Genetic sequence comparisons are often used to try to establish relationships in evolution. But as Robert Deyes, writing over at Access Research Network, shows, the molecular "clock" often conflicts with the "tree of life.":

Writing over a decade ago, UCLA biologists Laura Maley and Charles Marshall noted how genetic sequence comparisons carried out between different animal phyletic groups can lead to significantly different interpretations of evolutionary relationships depending on which species is chosen to represent each group (Ref 1). Such a finding should raise concern amongst protagonists of molecular systematics who today use sequence data to determine evolutionary relationships. Yale University's Gavin Naylor showed just how inaccurate such comparisons could be in the context of the vertebrate evolutionary tree (Ref 2). Mitochondrial DNA sequence analyses of 19 different taxa generated an astounding result- frogs and fish were clustered in the same clade as chickens even though "strong morphological and fossil evidence" did not show these as being in any way related by a common ancestor (Ref 2). The same mitochondrial DNA sequences placed echinoderms- which include starfish and sea urchins- in closer proximity to the vertebrates than amphioxus even though, being a chordate, we would expect amphioxus to be closer (Ref 2). That is, if we give the evolutionary tree any credibility. Given such anomalies, one should be cautious about stating what we really do know about the evolutionary relationships between different classes of vertebrates. Nevertheless molecular biologist Thomas Sakmar and his colleagues from the Rockefeller University seemingly threw caution to the wind several years later when they redesigned the rhodopsin molecule- a visual, light perceiving pigment that is ubiquitous throughout nature (Ref 3).

Also just up at The Post-Darwinist, Denyse O'Leary's news and culture blog on the intelligent design controversy:

Expelled DVD released today, to brisk sales, more hit reviews

Great offer! Get Ben Stein's Expelled - plus new book and earlier ID films

 British physicist David Tyler looks at a recent find in cichlid fish which has been vastly overhyped as evidence for new species. He means hype like this Nature News story (1 October 2008), which proclaims "What you see is how you evolve: Differences in vision could give rise to new species."

Here's the abstract of the paper he discusses:

Speciation through sensory drive in cichlid fish

Ole Seehausen, Yohey Terai, Isabel S. Magalhaes, Karen L. Carleton, Hillary D. J. Mrosso, Ryutaro Miyagi, Inke van der Sluijs, Maria V. Schneider, Martine E. Maan, Hidenori Tachida, Hiroo Imai & Norihiro Okada

Nature 455, 620-626 (2 October 2008) | doi:10.1038/nature07285 Abstract: Theoretically, divergent selection on sensory systems can cause speciation through sensory drive. However, empirical evidence is rare and incomplete. Here we demonstrate sensory drive speciation within island populations of cichlid fish. We identify the ecological and molecular basis of divergent evolution in the cichlid visual system, demonstrate associated divergence in male colouration and female preferences, and show subsequent differentiation at neutral loci, indicating reproductive isolation. Evidence is replicated in several pairs of sympatric populations and species. Variation in the slope of the environmental gradients explains variation in the progress towards speciation: speciation occurs on all but the steepest gradients. This is the most complete demonstration so far of speciation through sensory drive without geographical isolation. Our results also provide a mechanistic explanation for the collapse of cichlid fish species diversity during the anthropogenic eutrophication of Lake Victoria.

Tyler comments:

"The strongest evidence yet" involves a correlation between the visual system, body colour and ecology. Instead of this being used to support a hypothesis of sexual selection based on body colouration, the authors claim to have demonstrated sexual selection in action. This has been picked up by the media as fact: "a fish species in the cichlid family has been observed by scientists in the act of splitting into two distinct species in Lake Victoria" (Source). The cover of Nature proclaims that this is "a textbook example of evolution in action".

Let us suppose that the hypothesis is tested and confirmed, and the "sensory drive speciation" is validated. What are the implications for our understanding of evolution? It means that an ancestral fish population can split into two or more populations on the basis of colour. The daughter populations have differences in sensitivity to light frequencies and differences in body colouration. These may be accompanied by other ecological adaptations. There is no new genetic information - just fine-tuning of existing genetic systems. There is no evidence that these new species lack the potential to interbreed. Indeed, the differences are so slight that hybridisation to produce fertile offspring can be predicted with some confidence.

Talk about textbook examples- as the study authors themselves observe, for their particular proposed path by which new species may occur, "empirical evidence is rare and incomplete." Now, to their delight, they may have finally found an example (if the two schools of fish don't just interbreed back into hybrids after a few decades).

The problem isn't with the researchers, who sound suitably cautious. It's the pop science media that jump on something like this and make far more of it than the current state of knowledge would justify. That wouldn't matter if they were just speculating about some celeb's bumpy tummy, but unfortunately, they help skew science textbook and science teaching. Tyler observes,

The punchline: ID scientists are not opposed to the teaching of evolution in schools, but want it taught properly - allowing critical appraisal and the recognition of spin. Let speciation in cichlid fish enter the textbooks, not as a proof of evolution, but as an example of how evidence is brought to bear on current hypotheses of the origin of species.

That would be higher quality teaching, but would lead to too many embarrassing questions. My guess is, both the pop sci mags and the textbooks will stick to "proof of evolution"for the present.

Also just up at The Post-Darwinist: Darwinism and popular culture: Still not clear how mind emerges from mud ,

"Don't be fooled by their reputation for altruism and free love – bonobos hunt and kill other monkeys just like their more vicious chimpanzees cousins, according to new research," Ewen Callaway tells us in New Scientist (13 October 2008), revealing that

"Bonobos are merciless," says Gottfried Hohmann, a behavioural ecologist at Max-Planck Institute for Evolutionary Anthropology in Leipzig, Germany. He witnessed several monkey hunts among bonobos living in the Democratic Republic of Congo, and says, "they catch it and start eating it. They don't bother to kill it". Yet unlike chimps, bonobos live in female-centred societies where sex, not aggression, settles differences and enforces social order.

I'd wondered when all that "bonobos could teach humans a thing or two" stuff would finally hit the bottom of the vast circular file of pop science.

The rest of the article is basically people talking around an inconvenient discovery. My favourite line: "Some anthropologists suggest that in the million or so years that separate bonobos from chimps, bonobos lost their appetite for violence."

Gentle reader, remind me of that if they are ever ripping us both to pieces, eating as they go.

See "A defense of Apes r us - an insider look at the pygmy chimpanzee enthusiasts" for the "loving ape" view

and

"Apes R Not Us, and we have to get used to it, revisited!" for the skeptical view.

Also just up at The Mindful Hack: Language: Students cannot form logical position about television's impact?

MercatorNet “Navigating Modern Complexities” has kindly published my recent article on getting good marks, “The payoff for straining the brain: Does self-discipline beat intelligence? What about a good night’s sleep?”(October 8, 2008):

When researchers examined the final grades of 164 Grade Eight students, together with their acceptance or rejection from a prestigious high school, they found that “scholarly success was more than twice as dependent on assessments of self-discipline as on IQ.” Students with more self-discipline—meaning that they would sacrifice short-term fun for long-term gain—were more likely to improve their marks during the school year than those who wouldn’t sacrifice fun. By contrast, a high IQ did not predict a rise in grades. Obviously, this won’t surprise an experienced teacher or a mature parent. But it bears repeating all the same: Modern neuroscience is not overturning millennia of experience; it is filling out what the other disciplines already tell us. Our brains are very plastic organs, and paying attention determines the areas in which they develop. Like our bodies, brains must be exercised effectively to achieve our goals. That is why self-discipline is as important to brain exercise as to body exercise.

Go here for the rest.

Also just up at The Mindful Hack ...

Artificial intelligence: Computers do not think, they "shuffle bits"

Artificial intelligence: Getting computers to pretend to converse is an " extremely hard computational problem"

Spirituality: Churches nobody goes to any more vs. the "ancient and ever new" ones

Spirituality and the arts: High time someone said this

The Mindful Hack is my blog that supports The Spiritual Brain (Beauregard and O'Leary, 2007) .

Years ago, I met Michael Behe, American biochemist and author of Edge of Evolution, and he - then and always - struck me as a scientist who needed to witness to what science is supposed to be, against the spirit of the age.

Born in the wrong time, he was. In a time when scientists exist to provide proof for fascistic atheism.

Darwin's theory of evolution is promoted in order to make atheism work.

Behe could not make Darwin's theory work because the theory is not true to the reality of life. And he was not willing to buy into the many ways that others cope with that fact, and go on with their careers.

Political correctness demands that he either make the theory work, or pretend to. But he can't because it is not true.

Of course, hordes of grantsmen are willing to pretend that it is true. The sponsors of theories like the peacock's tail and the big bazooms theory of human evolution prance and dance before the grants committees. So?

Surely we have all been here before. Flatuent profs and glad rag-waving teachers, to say nothing of eager, agreeable museum docents. The sort of people whose position depends on agreeing with whatever is going down.

But they cannot make their shibboleth true by an exercise of the will alone.

No wonder Behe is so hated. Anyway, here is a podcast with Behe:

How Michael Behe Came to Doubt Darwin's Theory

Click here to listen.

This episode of ID the Future features a clip from national radio host Michael Medved's intriguing interview with CSC senior fellow and biochemist Michael Behe. How did Behe, author of Darwin's Black Box and The Edge of Evolution first come to doubt Darwin's theory? Listen in and find out.

Also just up at The Post-Darwinist

Darwinism and high culture: "Exactly why we do things this way is never a question that is asked"

Startling idea for a debate: Evidence really matters ...

Intellectual freedom: Post-modernism the key threat?

Christian mathematician John Lennox vs. former Christian science writer Michael Shermer, on God, design, and all that

In "Faith Beyond the Frontal Lobes" (Washington Post, September 27, 2008) Michael Gerson offers a common sense corrective to rampant materialism in neuroscience. Reviewing Andrew Newberg's work with meditators, which Mario and I discussed in The Spiritual Brain, he notes,

Human beings routinely have experiences that are not commonly associated with normal consciousness yet seem more real than normal consciousness. "There is something in the brain that facilitates and rewards that type of experience," Newberg says, "and our brain desires to make sense of it."

This leads some, of course, to reductionism -- the assertion that a physical basis for transcendent experience proves there is no such thing as transcendence. It is an evolutionary joke on humanity -- perhaps useful, but not accurate -- because everything explainable is thus illusory.

But this view is not more "scientific" than other views. It involves a philosophic materialism that is entirely faith-based. We know, for example, that a complex series of physical, hormonal changes helps bond a mother to her newborn child. Does this mean that parental love is a myth? Only according to the philosophic claim that chemicals exhaust reality. Is it not equally possible that a cosmos charged with transcendence might organize itself in such a way that human beings can sense transcendence?

Yes, it is equally possible. And that is a better explanation than reducing ideas to chemicals. Put another way, the chemicals that help mothers bond to newborn children don't help us understand why there is a black market in babies for infertile women who have never experienced such chemicals. Nor do they help us understand Mother Theresa and her Missionaries of Charity, who provided homes for thousands of children, even though she became a nun and never tried to have any children herself.

Neuroscience can help us understand some important things about human beings, but it will be the most use if it is treated as one source of information, rather than as a reductionist explanation - especially of subjects like spirituality.

For example, Gerson notes that some people's genes might not predispose them to spiritual experiences. Perhaps, but many spiritual traditions do not emphasize personal experiences; they are viewed as a gift that can become a distraction from the main business of learning to live as a whole human being.

See also:

"Neuroscience: Getting beyond the mind-body problem

"Neurotheology": Bad neurology and bad theology?

Neuroscience: Meditation really can change the brain

The recent USA Today op-ed fantasy that Britain does not suffer from controversies over intelligent design (because "theistic evolution" has brought such harmony to Brit land) is an instructive example of just what’s wrong with legacy mainstream media in general. The problem for Mark I. Pinsky's "Science and Faith the British Way" was its timing: The puff piece ran just as the Michael Reiss affair was blowing through the independent blogs.

Synopsis: The Royal Society attracted attention across the globe by firing education director Michael Reiss. As of October 4, 9:00 am EST, the Google search "Michael Reiss" "Royal Society" turned up 71, 500 hits, and blogging on the subject abounds. And the people who drove Reiss from his job (the sinner in the hands of an angry god affair), have earned condemnation on both sides of the controversy over evolution and intelligent design. (Reiss, a Church of England clergyman, is a convinced Darwinist, and his sin was suggesting that terms like "creationism" and :"intelligent design" be spoken aloud in class in order to tell students that they are wrong and that Darwin is right. But the fact that he is a clergyman caused prominent scientists to question his right to hold the education director's post anyway.)

Many Americans and Canadians found out about Reiss's sacking through blogs, and many lively public discussions ensued.

But along come the editors and author at USA Today and make clear their assumption that North Americans know nothing about the world that’s not on prime time Boob Tube.

So they publish a blog column that – in the context – would be outrageous if it were not so obviously and ridiculously false to the true situation in Britain.

Just being on the Internet does not transform legacy media into new media.

The basic legacy media principle is that you have no access to information apart from what they tell you.

It is a three-stage process: 1. They talk. 2. You listen. 3. You believe.

Only one problem: It doesn't work that way any more.

This is not the early 19th century. North Americans do not wait six weeks to find out what is happening in London; we know as soon as Brits do. And we now have lots of independent sources of information.

So legacy media - online or not - are spinning tales for a shrinking population, as their plummeting circulations show.

Those circulations are never coming back. And this little vignette is a window into one reason why.

The following stories will give you some idea of recent developments in the intelligent design controversy in Britain:

How angry is the Brit God of Science? Pretty angry, it seems ...

So they actually need to explain this? Britain's Royal Society is considering casting out God ...

Intelligent design and popular culture: The BBC spin on British creationism

Will Brit “faith and science” heavyweights speak up after education director’s firing?

Failed Brit Darwinist Michael Reiss: "A Sinner in the Hands of an Angry God": Synopsis of a Play in Three Acts

Intelligent design and high culture: Philosopher says teaching students about intelligent design should be okay - with qualifications (Here in evil, backward North America, the atheist philosopher was not driven from campus for his views.)

Darwinism and popular culture: The Anglican Church's non-apology to Darwin

Other stories at The Post-Darwinist:

Darwinism and popular culture: Only trolls would carry out Gallagher's orders, but for some reason he wants them carried out by gentlemen.

Darwinism and popular culture: Darwinian conservatism means "disintegration of morality"?

Theistic evolution: Straw men forked? Arguments for intelligent design addressed? Pigs fly?

Science and society: Here a tic, there a tic, everywhere a heretic ... Darwinism and popular culture:

Taking the fun out of fundamentalism - no hope for the one who does not accept ...

Both explained by psychiatrist Dr. Jeff Schwartz:

The easiest way to understand the difference between the mind and the brain is - the brain is a piece of biological matter ( protoplasm) in your skull. That's the brain. It's a thing; you can hold it in your hand. The mind is your experiences, and especially for scientific purposes your attention and attention focusing capacity so they aspect and the way in which you focus attention on your experiences.

and put to music by Marcia Bauman!

Hat tip Stephanie West Allen at Idealawg.

Also just up at The Mindful Hack

Social psychology: "Only the lonely"? Yes, abstract concepts can generate physical sensations - for better or worse

Near death experiences: Large project to study up to 1500 cases - possible new insights into relation between mind and brain

Evolutionary psychology: Do people see faces in cars?

Spirituality: A conventional sad tale does not transform into a spiritual memoir just because God is hat tipped