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Monday, October 18, 2010

Critical Thinking about Religion?

Frans de Waal is a biologist specializing in primate behavior—mostly non-human primates. He wrote an article for The New York Times on Morals Without God.

Like so many others, de Waal can't imagine what kind of morals and ethics a society would create without guidance from supernatural beings.
Even the staunchest atheist growing up in Western society cannot avoid having absorbed the basic tenets of Christian morality. Our societies are steeped in it: everything we have accomplished over the centuries, even science, developed either hand in hand with or in opposition to religion, but never separately. It is impossible to know what morality would look like without religion. It would require a visit to a human culture that is not now and never was religious. That such cultures do not exist should give us pause.
I do not accept that my society is steeped in Christian morality. I believe that Christianity has borrowed some very sound ethical principles shared by all societies and tried to make them its own. That does not mean that our wish to discourage murder and theft is a Christian value.

Furthermore, those values that are uniquely religious—such as banning contraception, prohibiting gay marriage, and rejecting evolution—are frequently the very ones that are rejected by modern Western societies.

It is NOT impossible to know what a society would look like without religion. It would look very much like the societies of Western Europe. Those societies have retained the moral and ethical values that pre-date and supercede religion and they have rejected the values of Christianity that they have outgrown. In countries like France, Belgium, the Netherlands, and Denmark citizens are rapidly approaching the point where religions are completely irrelevant. The Pope can continue to hold Sunday mass at St. Peter's and he can create a bevy new saints every year, but hardly anyone will care. Most of them don't even care today. In fact, most Canadians don't care even though more than 40% of us are nominally Roman Catholic.

I'm surprised that de Waal doesn't mention this since he is from the Netherlands and he makes this an important part of his opinion piece in The New York Times article.

It's true that no historical human cultures have been free of superstition. Almost all of them believed in magic. Our ancestors thought there were gods who controlled the weather and they feared evil gods who would do them harm. They believed in magic potions, fairies, and dragons. They believed in lucky numbers and developed elaborate rituals to avoid bad fortune (don't let a black cat cross your path).

The fact that all past cultures were highly superstitious is interesting, but it certainly doesn't trouble me the same way it troubles Frans de Waal. He said, "That such [non-superstitious] cultures do not exist should give us pause." Why? Is it hard to explain why older cultures believed silly things that aren't true?
Other primates have of course none of these problems, but even they strive for a certain kind of society. For example, female chimpanzees have been seen to drag reluctant males towards each other to make up after a fight, removing weapons from their hands, and high-ranking males regularly act as impartial arbiters to settle disputes in the community. I take these hints of community concern as yet another sign that the building blocks of morality are older than humanity, and that we do not need God to explain how we got where we are today. On the other hand, what would happen if we were able to excise religion from society? I doubt that science and the naturalistic worldview could fill the void and become an inspiration for the good. Any framework we develop to advocate a certain moral outlook is bound to produce its own list of principles, its own prophets, and attract its own devoted followers, so that it will soon look like any old religion.
This is really hard to understand. On the one hand, de Waals admits that we don't need God to make us moral. On the other hand, he suggests that our society is steeped in Christian morality. He seems to be saying that religion is important even if God is unnecessary.

One of the essential hallmarks of critical thinking is skepticism, especially skepticism about your own personal beliefs. One should always be prepared to question one's own assumptions.

One way of doing this is to look for evidence that will back up or refute your assertion. In this case, Frans de Waal should be asking himself whether there are any examples of societies that are adopting naturalistic worldviews and abandoning religion. If there are such societies, then is it true that they are in the process of evolving prophets and devotees and forming another kind or religion?

I've been in Europe many times over the past decade and I've not seen any evidence of this new religion that's supposed to look just like any old religion. There's no evidence of this new form of religion in North America either. I currently live in a very secular society in the suburbs of Toronto. Half of the people in my immediate neighborhood are non-believers and most of remainder do not agree with the moral and ethical tenets of any religion—especially Christian ones.

None of the non-believers in my neighborhood seem to have a pressing need to find another kind of religion to replace the one they've discarded. We are happy that Canada legalized gay marriage, prohibits capital punishment, allows abortion, promotes gender equality, and defends the right of every Canadian to have affordable access to health care. We don't need prophets and priests to tell us that this is good for society.

Frans de Waal is wrong to claim that our ethics and morals are derived from religion. He is wrong to claim that past belief in silly superstition is evidence that those superstitions can't be discarded. And he is wrong to believe that when societies discard religion they will be faced with such a void that they will have to re-invent religion.


Sunday, October 17, 2010

Lies, Damned Lies, and Medical Science

 
Here's an article from the Atlantic that everyone should read: Lies, Damned Lies, and Medical Science. It highlights the efforts of John Ioannidis to discover what's true and what's not true about modern medical research publications and clinical trials. I think this is going to become one of the hottest topics in science within a few years. The fallout will be horrendous when the public realizes that doctors are not as scientific as we thought.

Some interesting quotes from the article should prompt you to follow the link to the Atlantic website.
It didn’t turn out that way. In poring over medical journals, he was struck by how many findings of all types were refuted by later findings. Of course, medical-science “never minds” are hardly secret. And they sometimes make headlines, as when in recent years large studies or growing consensuses of researchers concluded that mammograms, colonoscopies, and PSA tests are far less useful cancer-detection tools than we had been told; or when widely prescribed antidepressants such as Prozac, Zoloft, and Paxil were revealed to be no more effective than a placebo for most cases of depression; or when we learned that staying out of the sun entirely can actually increase cancer risks; or when we were told that the advice to drink lots of water during intense exercise was potentially fatal; or when, last April, we were informed that taking fish oil, exercising, and doing puzzles doesn’t really help fend off Alzheimer’s disease, as long claimed. Peer-reviewed studies have come to opposite conclusions on whether using cell phones can cause brain cancer, whether sleeping more than eight hours a night is healthful or dangerous, whether taking aspirin every day is more likely to save your life or cut it short, and whether routine angioplasty works better than pills to unclog heart arteries.
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Still, Ioannidis anticipated that the community might shrug off his findings: sure, a lot of dubious research makes it into journals, but we researchers and physicians know to ignore it and focus on the good stuff, so what’s the big deal? The other paper headed off that claim. He zoomed in on 49 of the most highly regarded research findings in medicine over the previous 13 years, as judged by the science community’s two standard measures: the papers had appeared in the journals most widely cited in research articles, and the 49 articles themselves were the most widely cited articles in these journals. These were articles that helped lead to the widespread popularity of treatments such as the use of hormone-replacement therapy for menopausal women, vitamin E to reduce the risk of heart disease, coronary stents to ward off heart attacks, and daily low-dose aspirin to control blood pressure and prevent heart attacks and strokes. Ioannidis was putting his contentions to the test not against run-of-the-mill research, or even merely well-accepted research, but against the absolute tip of the research pyramid. Of the 49 articles, 45 claimed to have uncovered effective interventions. Thirty-four of these claims had been retested, and 14 of these, or 41 percent, had been convincingly shown to be wrong or significantly exaggerated. If between a third and a half of the most acclaimed research in medicine was proving untrustworthy, the scope and impact of the problem were undeniable. That article was published in the Journal of the American Medical Association.


[Hat Tip, again to John Wilkins]

Mark Anthony Signorelli Doesn't Like Darwinians

 
According to his blog posting Mark Anthony Signorelli is, "is a poet, playwright, and essayist." He has a very strong opinion about evolution and the "Darwinists" who promote it [The Jurisdiction of Science]. His main point is that anyone should be allowed to criticize modern evolution and I agree with him on that. However, just as there's good science and bad science, there's also valid criticism and not-so-valid criticism. The not-so-valid criticism often comes from people who don't understand evolution.

Here's how Signorelli ends his rant. Judge for yourself ...
The fact that our intellectual climate is such that so many merely scientific thinkers so consistently and so brazenly offer up their lame insights on the most momentous of topics does indeed constitute an essential aspect of our present barbarism. The attempt to understand the entirety of human existence in biological terms has less of philosophical seriousness about it, and more of professional pride. We would find ourselves in a very nearly analogous situation if a conclave of plumbers began writing books, asserting that water was the essential element in all nature, that our thoughts could best be understood as so many conduits to our actions, and that society itself is nothing other than a complex structure of pipes, aqueducts, and irrigatory canals, sending and receiving every life-giving benefit. Such a mode of philosophizing might be enjoyable for a while, but it could never be persuasive, and it could never be right. In both cases, we would recognize that the hard labor of authentic thought was being replaced by the facile application of a vocational jargon. In both cases, we would conclude that a form of knowledge, immensely valuable in its own sphere, had been distorted and falsified, by being rashly extended far beyond that sphere.

And this is why the Darwinians so constantly complain about hostile foreigners intruding into their sovereign territory of biology: in order to distract us from the reality of their own imperial ambitions. There is one enormous fact about the contemporary intellectual scene, and it is not the fact that non-scientists are relentlessly asserting their opinions on scientific questions; it is the fact that many scientists are now in the incurable habit of relentlessly asserting their opinions – their very dopey opinions – on a range of philosophical and cultural issues. And this is a situation that is infinitely more perilous and revolting than if the opposite were the case, because it means that those persons who, by trade and by training, are least competent to judge mankind’s most momentous questions are precisely the ones who are more and more commonly doing just that. We should not be distracted from this terrible reality by the Darwinians incessant howling about the rest of us critiquing their opinions; rather, we should recognize their noise for the rhetorical feint that it is, but one more tawdry polemical maneuver utilized by the proponents of an ideology that is false, ignorant, and dishonest to its core.
Let's be clear about my complaint. It's not that scientists are making foolish statements about evolutionary psychology—that's one area where Signorelli and I agree. My compliant is that he writes an essay on the more general topic of why poets should be allowed to criticize science—an essay that criticizes scientists (like me) who get upset when people misrepresent science in order to advance their personal agendas. The irony is that in this very essay Signorelli reveals a serious lack of understanding of the science behind evolutionary biology beginning with use of the creationist term "Darwinians" to describe all modern evolutionary biologists.

There are good poets and bad poets. It would be wrong to criticize all poetry just because you've read some bad poets. Right?

I agree with this ...
Yet if evolutionary theory does have broad consequences for the study of ethics or the study of the arts – as we have been told with greater and greater frequency of late – then it is a theory which may be fairly considered, and fairly criticized, by scholars in the fields of ethical philosophy or literary criticism. This should be a perfectly uncontroversial matter. To maintain that evolutionary theory needs to be taken seriously by humanist scholars, while simultaneously forbidding those same scholars, under penalty of the severest invective, to weigh the rational substance of evolutionary theory, is a piece of impudence so raw and ridiculous that it could only be performed in this most outlandish of ages. Whatever absurdities were perpetrated in the past by Freudian and Marxist theorists, they never retorted to objections towards their ideological reading of texts by saying, “you are no psychologist,” or “you are no economist.” If the Darwinians wish their theory to be taken seriously outside the laboratories of the biology departments, then they simply must accept the fact that it has become a fair subject of refutation to the entirety of the educated community.
Let's all try and distinguish between the proper science of evolution and evolutionary theory and the abuses perpetrated in it's name. Let's not make the naive assumption that "refuting" the worst abuses is equivalent to questioning what goes on in biology departments. That's silly.

We all have worldviews that shape our opinions. Here's one ...



[John Wilkins made me post this.]

Friday, October 15, 2010

Brother André and the Million Person Funeral

 
Brother André will become Saint André this Sunday. The press in Canada is all agog over this event. Here's an old video from 1982 relating a bit of history.



Almost every article and TV show mentions the million people who were present at Brother André's funeral. Clearly there were not one million people at the funeral as the CBC newsreels from that time clearly shows only a few thousand at most. Other media reports say that one million people filed past Brother André's coffin and this is a more reasonable claim.

Brother André died just after midnight on January 6, 1937. This is the middle of winter in Canada. His body was prepared and laid in a coffin at St. Joseph's Oratory in Montreal. You can see pictures of him lying in state by following the link to the CBC archives. The funeral was held on January 12, 1937.

Let's assume that the body was ready for viewing at noon on January 6th and remained on view until noon on the day before the funeral. According to press reports, St. Joseph's Oratory was open 24 hours a day so that people could pay their respects. That means that 1,000,000 people (one third of the population of Quebec and far more than the entire population of Monteal) filed past the coffin in 5 days (120 hours). That means a constant stream of people every single minute over five days moving at a speed of about 2 Km/hr (assuming 0.5 m between people). That's a slow walking pace so it's perfectly feasible that one million people could have climbed up to St. Joseph's Oratory in the middle of a Montreal winter to view Brother André's body.

Feasible, but not very likely. Perhaps it was a miracle?



Saints, Scientists, and Miracles

 
Rosie Dimanno is a well known journalist who writes for The Toronto Star. Sometimes she's an investigative journalist and sometimes she's just expressing her opinion. Often it's hard to tell the difference.

Ms. Dimanno is in Rome to witness an important (to her) event this Sunday (Oct. 17, 2010). Pope Benedict XVI will create six new saints on that day, adding to the list of over 10,000 Roman Catholic Saints.1. One of these new saints will be Brother André of Montreal. This explains one of the reasons why Rosie is in Rome—she's Canadian. She also appears to be in sympathy with gullible, devout, Roman Catholics. That's three other reasons.

Ms. Dimanno has written several columns on Brother André and his elevation to sainthood. Her goal is to show that the process is rigorous and scientific. According to the church, it's not just anyone who becomes a saint—you have to provide solid evidence that the candidate performed miracles while living and especially after dying. As you can imagine, this kind of rigorous proof is quite a challenge. This explains why there are only 10,000 saints.2

Here's a list of Rosie Dimanno's recent columns on this event.
Dimanno is entitled to her delusions. That's not a problem for me. What I object to is her claim that the existence of miracles has been scientifically documented. This claim was put forth most forcibly in her column of Wednesday, October 13, 2010: "Brother André's case for sainthood led by man of science."

She's referring to Mario Lachapelle who has a Ph.D. in "medical and biological research." At the age of 41, Lachapelle became a Roman Catholic priest and he is now assistant general of the Holy Cross Congregation in Rome. Brother André—soon to be Saint André—was a member of the Holy Cross Congregation in Montreal. The scientist-priest, Mario Lachapelle, grew up in Montreal and wrote a master's thesis on Brother André and his spirituality.

For the past few years Mario Lachapelle has been the vice-postulator in the Brother André case. He is responsible for showing that a miracle occurred and that it can only be attributed to Brother André (after his death). The case they choose was that of a nine year old boy who was injured in an automobile accident near Montreal.

Here's how Lachapelle describes the case, "Here was someone who was considered dead and one week later he was playing with his Nintendo." According to Rosie Dimanno, the miracle has to meet four conditions: (1) the cure has to be permanent, (2) it has to occur shortly after praying to the saintly candidate, (3) no other gods, angels or saints could have made the miracle happen, and (4) "... the acid test is convincing the tribunal that the healing is scientifically unexplainable given existing medical knowledge, which means depositions from attending physicians and experts in the field completely uninvolved with the case."

After a thorough investigation it was determined that the boy was in an irreversible coma and he recovered fully after his family prayed to Brother André. There is no other possible explanation. It had to be a miracle. Welcome to sainthood, Brother André.

The implications of this proof are profound. It's nothing less than proof of the existence of God. It's also proof that God is Roman Catholic. Five other proofs just like it will be revealed this Sunday. I can't imagine why five billion people won't immediately convert to Roman Catholicism. I know I'm going to talk to my friend the priest on Monday morning.

Science will have to be re-defined.


1. Several of them are my direct ancestors: e.g. Saint Begga of Heristal (613-693), Saint Itta (592-692). These are ancestors of Charlemagne so chances are you are also descended from several saints if you have European ancestors. Celibacy is not one of the requirements for sainthood.

2. There are a slew of potential saints in the pipeline, including several Canadians, but the rate seems to have slowed down in the past thousand years. There are more than 10,000 dead saints who can perform miracles. There are dozens of seraphim and angels, including more than a dozen archangels. There's Satan and his buddies and, of course, The Big Three. That's a lot of supernatural beings for a monotheistic religion.

Science Blogs vs Scientific Literature

 
Royce Murray is a highly respected scientist. He doesn't like science blogs, a point he makes in an editorial published in Analytical Chemsitry [Science Blogs and Caveat Emptor].

David Kroll discusses Murray's ignorance of scienc blogs in an article on Terra Sigellata [“The current phenomenon of ‘bloggers’ should be of serious concern to scientists”]. I urge you to read Kroll's article to see why Royce Murray is so wrong about blogs.

I'd like to make another point. Murray begins his editorial with ...
If you are a science scholar, you hope that all scientific articles that you read are grounded in fact. There is a lot of background information to guide you, including statistical data on what professional journals are read widely, with papers therein that produce citations by other subsequent papers and in general, influence the direction of forthcoming new science. As scholars publishing in professional journals, we are schooled in the importance of factual reliability and impact of articles we read in science journals. In terms of impact, we know of various collective valuations of journals through metrics like the so-called “Impact Factor”. By extension, editors and reviewers reinforce the meaningfulness of Impact Factors by explicit attention to the reliability of submitted articles; if the Scientific Method has not been adequately followed, then there should be a downwardly adjusted evaluation of impact. The picture of scientifically grounded innovations feeding progress in science is well established. I firmly believe that this system has served science well and that the scientific literature has provided generally reliable information and vast benefits to society over the centuries to the present and will continue doing so into the future.
I don't disagree with the final conclusion; namely that publication in scientific journals has served science well over the past 150 years. However, I do disagree with the general tone of this paragraph because it fails to recognize the poor quality of many papers that are published in the scientific literature. The focus on "impact factor" is especially disappointing since it caters to "me-too" science and not true innovation and risk-taking.

Royce Murray's criticism of science blogs would be a lot more credible if he were more honest about the limitations of the scientific literature. The lack of credibility in the scientific literature is often responsible for bad journalism and leads to an incorrect view of science among the general public. How many times have you seen an article in the popular press that's based on a bad scientific paper? How many times do we have to read about new cures for cancer before we admit that the scientific literature isn't all it's cracked up to be? And let's not even talk about fields like evolutionary psychology.

Fact is, the peer-reviewed scientific literature hasn't been very successful at weeding out bad science. It's about time we recognized this and tried to find a way to fix it. One of the advantages of blogs is that they frequently highlight the bad papers that make it into the scientific literature—they also point to the good papers.

Before blogs, there was no good way for the scientific community to critique the scientific literature. Some scientists think that papers in the peer-reviewed scientific literature should be immune from such criticism from the outside. They think that the only criticism should come from within the scientific literature. In other words, if you don't like a paper you have to publish another paper refuting the science.

One of the strange things about this attitude is that those very same scientists are very happy about issuing press releases and very happy to have their work praised in the popular press.


Thursday, October 14, 2010

Philosophers, Science, and Creationism

Investigating the boundary between science and religion

Richard Johns is a Sessional Instructor in the Department of Philosophy at the University of British Columbia. He came to my attention because he just posted a note on Uncommon Descent where he points us to a paper he recently published. Here's the link to his posting: The Limits of Self Organization.

You know as well as I do that anyone posting on that blog is a creationist, specifically an Intelligent Design Creationist. Thus, it won't surprise you to read that his work supports that version of creationism even if the paper itself doesn't mention Intelligent Design Creationism. (Where have we heard that before?)
I’m writing to tell people about a paper of mine that was published in Synthese last month, titled: "Self-organisation in dynamical systems: a limiting result". While the paper doesn’t address intelligent design as such, it indirectly establishes strict limits to what such evolutionary mechanisms as natural selection can accomplish. In particular, it shows that physical laws, operating on an initially random arrangement of matter, cannot produce complex objects with any reasonable chance in any reasonable time.
Synthese is "An International Journal for Epistemology, Methodology and Philosophy of Science." It is not a science journal. Please keep that in mind. Here's a link to Richard Johns' article published online last month [Self-organisation in dynamical systems: a limiting result]. Most of you won't be able to see that article so he kindly provided a link to Pre-published version.

The abstract makes you sit up and take notice.
Abstract
There is presently considerable interest in the phenomenon of “self-organisation” in dynamical systems. The rough idea of self-organisation is that a structure appears “by itself” in a dynamical system, with reasonably high probability, in a reasonably short time, with no help from a special initial state, or interaction with an external system. What is often missed, however, is that the standard evolutionary account of the origin of multi-cellular life fits this definition, so that higher living organisms are also products of self-organisation. Very few kinds of object can self-organise, and the question of what such objects are like is a suitable mathematical problem. Extending the familiar notion of algorithmic complexity into the context of dynamical systems, we obtain a notion of “dynamical complexity”. A simple theorem then shows that only objects of very low dynamical complexity can self organise, so that living organisms must be of low dynamical complexity. On the other hand, symmetry considerations suggest that living organisms are highly complex, relative to the dynamical laws, due to their large size and high degree of irregularity. In particular, it is shown that since dynamical laws operate locally, and do not vary across space and time, they cannot produce any specific large and irregular structure with high probability in a short time. These arguments suggest that standard evolutionary theories of the origin of higher organisms are incomplete.
All the code words are there. There's no way the editors of Synthese could be unaware of the implications of this work. It purports to be evidence of the existence of God. We can safely conclude that the discipline of philosophy has admitted the possibility that science could prove the existence of God.

(Don't bother reading the paper. It's one of those complicated lines of argument involving lots of mathematical equations. There probably aren't more than a few dozen people in the entire world who can understand the paper and offer objective criticism. I don't know if any of them reviewed the paper—I suspect not, but what do I know?)

Richard Johns concludes that current evolutionary theory is incomplete.
I have argued that there is an important limitation on the kinds of object that can appear spontaneously in a dynamical system. Such systems, with laws that operate locally and invariantly across space and time, are able to control only the local structure of the state. The state as a whole is therefore uncontrolled, except insofar as it is constrained by the local structure. This led us to the Limitative Theorem, which says that an irregular object, i.e. one that is largely undetermined by its local structure, cannot easily be produced in a dynamical system. Indeed, it was shown that its production is no easier than the appearance of an object of very similar size in a purely random system.

This result, while relevant to biology, does not of course contradict the theory of evolution in its most general form, i.e. that life evolved through a process of descent with modification. This is just as well, since the historical process of phylogeny is very well supported by the evidence. Nevertheless, the Limitative Theorem does suggest that the currently recognised processes driving evolutionary change are incomplete.
Doesn't this create some problems concerning the border between science and philosophy? You betcha, and Richard Johns is fully aware of the implications. Here's what he wrote on his blog [Why should self-organisation be limited?].
My theorem is also pure doom and gloom. Let's be honest: It offers no positive suggestion at all.

Can such negative claims be part of science? It is often said that a scientist must propose hypotheses that are empirically testable. That's not really true, however. While that's a big part of science, a lot of good scientific work is indeed negative. Much useful work is done by experimentalists who show that, while hypothesis H might predict empirical result E, E doesn't actually occur. Also, while most theorists are busily showing that H predicts E, other theorists very helpfully point out that H doesn't really predict E at all, even though we thought it did. A really negative scientist might even show that no hypothesis of a certain type will ever predict E.

I'm afraid I'm one of those really negative scientists. I've shown that no hypothesis in a very broad class predicts the existence of complex living organisms. More precisely, life cannot self organise in any dynamical system whose laws are local and invariant under spatial translation.
This is a very important point. Is it scientific to show that something cannot happen? I think it is.

Let's take a simple case like group selection. George Williams made a name for himself back in the 1960s by presumably showing that group selection could not occur by any known mechanism of evolution. Nobody, as far as I know, suggested that he wasn't being scientific. Lamarckian evolution is anther example. Although it's theoretically possible to pass on acquired characteristics, we discount that possibility because we can show that the connection between phenotypic changes and altering the genome rules out Lamarckian inheritance as a general mechanism of evolution.

If showing that something is theoretically impossible is valid science in some cases then why do we declare that attempts to do the same thing by Intelligent Design Creationists are automatically ruled non-scientific?

Richard Johns faces a special problem because he seems to have bought into methodological naturalism as a limitation on science. Again, from his blog ...
At this point a worrying possibility emerges. This no-go theorem is so broad that it rules out just about any naturalistic theory of the origin of life! It certainly seems to rule out all the naturalistic theories presently proposed. Yet, the whole business of science is to provide natural explanations for phenomena, so this result is unscientific after all. (Even if it is technically correct, take note.)

Well, this is an awkward business! What are we to do?
Indeed. What is he to do? Let's assume, for the sake of argument, that Johns has made a reasonable case for his argument. Let's assume that there may be ways of showing that life is impossible under the known laws of chemistry and physics. Is that science? Does it fit into the restriction of methodological naturalism?

I think the answer to the first question is "yes." It may be bad science, it may even be really bad science, but it's still science to investigate whether completely naturalistic explanations can account for life as we know it.

Let's not pretend to be naive. If there's no naturalistic explanation then there has to be some other kind of explanation.
So I think we have to broaden our horizons, and be open to new kinds of explanation. Perhaps it won't be that bad? And we have no other choice, if we want our explanations to be true.
We know what that means. By ruling out naturalistic causes, we are forced to consider supernatural causes. Is that what makes Richard Johns' work unscientific but not that of George Williams and many other theoreticians of biology? 'Cause if that's what methodological naturalism is all about then it's an ass.

I think everything is fair game for science. Our goal is not to develop rigid rules that make us feel good by ruling our opponents out of bounds just because we don't like their conclusions. Our goal should be to show that they are wrong.

I fully expect that people like Wesley Elsbery and Jeffrey Shallit and will show us why Richard Johns is wrong, just as they did for similar arguments by Bill Dembski. As they do that, Elsbery and Shallit will be practicing science as a way of discovering truth. It would make no sense to declare that Richard Johns has stepped outside the realm of science but Elsbery and Shallit remain inside its boundaries.

The Intelligent Design Creationist attacks on evolution are wrong because they are bad science, not because they are not science.


Wednesday, October 13, 2010

The Recurrent Laryngeal Nerve Must Have a Rational Design

 
Casey Luskin is at it again. The Intelligent Design Creationists are trying to argue their way out of the obvious implications of the path taken by the recurrent laryngeal nerve, especially in giraffes.

Now they're saying that, far from being an example of sloppy design, the path of the nerve has to have some selective advantage according to science. Thing is, you need to have a proper understanding of evolution in order to discuss this intelligently.

Enjoy, while keeping in mind why we call them IDiots [Wolf-Ekkehard Lönnig: Under Neo-Darwinism, the Recurrent Laryngeal Nerve Must Have a Rational Design.


Tuesday, October 12, 2010

Which Country Has the Best Brains?

 

BBC News has an article on which countries produce the most Nobel Prize winners: Which country has the best brains?.

So, which country has the best brains? I love the answer given by John Wilkins, "Surely not the one that cannot work out per capita rates of Nobel Prizes."


A Canadian Atheist Accommodationist

 
Canadian Atheist is a blog run by several Canadian atheists (hence the name ). One of them is Brent Kelley, an undergraduate at the University of Alberta in Edmonton, Alberta, Canada.

Here's what Brent said in today's posting: The Atheist Disposition,
Almost everybody I talk to seems to disagree with the “militant” positions that firebrand atheists such as Dawkins and PZ take. They feel they are too extreme and that their outlook too rigid.

I might disagree to some extent, but that’s not the point. The point is that the great atheist leaders that many atheists regard so highly are often viewed by outsiders as extreme, unreasonable, and ridiculous. Even those who agree with our cause often feel this way. Which means that if we’re trying to get the public on-board with our ideas and opinions, we’re failing.

We need to work on our image. I’m not sure where to start, but perhaps approaching the problem from the ground up is a nice way to start tackling the issue. What I would suggest is for atheists everywhere to be a little more friendly to not only one another, but also to others outside their atheist circle of friends. Before you attack a theist’s beliefs, ask yourself if the argument is worth it. You probably wont change their mind anyway. Instead, perhaps you could start up a discussion about science and try to explain the scientific viewpoint on this or that. Slowly and gently introducing them to the worldview of scientific naturalism might make them more receptive to atheism and critical thinking. And be open to their ideas too, you might even learn something. Do whatever, just don’t get into a shouting match and reinforce the stereotype that atheists are argumentative, unfriendly, and annoying.
[emphasis in original]
Why not visit their blog and post a comment? I did.


Teach Your Children Scientific Literacy

 




[Hat Tip: Greg Laden]

Monday, October 11, 2010

The Casey Luskin Lesson Plan on Teaching the Controversy

 
I often criticize the Intelligent Design Creationists for not coming up with anything other than criticism of evolution. That criticism is perfectly justified as we can see in Casey Luskin's latest posting on Evolution News & Views: Back to School Lesson Plans That Actually Help Students Understand Evolution. He's even gone as far as proposing a lesson plan on evolution for grades 4-7. One of the important parts of that lesson plan is the challenges to evolution.

It's Monday, and it's Thanksgiving Day in Canada, so I'm taking a bit of a break. Let's have some fun with Luskin's lesson plan. I'll quote each of his points with a brief response.
Step 3: Learn About the Case against Evolution (1.5 hours). Now students will learn about some of the science that challenges evolution. Watch the DVD Icons of Evolution.
- Ask students to explain the difference between microevolution and macroevolution.
This is far too complicated for public school students. The simple answer is that microevolution describes changes occurring within populations and macroevolution describes the history of life. Macroevolution includes things such as speciation that are not part of microevolution and it also includes things like asteroid impacts, ice ages, and drifting continents in order to explain the history of life. There's an important part of evolutionary theory called "Hierarchical Theory" where proponents argue for higher-level mechanisms of evolution such as species selection. They aren't part of microevolutionary explanations. Thus, microevolution is necessary but not sufficient to explain macroevolution [Macroevolution].
-The video mentions the Galápagos finches. Do the finches represent an example of microevolution or macroevolution?
It's on the border between microevolution and macroevolution. The value of the work on the Galapogos finches is that the results suggest how new species are formed. They formed from a combination of physical isolation events (different islands) plus microevoutionary events involving natural selection, and random genetic drift. Such speciation events occurred repeatedly in the history of life and these studies show how they can be explained by purely natural causes.
-The video mentions mutations in fruit flies which gave fruit flies an extra pair of wings. Were these fruit flies able to fly better and survive with the extra wings?
No.
-Are mutations helpful or harmful? Ask for examples of harmful mutations? How about helpful ones?
A harmful mutation is one that decreases fitness. There are hundreds of examples of genetic diseases in humans. A beneficial mutation is one that increases fitness. Antibiotic resistance in bacteria is a classic example but so is HIV resistance in humans. Dozens of field studies have shown that beneficial mutations can arise fairly quickly in populations that are challenged by environmental change. Molecular data documents thousand of beneficial changes to genes and enzymes over time.
-What was the Cambrian explosion?
The Cambrian Explosion was a period in the history of life where we see the appearance of new types of animals. The dates are approximately 500 million years ago and the time frame for the visible appearance of these groups ranges from 10-50 million years. It's important to note that the fossils of the Cambrian don't look like any species that are alive today and they don't contain any examples of land life. It's also important to note that the Cambrian explosion doesn't apply to plants, fungus, protozoa, and bacteria.

What caused the appearance of primitive animal groups 500 million yeas ago, over a period of tens of millions of years? Scientists don't really know but there are lots of ideas on the table. One thing that's very clear from molecular evolution is that the origin of the various lineages (phyla) goes back several hundred million years.
-Does the fossil evidence show that species have evolved by small gradual changes, or large sudden changes? Do fossils support Darwin’s theory? Why or why not?
The are many examples of slow gradual changes over millions of year but there are also examples of patterns called Punctuated Equilibria. In these examples you see very small changes—such as the speciation events in the Galapagos finches—happening at the time of speciation. In other words, the fossil record mimics the sort of thing you see in the Galapagos islands where the small changes occurring at speciation are quickly fixed in the population within ten or twenty thousand years. There's hardly any fossil record of the intermediates showing the transition between these closely related species.

There's nothing in the fossil record suggesting that large sudden changes can occur rapidly. That's a lie propagated by creationists who don't understand evolution and who have a religious agenda that interferes with their ability to do science.
-The video also mentions the origin of life. Does the evidence support the claim that the building blocks of life were present on the early earth? Why or why not?
The origin of life is an interesting scientific problem that hasn't been solved. Although it has nothing to do with evolution, it's clearly related. Some scientists think that life arose in a primordial soup containing abundant supplies of all the necessary building blocks we see today. There is plenty of scientific evidence that some of these building blocks—such as simple sugars and amino acids—can arise spontaneously. In fact, many of them have been detected in outer space. Other scientists prefer scenarios where life began much more simply with very small, highly abundant, chemicals that are still around today in the oceans. It will be interesting to watch for new discoveries as you grow up because science is poised to make significant advances in these areas.

You should keep an open mind on this question and watch for new discoveries from religious leaders that will help you understand the origin of life. It's possible—alghough not very likely—that religious organizations such as The Discovery Institute will come up with a scientific explanation of how, and when, God created life on Earth.
-Compared to humans, was the first life simple or complex? How about compared to a calculator, computer, or cell phone? Are living organisms more or less complicated than human technology? What do students think?
All available scientific evidence points to a common ancestor that was much more simple than humans, or most other species that are living today. Those primitive ancestors are much less complex than a modern computer because, in addition to having only a few hundred genes (at most), the internal cell biology and biochemistry was undoubtedly sloppy and inefficient. No modern machine is anything like that.

We are at the stage in technology development where it is possible to build better life forms than those that evolved naturally and you should look forward to learning about these new artificial forms of life in the next few years. You might even want to think about a future career in science so you can learn this technology.


The Great Accommodationist Dud: Round 2

 
Point of Inquiry is a series of podcasts financed by the Center for Inquiry. Chris Mooney is one of the people CFI pays to produce the podcasts. He decided to continue the accommodationist debate with PZ Myers and selected the moderator from round 1 to step in for him on the podcast. Unfortunately, Jennifer Hecht doesn't understand the concept of "moderator" so the podcast ends up being Jennifer and Chris against PZ.

PZ does a good job but it's tough defending yourself against two people who are coming at you from very different directions. Jennifer Hecht does not sound very convincing to me. She seems to believe that "a little bit of religion" is perfectly compatible with science and shouldn't be challenged. Towards the end of the podcast, Chris tries to bring up the fact that there are people who find the Gnu Atheists annoying and offensive. PZ replies, very effectively, by pointing out that many people find Chris Mooney annoying, arrogant, and offensive but they aren't telling him to shut up! I would add Jennifer Hecht to the list of people I find arrogant,1 annoying, and offensive.

Here's the podcast, it's a better utilization of your time than the first round was.

PZ Myers, Jennifer Michael Hecht, and Chris Mooney - New Atheism or Accommodation?


1. By my definition, you aren't "arrogant" if you are right. You are only arrogant when you are close-minded and wrong.

Sunday, October 10, 2010

Is Thanksgiving Day a Religious Holiday?

 
Tomorrow is Thanksgiving Day in Canada. It a holiday marked by good meals and getting together with friends and family. I've never thought of it in any other context. But then, I treat Christmas the same way (except there are presents).

Douglas Todd is a columnist for the Vancouver Sun and he has a very different view of thanksgiving as expressed in his article: At Thanksgiving, do atheists feel grateful?.
Are atheists thankful? And, if so, to whom? Or what?

In the Pacific Northwest, which has the highest proportion of non-religious people in North America, Thanksgiving is not always simple for those who do not believe in a transcendent reality.

How do the almost two out five British Columbians who say they have no religion, and especially the 16 per cent who are atheists, approach a festive day that encourages humans to express a sense of thankfulness, particularly for life itself being a gift?
What is it with people who believe in supernatural beings—especially in those Gods who need to be thanked from time to time? Why are these believers completely incapable of seeing anyone else's point of view? Is there something about believing in "transcendent reality" that affects their brains?


Friday, October 08, 2010

The Great Accommodationist Dud

 
I watched the whole three hours streamed live on the conference website. It was about as exciting as watching paint dry except that drying paint doesn't make you angry. All four panelists managed to miss the point.

It wasn't until we got to the very last question that anyone grasped the important point; namely, that PZ Myers and Vic Stenger have very different goals than Chris Mooney and Genie Scott.

Chris and Genie want people like PZ and Vic to keep a lid on it because the Gnu Atheists are making their life more difficult. Tough. There's no reason why PZ and Vic (and the rest of us) have to share their goals just because they think they're more important than getting rid of religion.

And why did Vic and PZ allow Genie to get away with defining science as methodological naturalism?

I was very disappointed in everyone on the panel, and in the moderator.


Carnival of Evolution #28

 
I've been so busy lately that I forgot to mention the latest Carnival of Evolution. This is doubly embarrassing because it features one of my favorite blogs [Carnival of Evolution #28 - Featuring Sandwalk].

Be sure to answer the survey questions ...
WELCOME to the 28th edition of Carnival of Evolution! This time the carnival has returned home. Not since the first edition back in August 2008 has an edition been posted here. That is cause for celebration, so let's do that with a little survey. I am interested who reads Carnival of Evolution, so please spend the next two minutes tops taking this brief survey about yourself and CoE. Results will then be posted here for the bemusement of all.


Thursday, October 07, 2010

The Velvet Underground of Molecular Biology

The Velvet Underground was a New York rock band in the 1960s. It was never very popular and never made much money but it's said to have influenced many other, more successful, bands.

Chad Orzel asks you to identify The Velvet Underground of Science by which he means an individual who isn't very famous but had a huge impact on science. Naturally, he has an example from physics.

I have an example from molecular biology. Max Delbrück (1906-1981) was one of the founders of the 'phage school (along with Salvador Luria). Delbrück began his science career as a physicist but when he went to the USA he switched to biology and soon became interested in bacteria and bacteriophage.1 During the 40s, 50s, and 60s he had a huge influence on the members of the 'phage group who used to meet regularly at Cold Spring Harbor where Delbrück taught a summer course in 'phage genetics.

Jim Watson, Matt Meselson, Franklin Stahl, Gunther Stent, Seymour Benzer, Edward Kellenberger, and Alfred Hershey are just a few of the scientists who were directly influenced by Delbrück. They all got together to contribute to Phage and the Origins of Molecular Biology in 1966. The book was a Festschrift in honor of Max Delbrück on his 60th birthday.

There were many more second and third generation scientists who grew up in the 'phage group. My own supervisor used to refer frequently to Delbrück's "Principle of Limited Sloppiness" as an effective way of doing science.

Delbrück, Alfred D. Hershey, and Luria won the Nobel Prize in 1969 but he (Delbrück) is still not very well known among today's students. I think that every biochemistry and molecular biology student should have to read The Eighth Day of Creation by Horace Freeland Judson in order to learn the history of their field.

They might discover that much of what they think of as "modern" was actually understood almost half a century ago.


Photo Credits: Top: Delbrück in the early 1940s from Wikipedia. Bottom: Delbrück and Luria at Cold Spring Harbor in 1953.

1. Physics was too easy—he wanted more of a challenge.

Three Conundrums

 
Razib Khan over at Gene Expression is discussing a recent article on epigenetics and other "revolutions" in molecular biology. Check out Razib's postings: Arise the vehicle! Arise the cell! and Epigenetics – what revolution?.

The article in question is by Steve Talbott1 and it's published in The New Atlantis: Getting Over the Code Delusion. Here's how the editors introduce the article ...
Editor’s Note: This is the first in a planned set of essays by Mr. Talbott explaining the significance of a revolution in genetics and molecular biology that has only just begun to receive public attention. Although this essay is at times necessarily tech­nical, we trust that our readers will not find it prohibitively so — and we have appended a modest and informal glossary to help smooth the path.
You all know where this is going, don't you?

Talbot sets up his "revolution" by describing several problems.
A number of conundrums have helped to nudge molecular biology toward a more contextualized understanding of the gene. To begin with, the Human Genome Project revised the human gene count downward from 100,000 to 20,000–25,000. What made the figure startling was the fact that much simpler creatures — for example, a tiny, transparent ­roundworm — were found to have roughly the same number of genes. More recently, researchers have turned up a pea aphid with 34,600 genes and a water flea with 39,000 genes. Not even the "chimps are human" boosters were ready to set themselves on the same scale with a water flea. The difference in gene counts required some sort of shift in ­understanding.
I've addressed this before. Knowledgeable experts in the field were predicting 30,000 genes at least as far back as the late 1960s. Their predictions were very close to the mark [False History and the Number of Genes] [Humans Have Only 20,500 Protein-Encoding Genes] [Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome]. Steve Talbot hasn't done his homework. This isn't a very auspicious beginning.
A second oddity centered on the fact that, upon "deciphering" the genetic Book of Life, we found that our coding scheme made the vast bulk of it read like nonsense. That is, some 95 or 98 percent of human DNA was useless for making proteins. Most of this "noncoding DNA" was at first dismissed as "junk" — meaningless evolutionary detritus accumulated over the ages. At best, it was viewed as a kind of bag of spare parts, borne by cells from one generation to another for possible employment in future genomic innovations. But that’s an awful lot of junk for a cell to have to lug around, duplicate at every cell division, and otherwise manage on a continuing basis.
In this day and age, anyone who equates junk DNA with non-coding DNA isn't worth reading. They've lost all credibility as far as I'm concerned.

Talbott explains the solution later on in his article when he says ...
So what’s going on? These puzzles turn out to be intimately related. As organisms rise on the evolutionary scale, they tend to have more "junk DNA." Noncoding DNA accounts for some 10 percent of the genome in many one-celled organisms, 75 percent in roundworms, and 98 percent in humans. The ironic suspicion became too obvious to ignore: maybe it’s precisely our "junk" that differentiates us from water fleas. Maybe what counts most is not so much the genes themselves as the way they are regulated and expressed. Noncoding DNA could provide the complex regulatory functions that direct genes toward service of the organism’s needs, including its developmental needs.
Anyone who states or implies that there is a significant correlation between total haploid genome size and species complexity is either ignorant or lying.

Larry Moran
Genome Size, Complexity, and the C-Value Paradox
"Organism rise on the evolutionary scale"? Has Talbott done any research at all for this article? His understanding of evolution is no greater than kindergarten level if he believes that there's an evolutionary scale with us near the top.

The idea that noncoding DNA contains sequences that govern gene expression has been with us for fifty years. That's hardly revolutionary. The idea that the amount of junk DNA in a genome equates to complexity has been soundly disproven. The idea that humans might need a million base pairs of DNA to control expression of every gene is ludicrous and has absolutely no evidence to support it. In fact, nobody I know has ever shown that mammalian genes require more regulatory sequences than insect genes or those of crustaceans (water fleas). What we have here is a perfect example of The Deflated Ego Problem.

What about the third "conundrum"?
Another conundrum — perhaps the most decisive one — has been recognized and wrestled with (or more often just ignored) since the early twentieth century. With few exceptions, every different type of cell in the human body contains the same chromosomes and the same DNA sequence as the original, single-celled zygote. Yet somehow this zygote manages to differentiate into every manner of tissue — liver, skin, muscle, brain, blood, bone, retina, and so on. If genes determine the form and substance of the organism, how is it that such radically different cellular architectures result from the same genes? What directs genes to produce the intricately sculpted and differentiated form of a complex organism, and how can this directing agency be governed by the very genes that it directs?
We've known the basic answer to this "conundrum" for about five decades. Talbott's idea of a revolution is very strange.

Don't bother reading the article in The New Atlantis. There's nothing "new" there and it may make you very angry.


1. Steve Talbott is a Senior Researcher at The Nature Institute. "My primary undertaking right now is a critique of conventional science with a view toward establishing the foundations of a new, qualitative science. The project, which requires an extraordinarily radical assessment of contemporary habits of thought, is headquartered here."

Tuesday, October 05, 2010

The Accommodationist Debate

 
I wish I were going to be in Los Angeles next weekend at the Secular Humanism Conference.

I would definitely attend this session ...
Science and Religion: Confrontation or Accommodation?

How should secular humanists respond to science and religion? If we champion science, must we oppose faith? How best to approach flashpoints like evolution education? A wide-ranging examination featuring a spectrum of distinguished panelists:

* Jennifer Michael Hecht (moderator)
* PZ Myers
* Eugenie Scott
* Chris Mooney
* Victor Stenger
I sure hope it's going to be on YouTube!


2010 Nobel Prize in Physiology or Medicine

 
The 2010 Nobel Prize in Physiology or Medicine was given to Robert G. Edwards "for the development of in vitro fertilization". They should have added "in humans."

This is a technological achievement, one that was based on years of work with other animals.

I do not favor awarding Nobel Prizes for technology. I prefer to give the science prizes to those who have advanced our fundamental understanding of the universe. This prize is for medicine, which is technology, so it doesn't violate any rules. But in the past the prize in Physiology or Medicine has usually been for basic research.

It worries me that there may have been non-scientific motives behind this year's selection. We saw a horrid example of that last year when the Nobel Peace Prize was announced and I hope this isn't a trend.

Here's an example of how the award is being treated in the press [British IVF pioneer Robert Edwards gets Nobel Prize].
As well as leading to a host of new treatments for infertility, the work also founded the principles behind stem cell research, cloning and techniques that would allow couples to prevent passing on inheritable diseases to their children.

Christer Höög, professor of molecular biology at the Karolinska Institute in Stockholm, and a member of the Nobel Prize Committee, said the birth represented a "paradigm shift"

"It showed for the first time that it is possible to treat infertility," he said.

Prof Edwards' work was highly controversial at the time and there was strong opposition to what was seen as 'playing God' and the research had to be privately funded.
The good news is that the Vatican is really, really, pissed! [Vatican official criticises Nobel win for IVF pioneer]. I think it's because the Roman Catholic Church is pro-life.


The Edge of Evolution

There are two main problems with Intelligent Design Creationism. The first is that the IDiots never have anything positive to offer by way of explanation. They complain about how evolution can never do this or that but they never give us a better explanation based on their beliefs. The second problem is that the IDiots often get their science wrong when they complain about evolution. Sometimes this is deliberate, but in many cases it's because they just don't understand what they're criticizing.

Their criticisms of evolution are based on the notion of a false dichotomy. They think that there are only two choices: their conception of evolution, or Intelligent Design Creationism. Thus, if they can refute their version of evolution it follows that creationism must be true.

People often make the claim that Intelligent Design Creationism isn't science. That may be true if you only think of it as promoting the idea of an intelligent designer but even there it depends on how you define science. However, much of the Intelligent Design Creationism literature isn't about defending creationism, it's about attacking evolution and those arguments definitely fall within the definition of science. As scientists, we have to deal with all the objections to evolution no matter what the motives of the challengers.

I think it's somewhat simplistic to dismiss all the Intelligent Design Creationist literature on the grounds that it's not science. Some of it has all the earmarks of science, it's just bad science. And bad science isn't limited to IDiots. I think there are many Theistic Evolutionists who are also guilty of promoting bad science and there are many atheist scientists who are just as guilty. The peer-reviewed scientific literature is full of examples.

Although it makes my American friends cringe, I favor teaching the controversy. It's the only way to show students the difference between good science and bad science.

Some of the Intelligent Design Creationists can craft pretty convincing arguments against evolution. It takes a lot of work to refute them. I going to give you an example of such an argument from The Edge of Evolution by Michael Behe. Let's see how you do.



The Two Binding Sites Rule

Behe's version of the history of life requires a God who intervenes quite frequently to create specific mutations that are almost impossible to account for by random mutation. Behe makes a good case for the problems with random mutation. In fact, his arguments are similar to those put forth by the mutationist camp—a group that I'm in sympathy with. Most biologists would not be able to refute Behe's arguments because they would agree with some of his false premises.

Behe's "Two Binding Sites Rule" is a good example. He argues that in order for two proteins to interact, evolution needs to create a small patch on the surface of each protein where five or six amino acid side chains become compatible with binding. Some of these changes could be neutral so they could arise independently but the analysis of hundreds of known binding sites shows that many of the mutations would be detrimental if they occurred by themselves—a single charged amino acid residue on the surface, for example.

It looks like you need to wait for three or four specific mutations to occur simultaneously in order to get a moderate interaction between two proteins that did not originally bind to each other. And these can't be just any proteins, they have to be proteins where there is a selective advantage to forming a complex. The example I've chosen is a bacterial photosynthesis reaction center where four polypeptides (gold, blue, green, purple) interact with each other and with multiple cofactors (space-filling molecules) to form a very complicated structure. Presumably, there was a time in the past when some of these proteins didn't bind to each other or to the cofactors. Over time, evolution favored variants that could form the complex. How could this happen according to evolutionary theory?

Studies on in vitro mutagenesis show that the probability of forming any de novo binding site is very low. For example, it's quite difficult to engineer specific antibodies that will bind to a particular antigen. The data shows us that you need a library of more than one billion antibody molecules in order to get one that will bind. Those one billion mutations are far from random. They are engineered so that they are confined to a small patch on the surface of the antibody where it is known that other proteins can potentially bind.

Behe argues from this evidence that the probability of creating a new binding site by random mutations is exceedingly small. So small, in fact, that such mutations would only arise in very large populations after several hundred million years of evolution. He bases his argument on some experiments he describes in the first few chapters or his book.

Behe points out that it is sometimes very difficult for the malaria-causing parasite, Plasmodium falciparum, to develop resistance to some drugs used to treat malaria. That's because the resistance gene has to acquire two specific mutations in order to become resistant. A single mutation does not confer resistance and, in many cases, the single mutation is actually detrimental. P. falciparum can become resistant because the population of these single-cell organisms is huge and they reproduce rapidly. Thus, even though the probability of a double mutation is low it will still happen.

If the probability of a single mutation is about 10-10 per generation then the probability of a double mutation is 10-20. He refers to this kind of double mutation as CCC, for "chloroquine-complexity cluster," named after mutation to chloroquine resistance in P. falciparum.1 Behe's calculation is correct. If two simultaneous are required then the probability will, indeed, be close to 1 in 1020.

Let's see how this relates to the evolution of protein-protein interactions. Here's how Behe describes it on page 135 of his book.
Now suppose that, in order to acquire some new, useful property, not just one but two new protein-binding sites had to develop. A CCC requires, on average, 1020, a hundred billion billion, organisms—more than the number of mammals that has ever existed on earth. So if other things were equal, the likelihood of getting two new binding sites would be what we called in Chapter 3 a "double CCC"—the square of a CCC, or one in ten to the fortieth power. Since that's more cells than likely have ever existed on earth, such an event would not be expected to have happened by Darwinian processes in the history of the world. Admittedly, statistics are all about averages, so some freak event like this might happen—it's not ruled out by the force of logic. But it's not biologically reasonable to expect it, or less likely events that occurred in the common descent of life on earth. In short, complexes of just three or more different proteins are beyond the edge of evolution. They are lost in shape space.
We're all pretty knowledgeable here but how many of you can immediately refute that argument? If you can't then you have no business accusing Behe of being stupid or silly and of dismissing his book as just another example of creationist ignorance. The correct explanation of the problem will undoubtedly appear soon in the comments. Before peeking, why not try and see how you would answer Behe if you were debating him in front of a large audience of creationists?


1. Behe may have been wrong about the specific chloroquine resistance mutation he used as an example. The two mutations may not have occurred simultaneously. Nevertheless, the principle is sound. If the single mutations are detrimental then you need both to get resistance and the probablity of two such mutations occurring together is 10-20.

Sunday, October 03, 2010

Meeting God in Montreal

 
Brian Dalton is Mr. Deity. If you haven't been watching all the episodes over the past few years then go to the website and buy the DVD. You won't regret it.

Brian is as funny in person as he is on the videos. He explained how "Mr Deity and the Virgin" was inspired by a debate he saw on TV.

Brian's wife, Amy Rohren, plays "Lucy" (Lucifer, Satan), Sean Douglas plays Jesus, and Jimbo Marshall is God's chief of staff.



One of my personal favorites is "Mr. Deity and the Really Unique Gift."



A No-Brainer

 
It's been a week since I issued A Challenge to Theists and their Accommodationist Supporters.
This brings me to my challenge. I challenge all theists and all their accommodationist friends to post their very best 21st century, sophisticated (or not), arguments for the existence of God. They can put them in the comments section of this posting, or on any of the other atheist blogs, or on their own blogs and websites. Just send me the link.

Try and make it concise and to the point. It would be nice if it's less than 100 years old. Keep in mind that there are over 1000 different gods so it would be helpful to explain just which gods the argument applies to.
There have been over 500 comments on that posting and dozens of attempts to meet the challenge, ranging from the fact that Babylon hasn't been re-built to variations of the old Cosmological and Ontological Arguments that have been around for centuries.

I think it's fair to say that nobody came up with anything that even remotely resembles a modern "sophisticated" argument that the Gnu Atheists are ignoring. Therefore, I declare victory.

From now on, whenever any accommdationist or theist accuses me of not having studied philosophy or theology I'll point them to my post and remind them that the Emperor really doesn't have any clothes. That includes a few people who sent me email messages explaining why they wouldn't lower themselves to post a comment on my blog. They implied that they still had some really good arguments for the existence of God but they aren't going to reveal them to me because I wouldn't understand them.


Saturday, October 02, 2010

Friends in Montreal

 
Seanna Watson, Steve Watson, Sue Strandberg, and a photo bomber.


This photo is from last night after dinner. Today at noon I was witness to the strangest phenomonon—before we could sneak away for lunch, there were no less than 14 people who deliberately took photographs of this man. Sometimes I had to photograph him with various people using their cameras.1 What is it about this guy? He's not particularly photogenic.


1. Nobody wanted me in the pictures!

Good Montreal Atheists

 
Yesterday we were part of a live podcast moderated by three Montreal Atheists; Jacon Fortin, Ryan Harkness, and Jeffrey Jones. They talked about dicks and how to be one. Phil Plait would not have been pleased!

You can hear the podcast on their blog The Good Atheist [The Good Atheist Podcast: Episode 107].



Friday, October 01, 2010

The Sound of Science

 
This is cute, but it's also deeply troubling.

I really don't like Darwin worship. It's true that I think he was the greatest scientist who ever lived, but science has moved on since 1859. Modern scientists respect, but do not worship, the past.

There are a couple of other problems with the lyrics. I'm confused about the reference to "theory" as some kind of "abstraction" and I don't like the implication that we go back and read Darwin to refresh our memory about modern evolutionary theory.

I also don't like the simplistic explanation of how real science is done. It's a common myth that publishing a peer-reviewed paper is the only way to do science. There are two things wrong with this mythology. First are the obvious exceptions, Origin of Species being one of them. Second, there's plenty of bad science papers in the peer-reviewed literature. Publishing in the peer-reviewed literature is neither necessary, nor sufficient, as a measure of good science.



[Hat Tip: Greg Laden]

Tuesday, September 28, 2010

Montréal

 
I'll be in Montréal, Québec, Canada this weekend attending the Atheist Alliance International (AAI) convention, Atheists Without Borders (Atheés Sans Frontières).

I'm arriving around 6pm on Thursday and leaving Sunday afternoon. Anyone else going? Contact me by email so we can get together. Maybe food and beverages on Thursday evening? (My address is at the top of the left sidebar.)

Most of Montréal is on a large island in the middle of the St. Lawrence river. The site was occupied by the St. Lawrence Iroquois when the first Europeans arrived in the 1530's. They had established a large village called Hochelaga but this village was largely deserted by the time Europeans constructed the first settlement in 1611.1 My ancestor, Barthélemy Montarras, was a soldier in the Compagnie Froment, Le régiment de Carignan, based in Montréal around 1665.

The dominant feature of the city is Mont Royal (Mount Royal) a group of hills right in the middle of Montréal island. The hills were first scaled by Jacques Cartier in 1535. A wooden cross was erected in 1635. The giant illuminated cross that we see today was built in 1924.

Montréal has several half-decent universities but, more importantly, it has many excellent bistros and cafés. I hope to try several of them this weekend. There are some special dishes that you just can't get in Toronto—or if you can get them, they're not nearly as good. It's sad that some of my friends won't be able to sample the smoked meat or the poutine due to restrictions imposed by their doctor.



1. Quebec City was founded in 1608. Santa Fe, New Mexico in 1608 and the Mayflower arrived in Massachusetts in 1620.