## Tuesday, September 30, 2014

### Recapitulation

[1.] See Alex T. Kalinka et al., "Gene expression divergence recapitulates the developmental hourglass model," Nature, Vol. 468: 811-814 (December 9, 2010); Brian K. Hall, "Phylotypic stage or phantom: is there a highly conserved embryonic stage in vertebrates?," Trends in Ecology and Evolution, Vol. 12: 461-463 (December, 1997); Andres Collazo, "Developmental Variation, Homology, and the Pharyngula Stage,"Systematic Biology, Vol. 49:3 (2000).

## Sunday, September 28, 2014

Accompanying the funny cartoon below was an explanation by a blogger about why chimps are super-smart and we humans shouldn't think too highly of ourselves.  The cartoon itself seems aimed at reducing all human exceptionalism to a primate urge. (I think the urge for academics to outpublish each other is more easily traced to that urge.)  It makes better humor than philosophy.

Basically chimps are pretty good problem-solvers (and so are octopi for that matter) and they more or less form a sort of strategy or cognitive map of a situation to deal with or navigate a particular problem.  What the psychologists are calling metacognition in this case is recognition of underdetermination or sense of (a lack of) certainty.  In fact, any ability to revise that map of the problem space is in some sense metacognition.

Of course, many animals have brains that recognize all sorts of things:  faces, predators, disorder, direction of motion, spatial relationships.  An animal that finds a better vantage point when the view is unclear is doing something analogous; investigating when the cognitive map is hazy is a similar instinct for any problem-solver like a raven or an ape.  Can there be much effective problem-solving there without some recognition of underdetermination, without some sense of uncertainty bordering on confusion?  It seems like lumping that in with the way humans think about their thinking is extrapolation-turned-polysemy.  It stretches credulity.

But the fact that a chimp can recognize when the cognitive map is shaky-- it seriously raises the question of whether a chimp has what it takes to do evolutionary science.  ;-)

## Saturday, September 27, 2014

### Jerry Was A Man

I didn't plan the title of my post... It leapt from my fingers as I started typing and the title of the famous science fiction short story somehow seemed appropriate.

I came across a post from Jerry Coyne, anticreationist extraordinaire, which exemplifies for me and reminds me just how bankrupt the materialist, secularist view of humanity really is.

When a male lion invades another group and kills the cubs, when a chimp tears another chimp to bits, those are just bits of nature, and aren’t seen as wrong.  And the amorality of nature is touted even by those who realize that our primate relatives show rudiments of morality, . . . . is it really true that all of nature, including primate societies, must be seen as amoral, while human actions must be judged by this thing called “morality”?

### Stephen Asma and the Cuvier-Geoffroy Debate

The reviews of Following Form and Function are intriguing to say the least.

http://embryo.asu.edu/pages/essay-cuvier-geoffroy-debate

The Cuvier-Geoffroy Debate?  Never heard of it.  Sounds interesting.

Yet, it surprises me to find that recapitulation precedes both Darwin and Haeckel, and that structuralism seems to have had a rich pre-Darwin history.
Serres had been influenced by the theoretical developments in German biology, most notably by early versions of the recapitulation theory proposed by Carl Friedrich Kielmeyer in 1793 and Johann Friedrich Meckel’s theory of arrests of development in 1811. Like Meckel, Serres believed that it was necessary to study the transitional forms of embryos to understand the permanent adult forms of vertebrates. Doing so, he assumed, would reveal that the developed forms of the lower classes of animals – invertebrates, for example –mimicked the intermediate embryonic forms of higher vertebrates. This idea of development was expressed in the Meckel-Serres Law, and distinguished from the later evolutionary accounts of the recapitulation theory proposed by Ernst Haeckel. Serres’ idea of arrests of development, and Geoffroy’s understanding of it, was transcendental rather than evolutionary. For transcendental anatomists like Serres and Geoffroy, the semblances discovered in embryonic stages reflected a particular metaphysical view of life and a philosophy of anatomy exemplified by Geoffroy’s principle of the unity of composition. The similarities inferred by these kinds of embryological studies did not necessarily represent the similarities of structure between vertebrates and invertebrates as an actual empirical fact of transformation from one species to another (i.e. an evolutionary account), but rather they represented the abstraction of an ideal type required by anatomists to form general laws of development and morphology in biology (i.e. a transcendental account). In other words, the principle of unity, the theory of analogies, the theory of arrests of development and the search for homologies were all regulative principles that served as conditions for the possibility of scientific discoveries in the field of anatomy.
- See more at: http://embryo.asu.edu/pages/essay-cuvier-geoffroy-debate#sthash.RsjBneyG.dpuf

## Tuesday, September 23, 2014

### Secular creationism on the rise in molecular biology!

From Jerry Coyne [emphasis mine]:
Virtually all of the non-creationist opposition to the modern theory of evolution, and all of the minimal approbation of [Coyne's University of Chicago colleague James] Shapiro's views, come from molecular biologists. I'm not sure whether there's something about that discipline (the complexity of molecular mechanisms?) that makes people doubt the efficacy of natural selection, or whether it's simply that many molecular biologists don't get a good grounding in evolutionary biology.
LOL

(I thought I heard for the last 15 years that evolutionary theory was molecular biology...)

I guess these molecular biologists are ... SECULAR CREATIONISTS!

## Monday, September 22, 2014

### Protostome vs. Deuterostome

Larval Transfer in Evolution in Horizontal Gene Transfer. . . .

## Sunday, September 21, 2014

### Pulled Punches: Haeckel's Embryos in Peer Reviewed Literature

First I'll talk about the peer-reviewed literature that Randy Olson brings up, and then I'll bring up some peer-reviewed literature that contradicts him.

In Randy Olson's "Pulled Punches" extra for his Flock of Dodos, Olson references an article in The Quarterly Review of Biology ...  and mentions the "peer-reviewed" status of said journal to bolster his claims about Haeckel's embryos.  As I've expressed elsewhere, I find Olson's choice of this particular example (which he says he picked for personal reasons--presumably because he thought himself particularly knowledgeable on the subject) of that particular book (Icons of Evolution) to represent Intelligent Design to be a loaded choice.

The authors of Olson's touted article have been key figures in the neo-Darwinian public policy think tank NCSE (National Center for Science Education) which is dedicated to having neo-Darwinian theories and hypotheses taught uncritically, and to discrediting Intelligent Design by conflating it with creationism and by promoting ad hominem arguments, and which played a key role in the mistreatment of Richard Sternberg at the Smithsonian.  Kevin Padian in particular dislikes Wells' criticism of his dino-bird theories, even though Wells' criticism is probably tame compared to that of paleornithologist Dr. Alan Feduccia.

At any rate, Padian and Gishlik's article seems to claim that Wells did not publish research-based papers after getting his PhD nor did engage in any research, a claim contradicted by Carolyn Larabell.  The appearance of this spewing of "pro-science" blatherskite in Quarterly Review says more about the journal than it does about the article.  No amount of peer review can make a journal avoid libel, it seems.  Nor apologize for it.  The fact that Quarterly Review has become a haven for this level of attack on Jonathan Wells, an attack all the more cheapened by associating Dr. Wells with a fictional murderous con artist (in the title no less), demeans its status as a scholarly journal. Why haven't we heard about the Talented Mr. Richards and the Talented Mr. Gould?

It was not long after that creationists and advocates of intelligent design ignited thousands of websites in an electronic auto-de-fé wherein Haeckel's reputation and that of Darwinian theory were generally sacrificed to appease an angry God...

(Robert J. Richards, "Haeckel's embryos: fraud not proven," Biology & Philosophy, Vol. 24:147-154 (2009).)
http://www.evolutionnews.org/2012/10/darwin_lobbyist_1065151.html

Contrary to the evolutionary hourglass model, variations in the adult body plan are often foreshadowed by modifications of early development. ... These modifications of embryonic development are difficult to reconcile with the idea that most or all vertebrate clades pass through an embryonic stage that is highly resistant to evolutionary change. This idea is implicit in Haeckel's drawings...

## Saturday, September 20, 2014

### Going Nuclear: Saving Vertebrate Phylogeny

From the abstract for "Going nuclear: gene family evolution and vertebrate phylogeny reconciled":

Gene duplications have been common throughout vertebrate evolution, introducing paralogy and so complicating phylogenetic inference from nuclear genes. Reconciled trees are one method capable of dealing with paralogy, using the relationship between a gene phylogeny and the phylogeny of the organisms containing those genes to identify gene duplication events. This allows us to infer phylogenies from gene families containing both orthologous and paralogous copies. Vertebrate phylogeny is well understood from morphological and palaeontological data, but studies using mitochondrial sequence data have failed to reproduce this classical view.
[emphases mine]
The abstract continues to save the day: "Reconciled tree analysis of a database of 118 vertebrate gene families supports a largely classical vertebrate phylogeny."  In other words, reconciled tree analysis picks the tree that contains the fewest departures/epicycles from the phylogenetic picture from morphology and paleontology.

## Friday, September 19, 2014

### Punches Pulled: Michael Behe Doesn't Care

In his "Punches Pulled" extra for his film Flock of Dodos, Randy Olson goes through a list of things that he left out of the film supposedly to be nice (i.e. to appear less hostile) rather than to keep his film from becoming a schlockumentary.

I direct your attention to his coup-de-gras.  He admits that he talked so long to Dr. Michael Behe that he felt tired afterward.  Tired?  Was there a debate that didn't make it into the film?  (He stresses in the film that two other interviewees he didn't debate about evolution because they didn't have the background.  Maybe he engaged Michael Behe about his then-forthcoming book Edge of Evolution, a book that discussed the powers of mutation and selection in detail; Flock implies that Behe wasn't doing anything in 2006 other than glorying in the publishing success of Darwin's Black Box.)

In fact, there is almost nothing from his very long talk with Dr. Behe other than the Mt. Rushmore analogy.  Briefly the film dwells on the mousetrap analogy--something more central, but is completely weak on it; if the film had got some of Behe's responses to Ken Miller's criticisms, there might have been some substance to the segment.  But it's "Mt. Rushmore" that you hear from the lips of Behe.  There's a lot more to ID concepts than a Mt. Rushmore analogy, but it seems to be on the basis of that analogy that Olson anticlimactically dismisses ID at the end of the film.  Did they talk about Mt. Rushmore and mousetraps for hours, or did they get into mutation frequencies and malaria?  What tired out poor Randy?

But I digress. This coup-de-gras that Olson so graciously left out of his film is that Michael Behe doesn't care. That's right, folks, he doesn't give a scat, and Olson has the goods.  More specifically, at the end of what was for Olson a long, grueling interview (Behe appears as relaxed as he did at the beginning of the interview), Olson baits Behe on the politics with which Flock is so deeply concerned.  On how the politics affects him, Behe responds that he doesn't have a personal stake in what gets taught to kids in public school because, like so many teachers (here and here), he doesn't send his kids to public school.  Perhaps, as a devout Catholic, he would never consider that option anyway.  We don't know what followed that sound bite--perhaps a fuller explanation of his "yes and no" answer--nor do we have any idea what was so darn tiring about sitting around outdoors having a relaxed conversation.

## Thursday, September 18, 2014

### p-values

The concept of p-value might just be the most central idea to the notion of counterflow, design, etc.

This is the Fisherian idea that I was taught in biology class at university, and the idea that Dembski has argued is more fundamental to theory choice than the likelihood inference that Elliot Sober promotes.

### Lobe-finned Fish, Amphibians, and Devolutionary Processes

So earlier this week I was thinking about von Baerian development and considering a specifically non-recapitulatory view of The Vertebrate Embryo and was thinking, "Could the majority of fish be considered more specialized in terms of the general vertebrate pattern, with the more amphibian-like fish being the archetype rather than the specialization.

Lo and behold, I came across something in Stuart Kauffman's work that evidence seems to have been mounting that the swim bladder came from the lung, not the other way around!  It would be even more intriguing if the archetype for fish were something even more like an amphibian, say a sarcopterygian like Tiktaalik, rather than the more numerous actinopterygians.  The actinopterygians depict for us how (bony) fish are different from other vertebrates.

Now, is it possible that we could learn things about vertebrate development thinking this way much more efficiently than we could with this quasi-Haeckelian recapitulatory progressivism?

The story as I knew it was that fish somehow developed a swim bladder around the time they replaced cartilage with bone.  Since utility is the mother and father of invention in the Darwinian world, the usefulness of swim bladders for pelagic swimming was sufficient to explain their existence.

If it turns out that lungs were adaptation preceding tetrapods by ages, well then that too is just what one expects in Darwinland.

It's important to remember that evolutionary logic means never having to say you're sorry.
. . . in 2009, just three years ago . . . the purported fact that 95 percent of the human genome "might as well not be there" was an embarrassment "for creationists," whom in typical Darwinian fashion Dawkins conveniently conflates with intelligent-design advocates. Junk DNA is just what a Darwinist would expect, in other words. Cut to 2012, and now the evident fact that "junk DNA" isn't junk at all but is instead vital for life has become "exactly what a Darwinist would hope for," namely, "to find usefulness in the living world." That is, heads you lose, tails I win. . . . suspiciously convenient self-contradiction. Ah well, as we knew already, being a Darwinist means never having to say "I was wrong."
But it's not a self-contradiction. With Evolution-Did-It , whatever direction the evidence points is just what Dr. Pangloss would expect, because evolution as a theoretical framework can accommodate almost anything.

Even if the upward trends of progressive (teleological) evolution makes more sense for the historical framework that the evolutionary research program has pursued, what value might there be in more devolutionary hypotheses being assumed.  (Devolution is not nearly as satisfying and validating to Darwinism as complexity-building evolution.)  The alligator is a reptile that is considered the pinnacle of reptilian evolution nor a transition animal but a sort of devolved representative of warm-blooded archosaurs.  Ceolocanths are believed to be derived from sarcopterygians.  The TTSS1 pump might be better thought of as having devolved from the flagellum.  The mimivirus might best thought of as having devolved from a cellular creature.  Maybe Tiktaalik, like the alligator is a throwback, an amphibian that thinks its a fish.  Cynodonts might be better understood as a devolution from monotremes.
The evolutionary relationships of the fossil [for the eutriconodont mammal Yanoconodon] suggest that either the "modern" middle ear evolved twice, independently or that it evolved and was then lost [i.e devolution] in at least one ancient lineage.
Or maybe some are mosaics because phylic boundaries, as we know them, are a trend, not a rule (otherwise, how would either mosaics or missing links be possible?).  Now, Archaeopteryx is no longer the missing link it pretended to be in our textbooks.  It is, for now, more like the coelocanth or alligator.  It is a mosaic that represents the diversity of archosaurs (though not as radically as ceratopsids which had apparently "recapitulated" and rediscovered their four-footed roots.  And if quadruped representatives of the archosaurs were there all along, like the elusive coelocanths, they simply flew under the paleontological radar and avoided the fossil record as many group likely have.

All this puts me in mind of this structuralist (and narrative-agnostic) formulation by Dr. Richard Sternberg:
The approach I am taking to this problem is a variant of structural realism, by which I mean that biological phenomena are manifestations of logico-mathematical structures. This perspective is orthogonal to the origins debate, if you will, because all historical actualities are understood to be space-time instances of pre-existing non-temporal possibilities. Within this context one can accept all that is empirically valid in evolutionary biology, while not axiomatically dismissing the position that structures as well as their “real” instantiations have an intelligent cause.

## Wednesday, September 17, 2014

### Baez on Information Geometry

I think I've struck some gold here concerning information geometry in a series by John Carlos Baez.

Start with part 8 where Baez gets into the relationship to evolution.  Some reminder about thermodynamic models:
Physicists love to think about systems that take only a little information to describe. So when they get a system that takes a lot of information to describe, they use a trick called 'statistical mechanics', where you try to ignore most of this information and focus on a few especially important variables. For example, if you hand a physicist a box of gas, they'll try to avoid thinking about the state of each atom, and instead focus on a few macroscopic quantities like the volume and total energy. Ironically, the mathematical concept of information arose first here—although they didn't call it information back then; they called it 'entropy'. The entropy of a box of gas is precisely the amount of information you've decided to forget when you play this trick of focusing on the macroscopic variables. Amazingly, remembering just this—the sheer amount of information you've forgotten—can be extremely useful... at least for the systems physicists like best.
He goes on to say that in biology, there is a lot less information in the system that can be forgotten... This goes back somewhat to the use of "entropy" to correlate to different kinds of information.  The (average) loss of uncertainty/entropy in Shannon information, for example. He goes on to talk about alleles as rival hypotheses.
The analogy is mathematically precise, and fascinating. In rough terms, it says that the process of natural selection resembles the process of Bayesian inference. A population of organisms can be thought of as having various 'hypotheses' about how to survive—each hypothesis corresponding to a different allele. (Roughly, an allele is one of several alternative versions of a gene.) In each successive generation, the process of natural selection modifies the proportion of organisms having each hypothesis, according to Bayes' rule!
It appears that this approach looks at information in terms of a distance from a destination state of stability.  So in that sense, it is more about relative information.
But what does all this have to do with information? . . .  first discovered by Ethan Atkin. Suppose evolution as described by the replicator equation brings the whole list of probabilities p — let's call this list —closer and closer to some stable equilibrium, say q.  Then if a couple of technical conditions hold, the entropy of q relative to p keeps decreasing, and approaches zero.   Remember what I told you about relative entropy. In Bayesian inference, the entropy relative to p is how much information we gain if we start with as our prior and then do an experiment that pushes us to the posterior q. So, in simple rough terms: as it approaches a stable equilibrium, the amount of information a species has left to learn keeps dropping, and goes to zero!  . . .  You can find [precise details] in Section 3.5, which is called "Kullback-Leibler Divergence is a Lyapunov function for the Replicator Dynamic". . . .  'Kullback-Leibler divergence' is just another term for relative entropy. 'Lyapunov function' means that it keeps dropping and goes to zero. And the 'replicator dynamic' is the replicator equation I described above.  . . .  [This approach] uses information geometry to make precise the sense in which evolution is a process of acquiring information
Baez offers some background to this in Gavin E. Crooks' Measuring thermodynamic length and in part 1 of his series.
But when we’ve got lots of observables, there’s something better than the variance of each one. There’s the covariance matrix of the whole lot of them! Each observable $X_i$ fluctuates around its mean value $x_i$… but these fluctuations are not independent! They’re correlated, and the covariance matrix says how.
All this is very visual, at least for me. If you imagine the fluctuations as forming a blurry patch near the point $(x_1, \dots, x_n)$, this patch will be ellipsoidal in shape, at least when all our random fluctuations are Gaussian. And then the shape of this ellipsoid is precisely captured by the covariance matrix! In particular,
the eigenvectors of the covariance matrix will point along the principal axes of this ellipsoid, and the eigenvalues will say how stretched out the ellipsoid is in each direction!

As I recall, the eigenvalues will be in bits of error in terms of the units of the parameters.

### Relative Entropy in Evolutionary Dynamics.

Marc Harper has a post about "Relative Entropy in Evolutionary Dynamics" (among "entropy and information" here) that is is potentially very useful for relating the Fisher Information metric to the information to be found in traversing sequence space.

Harper also has a related article published as "Information Geometry and Evolutionary Game Theory," from which I'm adding the example below to a previous post.

## Tuesday, September 16, 2014

### Adleman's K-potency and Kauffman's Atoms

One of the motivations for the sequence-space probability dispersion matrix is that as a model it might estimate the computational depth of nucleotide sequences, or the relative depth between two nucleotide sequences.   How deep is a given nucleotide sequence?

Kauffman writes in a recent foreword that the universe has produced every kind of atom it could produce (an ergodic process, whereas enumerating the realizable proteins is a non-ergodic process), but Leonard Adleman has elsewhere written in "The Rarest Things in the Universe" (among "entropy and information" here) that atoms with higher counts of protons than we've thus far encountered could be considered to have larger depth (and thus be somewhat analogous to Kauffman's sequences).
I am not a physicist, but I suppose it is possible to theorize about an atomic nucleus with a million protons. But what if I want to create one? It appears that producing transuranic elements takes huge amounts of time/energy and the greater the number of protons, the more time/energy it takes. It is even conceivable (to me at least) that there is not enough time/energy available (at least on earth) to actually produce one. Like the prime factorization of $2^{1,000,000}-1$, it may exist in theory but not in reality. On the other hand, physicists from Russia and America, using lots of time/energy, have created an atomic nucleus with 118 protons called Ununoctium. Ununoctium is analogous to Childers’ prime factorization; both exist in reality; both were very costly to create.
In his 1979 paper "Time, Space, and Randomness," Adleman develops an idea about "K-potency" motivated by an analogy with thermodynamics, specifically chemical reactions that take much less time going in one direction than the other.

This approach to "one-way functions" is important to crytography, incidentally.  His definition for K-potency follows here:

## Monday, September 15, 2014

### Inexplicable Caprice From Top to Bottom

Oh sure natural selection's been demonstrated . . . the interesting point, however, is that it has rarely if ever been demonstrated to have anything to do with evolution in the sense of long-term changes in populations. . . . Summing up we can see that the import of the Darwinian theory of evolution is just unexplainable caprice from top to bottom. What evolves is just what happened to happen.
- Stanley Salthe

[There are] hundreds of other evolutionary scientists (non-creationists) who contend that natural selection is politics, not science, and that we are in a quagmire because of staggering commercial investment in a Darwinian industry built on an inadequate theory.
- Suzan Mazur

## Saturday, September 13, 2014

### Randy Olson's Creationist Shill

I was tired of being told that my structuralism reduced to "creationism" by those who have no understanding of either.
-- Richard Sternberg
Randy Olson, in his documentary Flock of Dodos that purports to be an objective inquiry into Intelligent Design both as a (possibly) scientific enterprise and as a social phenomenon, talks about a subject interviewed at an ID convention who claimed to be a Darwinist but later seems to have not been.

This subject seemed noteworthy, Olson seems to present, because it seemed unusual to have a non-creationist spouting a teach-the-controversy view, let alone attending an ID conference as something other than a heckler or guerrilla documentarian.   Olson's big reveal is that this Darwinist is John Angus Campbell who is (or was) a Fellow at the Discovery Institute.  Olson is vague on this point and seems to rely on the audience to assume that Campbell's warm relationship with ID is in conflict with his conception of Darwinism.

Olson elsewhere does include footage of Michael Behe saying he believes in common descent and macro-evolutionary speciation events, and Olson presents Behe as the spokesman for ID in vague terms ("some say" he is the leading expert on Intelligent Design), so it would seem that Behe embraces some form of Darwinism being more or less convinced of several important tenets.  Behe is certainly not Darwinist enough for Olson, since he not only denies the sufficiency of natural selection for certain macroevolutionary feats but he also thinks that the influence of an intelligent agent is better explanation that the other rivals of the selectionist point of view.  (Olson's film implies that Behe is the leading idea-man of what he obviously considers an anti-evolution movement.)

## Thursday, September 11, 2014

### Against Neo-Darwinism or Against Evolution?

The nexus of Pro-Darwin lobby (teachers, pundits, parents, etc.) and biology practitioners worried about the political status of evolutionary science often work together to make this worse, and not simply by hateful negative attacks on their opposition or by failure to dumb it down sufficiently. (A point not made well by Flock of Dodos.)

As with many evolution-related issues, there is at best a double-message going out there. One is that neo-Darwinism has never had any serious deficiencies and therefore never needed any balance or controversy taught, which has been a useful tactic of the NCSE for years. (Whether this is a vestigial behavior--the "pro-science" lobby has evolved much more slowly than the "anti-science" crowd--or whether this is the inherent defensiveness of a dominant paradigm is a story for another time.)  The other message is that there is vigorous, healthy debate over what the processes and mechanisms of evolution are, but that since almost all of these are believers in both methodological naturalism and the power of known forces to explain everything, the commonly taught evolutionary hypotheses are unassailable facts (or should be taught as such at any rate).

The former message has certainly hurt Darwinism.  How much criticism has there really been against Richard Dawkins by the "pro-science" coalition for his extreme neo-Darwinistic reductionism?  Randy Olson's poker-players don't seem bothered by him.  The closest that Olson gets at all to noting any challenge to neo-Darwinism (or that there is any diversity in the academic ecosystem) is lumping "process structuralism" in with ID at some point (the "teach the controversy" segment, I think).  The fact that Olson can implicitly charge ID as a God-Did-It approach (as his editing choices convey) but not recognize the extent to which much of evolutionary literature has boiled down to Selection-Did-It or Evolution-Did-It says much.  In fact, the ideas about how it happened and the mechanisms involved are so complicated at this point, that overconfidence concerning natural selection through most of the 20th century (and continuing now) seems both naive and quaint.  I was taught in college that microevolution = macroevolution, essentially, as a fact. As Stuart Newman has pointed out, this overconfidence, while achieving political mileage in jurisprudence, has hurt public perception of evolutionary teaching in general.

Meanwhile Michael Ruse has attacked creationism (no doubt including ID in it) of being more selection-obsessed than the evolution crowd, without (until perhaps lately) giving any credit to this sociological effect.  If people tend to conflate anti-Darwinism with anti-evolution, maybe it's because too often the "pro-science" crusaders have conflated Darwinism with evolution.

The second message potentially hurts the general prospect of evolution partly because of this (wait, what do you mean it isn't as simple as natural selection and microevolution?), but also because Selection-Did-It is more obviously replaced by Evolution-Did-It.  Evolution has become the Dark Energy of the 21st century.  No one agrees what Dark Energy is or how it figures into physics, but Something is causing the galaxies to diverge over time; new species with novel structure and organs have appeared over time and therefore Evolution is the name given to that Power at work. The entire scientific community starts to a resemble a jury that have very conflicting ideas about how the defendant committed the crime and where he committed it, based on contradictory evidences and contradictory interpretations, but are (almost) unanimous in their belief that he is most definitely guilty based on the evidence. (Half the jury are okay his religion, half are okay with his race, and only a few don't like his face, so you can't say they are unanimously prejudiced.)

But if we give the name "Evolution" to the basic pattern being investigated--the changes in biological diversity over geologic time on Earth, the explananda rather than the explanans--neither Intelligent Design in general nor Discovery Institute in particular are any opposition to this.  The fact that you can be a creationist within the ID framework, as you can be an evolutionist like Michael Behe, or anything in between, is part of the guilt-by-association tactics by "pro-science" Big Darwin.  What the "pro-science" lobby find so threatening about the "Big Tent" of ID is that (a) that it is mostly consonant with theism  (i.e. "makes it possible to be an intellectually fulfilled theist") rather than dissonant, and (b) the usual tactics against Young Earth Creationism do not begin to address it.
(Again, two messages:  (1) Creationists are not to be trusted because they are evolution-denying hayseeds.  (2) ID theorists like Michael Behe who largely embrace evolution are still creationists because they don't rule out theories consonant with "supernatural causation."  Collectively, these messages amount to double-speak.)
Certainly, you can be a skeptic of neo-Darwinism without doubting Big Evolution.  What Suzan Mazur's work has achieved, perhaps more than anything else, is documenting the stifling effect the neo-Darwinian Synthesis has had on biologists and selection skeptics.  But calling evolution skeptics "evolution deniers" (a trope that analogizes with Holocaust denial) is partly ugly political tactic and partly "physics envy" (the idea that biology vies with physics for ontological validity, e.g. in elevating the theoretical status of evolution to that of gravity).  Many ID theoreticians believe in some version of selection-oriented evolution and common descent, many are skeptics of one or more accepted evolutionary hypotheses, and some do think the whole evolutionary narrative is a mostly unproductive concept.

The crumbling of the neo-Darwinist edifice has hurt Evolution in more than just a PR sense.  If science, as the ACLU has asserted through Judge Jones, is what scientists do, then neo-Darwinism is the strongest, most worked out, and most explanatory theoretical framework for evolution.  If it is really as weak as it appears to be, it calls for some serious skepticism of the explanans of evolutionary science, if not the explananda.

Perhaps the biggest failing of Randy Olson's Flock is the attempt to only cast Intelligent Design as a sociological phenomenon (driven by philosophical motives) and does not really get close to doing the same with his own camp, despite his belief in his own objectivity.  He shows some of this at work, but doesn't make it part of his documentary's explanation.  The explanation he gives concerning them is that they are so erudite (he helps make this point by displaying definitions for the big words they use) that they make poor evangelists for his gospel of truth.

http://www.darwinscholars.com/how-to-enrollschedule.html
http://www.evolutionnews.org/2014/06/why_does_biolog087231.html
http://www.evolutionnews.org/2010/02/how_to_play_the_gene_evolution032141.html

http://www.bcse-revealed.info/bcse/bcse.rev/Main/CognitiveDissonance.html
http://www.bcse-revealed.info/bcse/bcse.rev/Main/FreedomPluralismAndDeception2.html
http://bcse-revealed.blogspot.com/index.html
http://bcse-revealed.blogspot.com/2006/11/bcse-educational-incompetence-and.html

Gould's comments on von Baer's Law
http://darwinianfundamentalism.blogspot.com/2007/06/abscheulich-atrocious-stephen-jay-gould.html

http://www.evolutionnews.org/2011/10/wheel_of_fortune_new_work_by_t051621.html
http://www.evolutionnews.org/2014/06/more_strong_exp087061.html
http://www.evolutionnews.org/2009/10/dollos_law_the_symmetry_of_tim026721.html

http://www.evolutionnews.org/2007/02/hoax_of_dodos_pt_1_flock_of_do003132.html

http://www.suzanmazur.com/?p=20
http://www.suzanmazur.com/?p=259

### Jack Szostak and the Creation of Life

http://www.suzanmazur.com/?p=259

## Saturday, September 6, 2014

### links: Peer Reviewed Journal Defends Recapitulation

http://ncse.com/creationism/analysis/richardson

Michael K. Richardson "highly conserved" embryos
no highly conserved embryos
http://www.toriah.org/articles/richardson-1997.pdf

http://www.evolutionnews.org/2011/06/haeckels_embryos_make_multiple047321.html#backfn6

http://www.evolutionnews.org/2011/07/three_flawed_evolutionary_mode048541.html

http://www.ichthus.info/Evolution/DOCS/Richardson2.pdf

http://www.talkorigins.org/faqs/wells/iconob.html#raraff2

Recapitulation is dead!  Long live Recapitulation!

### Flock of Dodos Shows Randy Olson Engaging in Triviality

At a high school level, the aim of the [text]book is to convey some basic concepts of biology, not to confuse students with the complexity of a subject.
- Alan D. Gishlick, NCSE
Unrelated to my viewing Flock of Dodos, I had recently started looking through The Origin of Animal Body Plans (Wallace Arthur, 1997) and The Shape of Life (Rudolf Raff, 1996).  Figure 2-7 in Arthur shows Haeckel's embryos but attributes them to a figure from Embryos, Genes, and Evolution.  Raff uses the same figure and actually does name it as ultimately from Haeckel and qualifies it as "exaggerated," but Arthur gives no indication that they are obsolete or exaggerated.  Neither author uses the diagram for merely historical value but to illustrate vertebrate similarities in the phylotypic stage.  One might argue that they are not textbooks, but the 2002 Biology featured above is certainly a textbook, and so was Futuyma's Evolutionary Biology, and the other textbooks highlighted by Dr. Wells.
My copy of The Cell from the LIFE Science Series has drawings clearly based on Haeckel's artwork on page 103 (1964 edition), a page I clearly remember from my school library in the '80s. Figure 1-36 of Molecular Biology (1994) uses an illustration from 1874 as paradigmatic. Yet Flock would have its audience believe that these illustrations went out of fashion shortly after 1914.  Science reporter James Glanz wrote ["Biology Text Illustrations More Fiction Than Fact," 4/8/01] for the New York Times in 2001 that the "drawings were reproduced in textbook after textbook for more than a century."
Indeed, Glanz pointed out that one of the biology textbooks recycling Haeckel's embryo drawings was co-authored by none other than Bruce Alberts, then-head of the National Academy of Sciences [emphasis mine]:
I remember seeing these same images both in college and in earlier education, and despite what Randy Olson claims, the textbooks in which I saw them used them as iconic evidences of evolutionary reality.  Olson makes no bones about idolizing Stephen J. Gould, and yet Gould himself claimed less than 20 years ago that Haeckel's drawings were still being used in many "if not most" textbooks.  Eugenie Scott of the NSCE had acknowledged (and defended) the fact.  Even P.Z. Myers has admitted it.

I'll jump ahead to my main point here, and work my way back to it.  You'll mostly hear two conflicting ideas about Haeckel's embryos depending on whom you ask.  Either they are being used because they are basically correct, or they haven't been used in years.  (Few would probably react with as much umbrage as Stephen Gould at the obvious fakery of the images.)  Olson, maker of the anti-Intelligent Design documentary Flock of Dodos, uses the issue of Haeckel's embryo drawings to present Jonathan Wells as a mass market hack, implicitly comparing his book Icons of Evolution to supermarket tabloids.  Wells' criticism of the use of  these embryos was published in the peer-reviewed journal The American Biology Teacher in 1999.  The Discovery Institute has pointed out several current textbooks that use them.  Recently I browsed through The Shape of Life, a modern evo-devo book that does point out the "hour glass" of ontogenic development, also uses a variation of Haeckel's illustrations.

Olson has since defended his retention of his treatment of Wells in the film by retorting that it is a trivial issue whether Haeckel's embryos are actually still used.  This however is exactly the trivial point that Olson uses for his hatchet job on Wells, to demonstrate somehow that Wells either invents things or hasn't done his homework.  In fact, either Olson invented something or didn't do his homework.  If this was such a trivial point, why of all the points in Icons of Evolution did Olson pick this one?  In Michael Moore-esque fashion, Olson hands a biology textbook to a Darwin critic and asks him to find Haeckel's embryos, as though the existence of such a textbook was meaningful. (Perhaps this demonstrates the harm that evolutionary logic has done to thinking in general.)  Why did Olson mislead the audience about a "trivial" point in a book that has little to do with explaining ID but rather criticizes the misinformation used in teaching evolutionary biology?

Olson has been so on top of the "anti-science" crusade that over the years his mother sends him updates on what the poor anti-science rubes in her part of the country, which eventually led to Flock.  Olson, who has spent most of his life dedicated to understanding marine ecology specifically in light of the Darwinian narrative, is yet another disinterested third party reporting objectively on Intelligent Design.  About the only thing that Olson presents favorably for ID is expressing his surprise that ID conventioners seemed well-dressed, educated, and obsessed with scientific details, and that they weren't the provincial trailer trash that he very evidently was anticipating.  The footage of him sitting in his hotel room the night before the convention talking in a mock country drawl makes me wonder whether his whole idea for the film had to change when he didn't find the sort of people there he hoped to find.

Dr. Jonathan Wells has extended his Cracked Kettle analogy to Olson's defense of the disinformation he knowingly left in his documentary Flock of Dodos.

It is worthwhile to note that soon after claiming to not want to stoop to childishly satirizing the ID group (which is laughable since the whole point of the movie is to present the ID crowd as the biggest bunch of "dodos"-- pro-evolutionary figures are criticized for not making the truth accessible to the poor unwashed), Olson immediately launches into a strawman attack on ID.  He has a short interview with Michael Behe that gets into a very rough analogy, and from there starts making "sub-optimal design" arguments.

If one had any doubts that Wikipedia apparently winks its eye at neo-Darwinian activists, he could  look at the entry for Flock of Dodos.  If there was an even-handed arbitration at the site, it would have mentioned the Discovery Institute's rebuttal to the claim that Haekel's embryo drawings aren't used.   Frankly, I'm surprised that it even mentions the Institute's challenge to Olson's gross disinformation about the Discovery Institute's budget (not to mention how their budget compares to the overwhelming stacks of money that fuel the pro-Darwinian evolutionary paper mill).  Wiki's misleading assertion that "[t]he film gives equal air time to both sides of the argument"is enough to telegraph that Wikipedia is promoting the film as some sort of even-handed presentation.

Even Eugenie Scott acknowledged that Haeckel's embryos are still used!

Actually, the rise of Intelligent Design while a thorn in the NCSE's side has been good for business.  In the decade leading up to 2007, the alarm bells about a coming repressive age of theocracy drove their budget from \$250,000 to \$800,000.  But the NCSE is just one lobby at the forefront.  The actual money driving the entrenched paradigm is the money that pays for the thousands of papers on evolutionary science that present their findings in a neo-Darwinian framework (a la Panglossian manner highlighted by Stephen Gould in his famous "Spandrels" paper).

Among the "Pulled Punches" which Olson claims, he shows Jack Cashill off the top off his head echoing Wells' dates about Gould but getting the dates wrong.  He says "25 years" between 1995 and when Gould last published a rebuke of the Haeckel drawings, where Wells had in mind "over 20 years" between 1977 and 1999/2000, the latter date when Gould says Haeckel's drawings are used in "many (if not most)" textbooks.  Olson refutes Cashill as a strawman for Wells in "Pulled Punches" by interviewing a former student of the late Gould who cites his lambasting the drawings in a campus lecture in 1975 (criticizing the post-1914 image recycling that Flock implies never happened).  Wells might be overly judgmental about Gould's relative silence on the subject (especially during the time period he was helping "pro-science" establish U.S. law on what could be said about evolution in science classes), it would be helpful if he would give the precise dates.  Again, Olson later admitted that he was wrong about the drawings not being used, but that this doesn't change anything (because being a Darwin believer means never having to say you're sorry--you're still basically right no matter how the facts turn out).

What is perhaps even more ironic than Olson's accusation of harping on trivialities is the idea conveyed by Flock that the acceptance of the neo-Darwinistic narrative (and with it the unquestioning acceptance of related evolutionary hypotheses as undisputed facts) is waning because evolutionary eggheads are so far above us mentally that they can't convey these truths with the sort of catchphrases and simplistic pictures/narratives that the rest of us rubes are starving for.  If Olson did indeed read Icons of Evolution (and perhaps he didn't), a central point went over his head.

The reason that Haeckel's drawings weren't more criticized or noticed (at least before Richardson and Gould and Wells brought them back into the light) is because of their simplicity.  They make the "truth" more obvious to the poor unwashed than it would be simply presenting the facts.

## Friday, September 5, 2014

### Randy Olson's Flock of Anti-Creationist Statism

Early in his documentary Flock of Dodos, Olson starts framing the controversy as a red/blue political issue, and his entire presentation taken as a whole seems to emotively suggest an equation: ID = Creationism = Fundamentalism = Conservatism = G.W. Bush, actually promoting the divide that he is supposedly reporting on objectively.  Olson seems to go out of his way to make these impressions, at one point having the camera lingering dramatically on a picture of G.W. Bush in case the viewers haven't yet associated evolution skepticism with the political divide.  Early in his presentation, he suggests that there was a time that the U.S. was "red white, and blue" before dividing into just "red and blue" states.  A previous post earlier this year concerned the political significance of the phrase "Bush-appointed judge"; Olson uses the phrasing "Bush appointee" to denote the plagiaristic Judge Jones.  He also manages guilt-by-association (see here and here) in linking a bunch of divisive social issues to the Discovery Institute via a "tree" analogy used in the notorious "Wedge Document," and neatly avoids the question on whether the Institute takes a stand on any of these these issues.

An important nuance that is lost on most anticreationists like Olson and most of the poker-playing evolutionary Ph.D.s who rail polysyllabically against the theocratic bogeymen is that the neo-Darwinist guardians of truth are the ones who have successfully used federal power to silence opposition and criticism.  And yet one of these poker-playing Darwinists opines dramatically and righteously that allowing students to be misled in school threatens "the foundations of democracy."  It would seem that, if true, this would mean that democracy is best served by presenting evidence for and against.

Olson presents as a sort of cynical stratagem the idea that the "teach the controversy" approach has its roots in liberal ideas of pluralism and multiculturalism (which probably motivate John Angus Campbell).  Olson, on this point and others, shows his alignment with the Barbara Forrest's "trojan horse" conspiratorial propaganda (see Luskin's Salvo response), which is also set up by his colleagues' concepts of Evolutionary Wars EWI and EWII, in which a town school board embraces Intelligent Design after federal intervention in squelching creationist material (or so Flock states).  Yet, he never questions nor presents questions on whether there is something inherently authoritarian about centralized government control (guided, naturally, by the poker-playing elite) of what parents choose their children to learn as science.  But this is nothing new to the "pro-science" lobby.

Noteworthy in the movie is that Olson claims that he would have liked to have debated two of his interviewees about evolution but that they weren't sufficiently knowledgeable.  Yet, he never fires his challenges at Dr. Michael Behe.  ("What scientific data supports these concepts, Dr. Behe?" is never heard.)  While the film admits that Behe believes generally in macro-evolution and common descent, evolutionary ecologist Randy Olson is content to leave off the interview with the Mount Rushmore analogy, as though that represents the totality of ID concepts.  He doesn't present Behe with any criticisms to the mousetrap analogy, which should be a pretty simple exercise for someone as steeped in evolutionary science as Olson.  Maybe Olson was afraid of "looking like a dodo."  In fact, Mount Rushmore is the strawman on which Olson will base the film's summary of ID: that it is a concpet that never gets past the subjective to the quantitative.  To do this, he presents Behe as somehow the leading scientific figure in ID (curiously, an evolutionist who is ironically is representative of the what Olson depicts as a fundie conservative "anti-evolution" bloc).

Would it not have been extremely informative if Olson would have interviewed Behe (or someone else) who could have answered how Behe's concept of "irreducible complexity" relates to Dembski's concept of "design inferences"?   Aside from confining ID to Mount Rushmore-esque impressions, Olson interviews Dr. Jonathan Wells about one aspect (I'll discuss this grievance in a later post) of the one book mentioned that doesn't even discuss the merits of Intelligent Design.  Icons of Evolution is focused on the simplistic, flimsy, and misleading teachings that "explain" the Modern Synthesis to unknowing students.  It is an important book because many "pro-science" advocates state that ID is unimportant to consider because of all the things neatly explained already by the Modern Synthesis.  But it begs the question why Olson avoids any meat of ID theorists before he announces his verdict.