Materialism or Bust

Yet to be published...
There is a considerable amount of double-think promoted around the relationship of chemical evolution to biological evolution. I had a hard time figuring out what "Origins of Bust" (as it is referred to several times) was supposed to mean, or whether it may be presumed to have any shared understanding. What Mr. Downard means by "Origins or Bust" is "if life did not (and cannot) originate naturally, then it did not (and cannot) have evolved." Mr. Downard may well be knowledgeable enough to know that the Intelligent Design framework does not require there to be no macroevolution (though for many of us the continued lack of a suitable mechanism for the "theory" makes the evidence for macroevolution seem that much sketchier), so it's possible that he is simply drawing attention to things that are largely irrelevant to Meyer's arguments.

Aside from this though, I find Mr. Downard's understanding of this so-called "trope" misrepresents what I think and what I think many others of us think who find this mystery so compelling against naturalism. If the "origin of life" problem points to a need for an intelligent cause because the sum total of all unintelligent causes described/predicted by physical laws are collectively insufficient, then invoking that intelligent cause in other situations where material causes are categorically insufficient does not "multiply entities beyond necessity." There are plenty of problems within the macroevolutionary scheme--even without looking at the explanatory hurdles of the "origin of life" problem"--that speak to a need for an intelligent cause for macroevolution even for many who find the "reptile-to-mammal" evidence compelling.

To go back to Mr. Downard's understanding of "origin of life" significance for so-called "science deniers," a teleological cause for origin of life does not necessitate a teleological cause for biological diversity--but for many the necessity of teleological causation in the biosphere is more readily apparent in origin of life, and if it's necessary for life to start it makes people wonder whether it might be a better explanation for other things that appear to be designed for a purpose. The secular miracle of abiogenesis is supposed to remain a blank check on explanatory power--and everyone pretends that it must have perfectly reasonable (i.e. natural) explanation because almost ever since Darwin we have been pretending that science has always required that leap of faith. I think Mr. Downard's characterization is more apt description (however still imperfect) of how blindly optimistic the application of the apparent "success" of macroevolutionary theory has caused so many to suppose that we must be close to some coherent account on the origin of life, to the point of even supposing that some sort of natural selection also explains chemical evolution. It's "Naturalism or Bust," the contrapositive of what Downard imagines "creationists" typically have in mind.

Conveniently, it is forgotten how much work natural selection did in making the unificatory abduction seem to be better-supported than it was--except by those holdouts who still believe in the wonder-working power of selection. The "theory" of evolution, in whatever sense it has coherence, is a troubled theoretical framework. The "unificatory" power of Darwinian explanation seems to be not the least bit troubled (in the consensus groupthink of "tortucan" Darwinism) by natural selection becoming a less and less plausible mechanism. Selection turns out to have merely been an imaginary stand-in for what the "consensus" would like this yet-to-be-found mechanism to be capable of.  It becomes more acceptable when the paucity of coherence in the origin of life speculations is apparent.

consciousness

An interesting point.  If this is true, must it necessarily follow that consciousness reduces to physical laws? or does it mean that nature cannot reduce to physical laws?  (Note: I don't believe that Penrose is a reductionist though he may well be some sort of physicalist.) 

Many hard-core materialists believe by simply categorizing all difficult-to-reduce phenomena as epiphenomena they have made "a proper place for it."  But I think this is definitional gerrymandering. 

Reductio ad 'undesirum'

One might say this is a conundrum of the design inference:  Assuming for the moment that the biological world can be attributed to intentional design, is the most reasonable next inference--even if it can't be inferred scientifically but only on philosophical/religious grounds--that the designing intelligence is that which also caused and infused order into this universe?

A related concern (for some people) is this:  If that is the most reasonable inference after the design inference, should that consequence invalidate the design inference?   

Modified from its original form

Intelligent Interference vs. Creation

from The Emperor's New Mind by Roger Penrose

Perry Marshall dismisses ID as Old Earth Creationism because he seemingly is against any inference to the interference of an Intelligence that might turn out to be an Entity that resists scientific inquiry--or at least admitting any such inferences into science...  But in this broad characterization of what constitutes "Old Earth Creationism," how does Marshall's view differ?   

Marshall seems to be claiming at times that something has been introduced into the universe long after its beginning (which he accepts, I think, to be the consensus time of about 14 billion years ago).  Stardust somehow finds itself getting into interesting configurations over the course of 10 billion years and then, poof, God introduces information somehow, before there are cells intelligently manipulating their own genetic information, in a way that is a total game-changer.  Marshall asserts:

• In the history of the universe we also see the introduction of information, some 3.8 billion years ago. It came in the form of the Genetic code, which is symbolic and immaterial.
• The information had to come from the outside, since information is not known to be an inherent property of matter, energy, space or time. [bold emphasis in original; red highlighting is mine]

So ... at some point around 3.8 billion years ago, configurations in matter arise that aren't explicable in terms of the configurations that were there 3.9 billion years ago.  Why?  Because information is introduced from outside the space-time continuum that serves as the substrate for matter and energy, otherwise the information cannot be inferred to have been introduced without some qualitative difference that would invoke an abductive inference to ... design.  I can't help but wonder how this fails to meet Marshall's own broad criteria for God-of-the-gaps.

Is Perry Marshall the Reza Aslan of Intelligent Design?

There is a sense in which Perry Marshall almost neuters the relevance of Intelligent Design the way that Reza Aslan attempts to neuter the historical context of Christianity.  Reza Aslan appears to concede that the resurrection of Jesus could have been a historical event, and yet proceeds as though there was truly nothing extraordinary about what the historical Jesus did and said (that is, Jesus was an otherwise unremarkable man who was only later made remarkable because men invented a religion about him because he just may or may not have been an unremarkable man who happened to come back to life after suffering a gruesome death).  According to Aslan's book Zealot, since history is about what probably happened, historians can't infer improbable events (such as miracles) even though he sometimes argues that there is some historical plausibility to the resurrection. 

Marshall, on the other hand, appears to concede that a supernatural God may or may not be interjecting design into the natural world along its history; however, scientists just can't really make money doing science if we allow that there might be evidence of the need for an intelligence injecting information into natural processes.  (Huh?) We must only acknowledge such evidence in a hazy metaphysical sense (an ultimate sense) but never in any way that effects what historical conclusions we come to.  Because the scientist who thinks that a natural process is not solely sufficient to explain the prehistoric event has stopped the gravy train for producing papers about speculative (but "100% natural"!) events.

Marshall says that he has witnessed miracles personally.  But has he really investigated whether these "miracles" were merely natural events that aren't currently understood in the present paradigm and body of scientific knowledge?  Aren't such assertions just miracles-of-the-gaps until they eventually get explained away according to a consensus paradigm?  By calling these events "miracles" is he stating that there are good reasons to think that there is no "natural" explanation available in principle and therefore not likely to ever be found in anyone's lifetime ? or just no such explanation present at this time? --or is he vacuously asserting that since they are not repeatable natural events they can't provide scientific data?

I'm not equating these two men in terms of their sincerity or credibility.  I think Marshall is a much more sincere and credible figure than Aslan, but they are in some ways both masters of spin and presentation over content, and some of the similarity of their errors may be due to venturing outside their realm of expertise.  They both excel at marketing, and in either case, I think the effectiveness of marketing comes at the expense of conceptual clarity. 

Omniscience and Omnipotence in Evolution 2.0

The word 'omniscience' seems to play an important role in Perry Marshall's characterization of the Intelligent Design research program as a specie of Old Earth Creationism.  In at least two places (here and here) Marshall seems to claim that Stephen Meyer has brought in omniscience into their debate on Unbelievable.  What Meyer actually said (twice) was that Marshall seemed to be attributing a "near omniscient" knowledge to various kinds of cells.   

Before teasing apart what this means, let's look at one of Marshall's criticisms of neo-Darwinistic evolutionary theory:

Darwinists have this naive conception that random copying errors with natural selection have godlike powers and can do anything.
Of course this violates every principle of information theory and probability known to man; this is why Darwinists scream bloody murder any time someone brings up statistics. But it’s impossible for accidental processes to do this. They may as well believe in Superman or the Easter Bunny.

Marshall claims here that neo-Darwinism attributes to mutation+selection a near-omnipotence if not omnipotence.  However, the sort of omnipotence that neo-Darwinism claims for mutation+selection (+ even more accidental mechanisms such as genetic drift) is just the power to get from a prokaryotic cell even more simple than a bacterium to every "leaf" on the evolutionary tree.  But this is the same sort of power that Marshall claims for a "Swiss Army Knife" of mechanisms that are "in principle, capable of getting you [from] anywhere on the tree of life to anywhere else." Not truly omnipotent per se, but presumably capable of accounting for anything we've ever seen.

Drunkard's Search: The Many Problems With Perry Marshall's Conception of Intelligent Design

Annotated for clarity, another comment that is lost in moderator limbo:

April 21, 2017 at 2:58 pm

I recently attended a play (“Disinherit the Wind”) by Matt Chait in L.A. (who is definitely NOT a creationist in any generally accepted sense) after which a group largely composed of ID people applauded a monistic take on ID—not because they think its monism is correct but because it showed a serious grasp of both ID and the academic freedom that is desired for it.

There are many problems I have with the way ID is characterized on this site [Evolution 2.0].
  (1) It is generally difficult (if not impossible) to have a clear discussion about the claims made concerning ID without first having a clear discussion of what constitutes “miraculous” and “supernatural” (and whatever other related terms) in a scientific or meta-scientific sense. I agree with what Paul Brown wrote on [the] Meyer debate thread. You’ve defined god-of-the gaps so broadly that any abductive inference to X becomes an X-of-the-gaps if it’s possible for some new finding to make Y seem much likely than X. “Science” becomes by definition naturalism-of-the-gaps, with the gaps defined as anything not yet explained naturalistically (whatever “naturalistic” means). What Thomas Nagel writes here is a decent consideration of the “inference to best explanation”:   http://philosophy.fas.nyu.edu/docs/IO/1172/papa_132.pdf

The Drunkard's Search

  (2) There are some implicit assumptions about the relationship of science to paychecks that seem both unrealistic and philosophically flawed (i.e. both descriptively and prescriptively deficient).

  (3) It is not clear to me that even a young earth creationist would disagree with macroevolution in the sense that I see it construed here. In the range of being a theistic evolutionist (in the Behe sense) to being a baraminologist, I [think] there are people who are very interested in understanding what sorts of speciation are actually possible. It would be especially interesting to see you debate Cornelius Hunter, who draws very different conclusions from the same sorts of “overnight evolution” findings that you admirably draw attention to. 

Bill Nye peddles his "Junk" Science

Bill Nye the Clown Prince of Scientism and Secular Humanism has an entire show about how "science" can save us  ... from our antiquated sexual mores among other things.  Watch if you dare but prepare to be offended by almost everything that is said and done.  It says something that this man was the headliner for the recent "March for Science."  I agree with one thing in this video:  It certainly is junk, with regards to science, morality, or just good taste. 

I hope that even the NCSE can manage to be embarrassed by this 'robust display of vulgarity' from one of the apostles of "science literacy."  This is how Bill Nye (and the progressive scientism he is advocating) intends to "save the world."

Note: By "creationism" Bill truly means anything teleological that doesn't reduce us to being insignificant "specks" in a universe that exists as a value-free junkyard of cosmic debris:  

Irony meter: Bill wants us to stop embarrassing ourselves and subjecting children to harmful ideas.

Genomic DNA: Consilience "proof" of undirected evolution

ID (Intelligent Design) doesn't need common descent to be false (e.g., Michael Behe seems to accept common descent), but all theories of undirected evolution seem to require common descent.  Which means that to whatever degree common descent (CD) is not supported, undirected evolution is also not supported, since CD is one of the tent pegs of any specific theory of undirected evolution. 

One the key pieces of evidence for the "fact" of common descent of species through natural selection (plus some other assortment of mechanisms).

So, how accurate was our picture of the relationship of animal kinds based on morphology (looking at bones, organs, and tissues)?  The degree to which the fact of evolution is supported is supposedly measured by similarity of the tree of life before the flood of genomic DNA data to the tree of life based on genetics (i.e. a "parsimonious" tree of life that poses the fewest problems for a common descent narrative).

Here is one such comparison:

 

Tree changes:  Cnidarians (jellyfish) are actually more genetically similar to the more complex animals than ctenophores (comb jellies) even though they appear simpler (fewer morphological innovations).  Therefore, because of molecular studies, they are now assumed to have arrived later than jellyfish.  At least two groups of morphological deuterostomes are now thought to have much closer relationship to the other protostomes than to the chordates (vertebrates, tunicates) and starfish.  All the explanatory help of lumping the arthropods with the segmentally organized annelids (earthworms) is gone; instead, insects are closer to the simpler nematodes, and earthworms are more like molluscs (snails, squids) genetically.  Platyhelminthes (flatworms) are a significantly later development than previously thought.  Rotifers are closer to flatworms now than to roundworms, and the same goes for earthworms.

The only way that this confirms the tree story is that, loosely speaking, there is a correlation of morphological similarity and genetic similarity, which would be expected they are alike because of shared design or because of "descent with modification."  Only we weren't expected so much reworking of the trees assuming descent with modification.

Natural Selection: All Part of This Balanced Theory

Depending on how you define evolution, nearly everyone from hyperadaptationists like Richard Dawkins to young earth creationists believe that natural selection plays some role in diversification of species (i.e. evolution with a small "e").  But not even hardcore materialists all agree that natural selection is the primary mechanism that explains all the things that "have the appearance of design" in the biosphere.  This is the source of the contention between Paul Nelson and Jerry Coyne, and in fashion typical of biology academia, Jerry Coyne rallies the troops to aver triumphantly that Natural Selection must play some role in macroevolution, even though many of them believe that selection is a poor general explanation for biological innovation.

That is to say, selection is part of this balanced theory.  Which sounds familiar:

The ["part of this balanced breakfast"] claim is technically a legal requirement, but, like a Stealth Cigarette Commercial, the companies have hidden the obvious beneath the implications. After all — really! — if you're still hungry after eating a bowl of cereal, you don't cook yourself some bacon and eggs, or make toast. You just grab the cereal box and pour yourself another bowl.
In other words, your Choco Woofers are "part of this complete breakfast" in much the same way that chocolate cake is "part of a complete dinner": as a tasty dessert that doesn't add anything to the meal but calories.

And in much the same way that Natural Selection is part of the explanation of biological diversity as macroevolutionary descent with modification.

Part of this balanced explanation!!!!!

It's got what plants crave!
Here is further evidence that the theory of evolution (which one?) is as well-established as the theory of gravitation.   It might be better to describe it as an explanation in search of an actual theory. 

Programming Intelligence

Consider the use of cellular automata not simply, for artificial life, but for artificial intelligence.

How much programming does a cell need to develop into an animal of a given intelligence?

PZ Myers' Potty Mouth Proves Behe Right (or Mushroom Stories)

Years ago, in a court opinion stolen straight from the ACLU's amicus brief, Judge Jones the III claimed that ID could not be science because the ID scientists had not yet done the work in the lab of showing by experiment what natural selection could not do. 

Later Michael Behe would criticize Judge Jones' opinion on the grounds (among others) that that sort of lab work, while important, would produce results which would be simply be dismissed by critics as a failure to find the right conditions for evolution.

(13)  As a further example, the test for ID proposed by both Professors Behe and Minnich is to grow the bacterial flagellum in the laboratory; however, no-one inside or outside of the IDM, including those who propose the test, has conducted it. (P-718; 18:125-27 (Behe); 22:102-06 (Behe)). 
If I conducted such an experiment and no flagellum were evolved, what Darwinist would believe me? What Darwinist would take that as evidence for my claims that Darwinism is wrong and ID is right?

Prophetic!  Douglas Axe and Anne Gauger worked out just such an experiment, and only a prophet could have anticipated the response by the true believers in adaptationism.

Myers' argument gone to pot

At Panda's Thumb, P.Z. Myers dismisses Axe and Gauger's results as having a flawed protocol and points to a paper criticized in their work as succeeding where they failed:

Gauger and Axe are saying, "Ooh, we sh** in a pot and we couldn't even get mushrooms to grow in it,". . .

Meanwhile, the paper P.Z. Myers swoons over is about postulating lineages from an ancestral lineage.  How?  By working against natural selection and de-optimizing the effectiveness of the proteins.  (Note: Inventing a story about the improbable way the mushrooms must have grown is not the same as growing the mushrooms.)  Why did the proteins get just the changes that would make them sub-optimal in the right (pre-adaptational) way without breaking them, but preparing them?  Wouldn't the sub-optimality have made the organisms targeted for removal from the gene pool?  I know, I know... only an evolution denier would see a problem with that.  But why does natural selection stop doing its job precisely when Evolution needs it to? 

Paul Nelson's "Outrageous Lies"

Demonizing anyone advancing a teleological point of view is something that the neo-Darwinist research program has accomplished well.  Keep the debate focused on your opponents, and make your opponents look bad. 

Ed Brayton on ScienceBlogs claims to have found more evidence of "lying for Jesus":

Keith Miller said absolutely nothing that even remotely resembles what Nelson claims. Nelson, much to my surprise, was telling a baldfaced lie in order to make Keith Miller look foolish . . .  So not only did Miller not deny that a thief had stolen the items from his car . . . he explicitly agreed that a thief had stolen them. Nor did he claim that a “natural regularity” occurred. What he did dispute is the notion that human actions are somehow outside of the sphere of natural explanations.

Paul Nelson, apparently for comic effect, innocently if carelessly, states that Keith Miller (not to be confused with Kenneth Miller) would not phone the police if a thief broke into his car, since there is nothing about the evidence of the act---no inherent property of purposeful intent distinguishing it from any other natural cause--and, as Miller himself seems to explain this makes sense since a thief is just another bit of the natural world.  

Is Evolution 2.0 Question-Begging?

Oh, ok. So you're gonna make a lot of money, right? 
Yeah. 
Right. It's not yours? 
Uh...Well, it becomes ours. 
How is that not stealing?
... Uh, I'm not explaining this very well.
Okay...

How did evolution come about?  Well, you see, first there were cells that became smart enough to evolve and then they evolved to become even smarter at evolving.  Until they're super-smart!  See?  ... Hmmm.  This sounds awfully familiar.  

#comment1
I fully understand that how cells got to be so smart is a HUGE unanswered question. I agree that information always infers intelligent agents. And perhaps God is the answer. But my position is that living things are agents too and we can and should trace the progress from one evolutionary step to the next. I invite you to consider that the capacity cells have to evolve is a far more impressive miracle than, say, God beaming Zebras on to the savanna Star-Trek style where they suddenly appear eating grass.

It's not simply A huge unanswered question.  It is THE critical problem in terms of this "third way" approach having any real explanatory value in terms of purportedly supplying the completely naturalistic account for life that scientists have been purporting neo-Darwinism to be.  When you find a robot factory in the woods, is its presence there explained by the "fact" that the robots seem super-sophisticated?  It isn't explained by attributing intelligence to the obviously sophisticated factory.  It isn't even explained by attributing intelligence to the woods themselves.    

Does Perry Marshall Mispresent Intelligent Design?

 

The challenge continues to understand Perry Marshall's quasi-ID point of view.  It is almost as if Marshall is saying that rarefied design is philosophical proof of God's existence but of necessity there can be no be scientific proof of actual design because scientists "can't get a paycheck" with that sort of thing.  (While I disagree with Marshall on this point, I think he's hit upon something important: who, ultimately, is paying for the science--e.g. Joe Taxpayer--and what sort of science would they like their money spent on?)

At any rate, a possible elucidation of Marshall's antipathy toward the ID movement shows up in a response to a commenter's opinion about whether it makes more sense to attribute the intelligence to the evolving cells than to an "omniscient" designer's influence.  Marshall effuses: 

A Response to Perry Marshall

Part of my response (in moderator limbo since the first week of April) to Perry Marshall's explanation is below.  Marshall seems to argue on his blog that unless we attribute/limit all the intelligent design in macroevolutionary diversity to intelligence that is in the evolving organisms themselves, the recognition of intelligent design becomes a science-stopping God-of-the-gaps philosophy of science.

It is hard to understand your position in a way because sometimes you seem to making a design argument, and sometimes you seem to be arguing like Ken Miller that any influence God has had on history must somehow be undetectable. [Note: Actually, this is probably more like a BioLogos argument; Miller might argue that God refused to interfere with history altogether before Biblical events.] Near as I can tell, your version of a 3rd way is an attempt to keep theists from disengaging from the facts and/or basing their faith on certain scientific mysteries remaining mysteries. I can sympathize with that. In some ways you seem to be saying that the evidence for intelligent design stands regardless of the time frame that the information is put into the system. A lot of ID people would be on board with you there—except that most wouldn’t _require_ that the information be limited to the law-like behaviors of the universe and have specific evidential reasons (which you and others may disagree with) for rejecting that limitation.

Whether there is a coherent 3rd way depends on precisely what _is_ being added to the table and whether it is something more than a porridge of what is already on the table. It depends on whether one is proposing some sort of law that explains how watch-innovating factories are plausible (not merely possible) with no guiding influence. The reference to the Biocentrism book makes me suspect that the third thing being put on the table is a conscious universe akin to the thoughts of Thomas Nagel or Rupert Sheldrake, but somehow more dependent (in an unclear way) on material mechanisms. The problem with Sheldrake’s ideas (aside from the lack of academic engagement) is that they don’t present anything more clear than I have so far heard about the third way, although some of the things you’ve written sound like a front-loaded ID position. Positing a consciousness in cells and then arguing that cells can perform macroevolution over deep time because they are conscious, creative geniuses — if that is the hypothesis — is an intriguing hypothesis but seems like another extraordinary claim in need of extraordinary evidence.  If the “weak version” of 3rd Way is that “consciousness needs to be considered as a fundamental part of the problem and not merely epiphenomenal” then that much is easy to agree with. If one is applying the same sort of “in[de]finite departure” extrapolation to cell intelligence (as has been applied to mutation), that is the thing to be proved and that potential explanation has its own problems.

Ancestors all the way down

Significantly more complex V-ATPase

From PLOS One.  Discussed in more detail here. 

Two very distinct mechanisms, which most likely evolved independently, are employed for ATP-driven H⁺ pumps: the rotary mechanism of the V-ATPase and the alternating access mechanism used by the P-ATPases (Fig 1). The significantly more complex V-ATPase consists of 25–39 protein chains compared to a monomeric or homodimeric polypeptide for the P-ATPase. The operating mechanism for the V-ATPase is also more elaborate consisting of an electric motor-like rotary mechanism. In contrast, the P-ATPase operates by switching between two (E1 and E2) conformations similar to most allosteric mechanisms.

How do we measure "significantly more complex" in terms of bits? 
Mechanism is discussed in more detail here. 

no theory of the generative

http://www.cnsnews.com/commentary/david-klinghoffer/scientists-confirm-darwinism-broken

P.Z. Myers and the Bridge Hands Fallacy

In P.Z. Myers' universe all improbable outcomes are equally meaningless.  He states:

If I played bridge very, very fast, dealing out one hand every minute, that means I'd still have to wait 1.1 million years to get any particular hand you might specify ahead of time…and my life expectancy is only on the order of 10² years. Therefore, bridge is impossible. Similarly, if you add up all the nucleotide differences between me and my cousin, the likelihoods of these particular individuals is infinitesimally small…but so what? We're here.

No more unlikely than other hands

If I were to flip a coin 100 times, and the resulting pattern of coin flips exhibited inordinately high randomness deficiency, I could argue that the resulting pattern was no more special than a bit sequence with Kolmogorov complexity K(x) > 92 bits.  Using Myers' logic, that is.

But that would completely miss the point of what randomness deficiency is.  Myers is essentially arguing that since all microstates in a 'gas in a box' are equally unlikely, there isn't anything unusual about ending up in an improbable macrostate (like say, all the gas particles consolidated in one small corner of the box) since that particular microstate is no more unlikely that any of the quadrillions less special microstates.

If I am handed a Rubik's cube in a scrambled state, and I give it 20 turns and find it completely unscrambled, in Myers' world since this unscrambled state is just as likely to be generated as any other cube configuration, most of which are very disordered, we shouldn't be that amazed if the outcome is one of those highly ordered states.

Wait, you may say, don't highly unlikely coincidences happen all the time?  Sure they do.  If you expand your sample space to the space of all events, then there are myriads of ways to be surprised by coincidences--but then the bits of information needed to describe/prescribe exactly which of these quintillions of ways to be surprised was/will be instantiated approaches the logarithm of all the possible ways.   It's a one-in-septillion chance to be surprised in any one way, but you've bought a septillion lottery tickets by being willing to be surprised by any one of them.  But there will still be some limit to the number of lottery tickets even if one's 'universe of discourse' is the known physical universe.  As one approaches the limit of the Universal Plausibility Bound, one starts to exhaust the universe's capacity for producing accidental coincidences.  As the randomness deficiency approaches 450-500 bits, the sequence starts to be inexplicable in terms of chance alone, even with helpful distributions.

See Richard Dawkins below argue that coincidences are meaningless, in a very similar manner to P.Z. Myers, and consider why in a world in which "biology is the study of things that appear to be designed" it is important to be able to dismiss all incredible coincidences.  Are all coincidences meaningless, or do we generally need to apply reason to separate meaningless coincidences from meaningful coincidences? 

The Old Fact of Evolution

It seems as though evolutionary biology's status as a largely historical science is defended largely on the basis of a pre-established "fact" of evolution whose proof was provided essentially by Charles Darwin in 1859.

Since Darwin both the tree-like pattern of inheritance (phylogenetic trees) and the proffered explanation of natural selection as a plausibly sufficient mechanism have both come into question, and yet the "fact" established by Darwin is somehow protected from question, because of the attractiveness of a unifactory principle (however decrepit) is too powerful to sway one's true belief.  (Darwin said it, I believe it, that settles it!)  Michael Ruse puts it this way:

In dealing with the historicity argument, a great deal of confusion is brought in here by a failure to separate out certain aspects of the evolutionary endeavour.  Specifically, it is always useful to distinguish between three things that evolutionists are trying to do (Ayala 1978; Ruse 1984).  The first is that of establishing the fact of evolution.  This, of course, is what Darwin did in the Origin of Species through his unificatory argument.   Establishing that all organisms came from one or a few forms, by a natural, that is law-bound, process.  Then second, one has the question of paths, or phylogenies.  One is trying to trace out the actual history of life.  Did the birds come from the dinosaurs or straight from other reptiles?  Did humans evolve from Australopithecus afarensis, and was it the case that our ancestors got up on their hind legs and then the brain swelled up to the present size, or is the converse true?   Then third, one has the question of the mechanisms or causes: what is the force behind evolutionary change?

There you have it.  Darwin's plausible mechanism could have been essentially wrong, and the trees don't have to be real as long as one sort of tree or another might be imagined (the details are not important).  Assuming a theoretical framework for speculating endlessly creative adaptational forces allows us to attribute all sorts of things to natural processes despite not knowing how the laws of the universe allow macroevolution to actually happen on its own.  The important thing is that science can proceed by imagining how it might have happened.  As long as the framework allows us to imagine we have a general underdetermined answer to the big questions, the fact of evolution is well established--or is established through a confluence of inferences that do not rest on either particular mechanisms or on particular genetic/familial relationships.

Living species on the earth exhibit meaningful relationships to each other.  This much has been understood at least since Aristotle, and Darwin was certainly not the first to try to make sense of these relationships.  In fact, the taxonomies which Darwin depended on were the work of non-evolutionary thinkers.  That the technological similarities of animals with similar functional designs/Bauplans go all the way down to the level of genetic programming is not a surprise to modern theorists whether they are baraminologists, Darwinists, ID theorists, or other evolutionary thinkers.   The taxonomists gave us tree-thinking before Darwin.  The ability of an undirected natural process to do the extraordinary sort of innovation that is required for macroevolutionary Bauplan design is an open question in evolutionary biology.  Whence, then, the "fact" of macroevolution?    

Ken Miller Opposes Academic Freedom in the Name of ... Academic Freedom

The above picture was one newspaper's way of characterizing Tennessee's Anti-Evolution statute during the time of the famous Scopes Trial, which was really more about trying the statute than trying Mr. Scopes since the ACLU and Mr. Scopes' town contrived the suit as a stunt with the ACLU arranging in advance to pay Mr. Scopes' fine for breaking the law.

Ken Miller, who has been adamantly opposed to all things Intelligent Design, not only was a witness for the prosecution in the famous Dover trial, but participated in (what turned out to be) a public spectacle (during the trial) the sole purpose of which (in hindsight) was to frame the controversy with the Discovery Institute appearing to be on the side against academic freedom.

This act of media circus centered around some bad blood between the Discovery Institute and the Thomas More Law Center, as the TMLC was representing the Dover defendants and were attempting to strongarm various members of the DI into being expert witness without the advantage of their own independent legal counsel.  (Since Judge Jones arbitrarily expanded the scope of the case to rendering judgments against the DI and the ID Movement they represented--the ID movement as a whole was judged without their representatives having the benefit of legal defense--their concerns seem to be vindicated.)  It is unclear whether the TMLC intended this spectacle to shame the DI into throwing in, or preemptively clear themselves of blame in a nearly unwinnable case. 

Biology teacher and textbook author Ken Miller, who was neither much of a friend of either the TMLC or the DI, is at this event apparently to help blame the DI for the defendants' actions and the resulting debacle.  Instead of the Devil-made-me-do-it defense, the TMLC is enlisting Ken Miller to make the DI-made-me-do-it defense for their clients.  While simultaneously drumming up sympathy for the defendants (who were selfishly abandoned by the DI according to him), Miller remarkably drums up sympathy for the poor Dover biology teachers in this way:

But one of the things that I did want to remark about is we've heard a lot of rhetoric today about allowing discussion, and keeping Darwinism from being made a dogma, and don't we have the right to challenge it, and so forth and so on. It strikes me that this sort of rhetoric has a fundamental disconnect with reality. Because what actually happened in Dover, and all you have to do is read the papers, is after the board of education instructed first its teachers to read the statement about intelligent design, the teachers refused. And they deserve, I think, awards for courage, and they gave as their reason, the PA teacher code of ethics, which they all had to sign, to become teachers in the state of PA, and one of the, the provision of which is I will never knowingly present false information to a student. And if the issues here is academic freedom, how about the academic freedom of the teacher not to present false information. And in a sense that's what the case is about.  [emphases mine]

Here Kenneth R. Miller is claiming that the Dover case is really, when one gets to brass tacks, about the right of teachers to conscientiously object to teaching things that they have scientific reasons to think is incorrect.  I think I can predict what Miller would say to the question of whether teachers should be able to conscientiously object (with the support of the education faculty) to the uncritical teaching of undirected evolution without being in danger of losing their jobs.  Should teachers that do this be given "awards for courage"?  Has Miller ever gone on the record as advocating this sort of academic freedom? 

Here is the "false information" that the teachers did not want to read to their classes:

The Pennsylvania Academic Standards require students to learn about Darwin's Theory of Evolution and eventually to take a standardized test of which evolution is a part. Because Darwin's Theory is a theory, it continues to be tested as new evidence is discovered. The Theory is not a fact. Gaps in the Theory exist for which there is no evidence. A theory is defined as a well-tested explanation that unifies a broad range of observations. Intelligent Design is an explanation of the origin of life that differs from Darwin's view. The reference book, Of Pandas and People, is available for students who might be interested in gaining an understanding of what Intelligent Design actually involves. With respect to any theory, students are encouraged to keep an open mind. The school leaves the discussion of the Origins of Life to individual students and their families. As a Standards-driven district, class instruction focuses upon preparing students to achieve proficiency on Standards-based assessments.

The statement refers to Darwin's Theory as a "well-tested explanation that unifies a broad range of observations" but for which explanatory gaps "exist for which there is no evidence."  Here is what Kenneth Miller does not like about it:

So it basically is a statement that is systematically designed to undermine students' confidence in mainstream science, not just the theory of evolution, but in the whole validity of the scientific process, and the scientific method. It basically tells them, you can't trust science. And I think that's one of reasons why the teachers didn't like this at all. [emphases mine]

Because, as we all know, science--kind of like magic--only works if kids really believe in it.  If you can't wholeheartedly believe a theory, then you can't trust science.  It doesn't matter whether it's true that there are evidential and explanatory gaps in that "well-tested explanation"--it has to be taught as fact, because... because Science, that's why!  Believing in the potential inadequacy of a consensus opinion will cause the scientific method to be abandoned!  Eeeeeek!  Surely you agree, Mr. Feynman: 

Science is the belief in the ignorance of the experts.   

Oops. Perhaps Dr. Feynman didn't realize that all it takes to unseat a scientific theory (and science as a whole) is to tell kids that there is a book in the library that will give some information that will put a different spin on what they will hear in class, and they can read it on their own time! Wow!  Contrary to Dr. Feynman, one of the most brillliant physicists of the 20th century, Ken Miller seems to think that science is the belief in the total authority of the experts.

In Miller's mind it is unconscionable to force teachers to let the kids know about a book that presents a view they disagree with, but it's certainly okay to force teachers to teach Darwinian evolutionary theory without being allowed to teach any criticisms of that theory.  With the help of academic freedom activists like Miller, the federal court ruling for academic freedom was that a teacher is "free" to teach consensus thinking about biology and nothing else. This is the kind of freedom that requires a court order to silence the school boards elected by the students' parents (who, I believe, have much more of a stake in the students' philosophy of science than the teachers who are paid to teach their kids). 

Miller's sermon on academic freedom and why science-and-culture activists like the DI fellows are obligated to be witnesses on whatever terms the TMLC determine are best for their clients (what the heck does Miller care about that?), starts with a derisive scoff at the temerity of the DI to say that their recommended policy is not to require teachers to present ID material.  Richard Thompson cites DI material saying that school boards have the right (based on the academic freedom of both teachers and school boards) to "permit, and even encourage" the teaching of Intelligent Design.  Perhaps Prof. Miller is unaware of the distinction between being encouraged to teach something and being required to teach it.  Maybe that explains why he has such a muddled view of what it means to support academic freedom.  

Thompson equivocates about the relationship of DI policy to their obligation in the Dover case: "whether they [DI] wanted the school boards to [make their teachers] teach intelligent design or [only] mention it..." Wait a minute! It really doesn't matter whether the DI was recommending to the Dover school board that they have their teachers teach it or just mention it?  They are at fault either way?  This seems to be an indirect concession on TMLC's part that the reading of the statement (about neo-Darwinism as one competing origin theory) by the teachers instead of presenting ID material was already a concession made by the school board to the teachers, possibly because of the pressure being put on them by the Discovery Institute.  Why let students know about a book in the library if the teachers are were expected to use that book in the classroom???  There'd be no point!

Poor teachers!  Poor evangelical defendants!  BAD DISCOVERY INSTITUTE! 
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Post-Script:  Prof. Miller avows in this forum that it is disingenuous of the DI to cite Antony Flew as an advocate of design inference. However, it seems to be the case that Dr. Flew attributes his rejection of atheism to science based on a design inference:

 . . . Antony Flew has concluded that some sort of intelligence or first cause must have created the universe. A super-intelligence is the only good explanation for the origin of life and the complexity of nature, Flew said in a telephone interview from England.[emphasis mine]

Miller seems to believe that the DI should not cite anyone that doesn't agree with their particular version of ID.  Perry Marshall also makes Intelligent Design arguments even though he sharply disagrees, presumably like Flew, about what can be inferred about natural history with those design inferences.  I'll be examining Perry Marshall's views in the future.