Saturday, August 31, 2013

Michael Ruse States Why Darwin Should Not Be Publicly Challenged

Suzan Mazur, who wrote about the Altenberg 16 conference on the "Extended Synthesis," posted an e-mail chain conversation at her site: "From October 16 – 24, 2007, [Stanley] Salthe ran an email chain on the [Jerry] Fodor “Pigs” story with some of the science elites throwing in their two cents."

Said Stan Salthe:
“Folks – There’s not much new in this below, but, given Fodor’s prominence, and the place of publication, I thought I would pass it on.”
Michael Ruse, philosopher:
“In my opinion Fodor’s piece is grotesquely and immorally irresponsible – he has done no homework on evolutionary theory – to say that natural selection did not shape the guppy and the fruitfly is ludicrous of course, every creationist in north america is salivating today – even though, they are the people who push adaptation more than even me! think that this one won’t be used in the argument over what should be taught in schools?
Today, I am deeply ashamed to be a philosopher”
Stuart Newman, cell biologist:
“Fodor’s piece seems pretty reasonable to me, in fact, kind of obvious. To say that organisms at any stage of evolution have only a limited array of condition-dependent inherent characteristics, or developmental pathways, and selection can do no more than choose among these, has nothing whatsoever to do with creationism.”
Michael Ruse:
“You are very naive – it has everything to do with creationism – of course, to deny adaptationism is not to endorse creationism – but to write a piece slagging off natural selection in that way, is to give a piece of candy to the creationists – I am sure that duane gish has already incorporated this into his talks of course natural selection has to work on an array of given things, but this is not to deny selection – especially not through fodor’s silly arguments about analogies – and certainly not adaptationism the point of course is that fodor did not simply write a technical piece on adaptation – he wrote a piece flamboyantly denying selection in today’s climate, where we have just had two ultra right supreme court justices appointed, I think his behavior is somewhere between stupid and wicked
Emphases are mine. ... Apparently, Supreme Court justices who elect to not dictate to the states what is and isn't science might not agree with Judge Jones' schlocky philosophy of science and that makes them "ultra right."  Ruse has a moment here where he descends into "Duane Gish Syndrome."  Is he an anticreationist or a secular creationist? 

Random Thoughts on Schneider vs. Dembski: What Kinds of Information are Real?

Still thinking about Tom Schneider's ev simulation and these are the salient points:
  • What engineers mean by the "information" inherent in a complex, interactive machine is something different from Shannon information, something not necessarily synonymous to Kolmogorov information but certainly more closely related to it. 
  • Schneider thinks that Shannon information is the only kind of information there is--the only definition of information worth considering.  The references to Kolmogorov information that Dembski makes are lost on him.  Schneider is obviously very smart, very well versed in the sort of information he is concerned with, but like most that concern themselves with biology, he is oblivious to anything beyond the most mechanistic conceptions of information.
  • Jeffrey Shallit, by contrast, is interested in Kolmogorov information, but in his world, giving you a copy of a phone book you already possess has given you more information (a few bits more, to be precise) and a lot more information if the second book has a lot of the letters and numbers scrambled randomly.  Schneider would say that a completely randomized phone book would have zero information. There is something completely missing from both these conceptions.  
  • Hubert Yockey would have said that they were both confused.  Schneider would say that Yockey and Shallit were confused. Go figure.  About the only one who comes close to recognizing the fundamental problem is Gregory Chaitin, though he believes in Darwinism as well.  The only thing that they have in common is that they all seem to have very different justifications for dismissing Dembski. (I'm not certain that Chaitin dismisses Dembski, but he finds the informal arguments for evolution persuasive even though he thinks there is no real mathematical theory explaining evolution.)   
  • Schneider doesn't like that Dembski says that Schneider has claimed to produce what Dembski calls complex specified information (CSI) because he doesn't like that term. It does seem (need references) that Schneider has claimed to have literally "created information" and seems to have this in mind as support for the Cambrian Explosion not being really that strange.   
  • What Schneider has in mind by creating information is that natural selection could allow a co-evolution between varying binding sites and the binding molecule, so that both are refined.  To the degree that the emerging pattern is specific, I'm not sure that it's complex; to the degree that it is complex.   There is not much that is holistic about the problem--each nucleotide site can be refined more or less independently of the others--which makes it a very different problem than adapting an enzyme with highly cooperative sections.   
Generally, it seems that Schneider's implicit argument is:

  • Leading ID advocates claim that the Cambrian explosion is not explained by Darwinian models because in a evolutionarily short amount of time, the majority of body plan innovations, with their novel and unique architectures and developmental programs, all arose.  The body plans indication that enormous amounts of prescriptive information for development and hundreds of supporting protein specifications were developed for each arising phylum.
  • The ev simulation shows the specificity of binding sites being converged on to produce specific patterns that are informational and might be considered CSI. (Schneider disdains the concept of CSI so much that he doesn't thoughtfully consider how it might relate--or not--to Shannon information, so it's curious.  He is apparently incensed at Dembski for putting words in his mouth and then seems to argue that this is actually what he means by "creat[ing] information.")
  • Specificity of site recognition is an emergent kind of information, and phylum body plans, also being information, can presumably emerge as well.

     ____________________________________________________
         Ergo, the Cambrian Explosion is not hard to account for at all.

Now if we could just make a genetic algorithm to generate the specs for novel, working airplanes.... or for novel, working inventions in general...  As Ray Kurzweil would say, the singularity is near...

Thursday, August 29, 2013

Indirect Routes and Exaptation



http://www.evolutionnews.org/2012/08/did_michael_beh063271.html

8) Professor Behe excludes, by definition, the possibility that a precursor to the bacterial flagellum functioned not as a rotary motor, but in some other way, for example as a secretory system. (19:88-95 (Behe)).
I certainly do not exclude that bald possibility merely by definition. In fact in Darwin's Black Box I specifically considered those kinds of cases. However, I classified those as indirect routes. Indirect routes, I argued, were quite implausible:
Even if a system is irreducibly complex (and thus cannot have been produced directly), however, one can not definitely rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously. (DBB, p. 40)
University of Rochester evolutionary biologist H. Alan Orr agrees that indirect evolution is unlikely:
we might think that some of the parts of an irreducibly complex system evolved step by step for some other purpose and were then recruited wholesale to a new function. But this is also unlikely. You may as well hope that half your car's transmission will suddenly help out in the airbag department. Such things might happen very, very rarely, but they surely do not offer a general solution to irreducible complexity. (Orr, H. A. Darwin v. intelligent design (again). Boston Review [Dec/Jan], 28-31. 1996)
There is no strict logical barrier to a Darwinian precursor to a bacterial flagellum having functioned as a secretory system and then, by dint of random mutation and natural selection, turning into a rotary device. There is also no absolute logical barrier to it having functioned as, say, a structural component of the cell, a light-harvesting machine, a nuclear reactor, a space ship, or, as Kenneth Miller has suggested, a paper weight. But none of these has anything to do with its function as a rotary motor, and so none of them explain that actual ability of the flagellum.
A bare assertion that one kind of complex system (say, a car's transmission) can turn into another kind of complex system (say, a car's airbag) by random mutation and natural selection is not evidence of anything, and does nothing to alleviate the difficulty of irreducible complexity for Darwinism. Children who are taught to uncritically accept such vaporous assertions are being seriously misled.
- See more at: http://www.evolutionnews.org/2012/08/did_michael_beh063271.html#sthash.fpmfrfy5.dpuf

Wednesday, August 28, 2013

ideas

At the end of 
http://schneider.ncifcrf.gov/information.is.not.uncertainty.html
is a discussion that is hard to unravel because Schn almost always gives the example of conditional entropy of a decision point in the next base pair. 
Berry paradox:
http://www.cs.auckland.ac.nz/CDMTCS/chaitin/unm2.html
I think Elsberry references this and doesn't see its connection to his example function that searches program space for a Q-compressible string.
Chaitin:
http://www.cs.auckland.ac.nz/CDMTCS/chaitin/unm2.html
What happens if you start with this
    ``the first positive integer that cannot be specified in less than a billion words''
instead? Everything has a rather different flavor. Let's see why. 
The first problem we've got here is what does it mean to specify a number using words in English? This is very vague. So instead let's use a computer. Pick a standard general-purpose computer, in other words, pick a universal Turing machine (UTM). Now the way you specify a number is with a computer program. When you run this computer program on your UTM it prints out this number and halts. So a program is said to specify a number, a positive integer, if you start the program running on your standard UTM, and after a finite amount of time it prints out one and only one great big positive integer and it says ``I'm finished'' and halts.
Bernoulli's Principle:
They appeal to searches with “links” in the optimization space and smoothness constraints that enable “hill-climbing” optimization [32]. Prior knowledge about the smoothness of a search landscape required for gradient based hill-climbing,8is not only common but is also vital to the success of some search optimizations.9
Such procedures, however, are of little use when searching to find a sequence of, say, 7 letters from a 26-letter alphabet to form a word that will pass successfully through a spell checker, or when choosing a sequence of commands from 26 available commands to generate a logic operation such as XNOR [46]. The ability of a search procedure to work better than average on a class of problems is not prohibited by COI.10
http://schneider.ncifcrf.gov/paper/ev/dembski/specified.complexity.html
He shows that pHe shows that pure random chance cannot create information, and he shows how a simple smooth function (such as y = x2) cannot gain information. (Information could be lost by a function that cannot be mapped back uniquely: y = sine(x).) He concludes that there must be a designer to obtain CSI. However, natural selection has a branching mapping from one to many (replication) followed by pruning mapping of the many back down to a few (selection).
http://schneider.ncifcrf.gov/pitfalls.html
Treating Uncertainty (H) and Entropy (S) as identical OR treating them as completely unrelated. The former philosophy is clearly incorrect because uncertainty has units of bits per symbol while entropy has units Joules per Kelvin. The latter philosophy is overcome by noting that the two can be relatedif one can correlate the probabilities of microstates of the system under consideration with probabilities of the symbols
Claim of identicalWilliam Dembski in the book No Free Lunch stated that the two forms are mathematically identical (page 131)
-----------------------------------------------
http://schneider.ncifcrf.gov/paper/ev/dembski/specified.complexity.html
The random number generator used in ev is a deterministic function, yet the ev program clearly shows an increase in the information (as defined by Shannon) in the binding sites. (In other words, all the complex discussion and mathematics that Dr. Popescru puts out is a smoke screen that covers the simple situation at hand.) There is also the point from thermodynamics that information can be gained in a system (ie the entropy can go down) so long as there is at least a minimum compensating increase in the entropy outside the system
http://schneider.ncifcrf.gov/glossary.html#information
Information is measured as the decrease in uncertainty of a receiver or molecular machine 
----------------------------------------------
http://schneider.ncifcrf.gov/pitfalls.html
imagined flipping a coin 1000 times to get 1000 bits of information. . . . . So a random sequence going into a receiver does not decrease the uncertainty of the receiver and so no information is received. But a message does allow for the decrease. Even the same signal can be information to one receiver and noise to another, depending on the receiver!

Monday, August 26, 2013

notes on fitness function



http://www.godandscience.org/evolution/specifiedcomplexity.html
I think that one needs to think of the cases where the function is smooth and linear as the exception.  This is a case of a parameterized problem.


http://www.jackscanlan.com/2011/01/dembskis-idea-of-complex-specified-information-is-ironically-unspecified/

http://users.fred.net/tds///anti/william.dembski/
http://schneider.ncifcrf.gov/paper/ev/dembski/
http://schneider.ncifcrf.gov/paper/ev/dembski/claimtest.html
http://schneider.ncifcrf.gov/paper/ev/dembski/rebuttal.html



Saturday, August 24, 2013

Michael Ruse, Secular Creationist

Michael Ruse:
. . .  I think also in the present, for many evolutionists, evolution has functioned as something with elements which are, let us say, akin to being a secular religion. . . .  for Thomas Henry Huxley, I don't think there's any question but that evolution functioned, at a level, as a kind of secular religion. . . . I think Julian Huxley was certainly an atheist, but he was at the same time a kind of neo-vitalist, and he bound this up with his science. . . . it comes through very strongly that for Julian Huxley evolution was functioning as a kind of secular religion.  . . . I'm just saying this in a matter-of-fact sense -- I think that today also, for more than one eminent evolutionist, evolution in a way functions as a kind of secular religion. . . . in On Human Nature, [E.O.] Wilson is quite categorical about wanting to see evolution as the new myth, and all sorts of language like this. That for him, at some level, it's functioning as a kind of metaphysical system.* 
The New Atheists seem to hate Michael Ruse's soft touchy-feely liberalism.  Of course, I don't buy into the  Non-Overlapping Magisteria (NOMA) of Gould and Ruse (which feeds the "safe religion" dogma) much more than the idea that science and religion are at odds.  In the typical double standard, what we have in our universities is (a) pervasive preaching that religion is only safe if it has nothing to say about the nature of the universe, (b) pervasive eulogizing that science will die a painful death if scientific results can be used to imply non-material or extra-scientific causes, and (c) pervasive commentary on how science has liberated us from our silly superstitions about deity.

The Pharisees and Sadducees in the anti-creationist camp aren't always closing ranks.  I think anticreationism is a good name for the shared enthusiasm, in spite of the fact that the conflation of creationism with intelligent design is a ugly bit of equivocation, since it seems to be based on a fear of creationism being taken seriously.  No doubt, the usual suspects would say that I am tacitly agreeing with their conflation of ID with creation science and Young Earth creationism.  Rather, I am thinking of anticreationism as a sort of hysteria over the creationist bugbear that
(a) causes the afflicted to react against anything that threatens the authoritarian control of a scientific hierarchy, and
(b) causes the afflicted to respond to almost anyone (e.g. Rupert Sheldrake or David Berlinski) suggesting that science can point to non-material causes as though he or she were a creationist like Duane Gish.  (I also think of this as "Duane Gish syndrome.")

Ruse with trilobite tattoo
This is related to the habit of Dawkins, Prothero, and Eugenie Scott of being seemingly incapable of responding to anything other than Young Earth Creationism.  To Dawkins, David Berlinski is a creationist; to Prothero, Stephen Meyer is arguing based on the Book of Genesis; to Scott, if Dr. Rick v. Sternberg's neo-Platonism allows him to seriously critique baraminology, he might as well be a creationist -- after all "if it walks like a duck, and quacks like a duck ..."

Which puts me in mind of David Sloane Wilson saying that Jerry Fodor deserved the title of "secular creationist" (a term slightly less absurd than "creationist porn") for suggesting that science is not a prescriptive for the human condition.  Apparently, for Wilson whatever lies outside of Scientism is Creationism.

Perhaps we will have a repeat of the "Science Wars."  The New Atheists seem to hate Michael Ruse's soft liberalism, in spite of Ruse's complicity in the Edwards vs. Aguilard jurisprudence, a victory that atheists, materialists, secular humanists, positivists, and various anti-supernaturalists have managed to marshal against any attack on Darwinism ever since Judge Jones cut-n-pasted the ACLU's amicus brief into his ruling.  In spite of being an "ardent Darwinian," Ruse is apparently too postmodern for Positivism's heirs.

In a pettiness that seems to typify the New Atheists, Jerry Coyne slams Michael Ruse for identifying the wrong Hitchens brother (in fact, he desperately screencaps Ruse's mistake in case Ruse notices the obvious error--which he does).  For Coyne, this is the telling proof that Ruse is hopelessly confused.  Well, the first bit anyway.  Like Jeffrey Shallit obsessing over Schopenhauer attributions, Coyne takes Ruse to task over using the popular inaccurate version of the George Orwell quote: “There are some ideas so absurd that only an intellectual could believe them.” Coyne loves the original: “This is one of those views which are so absurd that only very learned men could possibly adopt them.”  Sadly, Coyne wasn't using the the Orwell quote to refer to neo-Darwinism or the New Atheist caricature of religious history.

Come to think of it, this also reminds me of a truly bizarre response that Daniel Dennett submitted for an article by David Berlinsky.  It was a bunch of random, excited pettiness bordering on schoolyard bullying, among other things focusing on Berlinsky's mistake with a gender pronoun (not making this up) and unwittingly revealed his own ignorance over the term "combinatorial explosion."  Berlinksy aptly called the response "a robust display of vulgarity."  I think Dennett is capable of much better, and it would be a kindness to attribute that outburst to something written during a drunken rage.

Then again, maybe there are responses so juvenile that only very learned men will attempt them.

Anyway, after Coyne gets through with the minor kvetches (not so minor that he doesn't assign them ordinal numbers for reference), he has used up all his energy educating us on the particulars of names and quotes that he waves his hands and leaves the humanism/atheism divide as an exercise to the reader.  He quotes a rather well-stated criticism from Ruse and focuses on the first word of the excerpt.  I'll fill in the blanks. You can be an atheist without bothering with the "human reason, ethics, social justice" that secular humanists attempt to incorporate into their view.  However, the New Atheists and the Secular Humanists seem to be pretty much on the same page with respect to what Ruse is saying in the quoted passage.  Coyne doesn't bother speaking to that, but dismisses Ruse on the basis of "Peter Hitchens," "Humanists," and a misquote.

Ruse earns enough contempt from Coyne as a bad sport that Coyne shies away from more name-calling, clearly sounding disappointed that Ruse doesn't appreciate the unprofessionalism.  PZ Myers is not so coddling, and wishes he had thought of "something better" (showing more contempt, presumably) to call Ruse than the 'clueless gobshite' he calls him.  To his credit Ruse has never called out Myers as an oozing pustule of rancor and absurdity.  One gets the impression reading Myers' response that he has no problem attributing both "[b]lind, unquestioning worship of our leaders" and "incessant fractiousness and dissension" to theistic religion, but considers it a great contradiction to say that, like theistic religion, either is true of the anti-religion complex of atheism, materialism, Scientism, "free thought," and secular humanism.  He doesn't correct Ruse on applying either description to theistic religion.

My guess is that what really irks Myers is that he doesn't like that Ruse is saying that people that hold to atheistic and materialistic worldviews often behave like fundamentalist proselytizers and that the American people have a legitimate interest in government schools not being used for such proselytizing  -- or at least, that the proselytizing not be so overt and obvious.  Eugenie Scott's response to Ruse on this score was that he was simply being "dumb." (To which he replied, "But while that may indeed be so, I am not sure that it is an argument."  I am quite sure it isn't, Michael.)

Are schools promoting a metaphysics of naturalism?  Are kids getting that picture from "the science" or from the way science is being taught?

Ruse acknowledges that what one finds compelling (or what kind of evidence one may be willing to admit) is guided by one's metaphysics:
But [Philip Johnson and I] did talk much more about the whole question of metaphysics, the whole question of philosophical bases. And what Johnson was arguing was that, at a certain level, the kind of position of a person like myself, an evolutionist, is metaphysically biased at some level, just as much as the kind of position of let us say somebody, some creationist, someone like [Duane] Gish or somebody like that. And to a certain extent, I must confess, in the ten years since I performed ["performed"?], or I appeared, in the creationism trial in [Epperson vs.] Arkansas, I must say that I've been coming to this kind of position myself.*
Michael Ruse again:
. . .  I think also in the present, for many evolutionists, evolution has functioned as something with elements which are, let us say, akin to being a secular religion. . .  for Thomas Henry Huxley, I don't think there's any question but that evolution functioned, at a level, as a kind of secular religion. . . . I think Julian Huxley was certainly an atheist, but he was at the same time a kind of neo-vitalist, and he bound this up with his science. . . . it comes through very strongly that for Julian Huxley evolution was functioning as a kind of secular religion.  . . . I'm just saying this in a matter-of-fact sense -- I think that today also, for more than one eminent evolutionist, evolution in a way functions as a kind of secular religion. . . . in On Human Nature, [E.O.] Wilson is quite categorical about wanting to see evolution as the new myth, and all sorts of language like this. That for him, at some level, it's functioning as a kind of metaphysical system.*  
I think that the same postmodernist sympathies in Ruse that make him very interested in social constructivism in science also simply can't abide the idea that humans have some exalted status in the natural order.  Ruse (2010) expresses skepticism in Fodor and Piattelli-Palmarini's proudly professed atheism because he suspects that they "just cannot stomach the idea that humans might just be organisms, no better than the rest of the living world. " Maybe they are simply seeing what the "ancient mind" called "the image of God."   Hey, if it looks like a duck and walks like a duck ...

Is it ironic that Ruse is complaining that Coyne and his fellow ultra-Darwinian materialists are ripping on him for bucking against Scientism when Ruse's response to Jerry Fodor's similar transgression was to denounce Fodor as "wicked" for not realizing the possible ramifications of Darwin doubt on U.S. public policy?  (Ruse is a English conservaphobe at a Canadian school, mind you, in spite of the enormous role he has played in U.S. science politics.)

Is it ironic that Ruse can feel conflicted about having to censor his postmodern second-guessing of "science's" claim to ultimate truth because of the political implications, while publicly condemning Fodor for "giving creationists a piece of candy"?  Isn't this just one secular creationist crusading against another?

Epilogue:  I wrote "anticreationism" for the lack of a better word at the time.  I just noticed that this is a term that Ruse uses to describe the NCSE.*  I'll add here that I think Ruse is right to think that the New Atheists have put at risk (God bless 'em) the hitherto successful method of NOMA:  Religionists can go on claiming to know the meaning of life, and we scientists will decide what is real and what their children will be told is real.  (Sounds legit.)
That Pigliucci's accusations of conspiracy unwittingly extend to people on his own side constitutes, in my opinion, further evidence that his zeal against creationism (as understandable as it is) has generated in him an illegitimate negative bias against anything that is in any way associated with creationism.  Once again, I believe Pigliucci's strong dislike for creationism is well-founded, but it appears to have caused him to miss the point of The Design Inference, whether the point of the book turns out to be correct or incorrect.  - Mark Velutic [emphasis mine]



Tuesday, August 13, 2013

Dr. Daniel Shechtman: The Nobel Prize Winner Who Dared to Question the Consensus


http://intelligentdesign.podomatic.com/entry/2013-08-12T17_29_49-07_00

On this episode of ID the Future, host David Boze examines the plight of Dr. Daniel Shechtman, recent winner of the Nobel Prize in Chemistry who once suffered much rejection and ridicule for threatening the consensus of the scientific establishment. Listen in and consider the parallels between Shechtman's once-heretical science and the modern-day rejection and scorn of the ID movement.




Thursday, August 8, 2013

-------

Each command produces 5 results.

Choose where to locate the five results.

Most random commands will be mapped to READ.

Writes to addresses above 255 will be wrapped to the buffer.
Command code remainders above 32 will be assumed to be data.

Tuesday, August 6, 2013

fitness and lesswrong


*http://lesswrong.com/lw/1zu/compartmentalization_as_a_passive_phenomenon/
*http://www.jackscanlan.com/2011/01/dembskis-idea-of-complex-specified-information-is-ironically-unspecified/

*http://users.fred.net/tds///anti/william.dembski/
*http://schneider.ncifcrf.gov/paper/ev/dembski/
*http://schneider.ncifcrf.gov/paper/ev/dembski/claimtest.html
*http://schneider.ncifcrf.gov/paper/ev/dembski/rebuttal.html

fitness for free:
*http://www.godandscience.org/evolution/specifiedcomplexity.html

Monday, August 5, 2013

missouri

http://im-from-missouri.blogspot.com/2008/07/why-courts-should-stay-hell-out-of.html
http://evolutionnews.org/2006/06/intellectualconservativecom_re002375.html
http://scienceblogs.com/tfk/2007/11/11/the-salem-hypothesis-explained/
http://evolutionnews.org/2006/08/find_out_about_true_religion_a002567.html


http://firstthings.com/onthesquare/2013/08/the-anti-science-canard
http://nationalreview.com/human-exceptionalism/354642/no-society-should-not-allow-3-parent-ivf-wesley-j-smith
http://discovery.org/a/2735
http://discovery.org/scripts/viewDB/filesDB-download.php?command=download&id=1186