Part 3 - Darwins Dilemma, Creationist Propaganda and Corrupt Christians

The previous post is available here.

Having ‘proved’ that fossils predating the Cambrian radiation are non-existent, and that all modern animal phyla appeared out of nowhere - in what the narrator describes as a “burst of creativity” - Darwin’s Dilemma the movie, then proceeds to ridicule Darwin the scientist. In their distorted reasoning, the creationist filmmakers think that if they can discredit a scientist that lived 150 years ago in Victorian England, somehow the audience will be convinced that the whole of modern science is erroneous. To initiate the strike against their biology bent Beelzebub, another carefully cropped quote is thrown to screen;

“Nothing distressed him more than the Cambrian explosion…” - Stephen J. Gould

For some unknown reason, creationists love Stephen Gould. Their infatuation may have something to do with a distorted view of Gould’s ‘punctuated equilibrium’ model; perhaps somehow the idea of a long stasis followed accelerated change translates to divine creation in the minds of simpletons? At any rate, Stephen Meyer or some other failed scientist from the Discovery Institute must have gotten this Gouldian morsel shorthand in a text message. They certainly didn’t get it from the page 238 of The Panda’s Thumb, the book in which Gould uses it to illustrate the lack of discrepancy between long past Darwinian predictions and modern paleontology.

It is certainly true that Darwin struggled with the lack of fossils predating the Cambrian radiation, speaking to intermediate fossils in Chapter 10 of the Origin of Species he wrote;

“Why then is not every geological formation and every stratum full of such intermediate links? Geology assuredly does not reveal any such finely graduated organic chain; and this, perhaps, is the most obvious and serious objection which can be urged against my theory.”

Of course, as with the Richard Dawkins quote yesterday and the Gould quote above, Darwin is here using the presupposition of a question as a lead to his explanation. And although the film in question is in the habitat of mining only the presumptive portions of these literary tools, the authors’ answers usually follow. In the case of Darwin’s true dilemma alluded to in the Origin of Species quote, he explains later in chapter 10 that,

“The explanation lies, as I believe, in the extreme imperfection of the geological record…. we continually overrate the perfection of the geological record, and falsely infer, because certain genera or families have not been found beneath a certain stage, that they did not exist before that stage. In all cases positive paleontological evidence may be implicitly trusted; negative evidence is worthless, as experience has so often shown…
Those who believe that the geological record is in any degree perfect, will undoubtedly at once reject my theory. For my part, following out Lyell's metaphor, I look at the geological record as a history of the world imperfectly kept and written in a changing dialect. Of this history we possess the last volume alone, relating only to two or three countries. Of this volume, only here and there a short chapter has been preserved, and of each page, only here and there a few lines. Each word of the slowly-changing language, more or less different in the successive chapters, may represent the forms of life, which are entombed in our consecutive formations, and which falsely appear to have been abruptly introduced. On this view the difficulties above discussed are greatly diminished or even disappear.”

Basically stated, what Darwin was implying was that, due to erosional processes, fossils are rare in the first place, and the oldest of all-the-fossils on Earth are rarer still. And he further predicts that despite these natural conditions, predecessor fossils are there and will be found as time proceeds and paleontological excavations are made. Darwin was right on-target with this prediction. In the 150 years since publication of the Origin of Species, numerous fossils have been unearthed, including those of the Ediacara biota, some from the Doushantuo formation and even the fascinating Markuelia fossil embryos – all predating the radiation vent! But, alas I guess these fine fossils don’t count… After all, as Paul Chien the head of the Discovery Institute’s paleontology section tells us in the film,

“to the paleontologist, the lack of intermediate fossils is well known.”

And Paul Chien should know, because he’s Chinese! As he later explains, “the Chinese community is honest about these problems and tries to explain them outside of Darwin.”

In addition to having an Asian heritage on his side, Paul Chien is a fellow of the Discovery Institute where he helps ‘spread the good word’ by translating Christian pseudo-science into the Chinese language. The worst part of Chien’s resume is that he’s also a biology professor at the University of San Francisco – tsk tsk San Fran.

Chien’s appearance marks a second transition point in the film’s diabolical plot. Leaving the fossils in the past, the modern sciences of evolutionary development and molecular genetics take center stage. In concert with this changeover is implementation of a new strategy – drawn the audience with science-ish jargon and convince them of life’s irreducible complexity. Leading this new front is Steven Meyer himself; holstered at his side is information theory. Brandishing this weapon he aims to shoot down “Neo-Darwinist storytelling” – by showing that modern genetics has nothing to do with evolution…


CONCLUDED - IN PART 4



Condon, D. (2005). U-Pb Ages from the Neoproterozoic Doushantuo Formation, China Science, 308 (5718), 95-98 DOI: 10.1126/science.1107765


Dong, X., Donoghue, P., Cunningham, J., Liu, J., & Cheng, H. (2005). The anatomy, affinity, and phylogenetic significance of Markuelia Evolution Development, 7 (5), 468-482 DOI: 10.1111/j.1525-142X.2005.05050.x

Morris, SC (1995). Ecology in deep time Trends in Ecology & Evolution , 10 (7), 290-294

Quammen on Darwin

Good write-up, swiped from Here

By ED KEMMICK – Billings Gazette

Charles Darwin, who fundamentally altered the way scientists view the world and whose ideas are nearly as inflammatory today as they were when he announced them to the world 150 years ago, was a quiet, kindly homebody who was literally sickened by excitement and dispute.
And though he is known now for one big idea, the theory of evolution by natural selection, Darwin spent his life, in the words of David Quammen, immersed "in the beautiful significance of tiny details."

Quammen [at right] is a science writer who lives in Bozeman. Having spent most of February and March delivering lectures on Darwin around the country, Quammen said he sometimes felt a little presumptuous, given that Darwin apparently never gave a single public talk on evolution.

"It was hard for him even to have a really animated discussion with one of his friends without being sick the next day," Quammen said.

Darwin is the subject of renewed interest this year because it is the 150th anniversary of the publication of "On the Origin of Species" and the bicentenary of his birth in England on Feb. 12, 1809.

Quammen is in demand because he has spent much of his career writing about evolutionary biology. He delivered a speech on Darwin at the Library of Congress in 2002, and in 2006 he wrote "The Reluctant Mr. Darwin," a short biography. He also served as general editor and wrote an introduction for a big, new illustrated edition of "The Origin" published in October.
He has lived in Bozeman since the 1970s and is now in his third and final year as the Wallace Stegner Distinguished Professor of Western American Studies at Montana State University.
He said he has been surprised "to find myself sort of a tinpot Darwin expert. ... I'm not trained as a scientist myself. I'm not an evolutionary biologist. But I've been in love with this guy and his work for a long time." ................

Link to Billings Gazette to Continue

Capturing the Superorganism or Reviving a Monster?

"The beauty of the dream vanished, and breathless horror and disgust filled my heart," so said Victor, a well established scientist from the upper east side of Transylvania Switzerland as he witnessed life cross the threshold of the lifeless and into his newly created monster – Frankenstein!

Well, OK – maybe quoting from Mary Shelly’s Frankenstein is a bit over-the-top, but a recent article published in the Journal of Evolutionary Biology has made me question whether or not Andy Gardner and Alan Grafen have created a monster of their own – one that they may eventually come to regret.

In a recent article (available as a PDF Here) titled “Capturing the superorganism: a formal theory of group adaptation,” Gardner, a Royal Society University Research Fellow, and Grafen, a Professor at Oxford University widely known for his work in statistics (most memorable to me for his mathematical modeling of Zahavian Handicaps), define, describe and quantify group adaptation and group selection as functional modes of natural selection.

On one hand the article is innovative in that it takes steps to cleanly differentiate between often befuddled concepts, like “kin selection” versus “group selection” and various interpretations of “fitness;” it also empirically formalizes (and limits) the group adaptation theory - indeed it lifts the theory to new heights. However, on the other side of the coin, the article (antagonistically in my mind) compounds any preexisting misunderstanding of these concepts by arguing for even greater expansion of analogy.

For example, the article tediously - though accurately - makes distinctions between various measures of fitness, including inclusive fitness, relative fitness, within-group fitness, personal fitness, between-group fitness, individual fitness and indirect fitness; but then, rather than provide simplicity and clarity to this dizzying collection of measurement methodologies, the article uses them as a foundation in support of further artificial constructs – namely groups as individual units or actors in natural selection.

The superorganism enters… [As a side note, there is a good E.O. Wilson interview (audio file) at NPR’s Science Friday website from last December in which he discusses the superorganism concept and his book of the same title – HERE]

Through their delineations, Capturing the Superorganism’s authors intentionally reveal that both the individual organism and the “group” as focal points of adaptation are only ‘maximizing agent’ analogies and that both are only intermediaries to ever fluctuating gene frequencies. Unfortunately, rather than arguing for a more reductive measure of selection, an all encompassing fitness-model or perhaps even a gene-centered perspective, they instead suggest viewing the process at a greater scale and wider focus.

Ironically, the article opens with a quote from Richard Dawkins’ Extended Phenotype;

“I have characterized inclusive fitness as ‘that property of an individual organism which will appear to be maximized when what is really being maximized is gene survival’... One might generalize this principle to other ‘vehicles’. A group selectionist might define his own version of inclusive fitness as ‘that property of a group which will appear to be maximized when what is really being maximized is gene survival’!

This excerpt, and the context in which it is constructed, clearly makes an argument against viewing the individual organism as a unit of selection and implies that any unit above that of the gene is so artificial as to be considered arbitrary. Key to this idea is the phrase “will appear to be maximized,” which means that it is not truly being maximized, but rather it is a merely an extension of the gene – a vehicle. A “vehicle” is precisely what a “group” represents, a vehicle composed of multiple smaller vehicles – all of which have a gene behind the wheel.

From the abstract: “Adaptation is conventionally regarded as occurring at the level of the individual organism.”

Perhaps individual organisms are ‘conventionally regarded,’ but not accurately so… Individual organisms may be units of reproduction, but they are not replicators. Genes lay at the core of all phenotypes; morphological, behavioral, social or otherwise - is it really convenient to think of natural selection as occurring at the level of the individual organism? Most successful organisms aren’t replicated in their entirety; rather it’s the successful, or surviving, genes contained within their DNA that are passed on with an increased probability of contributing to the genome of future generations. Genes are passed on, not whole organisms; if the analogy is not “true” for individuals, why up the ante and recommend adopting a level of biological organization that is even higher than an individual?

The authors admit that the Group Maximization Analogy (GMA) does have limitations;

“we find that there is a strong mathematical correspondence between the ynamics of gene frequency change and the GMA analogy in scenarios where groups comprise genetically identical individuals or where within-group competition is repressed. This correspondence reveals that, in such scenarios, natural selection acts to optimize group phenotypes for the purpose of group fitness maximization –i.e. group adaptation.”

According to the authors, group adaptation seems a best fit in those situations in which individual members have identical genomes (i.e. are “cloned”) or in those scenarios where competition is repressed (i.e. is “policed,” or controlled by an external agent). Wouldn’t these situations, one in which like-vehicles “strive” to move like-genes, and one in which a dominant phenotype exhibits some level of control (policing or chemical control via pheromones) over a less-dominant phenotype, also represent strong cases for a gene-centered, or an Individual Maximization Analogy?

Considering that within-group selection (i.e. genes by way of individual organisms) is inevitable, are there any cases, or models for group-selection that take this into account?

“We have found no formal justification for group adaptationism in any scenario in which within-group selection is permitted. Obviously, no real-world species will perfectly embody the ideal of zero within-group selection.”

OK, doesn’t such a finding impair the group model as an inclusive theory?

“…we emphasize that this is not sufficient grounds for abandoning the notion of group adaptation in evolutionary biology.”

Why not?

“The theory of individual-level adaptation is similarly based upon limiting assumptions, such as unbiased genetic transmission, which are not expected to be perfectly realized in any species; yet, it enjoys huge experimental and empirical success.”

True, however the individual-level adaptation model is also a “maximization analogy,” used as a tool, artificially constructed to demonstrate, measure and communicate what in actuality is occurring at a lower level - the level of the gene. Is that the purpose of the GMA, simply an additional tool to be used in exhibiting the effects of genetic frequency, and if so what is the benefit of up-scaling from the level of the organism to that of the group, or extending the phenotype to greater distances, bearing in mind that at the very least the individual is the unit of reproduction and any expansion of analogy is likely to cause even greater confusion?

“Our emphasis has been on formality and not generality – there is much work to be carried out to establish whether other scenarios will admit a group adaptationist view of social evolution. In the meantime, we suggest that it is safer to view social adaptations as occurring at the level of the individual organism, where they function to maximize inclusive fitness.”

Gardner et al. (2009). Capturing the superorganism: a formal theory of group adaptation. Journal of Evolutionary Biology DOI: 10.1111/j.1420-9101.2008.01681.x

The Rise of “Homo egocentricis”

Although it was literally a dark and stormy night, such weather conditions were but a novelty to the speaker – a scientist whom had spent the majority of his life scanning barren rocks and desiccated landscapes for fragments of fossil bone beneath the unrelenting and scorching sun of an East African desert. Yet, I can’t help but think that some level of instinctual fear naggingly tickled at his stomach as he approached the waiting crowd…

There was little doubt that villains - the arch enemies of reason and deniers of fact– concealed themselves among the many upstanding community members and university staff in attendance. This was, after all, Tallahassee, Florida. A city of the Southeastern Unite States, geographically located near the eastern extent of the so called “Bible belt.”

How would they react to being told that biological evolution is fact? Moreover, how would they respond to learning that Homo sapiens, despite an egocentric view of the world, have shared a common ancestry with other primates, and in fact, a common lineage with all life on Earth?

Actually, they responded remarkably well, much to the credit of Dr. Don Johanson.

By all accounts, the talk on Human Origins was a success. Dr. Johanson spoke with the confidence and familiarity that has made him a highly sought, world renowned lecturer and scientist.



He began the talk by discussing the development of his personal interest in anthropology as a child and quickly moved through a summary of the major fossil discoveries made during his lifetime - a true story of adventure and discovery. The lecture was given at an IMAX theater and included some fantastic images of hominid fossils and African landscapes; the presentation can be viewed in its entirety by going to the FSU Origins webpage HERE and clicking on the red-highlighted “Webcast” text to the right of Dr. Johanson’s photograph.

As a further suggestion, I’d recommend a quick look at a recent article by Kaye E. Reed of the Institute of Human Origins (which Don Johanson runs in Arizona) discussing the paleoecology of the Hadar hominin site in Ethiopia. The article discusses speciation and environmental transitions associated with Australopithecus afarensis.

Reed, K. (2008). Paleoecological patterns at the Hadar hominin site, Afar Regional State, Ethiopia Journal of Human Evolution, 54 (6), 743-768 DOI: 10.1016/j.jhevol.2007.08.013

“Punctuated Equilibrium is Garbage”

A fantastic lecture given by E. O. Wilson at Florida State last night!

It was a privilege to listen to such a distinguished scientist, expert naturalist and exceptional author. If only I was half as sharp today as he is at 79… The amount of technical knowledge, understanding and wit that he possess is only exceeded by his passion for the natural world – a true asset to the scientific community and to the planet as a whole.

Rather than listen to my second hand droning, checkout the link below to view the webcast directly - Courtesy of Florida State University.

Also, be sure to scope the “E.O. Wilson Biophilia Center” which is scheduled to open September 12, 2009.


By clicking on the link below you’ll be able to hear Ed Wilson talk about Darwin’s four great works:

1. Journal of Researches into the Natural History and Geology of the Countries visited during the Voyage of HMS Beagle Round the World (1845)

2. On the Origin of Species (1859)

3. The Descent of Man; and Selection in Relation to Sex (1871)

4. The Expression of Emotions in Man and Animals (1872)

As well as topics like;

The John Wayne Vs Woody Allen Model of Sexual Selection…

The Birth of Modern Psychology…

The two Tribes of Biologists - the Functional biologist and the Natural Evolutionist…

Religion as a Byproduct of Warring Tribalism…

The Plight of the Honey Bee…

The Potential for Life on Europa…

And don’t forget to listen for my favorite quote of the talk, “Punctuated Equilibrium is Garbage.”

UPDATE: Click on "WEBCAST" under Ed's picture at the website Here to listen.

The Adventures of Darwin, Alfred Wallace & Henry Bates

Lecture filmed 3/19/2009 at Florida State University as part of the Origins 2009 Celebration.

UPDATE: Click on "Webcast" under Sean's picture (here) to view.


Sean Carroll retraces the epic adventures of three scientists - Darwin, Alfred Wallace & Henry Bates – as they develop their ideas on evolution during the golden age of the theory’s development. Carroll then proposes that we are currently in a second golden age of learning.

To skip introductions, jump to about the 14:30 minute mark.

Defending Darwin

Just returned home from a week of fieldwork and observed the slight blogospheric bioturbation resulting from the letter sent to New Scientist by Dan Dennett, PZ Myers, Jerry Coyne, and Richard Dawkins.

Letter Posted at New Scientist – “Darwin was right"

Pharyngula – “Spanking New Scientist”
Why Evolution is True – “Darwin proclaimed wrong AGAIN; we fight back!”
RichardDawkins.net – “Darwin was right”
Sandwalk – “Blunt Talk from Four Evolutionists”

Read some of the author’s arguments in defense of the original article in the comments section of – “Why’s Graham so Glum: Lawton Critiqued”

Adaptation and Evolution in a Changing Climate

I haven't had a whole lot of time to blog the last few days, but I came across this quick write-up on Science Daily and liked the quote at the end, “We lose diversity with a rapid change, but always life finds a way. Some kind of life will fill the gap.”


Charles Darwin may have been born 200 years ago come Feb. 12, but his theory of evolution remains an everyday touchstone for modern biologists. And while the Origin of Species author might not have known the term “global warming,” he wouldn’t have been surprised that the environment is changing. He would, however, be astonished by the speed at which it’s happening today, researchers believe.

“Every species is under temporary permanence,” says Bill Saidel, an associate professor of biology at Rutgers University’s Camden Campus, where he teaches Animal Behavior and Behavioral Neurobiology. Darwin would have predicted changes in species’ habits and even changes in the environment, but the planet’s facing changes that are both drastic and unpredictable.

Saidel notes some already observed results of global warming today, like changing avian migration patterns and pH levels in oceans. But how would Darwin begin to determine how every species might respond to climate change? Most likely he’d begin by observing those habitats that are uniquely individual and well-defined.

This approach – researching one specialized habitat for insight into a larger understanding of evolution – is how Saidel conducts his own research at Rutgers–Camden. His interest in the exotic African butterfly fish is precisely because it has evolved two retinas in each eye, but only feeds from information derived from one. The fish’s highly specialized adaptations, from retina to brain, serve as a model for discerning the circuitry of feeding in all vertebrae whose visual traits aren’t as clearly segmented.

“This fish has much to teach us. It has adapted extraordinarily to a single unique environment. Yet, the consequences of a highly adapted species is that any change can be dire,” says Saidel.
Dan Shain, associate professor of biology at Rutgers–Camden, also researches highly specialized creatures: worms that thrive in the world’s most extreme climates. He studies them for insight into their adaptations and their unique cocoon production processes, which have biomaterial applications. Only the intensely frigid environs Shain once explored in destinations like Alaska aren’t as cold anymore.

This summer, the Rutgers–Camden researcher traveled to Denali National Park to observe ice worms, whose glacial habitats make them an ideal indicator species for climate change.

“Ice worms have been around at least a few million years and have been through many ice ages, but the change there now is dramatic,” Shain says. “I’ve been traveling to Alaska for 10 years studying ice worms. The mass of the glaciers is about half of what it was a decade ago.”

Disappointed, Shain didn’t find new specimens allegedly living in Eldridge Glacier. Even the glaciers he previously identified as housing a plethora of ice worms had sadly receded.

“The number of ice worms is radically down. We think ice worms are getting washed off the glaciers and they don’t have the capability to move up the glacier quickly enough,” he reports.

The issue of time is crucial to understanding the implications of global warming. Shain calls it “accelerated evolution” and predicts large-scale extinctions that even Darwin couldn’t comprehend. Species that can best adapt to this abrupt change will go on and multiply, leaving the world with less of a variety.

“We lose diversity with a rapid change, but always life finds a way. Some kind of life will fill the gap.”

Rutgers University (2009, February 10). Big Year For Darwin, But What Would He Make Of The Climate Change Ahead?. ScienceDaily. Retrieved February 11, 2009, from http://www.sciencedaily.com/releases/2009/02/090202113611.htm

Why’s Graham so Glum: Lawton Critiqued

Only 24 days into my blogging career and already I seem to have ruffled the feathers of a professional science journalist – not real sure if that’s a bad thing or not…

Well, in all modesty the feathers on this particular journalist seem to ruffle quite readily, so readily in fact that he’s been tousling them on several different science blogs during the past few hours. He’s posted comments and rebuttals on Evolving Thoughts, Evolutionary Novelties and where I happened to bump into him, at Larry Moran’s Sandwalk.

I guess a life of servitude to the public media can be stressful, at least for New Scientist writer Graham Lawton whose recent article “Why Darwin was wrong about the tree of life” graced the most recent cover of New Scientist titled “Darwin was Wrong.”

I’m really quite astonished at Lawton’s parrying and thrusting all over the blogosphere; it seems to me that any biology or science enthusiast could have predicted a little fallout resulting from the phrase “Darwin was Wrong” being placed on the cover of a popular science magazine. Indeed - I’d be shocked, if I were to discover that the generation of such hype was anything less than the premeditated goal of the magazine’s editorial staff.

In point of fact, Lawton himself states in the comments section of Sandwalk,

“I'm acutely aware that it is 50% journalism, 50% sales pitch”

So, why is Graham so glum? He’s clearly aware, as are most readers, that the cover is little more than a publicity stunt aimed at selling copy. He may be missing the very important point that although everyone recognizes the pitch, not everyone approves of the tactic.

Lawton, as well as the editorial staff of New Scientist, may think that sacrificing accuracy for the sake of profit is a respectable endeavor; however I would venture to guess that much of the magazine’s readership does not. In part, it may be that readership’s response to the cover that contributed to the comparatively apologetic tone of the article’s subsequent editorial (Editorial: Uprooting Darwin's tree tone).

At any rate, regardless of the profit margins involved in misrepresenting important biological contributions through creative cover making, why does Lawton continually assert that the article’s content somehow remedies the cover page?

I’ve read the article. It seems abundantly clear to me that Lawton’s goal was to firstly create an artificial dichotomy between Darwin’s branching tree concept and genetic studies involving horizontal gene transfer (HGT) and then, after accomplishing this, to pummel Darwin’s idea through literary biased language.

A few examples of Lawton’s biased language:

1. Speaking to the Tree of life project - “But today the project lies in tatters, torn to pieces by an onslaught of negative evidence”


2. “Many biologists now argue that the tree concept is obsolete and needs to be discarded”


3. HGT - “[This] bombshell has even persuaded some that our fundamental view of biology needs to change”


4. "For a while, this allowed evolutionary biologists to accept HGT without jeopardizing their precious tree of life”


5. Darwin’s concept - “We now know that view is wrong”
“Meanwhile, those who would chop down the tree of life continue to make progress”


6. "Having uprooted the tree of unicellular life, biologists are now taking their axes to the remaining branches”

Comparing Darwin’s tree (based on natural observation and inference) to modern molecular genetics may be stretch, but I’ll refer to the above listed blogs and their accompanying comments as opposed to laying out the arguments here…

Rather my point is very simple, popular science periodicals, as well as science journalists should strive to master the arts of clarity and accuracy; they should compose and present the resultant works in a creative and informal way that is both informative and enjoyable to the science enthusiast who partakes of them. To pursue the agitation of the informed readership and to encourage fundamentalists is – plainly and simply – wrong.

Science Journalism - “Journalism tends to have a stronger bias towards sensationalism and speculative theories than science, whereas science focuses more on fact and empirical measurement.” Lawton’s balance is askew...

As to my originally posed question at Sandwalk, “So, is the title an outright media ploy - pandering for profit – or, does Lawton lack some fundamental understanding of scientific progress?” This wasn’t a personal assault; it’s a critique of the New Scientist’s pandering and the article’s inability to distinguish between historic foundations and modern remodeling.

“Oh, and Johnny: sorry to disillusion you but I've got a pretty good understanding of scientific progress. You, however, lack a fundamental understanding of how the media works.” (Lawton)

Thanks for the disillusionment Graham, but you’ve made it abundantly clear how the media works with your comment at Evolving Thoughts,

“I really ought to make a sarcastic comment here about "really bad" bloggers, but that would be an oxymoron. (Only kidding - it's soooo much fun being rude to people on the internet, isn't it, and so much easier than being rude to them in person!)”

I do have a suggestion for the next New Scientist cover:

They’ll sell like hotcakes!

Update: Also a conversation at EvolutionBlog

Update 2: also at Pharyngula