions of every atheist. In other words, he thinks that atheism is a religion like Roman Catholicism or Voodoo. That's just plain nonsense.

Why is it so hard for believers to understand the absence of belief? After all, every single one of them doesn't believe in hundreds of Gods. The Pope doesn't believe in Thor or The Flying Spaghetti Monster. Neither did Hitler, Stalin, or Mao. When can we expect an apology from the Pope?

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[Hat Tip: Why Evolution Is True]

1. PZ Myers has just posted a list of Hitler quotations proving beyond a shadow of a doubt that Hitler was a firm believer in God. Very likely the same God that the Pope and Bill Donohue believe in.

Tom Chivers' Top Five Books on Evolution

 
Tom Chivers has posted a list of his top five books on evolutionary biology [Best evolutionary biology books, from Stephen Jay Gould to Richard Dawkins]. Here they are ...

1. Wonderful Life: The Burgess Shale and the Nature of History (1989)
   Stephen Jay Gould
2. The Ancestor's Tale: A Pilgrimage to the Dawn of Life (2004)
   Richard Dawkins
3. Genome: The Autobiography of a Species in 23 Chapters (1999)
   Matt Ridley
4. Darwin's Dangerous Idea: Evolution and the Meanings of Life (1995)
   Daniel Dennett
5. The Blind Watchmaker (1986) Richard Dawkins

I agree with Wonderful Life but it's a little bit dated. I agree with The Blind Watchmaker—it's a must-read book for anyone interested in evolution. The Ancestor's Tale is okay but it doesn't make my list. Genome has nothing to do with evolution. Darwin's Dangerous Idea is just about the worst book on evolution that's ever been written. Dennet's version of evolution is conceptually flawed and his diatribes against Gould are simply a vehicle for demonstrating his (Dennet's) misconceptions about evolution.

Here's my list of the top five trade books ...

1. Wonderful Life: The Burgess Shale and the Nature of History (1989) Stephen Jay Gould


2. The Blind Watchmaker (1991 edition) Richard Dawkins


3. Why Evolution Is True (2009) Jerry Coyne


4. Reinventing Darwin: The Great Debate at the High Table of Evolutionary Theory (1995) Niles Eldredge


5. Extinction: Bad Genes or Bad Luck? (1991) David M. Raup

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Get the Popcorn!

 
According to Wikipedia, Karl Giberson (right), "... holds two Bachelor's degrees from the Eastern Nazarene College, and both a Master's degree and PhD from Rice University." He teaches courses on religion and science at Eastern Nazarene College.

He also writes articles defending religion. His latest appears on the BioLogos website [Doing Battle with Jerry Coyne’s Army of Straw Men]. The purpose of that posting is to take on Jerry Coyne of Why Evolution Is True. Jerry Coyne, as most of you know, is one of those atheists who dares to challenge theists, even moderate ones. Coyne is definitely not an accommodationist.

Apparently Coyne and the other vocal atheists (I am one) are insufficiently versed in the subtleties of religion and science and Karl Giberson is going to set us straight in a series of upcoming postings. (You'll need several bags of popcorn to watch this.) Like many before him, Giberson is going to try and prove that the vocal atheists are attacking strawman versions of religion and not the really good stuff that intelligent people believe in. Have we heard this before? [The Emperor's New Clothes and the Courtier's Reply] [On the Existence of God and the Coutier's Reply]

Here's what Giberson finds most objectionable.

Some of the arguments I want to examine include:

1. The tendency of the New Atheists to lambast laypeople who acquired some wrong ideas in Sunday School studying religion, but to let them off the hook for the wrong ideas about science they acquired in the public schools. Most Americans spend way more time studying science in school than they do studying religion in church. So why is “religion” to blame for bad religious ideas but science gets off the hook for dumb science ideas?

Speaking of strawmen, has anyone ever met a New Atheist like this? All the New Atheists with a science background (e.g., Jerry Coyne) are vigorous opponents of bad science. Some of us have reserved our harshest criticism for those who don't understand science, especially those theists who claim that religion doesn't conflict with science.

2. In our debate on USA Today, Jerry Coyne contrasted the complicated theological doctrine of the incarnation—the most mysterious idea in all of theology—to the function of penicillin—one of the best-understood ideas in biology. This is not an appropriate juxtaposition at all.

Shame on you Jerry Coyne! That's not an appropriate comparison at all. The appropriate response to a theist who raises "the complicated theological doctrine of incarnation" is, "Who the fu heck cares!" First theists need to establish that God exists and only then can they advance arguments about how their god behaves. The argument with atheists is about the existence of God, not incarnation. Atheists don't give a damn about incarnation, or original sin, or how many fairies can dance on the head of a pin. Show me the fairies.

3. The phrase “philosophical consistency” is tossed around like it represents some simple set of rules that allow us to see how religion is cheating. If only it were that simple. Science all by itself has issues with philosophical consistency that Coyne apparently doesn’t see because, if I may hazard a guess, he hasn’t spent a lot of time wrestling with the deeper issues of science.

Oh Boy! This is going to be fun. Apparently science is just as philosophically inconsistent as religion! Can't wait to find out about that.

Stay tuned folks.

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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.

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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.

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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.

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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!

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

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)

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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.

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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?

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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.

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