Friday, September 23, 2016

Is Stuart Kauffman secular creationist?

Stuart Kauffman has long been preaching the efficacy of self-organization to make up for the general lack of efficacy of natural selection to explain functional complexity.  In his case, he generally isn't always accused of being a secular creationist.  Since the growing demand for an Extended Synthesis (since the "Modern Synthesis" is finally faring poorly in the public eye) since the Altenberg 16 turning point, it is getting hard to even fault Kauffman for pointing out the elephant in the room.

From p. 150 of Stuart Kauffman's At Home in the Universe:
Is the "canon of selection" the "quintessential statement" about a lack of purpose behind human existence because it is really difficult to .  Kauffman seems to be implying elsewhere that a new canon needs to .   It seems like nearly half the serious thinkers are relegating selection to a minor role; even though the Prime Suspect for the crime of accidental design probably is not guilty, and no one can agree on what combination of the milieu of evolutionary causes is responsible for the functional complexity of life, there seems to be 98% agreement on one thing, it must be an accident.  Kauffman is one of the definitive majority here and he goes on to explain why in the next few paragraphs:  The order in life must be accidental because biology is so woefully unpredictable.  Biologists are so often thrown for a loop that it can't be design.  Sounds more to me like biology does not investigate laws in the sense that physics  does, but that it investigates a perpetually clever technology, a technology for which it has become dogma to posit a mysterious origin in some law-like process--the orthodox version having selection as the central engine in that process. They can't agree on how such a process works, only that it has somehow worked and this theory that it has somehow is as well established as the theory of gravitation.

This is rather like somebody having been sent to prison by the unanimous vote of jurors who believe incompatible versions (based on incompatible evidence) of how the defendant Q committed the crime.   They all agree that he must be guilty (due to there not being any preferable suspect) but there is not much agreement beyond that point.  Juror #1 believes in scenario A because fact X makes scenarios B and C implausible; juror #2 holds to scenario B because fact Y makes scenarios A and C implausible; and juror #3 is certain that scenario C is correct because fact Z makes A and B ludicrous.  But they can join arms and say they are assured of defendant Q's guilt because someone's version must be correct.  It must be correct because if facts X, Y, & Z rule out A, B, & C, then that means that we're back to square one and the real criminal is still out there, and that is a justice-stopper, ladies and gentleman.

Thursday, September 15, 2016

Galton on the nature of invention

Also from Galton's Natural Inheritance:
An apparent ground for the common belief [in gradualism] is founded on the fact that whenever search is made for intermediate forms between widely divergent varieties,
whether they be of plants or of animals, of weapons or utensils, of customs, religion or language, or of any other product of evolution, a long and orderly series can usually be made out, each member of which differs in an almost imperceptible degree from the adjacent specimens. But it does not at all follow because these intermediate forms have been found to exist, that they are the very stages that were passed through in the course of evolution. Counter evidence exists in abundance, not only of the appearance of considerable sports, but of their remarkable stability in hereditary transmission. Many of the specimens of intermediate forms may have been unstable varieties, whose descendants had reverted; they might be looked upon as tentative and faltering steps taken along parallel courses of evolution, and afterwards retraced.  Affiliation from each generation to the next requires to be proved before any apparent line of descent can be accepted as the true one. The history of inventions fully illustrates this view. It is a most common experience that what an inventor knew to be original, and believed to be new, had been invented independently by others many times before, but had never become established.  Even when it has new features, the inventor usually finds, on consulting lists of patents, that other inventions closely border on his own. Yet we know that inventors often proceed by strides, their ideas originating in some sudden happy thought suggested by a chance occurrence, though their crude ideas may have to be laboriously worked out afterwards. If, however, all the varieties of any machine that had ever been invented, were collected and arranged in a Museum in the apparent order of their Evolution, each would differ so little from its neighbour as to suggest the fallacious inference that the successive inventors of that machine had progressed by means of a very large number of hardly discernible steps.
If that is a "fallacious inference" then how is any lineage inferred?

Tuesday, September 13, 2016

Evolution as Invention by Galton

Darwin's cousin Francis Galton discussed the innovative power of Natural Selection in his classic Natural Inheritance:
The hansom cab was originally a marvellous novelty. In the language of breeders it was a sudden and remarkable "sport," yet the suddenness of its appearance has been no bar to its unchanging hold on popular favour. It is not a monstrous anomaly of incongruous parts, and therefore unstable, but quite the contrary. Many other instances of very novel and yet stable inventions could be quoted. One of the earliest electrical batteries was that which is still known as a Grove battery, being the invention of Sir William Grove. Its principle was quite new at the time, and it continues in use without alteration.  . . . It seems to me that stability of type, about which we as yet know very little, must be an important factor in the general theory of heredity, when the theory is applied to cases of high breeding. . . .
Infertility of Mixed Types.--It is not difficult to see in a general way why very different types should refuse to coalesce, and it is scarcely possible to explain the reason why, more clearly than by an illustration. Thus a useful blend between a four-wheeler and a hansom would be impossible ; it would have to run on three wheels and the half-way position for the driver would be upon its roof. A blend would be equally impossible between an omnibus and a hansom, and it would be difficult between an omnibus and a four-wheeler .* [emphases mine]

Strangely, the copy of Galton's Natural Inheritance available in PDF form at is from Harvard's divinity school of all places.  The college's library stamp represents the testament of Christian scripture as an open book, with Psalm 119:169 cited on the left side and John 17:17 cited on the other.  The Hebrew words of the Psalm say "in Your word give me understanding," and the Greek words from the Gospel say "Your word is truth."

Tuesday, August 23, 2016

Deter Lucem Defends Hawking's Self-Birthing Universe

Suppose you ask a college professor, "Where does a baby come from?  How does a baby come to form in the womb?"

The professor says that there is a biological law of development that causes an ovum to develop into a baby and that this law requires an ovum to create itself from nothing.  You say that this sounds circular as though a baby comes to be because its potential existence makes it somehow necessary.  The professor sighs and tells you that you misunderstand him: The internal characteristics of the early embryo is what leads to the embryo existing; the existence of an embryo is inevitable based off of a bunch of different criteria that exist before the embryo really starts to expand into existence. 

Surely you would gather that this professor is either engaged in sophistry or has no idea just how logically unsound his reasoning is.  What I want to look at here is what happens when a physicist tries to turn cosmology into a universe-creating perpetual motion machine, and then laymen attempt to defend such reasoning.

Stephen Hawking has a knack for taking science and doing a whole lot of questionable philosophy beyond it (see bottom of this post), in spite of his sometimes dismissive attitude toward philosophy.  A particularly quotable example was brought to the spotlight in the 2015 Christian film God's Not Dead:
Because there is a law such as gravity, the universe can and will create itself out of nothing.  
The film is staged around several fictional presentations in which a college student is making a case for the existence of a Creator to an atheist professor's philosophy class.  The student Josh interprets Hawking's words thus:
Hawking is basically saying that the universe exists because the universe needed to exist, and because the universe needed to exist, it therefore created itself. 
Now, the original statement by Hawking is that there exists something (the law of gravity--which is inside or outside the universe?) that explains the necessity for and therefore the existence of the universe.  Like the Logos in the Gospel of John, gravity plays for Hawking the role of Firstborn of all Creation, eternal and present "in the beginning."

Amateur Darwinism apologist Deterlucem spends an entire Youtube webisode taking on these fictional arguments in the film, and takes issue with the above as though the character Josh is stating that Hawking means the form of our present universe was foreordained in "some cosmic plan."  Instead, Deter impatiently explains Stephen Hawking's assertion that the law of gravity requires the universe to spontaneously create itself from nothing:  
It's like I mentioned twice now, the internal characteristics of the early universe is what led to the universe existing--it's meaning [sic] the existence of the present universe was inevitable based off of a bunch of different criteria existing before the universe really started to expand into existence. 
"Expand into existence"?  Expanding from non-existence?  Now, even if we accept the law of gravity deterministically getting us from a pre-inflation early universe to the present universe with no speculative baggage (a big "if"), that process doesn't explain how we get the pre-inflation early universe "from nothing."  It's not clear that Deter has thought about his own words enough to know himself what he means by them.  This cosmic "just so" story sounds like a creation myth:
In the beginning was Nothing, and the Nothing expanded four-dimensionally into Something because of the Criteria, and Gravity caused the Criteria to hyperinflate the new Something into an immense universe of mass and energy, which through Cosmic Evolution eventually became the universe we see now.
What Deter has presented is something that Daniel Dennet calls a "deepity."  In its sensible, obvious interpretation (in this case, that the outcome of a deterministic process is explained by initial conditions), its meaning is trivial and irrelevant.  In its non-trivial sense (in this case, that a thing's early state explains how it came to be in that early state), it is absurd.  He does this through what Daniel Dennet calls "rathering."  Rather than an inevitable universe in the sense of being planned, laws like gravity endow a Nothing with awesome self-starting, universe-becoming powers.  Because Science.  This is one of those ideas that are so absurd that only intellectuals could believe them.  It is the intellectual version of the explanation for electrolytes in Idiocracy (note: Brawndo is something like Gatorade).
William Dembski points out the philosophical problems with Hawking's theological and causal interpretations of early universe 4-dimensional space as timeless and non-causal in several pages of the anthology Mere Creation.  

Lawrence Krauss is only slightly more nuanced when he explains that "nothing" is an unstable something.  If you have a "nothing" all by itself without matter or energy, it starts quivering and explodes into an enormous universe.  G.K. Chesterton once compared materialism to schizophrenia: both are characterized by reason without sense.  When reason is all by itself without sense, it starts quivering and explodes into a cosmological fantasy.  ". . . [T]he materialist's world is quite simple and solid, just as the madman is quite sure he is sane. The materialist is sure that history has been simply and solely a chain of causation, just as the interesting person before mentioned is quite sure that he is simply and solely a chicken. Materialists and madmen never have doubts."*

Poets do not go mad; but chess-players do. Mathematicians go mad, and cashiers; but creative artists very seldom. I am not, as will be seen, in any sense attacking logic: I only say that this danger does lie in logic, not in imagination. . . . The poet only desires exaltation and expansion, a world to stretch himself in. The poet only asks to get his head into the heavens. It is the logician who seeks to get the heavens into his head. And it is his head that splits.  
- Chesterton*

Friday, July 8, 2016

Local Fitness Landscape Mapped Out for Green Fluorescent Protein

Sharp peaks.

Cornelius Hunter quotes a recent article in Nature about GFP:
We were really surprised when we finally had a chance to look at exactly how the interactions between mutations occur. We also did not expect that almost all the mutations that are only slightly damaging on their own can destroy fluorescence completely when combined together.*

Quasispecies: Trapped in Sequence Space

Edward C. Holmes and Andre´s Moya make some interesting comments in "Is the Quasispecies Concept Relevant to RNA Viruses?" JOURNAL OF VIROLOGY, Vol. 76, No. 1, Jan. 2002, p. 460–462:

Friday, July 1, 2016

Unlimited Variation: The Dark Energy of Biology

Alfred Russel Wallace, the co-discoverer of natural selection, wrote in 1858 that his theory could be summarized as “indefinite departure from the original type.” “Indefinite departure” is in fact the central claim of the theory of evolution by natural selection. But it still hasn’t been observed. Richard Dawkins, Jerry Coyne and others keep trying to bully us into accepting that it is a “fact.” OK. Maybe it is. So give us the evidence. We have to read their books carefully to realize how meager it is. They still haven’t shown us that extrapolation.
Back in 2013 Tom Bethell wrote an interesting piece about the "central claim" of modern evolutionary theory.  As with many interesting articles of this nature, my attention was drawn to it by a caustic review by a renowned ID-hater, in this case the inimitable Jeffrey Shallit

Shallit pedantically quibbles about Bethell's criticism of Charles Darwin.  Darwin stated that there was no reason to suppose any limit to variations of forms, e.g. no reason a fish couldn't become an elephant through a long enough series of minuscule changes, which casts natural selection as Dr. Moreau's scalpel working at a geological pace. This has enormous relevance to the extrapolative nature of evolutionary theory, for it is the justification for what Wallace called (as Bethell points out) "indefinite departure from the original type." By "indefinite" Wallace meant that for practical purposes it can be considered infinite, the limits being so indefinitely far out as to not rule out any connection between the varied forms we see and the simplest cell.

It is this sense of extrapolation that is central to evolutionary theory, more so than either common descent or natural selection

In a particularly Dawkins-esque stroke, Shallit pounds the pulpit:
What we do see is evolution taking place today, and we have the fossil record that shows the changes in the past. You have to be particularly dense or dishonest to deny this.
In other words, we already know that any limits to variation don't matter to macroevolutionary theory, because macroevolution must have occurred.  We have these here fossils, and we know Mr. Darwin's speculations about them must be true because we observe limited variation now.  Accept the extrapolation or be denounced as a "denier"! Shallit and his audience stand ready to punish the deniers by pointing and laughing while simultaneous shaking their fists in furious rage. 

Shallit invokes speciation.  I'm not certain if everyone would agree on his instances of speciation (none of which he offers--it is left as an exercise to the reader), but perhaps he would be surprised to know that even most "Young Earth" creationists believe in some limited form of speciation.  In spite of considering himself an expert on pseudo-science, he doesn't even understand the nature of his favorite "pseudoscientific" bugbear, Young Earth Creationism.  He might also be unaware that even though undirected speciation may be necessary for macroevolution, it is not sufficient to explain macroevolution.  In fact, Cornelius Hunter, who is not a Young Earth creationist, does not deny ultra-fast adaptation or an old age of fossils.  Shallit seems to consider him a run-of-the-mill creationist.  It seems that Shallit does not recognize any significant differences among those he considers "creationists" (which for him includes ID advocates).    

All of this is probably lost on evolutionary materialists who depend on a quasi-Newtonian metaphor in which evolution is moving with a sort of inertia.  This is why Jerry Coyne can liken macroevolution to a train in motion (though it is also an artificially powered and directed machine) and Shallit can compare it to cosmological materials flying apart.  (Although, the hypothetical drive powering the quasi-infinite variation of evolution is, in epistemological status, somewhat reminiscent of poorly understood "dark energy.")  
As natural as a train in motion...  Give this choo-choo
enough time and it just might reach the Galapagos Islands. 

Thursday, June 30, 2016

The Engineer and the Chalk

In Charles M. Vest's speech at MIT in 1999 attributes the parable of The Engineer and the Chalk (or The Handyman's Invoice) to electrical engineering expert Charles P. Steinmetz:
I want to tell you a story about an incident in the career of Charles Proteus Steinmetz, the great electrical engineer.
In the early years of this century, Steinmetz was brought to General Electric's facilities in Schenectady, New York. GE had encountered a performance problem with one of their huge electrical generators and had been absolutely unable to correct it. Steinmetz, a genius in his understanding of electromagnetic phenomena, was brought in as a consultant -- not a very common occurrence in those days, as it would be now.
Steinmetz also found the problem difficult to diagnose, but for some days he closeted himself with the generator, its engineering drawings, paper and pencil. At the end of this period, he emerged, confident that he knew how to correct the problem.
After he departed, GE's engineers found a large "X" marked with chalk on the side of the generator casing. There also was a note instructing them to cut the casing open at that location and remove so many turns of wire from the stator. The generator would then function properly.
And indeed it did.
Steinmetz was asked what his fee would be. Having no idea in the world what was appropriate, he replied with the absolutely unheard of answer that his fee was $1000.
Stunned, the GE bureaucracy then required him to submit a formally itemized invoice.
They soon received it. It included two items:
1. Marking chalk "X" on side of generator: $1.
2. Knowing where to mark chalk "X": $999.
Thus Steinmetz left his mark in more ways than one in early 20th century technology and business. You will do the same in the early 21st century.
Because you too will know where to put the "X."
But Steinmetz lived in the age of iron machines. Your careers will play out in the age of knowledge and information.
Fifteen years ago, shortly before his untimely death, the author Italo Calivino wrote Six Memos for the Next Millennium. In his memo entitled "Lightness," he put it simply:
"I look to science to nourish my visions in which all heaviness disappears. Today, every branch of science seems intent on demonstrating that the world is supported by the most minute entities...
The iron machines still exist, but they obey the orders of weightless bits."
The iron machines obey the bits.

Thursday, June 2, 2016

PZ Myers: The Biology Does Work

Evolution 2.0
Perry Marshall is raising some eyebrows and saying some interesting things about his Evolution 2.0.   I mostly like what he has to say, although I don't think he is giving proper credit to what Intelligent Design is or where some of his arguments come from.  He presents 'Evolution 2.0' as a kind of bridge between evolutionary thinking and design intuitions (what started as 'Mere Creation') and this is essentially what Intelligent Design already is.  Marshall does seem to bring a lot of the collective arguments of Bill Dembski, Steve Meyer, and Mike Behe framed succinctly within the past 30 years of genetic discoveries.

However, the confusion is in no small part because of the willful conflation of ID with creationism by ID's critics.  'ID Creationism' is a worthless term that is nothing more than a dishonest advertising campaign co-developed by Barbara Forrest and the NCSE.  Its effect has been to shut down discussion before it happens, and I believe that was precisely the intention.  This ploy was opportunistic ideological propaganda "in a cheap tuxedo."  If this lame political stunt now ends up causing people to pick up a book like Marshall's, so be it.  In the end inquiring minds will probably find that Evolution 2.0 is simply the more evolution-friendly version of ID.  

An interesting exchange between Perry Marshall and PZ Myers appears online and I was struck by various attempts by Myers to dismiss an engineering perspective of biology.  This one stood out in particular:
Over and over again what you do is you tell me ‘well from my perspective as an electrical engineer this doesn’t work, it can’t work’ and I’m telling you yeah but biology does work, so maybe your perspective is wrong.
What does Myers mean by "biology does work"?  In context, he seems to be saying that even though perspectives from engineering and computer science cast doubt on the very idea of a coding system arising through natural, random processes, it does indeed work so phooey on perspectives outside the fiefdom of biology.  Does he mean that the science of biology gives us useful technology (e.g. penicillin) and therefore we shouldn't question that life had a spontaneous origin?  Or is he dogmatically asserting that in modern biology it is a matter of unquestioned orthodoxy that natural processes are sufficient to produce whatever exists?  Fossils therefore abiogenesis?

Marshall challenges (with a 3 million dollar prize) the realm of biology to generate a coding system through an undirected chaotic process, and Myers states that this challenge is a sham because he should be able to present the already naturally occurring genetic code as evidence that this can happen and thus get the prize.  He doesn't need to question his assumption that abiogenesis happened because "biology does work"!  It is obvious that he, like so many others in evolutionary biology, are completely unaware of just how much intellectual laziness is represented here. 

He then goes on to ironically accuse Marshall of assuming what he intends to prove.  While Marshall is simply using the same abductive argument championed by Stephen Meyer, PZ Myers is unaware that museums full of fossils do not demonstrate that our DNA has a perfectly coherent natural explanation.  He fervently believes no one should actually have to do the work of demonstrating the random genesis of a code to get that 3 million dollar prize.  Darwin's "one long argument" showed the world that science had no need for God, and since there is no God we know that amazing codes like DNA have a perfectly natural explanation, even if we don't know what that could be (RNA, crystals, abiogenetic molecules du jour). 

I wish that Myers had promoted Tom Schneider's work as proof of a randomly generated code.  Then there might be some interesting back-and-forth about what a coding system is vs. a lock-and-key system.  While I suspect that there are flaws in the applicability of Schneider's model to actual site recognition, the bigger flaw is in its applicability to the sorts of biological "innovation" that Wagner and others have tried to characterize. 

Myers also criticized Marshall for what he considers an 'appeal to authority'.  Now you have to keep in mind that to Myers a 'creationist' isn't necessarily someone who believes that the world was created in 6 days, a 'creationist' is anyone that thinks that there are evidential reasons for thinking that life is the result of a conscious, creative act.  This is never more evident than in Myers' insinuation that Perry Marshall is a creationist.  As a rabid anticreationist, Myers will not only belittle 'creationists' for citing other 'creationists', but will get much more upset if they cite a figure that has some weight and is not already discredited as being skeptical of neo-Darwinism.  When 'creationists' do this, it must be characterized as an 'appeal to authority'. 

But if you read carefully, you'll see that Myers doesn't think it's wrong to appeal to authority; he faults Marshall for not appealing to the correct authorities. 

Myers and likeminded crusaders against anti-science tend to dismiss the engineering/software analogy.  Dawkins and others embrace the analogy because they don't see the problem.  Regardless of the definitions, orthodox evolutionary biology has the unique problem of trying to explain how engineering happens without an engineer, how a coding system develops without a coder, how purposeful machines arise in entropy-ridden purposelessness.  The Myers approach is to claim that the analogies from digital engineering don't apply to the digital wetware in our bodies.  It is too different they claim because it is (a) complicated, (b) replicated, (c) fault-tolerant, and (d) so darn wet.  All that math and computer science that is applicable to artificial digital systems is therefore not applicable to biological wetware (except when it seems to confirm an evolutionary point of view, of course).  Biological matter is too different in its complicated, self-reproducing electrochemical wetness to be beholden to information principles.
Engineering analogies must not be applicable because fossils and stuff show that the "biology does work", and after all, there are random errors that follow known distributions.  Therefore we can safely conclude that all the non-randomness is due to the accidents of genome arrangement.  After all, hundreds of thousands of biologists show up for work each day, and do science, and get their findings published.  There's no need to demonstrate how such elaborate order arises from disorder, because evolutionary biologists already know that it did.  All this "brute force molecular biology" really has no place weighing in on the matter.  Myers can join Jerry Coyne here in lamenting how molecular biology is not bolstering evolutionary theory--the weed of secular creationism seems to be sprouting up in molecular biology.  Seems like we will have to extend the Salem Hypothesis to include molecular biologists. 

Pay no attention to any ramifications of Craig Venter's work.  Why?  'Cause biology does work already!  It works!  We're not going to give up a hundred years' worth of conjectures and plausibility stories for some preposterous "brute force molecular biology" experiments!  The biology has worked just fine without them.

Wednesday, May 25, 2016

PSA from Dr. Pangloss

For example epigenetics ...

Evolution -- the theory so malleable that every failure is really just a success in disguise. 

Thursday, April 7, 2016

James Shapiro & Why Evolutionary Theory Is Getting Unrecognizable

Recently I got to see a debate between Michael Ruse and Cornelius Hunter.  For the most part, Hunter argued that the facts of biology, mostly citing recent research, discredit an evolutionary explanation based on Darwin's original theory, esp. any theory dependent on common descent or positive selection.  For the most part, Ruse discussed what was historically so convincing to Charles Darwin.  This latter scheme, though it did not in any way rebut Hunter's points, seems to fit the mainstream approach. 

A similar pattern ensued in a debate a few years about ID with Michael Shermer and Donald Prothero on one side, and Stephen Meyer and Rick Sternberg on the other.  If memory serves, Shermer and Prothero mostly summarized the century-old argument for common descent for the audience, while Meyer and Sternberg attacked natural selection as a sufficient explanation.  (Reminder: ID in no way require common descent to be false, though it is quite at home in the anomalies in phylogenetics.)

With more recent mosaics (e.g. Tiktaalik and Pakicetus and other "missing links") in tetrapod evolution, the "overwhelming evidence" for "evolution as fact" seem to be an abductive inference based on fossil geology, comparative anatomy, and embryological similarity.  And now, as then in Darwin's day, a historical evolutionary process (whatever the mechanism) is compared to what a typically atheist/deist biologist presumes an anthropomorphized cosmic designer would or wouldn't have done.  This is the "one long argument" of Mr. Darwin and these theological arguments haunt science textbooks to this day. 

In an era of evolutionary thought where Darwin's Tree of Life is being discussed as an outdated concept and natural selection as maybe not being a central explanatory mechanism for macro evolution, it begs the question what biologists (or anybody) mean when they assert that "Evolution is a fact." "Evolution" may be the most overloaded term in all of science.  It refers to a historical "fact" and a "theory" of causation and a trivial phenomenon (microevolution) and a research program and a narrative (and a religion according to Michael Ruse).

James Shapiro, a fairly mainstream microbiologist and evolutionary biologist has written a book Evolution: A View from the 21st Century that challenges a lot of the assumptions of the mainstream Evolutionary Synthesis.  He differentiates between several key aspects of evolution.
General discussions of evolution, especially in the context of the “Intelligent Design” controversy, suffer from an unfortunate conflation in the minds of the lay public (and also of scientists) of three distinct questions:
[1] The origin of life
[2] The evidentiary basis for an evolutionary process
[3] The nature of evolutionary change
[emphasis mine]
When you think about, the 3rd item is all over the place right now.  There is no consensus on whether natural selection is a sufficient explanation for what Darwin used it to explain--the origin of all species--and that is an understatement.  The 1st item is in a similar state of disarray in terms of a coherent theory, but this is less surprising and more widely understood--and the chief reason why many theorists separate it from the Evolutionary Synthesis.  Now, the 2nd item is something that many, though not all, ID theorists either agree with or at least grant for argument's sake. Many ID theorists do dispute whether the evidentiary basis for common descent is as strong and coherent as neo-Darwinists and evolutionary materialists aver, but ID is generally not in conflict with an "evolutionary process" of some kind.
The one issue that has effectively been settled in a convincing way is the evidence for a process of evolutionary change over the past three billion years. The reason the answer to this question is so solid is that every new technological development in biological investigation—from the earliest days of paleontology through light microscopy and cytogenetics up to our current molecular sequence methodologies—has told the same story: living organisms, past and present, are related to each other, share evolutionary inventions, and have changed dramatically over the history of the Earth.* [emphasis added] 
How much an ID theorist agrees with a common "story" depends on what he means by "related to", "share", and "history."  Even a Young Earth Creationist might agree with these articles as stated, though Shapiro probably means "history" as the mainstream interpretation of the "fossil record" rather than simply as time.  But the majority of ID theorists, including Steve Meyer, Michael Behe, William Dembski, and even Jonathan Wells, seem to adopt or use the mainstream view of fossil dating. 

The central point of departure for Intelligent Design is whether there is a significant component of intelligence that is required for a complete explanation for the biological world.  But there is a real and general way in which both ID theorists and creationists see organisms as related to each other and sharing innovations in a non-Darwinian sense, an innovative relationship between living things that has unfolded in a dramatically changing diversity over Earth's history (whether a long history or short).  

And the question remains whether even the evidence for an evolutionary process, intelligent or not, is quite so strong without a prior conviction that all natural phenomenon have a strictly natural cause (where "natural" essentially means "material" or "physical").  As evolutionist par excellence Richard Lewontin said:
Our willingness to accept scientific claims that are against common sense is the key to an understanding of the real struggle between science and the supernatural. We take the side of science [defending science against "attackers"?] in spite of the patent absurdity of some of its constructs, in spite of its failure to fulfill many of its extravagant promises of health and life, in spite of the tolerance of the scientific community for unsubstantiated just-so stories, because we have a prior commitment, a commitment to materialism. It is not that the methods and institutions of science somehow compel us to accept a material explanation of the phenomenal world, but, on the contrary, that we are forced by our a priori adherence to material causes to [seek only material causes  in science]. Moreover, that materialism is absolute, for we cannot allow a Divine Foot in the door. The eminent Kant scholar Lewis Beck used to say that anyone who could believe in God could believe in anything. To appeal to an omnipotent deity is to allow that at any moment the regularities of nature may be ruptured, that miracles may happen.
And that, Charlie Brown, is the meaning of Slippery Slope. Somehow, this "Divine Foot in the door" didn't stop scientists like Isaac Newton, nor the many "creationist" scientists that preceded both Darwin and widespread Deism, from real, ground-breaking science. Somehow, in the absence of an "absolute" materialism, both common sense and the belief in a universe made comprehensible by a rational Designer made them expect an orderly world where miracle was exceptional but not excluded.

Wednesday, April 6, 2016

Non-Haeckelian Development

Some fun weirdness in the tangled “tree of life.”  Donald Williamson, a marine biologist who wondered why very different larval forms pop up willy-nilly in very different species, has a bold hypothesis.  Although his explanation is very heterodox (though it received serious support from Lynn Margulis) and is yet to be supported by any molecular data, what is much more fascinating is the extent of the problem his theory aims to solve, including the following oddities:
  1. Very similar larval forms appear in phyla with dissimilar adult body plans.
  2. Wholly different larval forms appear in the same phylum
  3. Some echinoderms are develop as protostomes, some as deuterostomes. 
  4. Some mollusks, annelids, sipunculids, and even some deuterostomes have rotifer-like trochophore larvae.
These larval variations not only challenge the Haeckelian expectations of neo-Darwinism, but they potentially put the whole protostome/ deuterostome division in question.  Here’s Williamson’s attempt to fit these larval epicycles into a Darwinistic history:

   … Brittle stars and sea urchins are very different as adults but share the unique pluteus form of larva. Why would similar larvae produce dissimilar adults [in different phyla]? Larval transfer proposes that the basic pluteus larva evolved only once, in a sea urchin, and was retained in this sea urchin’s descendants.  An ancestor of most existing brittle stars then acquired a pluteus larva by hybridizing with a sea urchin. 

    One member of this group, Kirk’s brittle star, develops directly from the fertilized egg, with no trace of a bilateral larva, and its blastopore becomes a mouth. It is, therefore, a protostome.  All echinoderm larvae are in a different developmental class, the deuterostomes, in which the mouth is a new opening; several echinoderms that have lost their larvae develop as deuterostomes. If Kirk’s brittle star lost its larva, it must have also adopted a fundamentally different pattern of cell division in the embryo. We believe, however, that Kirk’s brittle star has no larva because none of its ancestors hybridized with a sea urchin. The heart urchin Abatus cordatus and the three known species of sea daisies also have no larvae and develop as protostomes.  We suggest that this is the ancestral method of echinoderm development, and the pattern called deuterostomy came with the transferred larvae. 

  Two sea urchins, Lytechinus variegatus and Lytechinus verruculatus, are of the same genus, but the similar adults each develop from very different pluteus larvae. Such cases are difficult to explain if larvae and their corresponding adults evolved from one common ancestor.


It’s pretty curious stuff.  

Sunday, March 6, 2016

Theohysterical Characteristics of Hate Coordination in Censorship Activities of Daily Science

At the beginning of this year, a certain research article discussed the many special optimizations in the human hand that sets it apart from other ape hands in terms of manual dexterity and, by extension, tool use.  Call it the science of the opposable thumb:

Interesting stuff.  But don't base any of your studies though on their meticulous documentation and experiments.  As you might guess from the watermark, the paper has been RETRACTED due to "inappropriate" (and apparently, offensive) language.  Ming-Jin Liu et al used the C-word.  Yes, the word "Creator" appeared not once but twice in the paper.  P.Z. Myers and other intimidazi apparently bombarded PlosOne with protests against nasty so-called "intelligent design creationism" creeping in, and PlosOne finally noticed that the C-word had been carefully hidden in the front-page abstract.   (Sneaky ID devils.) 

The authors have since stated that the Chinese expression (perhaps Tian?) was improperly translated and should have been rendered as "Nature" for Western "ears."  Bowing low before the angry Darwinian gods proved pointless though, and the publishers would not accept revising the "Creator" language to either "nature" or even "evolution".   As Eugenie Scott and Barbara Forrest have taught us, if the eagle quacks like a duck, then it can't be an eagle, because it probably once was a duck and that makes it is just a duck pretending to be an eagle (or some such logical profundity), just like we are all really sarcopterygian fish, no matter how many millions of mutations and HGTs we may boast since our Tiktaalik phase.  Someone call Barbara Forrest, for she may want to add a new chapter to her Trojan Herring book!  Here's another attempt of unseemly religion to camouflage itself as Holy Science.  Changing "Creator" to "Nature" won't atone for this unpardonable sin because it would be known that these edits changed it from being an ID article to "passing for" a Science article.  But once a "creationist" text always a "creationist" text, and as the brave and wise luminary/logician Judge Jones III has opined, an ID article can't be a Science article. 

You can still download the article but note that it bears the scarlet letters branded on each page.  And yes, all this means the authors must be ... secular creationists!
Now, if only the thought police could scrub our Declaration of Independence of all this offensive language (as well as all public forums), we might finally be free from the freedom of expression. 

Saturday, March 5, 2016

the nature of insight

But then the kind of information that produces design of an algorithm or machine--or possibly a nanomachine made from amino acids--often requires insight, whereas the way that natural selection processes the information from the environment is much more like pedantry. *
And this classic gem, which could be said to Intuition, to Insight, to Revelation, to Wisdom herself, or to the Creator:
since feeling is first
who pays any attention
to the syntax of things
will never fully kiss you  *