Discussions in the comment sections of many posts on this site chaotically tend toward the strange attractor of one generally off-topic issue: Why does Creation/Evolution seem correct to you? It is usually a discussion between Creationists who believe that the scientific conclusions are based on faith, and Naturalists who believe that the Scientific Method is best tool ever invented to extract sense from chaos.

In the beginning, Natural Philosophers (now called Scientists) in the West all believed in the Bible. Bishop Ussher gave the final word on the age of the universe according to the Bible in the early 1600’s, and the Church had all the answers. But then the idea emerged that one can actually test Aristotelian conclusions (purely rational and based on “what everybody knows”) with observations. Copernicus demonstrated with careful observation and applied math around 1600 that only the moon itself orbited the Earth, and all the other planets circled the Sun. The church accepted this, as a philosophical observation, irrelevant to the place of Man in the Universe. Then Galileo made a gadfly of himself by publishing popular books mocking the Pope for publicly continuing in the preaching of Geocentrism when it was clear, with the aid of a telescope, that not only did the planets orbit the sun, but that some of those planets had moons of their own. Many moons, placed where Man couldn’t even see them without modern technology.

Well, it just snowballed from there. Newton, a devout Christian, developed math in the late 17th century that accurately modeled the behavior of pretty much everything that man could observe at the time (the Laws of Motion). And those models showed how things naturally happen, without need for divine intervention. Then  in the mid-19th century, J.C. Maxwell developed similar rules to explain electromagnetism (light, electricity, radio, etc). Discovery after discovery kept challenging the universally held beliefs in many areas. Gravity wasn’t related to nor caused by sin. Demons didn’t cause disease. The basic elements weren’t Earth, Air, Fire and Water. Air was a complex substance, but caloric and phlogiston weren’t. The planet and the universe steadily got wider and older and more complex as more and more evidence collected by true believers forced them to acknowledge that nature is as it is, and not how interpretations of the ancient texts described it.

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Duped from Ethics Gradient.

They’ve started advertising the DVD version of that infernal, mendacious, highly offensive, wilfully ignorant and misleading waste of megabytes known as Expelled. Bay of Fundie has scratched the surface of their advertising and revealed some new information.

Now, given that this is the DVD release of Expelled, it makes me wonder what kind of special features they’ll include. Of course no one can know for sure, but I have something of a wish list:

- a complete timeline of all the steps taken & communication entered into to secure the participation of such people as Richard Dawkins and PZ Myers, including a full explanation for the stark deviation from the premise of the original film: it was originally presented to Myers & Dawkins as a documentary named “Crossroads”, detailing the intersection of religion & science, which it clearly did not turn out to be, either by name or nature

- full, uncut, unedited interviews with the above-named

- a full explanation from the film’s producers of PZ Myer’s own expulsion from a screening of Expelled by security staff before he’d entered the theatre, despite the fact that he’d registered to attend under his own name and hadn’t attempted any kind of subterfuge, as was alleged early on by the producers (as well as an explanation of how Richard Dawkins, arguably more recognisable than PZ Myers, was allowed to enter unmolested)

- behind-the-scenes segments showing such things as exactly who comprised the audience in Ben Stein’s opening, paranoid address to college “students”and a clear explanation of Adolf Hitler’s alleged use Darwin’s theory of evolution to justify his horrific experiments

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The only animals you’ll usually find in municipal swimming pool are humans.  It’s the end of the year, though, and Maplewood, Missouri is one of many communities that invites dogs into the pool before draining the water.  Out of curiosity, I visited Maplewood’s pool today and saw numerous dogs anxious to hit the water.

Entering a swimming pool filled with dogs that don’t know each other presents some hazards, of course.  Therefore, children under the age of 12 are not allowed into the pool area.   Adults who do enter are asked to sign a comprehensive waiver of liability.

Once admitted to the pool itself, this is what you would have seen today.   Lots and lots of dogs.  I was there in the early afternoon, and probably saw 100 dogs in the pool.  The only hazard I experienced was that I almost tripped over a few dogs.   They were truly everywhere.  No one seemed distraught that most of the dogs were swimming naked.  Somehow, it’s very different when the naked animals are humans.

Yesterday, at the nearby pool of University City, a friend of mine reported that she saw 400 dogs in the water at the same time.

This swimming pool full of dogs and people reminded me that people and dogs have developed incredibly close emotional bonds.  And these bonds all happened over the past 20,000 years because, until then, there were no dogs on planet Earth.  In a blink of an eye, dogs evolved from gray wolves, thanks largely to neotony. The two species are still so closely related that they can still breed with each other.  To shake things up at the pool, then, I could have cried wolf, though I didn’t.

As I mentioned in two previous posts (here and here), I recently had the opportunity to attend several of the sessions of the “Future Directions in Genetic Studies” workshop at Washington University in St. Louis.

One of the speakers was Carl Craver of Washington University. Craver’s talk was titled, “The Reductionist Distortion of Behavioral Genetics,” a push-back against those who consider genetics to be essentially a gene-centered reductionistic enterprise.

Craver illustrated his talk with two examples of progress in genetic research in contemporary neuroscience: the study of mechano-sensation in C. elegans, and the study of learning in mice. Here his own synopsis of his basic points:

Although these examples involve the effort to explain behaviors in terms of lower-level mechanisms, they violate the assumption that behavioral genetics is or ought to be reductionist in the above sense. First, one must distinguish genetic intervention, in which genetic mechanisms are commandeered to intervene into higher-level systems implicated in a behavior, from genetic explanation, in which the genes are components in the mechanism’s behavior. Second, one must distinguish cases in which genes play a crucial background role in the development and maintenance of mechanisms underlying behavior without themselves being components in the mechanism from cases in which the genes are components in the mechanism. Third, even in cases where genes are components in the mechanisms underlying a behavior (as in the LTP case), their contribution is intelligible only in light of facts about higher-level mechanisms; explanatory reduction to genetics is not even a coherent possibility. The reductionist distortion of behavioral genetics introduces biases into our understanding of neural mechanisms that are distracting and misleading us in the effort to understand the neural basis of behavior.

According to Craver, genetics is not inherently reductionistic, nor should it be.  In order to best make progress in the neurosciences, we need to take an integrated view of how genes contribute. Taking this integrative approach would serve as an “antidote to reductionism.”

At the beginning of his talk, Craver distinguished neurophilosophers (”who use findings from neuroscience to address traditional philosophical puzzles about the mind”) with Craver’s own work as a “philosopher of neuroscience (who “study neuroscience to address philosophical puzzles about the nature of science”). [After hearing Craver speak, I purchased his recent book, Explaining the Brain: the Mechanisms and the Mosaic Unity of Neuroscience (2007). Some of the material in this post is from Craver's book].

According to Craver, neuroscience, which attempts to link various levels of explanation with double-sided arrows of causality, is not destined to be a reductive science.  It is important to recognize this, because characterizing any science as reductionist slants science policy decisions in a nonproductive way. Characterizing a field as reductive affects the allocation of resources. For instance, what university departments and projects should be funded?  To consider a field to be reductionist pushes away from what Craver considers the true goal of neuroscience: to improve the human condition-essentially, neuroscience is medical science, or at least it should be considered as such.

Craver described three versions of reductionism. For instance, consider “metaphysical reductionism,” which considers everything to be “physical.” Craver finds this approach “puzzling” and “esoteric,” as well as irrelevant to real life neuroscientists. Working neuroscientists actually do their work at this level. Consider also “explanatory reductionism,” which considers low-level explanations to be automatically blessed as privileged and fundamental. A third version is “methodological reductionism,” which advocates experiments in which we “intervene low and detect high.” For instance, we can alter a gene and strive to detect higher level behavioral changes. Craver nominated John Bickle as a good example of a methodological reductionist, in that Bickle tended to “leap from molecules straight to behavior.”

What are the alternatives to reductionism? One of these alternative approaches is the position Craver termed “autonomy, advocated by David Marr and Jerry Fodor.

The other major alternative approach would be integration, which actively seeks explanations that span multiple levels. Reductionism is “anti-integration.” Craver discussed some of the work with C. elegans, a small worm that “God created for neuroscientists,” in that it has only 302 neurons, it is completely sequenced and it is transparent. Craver recommended a website containing much information regarding the experimental work on C. elegans.

Using the integration approach, one will encounter many senses of “level,” when one considers possible “levels” of explanation. There are dozens of these, including levels of control, description, theories and implementation.  Whenever Craver discusses explanatory integration, however, he’s referring to mechanistic levels, the more primitive levels of mechanisms being embedded within the higher levels.

According to Craver, Integrative neuroscience provides a clear sense of A) what is a “level” and B) how to integrate levels. In the actual practice of neuroscience genetics is frequently not reductive. This is true because many neuroscientists are not truly obsessed with reductionism, and “what you find often depends upon what you’re looking for.” In order to provide more impressive explanations, “trans-genetics needs to be an integrated study,” because reductionism brings on a series of troubling biases.

For instance, reductionism emphasizes the internal over the external. It considers a simplified version of the environment. It causes complexity at higher levels to be legislated out of existence. It encourages us to buy into a simplistic “additivity,” causing us to assume that what we have learned about tiny parts in isolation can be scaled up automatically when considering behavior as a whole; reductionism thus causes an oversimplification of phenomena. Reductionism also encourages “disciplinary myopia,” encouraging the assumption that phenomena can be described exhaustively from merely one perspective.

Craver offered additional arguments for using the integrative approach:

a. Brain systems are likely to have hierarchical organization, and the integrative approach is the most promising approach.
b. The integrative approach encourages exploration–interest in multiple levels of explanation.
c. The integrative approach is robust; its findings are more likely to withstand scrutiny when attacked from the multi-disciplines.
d. Craver’s “clinical argument”: interpersonal research is less intrusive and it provides ways to restructure the environment, ways that are often at least as promising as the reductive approach of manipulating the genes.

In sum, Craver makes a strong case that we should pitch our research at multiple levels of argumentation using the integration approach, therefore avoiding the tendency toward reductionism.

I’m in the process of reading Craver’s book, which I find to be written persuasively and with precision. This is also the way Craver speaks and it is thus delightful to listen to his ideas, which are based on his intimate familiarity with both the science and history of neuroscience.

Anyone who has been following my interests at this site likely knows of my interest in trying to pin down what it is that constitutes a meaningful “explanation” (not simply in the sciences, but, e.g., in ordinary conversation and political advocacy). I will be posting on this topic repeatedly in the coming months. Like Craver, I often have an aversion to reductionistic explanations (I should be clear–I don’t object to explanations that involve lower level mechanisms, only those that do this to the exclusion of higher level explanations and emergent phenomena).  And like Craver, we need to do the sort of work Craver is doing, to keep explanations meaningful, to prevent them from devolving into expressions of pure emotion or dead-end reductionism, which comes in many forms.

As I mentioned in an earlier post, I recently had the opportunity to attend some of the sessions of the “Future Directions in Genetic Studies” workshop at Washington University in St. Louis. One of the talks was by Paul Griffiths, a Philosophy professor from Sydney, Australia, who discussed “The Distinction between Innate and Acquired Characteristics.”

Griffiths’ talk focused on the troubled use of the word “innate.”  Also troubled are various synonyms of “innate,” including “instinctual,” and “human nature.” These terms all seem to engender confusion more than anything else, because there is a wide variety of potential meanings to these terms.  Can’t we all agree on what it means to be “innate,” so that we can understand each other when we use that word? As you see from this post, Griffiths is not optimistic.

Griffiths spent the first part of his lecture unpacking quite a bit of history of the biology of behavior. Many prominent scientists weighed on the use of the term “innate” during the 20th century. They include a staunch critic of behaviorism, Zing yang Kuo, “a terrific writer,” whose 1920 article, entitled “How are our Instincts acquired?” Griffiths highly recommended (I can’t find that article, but here is another of Kuo’s articles). Griffiths also mentioned the “instinct theorists,” including William McDougall (Griffiths commented that many of these theorists were actually dualists). Another of the instinct theorists was Niko Tinbergen, who argued that there is something about animal instincts that cannot be reduced.

Konrad Lorenz was influential in the 1950s, promoting the idea that there could be instincts without vitalism. Lorentz argued that we needed a much more complicated sketch of neural mechanisms, essentially arguing that small instincts were “assembled by the environment.” In short, Lorentz kicked vitalism out of the mix. Griffiths then described the work of Daniel Lehrman, who “wrote that other great paper of 1953,” a paper entitled “A critique of Konrad Lorenz’ Theory of Instinctive Behavior.”  As Griffiths put it, “Here was an animal lover who is also an anti-nativist.” He then descibed C.H. Waddington’s concept of “canalization.” A bit vague on my understanding, I found this explanation of Waddington’s approach following the talk:

the degree to which a trait is innate is the degree to which its developmental outcome is canalized. The degree to which a developmental outcome is canalized is the degree to which the developmental process is bound to produce a particular endstate despite environmental fluctuations both in the development’s initial state and during the course of development.

In view of these many approaches, what scientists have meant when they have claimed that traits are “innate” has never been something easily discerned.  In fact, the term “innate” remains a highly confusing concept.

Griffith’s own view is that it is “unscientific” to say that behavior is “innate,” unless the claim is unpacked neurologically. In short, it is not an explanation to say that something is “innate.” In order to explain something, one must address how that trait came to be. This idea was summed up in the writings of P.P.G. Bateson, who was also concerned about the conceptual swamp that the word “innate” had come to represent. Referring to the use of the word “innate,” Bateson wrote “Say what you mean, even if it takes longer, rather than use a word that carries so many different connotations.”

What do people currently mean when they claim that something that is “innate?”  It’s still not clear.

Some people mean that the trait is typical of the species. In 1975, Stephen Stich argued that an “innate” trait is a trait that a person will manifest in the normal course of human development. This approach doesn’t really work, because there are many examples of traits that are common that nonetheless depend upon the environment.

Another approach is based upon what might be termed “adaptiveness.” Something that is “innate” is something that doesn’t closely track the environment through natural selection. As Khalidi wrote in 2007, “innate” traits are those that contain more information than the environment.

A third common approach is an analysis based upon “fixity.” Those traits that are “innate” are environmentally canalized; they are insensitive to the particular state of the environment. For instance, one can find lots of genetic variation in a population of sparrows, but they mostly turn out looking similar. This same idea can be found in the writings of Andrew Ariew (1996).

Griffiths concludes that “innate” is an “expression of an implicit folk-biological theory of animal nature.” According to this folk-biological theory, some traits of living things are expressions of an inner nature, whereas others are imposed by the environment. (more…)

Can one gene make a difference?  Absolutely.  One case in point is Tay-Sachs Disease, a physical condition  where the central nervous system begins to degenerate in a four to six month old child who, until the onset of the disease, appeared normal.  Individuals with Tay-Sachs disease have two copies of a genetic mutation, one copy inherited from each parent.  In a carrier of Tay-Sachs, only one gene is different when compared to non-carriers. That’s how important one gene can be.   When we’re talking about complex behaviors, though, can the “cause” really boil down to one gene?  It’s unlikely.

I recently had the opportunity to attend several sessions of the “Future Directions in Genetic Studies” workshop at Washington University in St. Louis. On Friday, I attended a lively seminar led by Gar Allen, who teaches biology at Washington University. His talk was entitled “What’s Wrong with ‘The Gene for . . .’? Problems with Human Behavior Genetics and How to Combat Them.”

Allen opened his talk by asserting that claims about the genetic basis for complex human behaviors and traits are “notoriously difficult to investigate and replicate.” There is a long and troubled history of claims that genes are the cause of various conditions. For instance, in 1969, Arthur Jensen became the center of a storm when he wrote that Caucasians were more intelligent than African-Americans, suggesting that there was a genetic basis for this difference. Jensen’s position has been heavily criticized by numerous scientists on numerous grounds.

Jensen’s genetics-based pseudo-science was one of many such “scientific” conclusions, of course. Even prior to Jensen’s announcement, the eugenics movement of the early 20th century gave rise to numerous unsubstantiated genetic claims. Allen’s PowerPoint presentation illustrated the long history of dubious genetic claims. That history extends to the present. Allen illustrated the recent history of such claims with photos of the covers of at least a dozen popular magazines, each of them touting newly discovered genetic “causes” for complex medical conditions or complex social phenomena such as alcoholism and violence.

Genes are easy to blame for behaviors even when genes are incorrectly blamed. The media loves these stories that a gene is responsible for “causing” complex social phenomena. They are happy to bring fame to the scientists making such claims. Unfortunately, the media finds it much less newsworthy when other scientists to urge caution regarding such claims, even when caution is urgently needed. And if you’re looking for big headlines detailing methodological flaws in the studies on which gene-behavior claims are made, don’t hold your breath.

According to Allen, we should be suspicious of many claims that a gene “causes” a behavior. Genes are all too often put on thrones, resulting in reification and essentialism rather than true explanation. Genes are always situated in complex environments, and that it is a rare day when a single gene could be serve as “the” cause of a complex behavior. All careful scientists who study genes and behavior know that genes are always part of a complex cascade of causation. Nonetheless, all too many “Gene for X” stories start boldly with the (unsubstantiated) claim, ignoring or downplaying serious methodological concerns.

Further, it is common to hear gene jocks confusing correlation with causation. As Allen noted, responsibly testing the true role played by any particular genotype is made especially difficult due to problems with defining the relevant phenotypes and the difficulty of accurately choosing a population to study. Allen used Dean Hamer’s study regarding the alleged genetic basis for homosexuality.

Hamer’s study triggered widespread interest. If true, Hamer’s conclusion that homosexuality had a “genetic cause” would help gays defend themselves against claims that being gay was a mere lifestyle choice. On the other hand, there were numerous difficulties with Hamer’s study that didn’t make headlines. Compounding the problem, Hamer has a reputation as one who is reluctant to publicly engage with his critics.

One of the main problems with Hamer’s study is that it is extremely difficult to define homosexuality. Hamer asked his subjects rate themselves using Kinsley’s sexuality scale. It doesn’t take much to see the problem with this method. For instance, consider people like U.S. Senator Larry Craig (of airport restroom fame), who appears to have sex with men but nonetheless refuses to consider himself to be a homosexual. Consider, also, the numerous men with conscious or subconscious homosexual impulses who have not (yet) acted on those impulses.

Allen raised other serious concerns with Hamer’s study: Is all same-sex behavior to be treated the same, to be considered as having arisen from the same source or cause? If so, why? In Hamer’s homosexual group, seven out of 40 of the subjects lacked the “homosexual” marker.” Hamer concluded that perhaps there was a different genetic marker that also caused homosexuality. Allen suggested another possibility that Hamer ignored: “Maybe there is no genetic marker.” Allen also questioned why Hamer’s search was limited to markers on the X chromosome.

The types of problems one can see with Hamer’s study are common with many other studies announcing the discovery of “the gene for.” Studies seeking to find the genetic basis for human behaviors tend to be reductionistic. They tend to ignore gene-gene and the gene-environment interactions (Allen warns that it can be very difficult to pin down what constitutes the environment in many cases). Further, many genocentric studies fail to

A) consider alternative hypotheses;

B) appreciate plasticity of development;

C) take account of hierarchical systems and emergent properties; or

D) recognize the rampant nonlinearity of biological processes.

I would add that these bold stories announcing “The gene for X” also ignore the concerns recently expressed in this article urging a reworking of the modern synthesis.

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There was to have been a broadcast debate today between a Creationist and a Biologist. Ray Comfort (of the Banana Proves Creationism fame) against PZ Myers (a.k.a Pharyngula). But the station wimped out, and broadcast Comfort in relative quiet comfort today, and will allow Myers to respond tomorrow morning (Weds. Aug. 6, 2008 10:00 CDT (GMT-5)) on WDAY

Here is Pharyngula’s play-by-play, blogged during the first 40 minutes of the broadcast.

The first response comment was:

A friendly reminder to turn all irony meters and bullshit detectors to the lowest sensitivity, lest they be vaporized.

with a reply at comment #73 that I appreciated

Try our new line of Comfort-standard(TM) industrial grade irony meters. 2-ga. internal wiring, 3×10^6:1 step-down transformers, military-grade ICs, massive dual-blade fast-trip circuit breakers and Safe-Shatter(TM) non-shrapnel-producing casings. Each unit is hand-assembled and burned in on a steady diet of AM radio and Bush administration ‘We’re turning the corner… really now, honest’ press releases. Autoranging, and rated to 30 TeraHaggarts. Don’t browse the web without one!

I’ve blown up electronic panels with inadequately specified parts in the past, with actual noise and smoke. So I “get” each of these units. Except, how many MegaDubyas are there in a TeraHaggert?

The July 11, 2008 edition of Science (available only to subscribers on line) includes an article entitled “Modernizing the Modern Synthesis,” by Elizabeth Pennisi, regarding a group of scientists who call themselves “The Altenberg 16.” They have gathered together to explore the need to revamp the modern synthesis. What is the “modern synthesis”? According to Wikipedia, the modern synthesis “bridged the gap between experimental geneticists and naturalists; and between both and palaeontologists, stating that”:

• All evolutionary phenomena can be explained in a way consistent with known genetic mechanisms and the observational evidence of naturalists.
• Evolution is gradual: small genetic changes, recombination ordered by natural selection. Discontinuities amongst species (or other taxa) are explained as originating gradually through geographical separation and extinction (not saltation).
• Selection is overwhelmingly the main mechanism of change; even slight advantages are important when continued. The object of selection is the phenotype in its surrounding environment. The role of genetic drift is equivocal; though strongly supported initially by Dobzhansky, it was downgraded later as results from ecological genetics were obtained.
• The primacy of population thinking: the genetic diversity carried in natural populations is a key factor in evolution. The strength of natural selection in the wild was greater than expected; the effect of ecological factors such as niche occupation and the significance of barriers to gene flow are all important.
• In palaeontology, the ability to explain historical observations by extrapolation from micro to macro-evolution is proposed. Historical contingency means explanations at different levels may exist. Gradualism does not mean constant rate of change.

According to “Modernizing the Modern Synthesis,” the modern synthesis thus holds that:

Organisms have a repertoire of traits that are passed down through the generations. Vacations in genes alter those traits bit by bit and if conditions are such that those alterations make an individual more fit, and the altered trade becomes more common over time. This process is called natural selection. In some cases, the new feature can replace an old one; in other instances, natural selection also leads to speciation.

The modern synthesis has guided biologists for the past 70 years. The obvious question, then is what has happened since then to necessitate any changes to the modern synthesis?

A lot has happened in the past half-century. DNA’s structure was revealed, genomes were sequenced, and developmental biologist turned their sights on evolutionary questions. Researchers have come to realize that heredity is not simply a matter of passing genes from parent to offspring, as the environment, chemical modification of DNA, and other factors come into play as well. Organisms vary not only in how they adapt to changing conditions but also in how they evolve.

One of the organizers of the group, evolutionary biologist Massimo Pigliucci stresses that the need for a reworking of the modern synthesis doesn’t mean that the overall theory of evolution is wrong (as “intelligent design” advocates will no doubt argue). Rather, the group is attempting to “better incorporate modern science and the data revealed by it.”

The Pennisi article serves as a succinct review of some of the new research that needs to be incorporated into evolutionary biology. Many of these developments “are nudging evolutionary biology away from a focus on population genetics-how the distribution of genes changes across groups of individuals-and toward an understanding of the molecular underpinnings of these changes.”

One of the basic ideas that needs to be incorporated is that DNA cannot do it all–biology is highly constrained by physics and this needs to be recognized. Evolutionary biologist Gunter Wagner explains that under the “old” modern synthesis, “the body plan is a historical residue of evolutionary time, the afterglow of the evolutionary process such that more closely related organisms share more features.” The “new” view is that body plans have internal inertia and evolution works around this stability.”

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There is yet another story going around about dinosaur and human footprints found together in ancient (maybe 4,000 years old!) rock. Here is the local credulous Texas take on the find.

All the previous pictures of contemporaneous dinosaur and human footprints provided by these people showed that humans used to have 19″ long feet with only 3 toes. This new isolated sample, long removed from its secret setting, is available to view in person by true believers. The dinosaur track might be real, but any anatomist or gait specialist could tell you what is wrong with the human footprint, and its intersection with that of the dinosaur. Any paleontologist want to comment on the dino-print?

If they really wanted actual paleontologists to believe the evidence, they would invite them to the site of the find to seek the rest of the footprint trail. As an attempt to gain credulity, they claim that over 800 x-rays were taken of the rock (one CAT scan?) after the human footprint was “revealed”. Um, I guess they need to prove that it is a rock through and through. Actually, the claim is that fossil footprints are made by compressing layers of rock, rather than in a soft single sediment layer where they are usually found. The scans reportedly show that both footprints distorted underlying layers.

The daughter of the discoverer has studied some geology, so she is skeptical of its evidentiary value as proof of a Young Earth. But Dr. Carl Baugh, the founder and director of the Creation Evidence Museum in Texas, hopes to get these pictures into Texas textbooks (and therefore all other states) under the Strengths and Weaknesses doctrine of the Discovery Institute.

Writing on a NYT blog, Olivia Judson argues that we should abolish “Darwinism.” Here’s what she means:

I’d like to abolish the insidious terms Darwinism, Darwinist and Darwinian. They suggest a false narrowness to the field of modern evolutionary biology, as though it was the brainchild of a single person 150 years ago, rather than a vast, complex and evolving subject to which many other great figures have contributed. (The science would be in a sorry state if one man 150 years ago had, in fact, discovered everything there was to say.) Obsessively focusing on Darwin, perpetually asking whether he was right about this or that, implies that the discovery of something he didn’t think of or know about somehow undermines or threatens the whole enterprise of evolutionary biology today.

Sounds good to me. That way, it will be more apparent that the Creationists are arguing against an entire phalanx of theorists, biologists, statisticians, geologists and biochemists (among others). Without the term “Darwinism,” it would be more apparent that the Creationists can’t win simply by claiming that a single man stands between them and our science classrooms. I agree with Judson that to call modern evolutionary biology “Darwinism” is like calling aeronautical engineering “Wrightism.”

I only disagree with Judson in one regard. She suggests that Darwin accomplished more in his lifetime than any of us could accomplish in two lifetimes. I would suggest that the proper number is ten or more, based upon Darwin’s far-ranging achievements. He was truly an extraordinary scientist and thinker.

I was surprised yesterday to find a post by Jerry Pournelle (well known SF author and technology columnist) on MensNewsDaily (a starkly conservative news magazine site with pretensions of middle-of-the-roadism). His column, Intelligent Design: Answers and Questions, is openly favorable to the premise that Intelligent Design and Global Warming denial should be taught in science classes.

I have read much by Pournelle, starting with his collaborations with Larry Niven in the 1970’s and ’80’s, and then his columns in Byte magazine, and his solo novels more recently. There is a strong Libertarian feel in his recent works (such as “High Justice”), where big corporations are the good guys and “liberal” governments merely stumbling blocks to progress or even survival. But he does write some great adventure stories. I was only mildly put off by the contention in “Fallen Angels” that embracing the global warming hoax would lead into international Luddism. I figured that it was just a plot device.

But now I see that the writings of Pournelle reflect an overall feeling that Nature and Man are but players on a stage that no mortal can understand. Perhaps it has something to do with his recurring close brushes with mortality. If you read some of his other columns at JerryPournelle.com, you’ll see that he champions all manner of oddball challenges to “Mainstream Consensus Science”. Sooner or later, one of these challenges may turn out to be valid. But historically speaking, successful challenges to the well established theories of thermodynamics and quantum theory are far between.

Absolutely! As long as we teach ALL of the controversies. This is some clever science/religion/humor.

In brief, Stephen Jay Gould proposed the idea that evolution is truly stochastic (a particular technical kind of random), that if we started evolution over as of a million years ago, we probably wouldn’t be here in our current form. That is, any evolutionary step is contingent on the history of steps that went before, each based on a combination of random mutation and environment.

I’ve read several posts about the new discovery today, and the best summary with accurate excerpts and clear analysis is this one from Pharyngula (PZ Meyers Myers).

In brief: A single experiment ran over 20 years, or 33,000 generations of bacterial cultures, where they froze a sample every 500 generations from each of 20 separate populations, all nurtured identically over the entire time with a particular set of stressful conditions. When a particular beneficial change occurred to the population, they could track back genetically and see what the genetic change was, and what probably allowed it to manifest in a visible way. Then they tried to get the same thing to happen again starting from various suspected branching points. In some cases, the same mutation happened again.

Of course, Michael Behe of the Discovery Institute quickly posted a sort of rebuttal to the idea that yet another piece of evolutionary theory has been proven, so Meyers took him to task. Behe claims that the experiment proves how incredibly unlikely such changes are, and therefore they need an Intelligent Designer to guide them. Apparently he missed the point that the complex series of changes did happen, and were repeatable, but only in a statistical manner. As opposed to in a pre-ordained, designed sort of way.

Or possibly his point is that God individually guides the evolution of laboratory E. Coli to fool scientists into thinking that supernatural intervention is unnecessary. It’s hard to tell.

[Admin note:  here is the description of the experiment by New Scientist]

You read that right! No reader of Dangerous Intersection, radical materialist or hard-bitten skeptic believes in science. To say otherwise is to give a false impression of what science actually is. Science is not something in which a person believes or does not believe. Science is not a belief system; it has no holy screeds or sacred tenets. It is merely a tool, a method of gleaning knowledge, and the language used in reference to it should reflect this.

What on earth am I ranting about? Well, it goes back a few years to the Discovery Institute, and spans all the way to the present with Ben Stein’s film Expelled. The intelligent design/evolution debate has become quite the pop topic, and hence, the endless battle of science vs. religion has come into everyday discussion as well. Everyday people in normal daily settings run through these issues, turning any public place into a potential battleground.

I’ve heard a lot of the less experienced science advocates say things about science that frankly aren’t accurate. While these people mean very well, they fail to frame their debates properly, and the content of the discussion suffers for it. Since science vs. religion has become as much a layman’s debate as an expert’s one, I think the time has come for those of us on the science side of things to agree on the language we should use.

I have no expertise in science, religion or philosophy, I have no refined understanding of the psychology of persuasion, and I am no orator. However, I still have the gall to make a few semantic suggestions for any person who plans to engage in a lengthy discussion on evolution, intelligent design, or the general clash between religion and science. My tips, and their justifications, are as follows: (more…)

For three decades I’ve puzzled about the idea held by Christian Fundamentalists that the Bible must be proven absolutely and literally true in every way, or else Christianity is false. The latter clause being accepted as silly, therefore most science of the 19th and 20th century is patently on the wrong course.

I think I finally get it: It isn’t so much about the whole Bible, as about a literal Adam and Eve and serpent and fruit. If one even momentarily entertains the idea that this particular tiny part of the Bible is allegorical, then where is the original sin? If A particular orphan named Adam didn’t bite of a particular forbidden fruit, then the underlying momentary lapse of ancestral judgment for which Christians claim God holds all living people responsible didn’t happen. Therefore Jesus died in vain, if one belongs to a congregation for whom Original Sin is The Big One.

Therefore, one must reject the geology, astronomy, and functional biology as was available to 19th century discoverers like Darwin. One must also reject all the subsequent discoveries that frustratingly and consistently reiterate his conclusions, like the periodic table, plate tectonics, cell biology, quantum theory, biochemistry, radiological dating, germ theory, cosmology, dark matter/string theory, genetics, chaos theory, and so on. If it can cast doubt on the timing or existence of biblical original sin, it must be wrong.

It makes perfect sense, in a narrow world view sort of way.

Many people still bristle at the idea that chimpanzees can have “cultures.” The evidence is accumulating, however, as documented in “Almost Human,” an article found in the April, 2008 edition of National Geographic. The article was written by Mary Roach, with incredible photos by Franz Lanting.

In 2007, an Iowa State University anthropologist named Jill Pruetz reported that while studying chimpanzees in the field (two years earlier) she noticed a female chimp:

Sharpening a branch with her teeth and wielding it like a spear. She used it to stab at a bush baby–a pocket-sized, tree dwelling nocturnal primate that springs from branch to branch like a grasshopper. Until that report, the regular makings of tools for hunting and killing mammals had been considered uniquely human behavior. Over a span of 17 days at the start of the 2006 rainy season, Pruetz saw the chimps hunting bush babies 13 times. There were 18 sightings in 2007. It would appear the chimps are getting creative.

Pruetz has spent more than four years studying the Fongoli chimpanzees (they are savanna-woodland chimps from eastern Senegal, across the border from western Mali). Pruetz has been habituating the Fongoli chimps (allowing them to get used to her) for the past three summers. She has done this hot, filthy and exhausting work six days a week, from dawn to dusk. She has gotten sick with malaria seven times. In the course of watching the Fongoli champs, she has also noticed them engaging in other behaviors unique to these Fongoli chimps: “soaking in a water hole and passing the afternoon in caves.”

Spearing bush babies is only the most recent of the many cultural behaviors documented regarding chimpanzees. Jane Goodall was the first to report seeing chimps making tools (for termite fishing). The world-famous bonobo named Kanzi has learned hundreds of symbols to communicate. This National Geographic article reports numerous other behaviors unique to various communities of chimpanzees have been documented. Some communities of chimpanzees use rocks to smash open nuts much like we would use hammers and anvils. Other champs chew leaves into a spongy wad to soak up water for drinking. Several communities of chimps cool down by a wading into pools of water. Numerous communities of chimpanzees throw rocks, sometimes as weapons and other times as part of displays.

The article notes that chimpanzees and humans share between 95 and 98% of their genomes. The article cautions, however, that this is “less meaningful than it sounds. Humans share more than 80% of their gene sequence with mice, and maybe 40% with lettuce.”

The author of this article, Mary Roach, was surprised to learn that chimpanzees’ yawns are contagious, “both among each other and to humans.” In the course of writing this article, she also learned that chimps laugh, and even get upset if someone laughs at them. They sometimes spit in disgust. Some chimps have been known to adopt other species of animals (one chimp named Tia adopted a small kitten).

Chimps get up to get snacks in the middle of the night. They lie on their backs and do “the airplane” with their children. They kiss. Shake hands. Pick their scabs before they’re ready.

The observations reported in this article certainly blur the cultural boundary between humans and chimpanzees. These sorts of observations will make many people upset, however. They want to believe that humans are sui generis among animals, of their own kind and that there is no real comparison, certainly no cultural comparison between humans and animals of any other species.  In fact, there are hordes of people who resist thinking of humans as animals at all (and see here) (and here and here).

Perhaps it won’t soothe the critics to view the situation in the way suggested by a famous evolutionary biologist:

It is perhaps less problematic to view the situation as does The Third Chimpanzee author Jared Diamond: Not that chimps are a kind of human, but that humans are a kind of chimp.

This is an article that truly transported me around the world. It made me feel that I was almost there, observing these magnificent animals. As I’ve commented before, this type of writing and photography is nothing out of the ordinary for the National Geographic.

I started thinking about the the “reductionist attitude” in presenting science when I read Erich’s Post To deal with “arrogant” scientists we need to move beyond reductionism and break the “Galilean Spell” (from May 7, 2008). Curricula seem to begin with biology, work through chemistry, and finally introduce physics. If English were taught categorically as science is now, students would go through phases in this order:

• Elementary English: Analysis of Literature (done orally)
• Intermediate English: Sentence structure, paragraphs, and essays (done graphically)
• Advanced English: Introduction to the Alphabet and Spelling Lessons

The alphabet of science is made up of basic natural “laws” as discovered by Newton, Maxwell, Mendeleev, Heisenberg, and so on. Sentences and paragraphs are like molecules and chemical syntheses. And finally you have enough structure to begin to see how biology works from cells (essays) through organisms (stories) and populations (novels).

One could be taught holistic science, building to the grand ideas from the simple ones. By constructing the ideas instead of breaking them down, the interrelationship and the interactions of the parts can be seen, as well as the nature and function of the parts themselves. A whole is never the sum of the parts; it is the sum of the interactions between the parts set on a foundation of the parts themselves. This becomes obvious when building, but is obscured when deconstructing.

No wonder Americans doubt the “theory of evolution”. Schools try to teach this advanced and universal concept without any foundation. By the time the basic laws of nature (whose interaction supports this conclusion) are introduced, the theory has been mentally discarded.

Why is it done this way? (more…)

Neil Shubin recently published a book celebrating the discovery of a life form that clearly constitutes a transitional life form: tiktaalik, a fish that crawled out of the water by use of its rudimentary limbs. In a post in which I described Shubin’s book (Your Inner Fish: A Journey Into the 3.5 Billion Year History of the Human Body (2008)), I argued that every life form is a transitional life form. We’re all on the way to something else, at least those of us who will leave biological offspring. But some life forms are more obviously transitional than others and no currently living animal is more obviously transitional than the platypus.

The May 8, 2008 issue of Nature (articles available online only to subscribers) announces: “Top Billing for Platypus at End of Evolution Tree.” The article starts out by describing the platypus, one of nature’s oddest creatures:

Seemingly assembled from the spare parts of other animals. The semi-aquatic monotreme is a venomous, duck-billed mammal that lays eggs, nurses it’s young and occupies a lonely twig at the end of a sparse branch of the vertebrate evolutionary tree.

The Nature article describes the findings of a study analyzing the genome of the platypus. It was conducted by Wesley Warren of Washington University in St. Louis, Missouri. The study found that the platypus genome contains both reptilian and mammalian elements.

The study also explains the emergence of the many odd features of the platypus. For instance, the platypus does produce true milk (although it doesn’t have true nipples). The new study shows that the platypus has the genes for caseins (milk proteins) which map in a way that corresponds to the protein mapping in humans.

This is a sign that one of the genetic innovations that led to the development of milk occurred more than 166 million years ago, and after mammals first split from the lizard-like sauropsids that gave rise to modern reptiles and birds.

The platypus results from a mix of reptile and mammal genes. “The genomic features of what are now two separate lineages can coexist in the genome of a single organism.”

Apparently the Pacific Justice Institute is suing a couple of Berkeley professors for putting up a website that explains evolution. The PJI apparently sues anyone who might constrain Christian evangelism in America, including in public schools. I read about this current suit here, on CitizenLink.org.

CitizenLink is a newsletter for Focus on the Family, a non-profit political action group for Pro-Life, evangelical Christian, and/or Young Earth education policies, but with redeeming social action programs. As long as they don’t mention candidates by name, they don’t have to pay taxes.

The legal claim is that evolution is a faith-based idea, and that the professors used Federal Grant money (National Science Foundation grant no. 0096613) as part of the funds needed to develop the site. Apparently the site disregards Creationist sources and ideology, and as such is religiously biased and violates the separation clause.

www.UnderstandingEvolution.com is full of references and citations, explanations, illustrations, and teaching guides to try to lead one to an understanding of many facets of what evolution is, and how it affects, well, everything. Topics include easy to follow answers for skeptics, like “How does evolution impact my life?”, “What is the evidence for evolution? ” and “What is the history of evolutionary theory?”. There are guides for teachers at all levels.

As such, this site has been a thorn in the side of Intelligent Design since 2004. Let’s see how much mainstream press this current nuisance suit attracts.

I was meandering in cyberspace, and stumbled onto this column by Australian Michael Ruse: The struggle between evolution and creation: an American problem. This appeals to me after all the news about Australian Ken Ham and his Creation Museum here in the U.S. The muse of Mr. Ruse is that the U.S. is vocally and publicly debating the science of evolution versus competing Biblical philosophies, and their roles in education and culture

But his main point is that this is just a symptom. Ever since the Scopes trial, the vocal Biblical Literalism Fundamentalist minority has been fighting for its life. Part of their claim is that evolution is not as values-neutral as proponents like to claim. Ruse agrees. Evolution theory was bolstered by Darwin’s books with his additions to the theory. But it might have stayed a quiet and intellectual revelation, had it not been for Darwin’s contemporary, scientific and social activist Thomas Huxley.

Huxley, who was known in the popular press as “Pope” Huxley, preached evolution-as- Christianity-alternative non-stop at working men’s clubs, from the podia in presidential addresses, and in debates with clerics, notably Samuel Wilberforce, Bishop of Oxford. Huxley, who invented for himself the religious label of “agnostic”, even aided the founding of the new cathedrals of evolution, stuffed as they were with displays of dinosaurs newly discovered in the American west. Except that these halls of worship were better known as museums of natural history.

Ruse follows the history forward to show why he considers this to be An American Problem. The rest of the world’s Christians are content to accept science for what it can provide, and leave to the Bible issues outside of what can be examined. But America was settled in part by religious extremists, exiled from England and other countries for their radical beliefs. This culture is diluted, but still present and very vocal. The founding fathers were well aware of this element, and set the nation up to minimize the damage that they can cause, while allowing them to be themselves.

As the orders of magnitude of scientific understanding kept expanding beyond the narrow scale of the Biblical universe, the Biblical Literalists had to draw a line. It was too late to hold at a geocentric universe, and much too late for a flat Earth. Sin and demonic possession as the causes of disease also gave way to germ theory without much of a fight. But spontaneous divine creation of man is now the sticking point. Any evidence or theory that contradicts direct and intentional divine creation is labeled unholy.

In America the battle between secular government and a theocracy is being fought in the guise of Evolution versus Intelligent Design (or whatever name Scientific Creationism is using). From the vantage of Australia, it is an interesting skirmish. Here in the Bible Belt, it scares me.

We have a nice brewery run by the Schlafly family in our town. A town already renowned for beer. But a relative by marriage is more famous than the beer because of her stance against women’s rights and against progress through knowledge. Yes, Phyllis Schlafly is in the local news with a new controversy. In brief, this Washington University Alumna has been offered an honorary degree, and the faculty is in an uproar.

Why? After all, my own commencement speaker (honoree of the year) at that institution was Bob Hope. He claimed to be the most degreed high school dropout in the world at that time. The link above goes to the article containing the full text of a scathing letter by the faculty about the choice of Schlafly, specifically from the Law School. The flap is because the faculty thinks that honoring an outspoken anti-intellectual with another degree would demean an institution of learning. At least Bob Hope says silly things on purpose.

Our own Erich had put a response up there, but I found the post it by browsing news involving Creationism, another educational priority of Ms. Schlafly. Quoth he:

The problem is that if Ms. Schlafly completely had her way, core values of true academics, including skepticism and tolerance, would be extinguished. Under those conditions, Washington University would cease to exist.

According to this article, essentially copied from the AP, Adnan Oktar, who writes as Harun Yahya, has been convicted of fraud. His extensive organization