Showing posts with label Schneider. Show all posts
Showing posts with label Schneider. Show all posts

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.

Sunday, October 13, 2013

The Whistling Herring

 "He eteþ no ffyssh But heryng red."

The dialogue's not perfectly accurate but is more or less the MirrorMask version of an old Yiddish joke:
What’s green, hangs on a wall, and whistles?
Gryphon: I give up, I think, no wait, wait… Fine. What’s the answer?
Helena: Okay. It’s a herring.
Gryphon: But a herring isn’t green.
Helena: You can paint it green.
Gryphon: But a herring doesn’t hang on a wall.
Helena: You can nail it to a wall.
Gryphon: But a herring doesn’t whistle!
Helena: Oh, come on. I just put that in to stop it from being too obvious.
This puts me in mind of Dembski's tractability condition.  (In more recent developments of algorithmic specified complexity, the tractability condition is built in as a feature of randomness deficiency.)  Even if it's true that a herring can be green because of paint, and even if it can be made to hang on a wall, the effect is to include anything that can be painted green and hung on a wall.  These increase the specificational resources of the target space so that it's no longer specific.  I can paint a squirrel green and stick it on the wall.  Or a carrot.  Or a handkerchief.  Which is precisely the joke. Once I include things that aren't normally, typically green, as well as things that don't typically, normally hang on a wall, the riddle becomes intractable.   

Thursday, September 5, 2013

Another blogger's thoughts on the _ev_ program

I forget whether I had already logged godandscience's thought-provoking article:

    http://www.godandscience.org/evolution/specifiedcomplexity.html

I also thought Dembski's point about ev's handling of the equality condition seemed relatively weak, but I've had some other thoughts on that since.  I have since had the feeling that the treatment of ev was a late decision in the development of Dembski's book, and he had the choice of either quickly shoehorning something about it into his book or deal with the postings that the book was sadly behind the times since there exist papers in which simulations are purported to create information.

Like the mound of papers theatrically stacked in front of Behe in Judge Jones' courtroom, there are constant allegations of refutations and counterexamples.

I'm less sure that ev demonstrates something real about the biological world, though the more I've thought about the less sure I am what exactly it does demonstrate.  (I think I know what Schneider was attempting to simulate, but that is a different question ultimately from what was actually demonstrated.)


Wednesday, September 4, 2013

Schroeder complexity


Schroeder claims that bit strings formed from random coin tosses, most probably, will have zero information content zero.  I'm not sure how he can argue that unless he happens to known the receiving machine in question.

But, taken very generally, it is an interesting question to ask, I think: what is the minimum Kolmogorov complexity of a message that would be recognized as a valid proof of Godel's Incompleteness Theorem (in English)?  Once you figure out a number, call that number N.

What would Schroeder assess the average Shannon complexity of the shorter such proofs to be?  (Schroeder thinks exclusively in terms of Shannon complexity.)  Would it be more than N?  Does it make a difference that state change from not understanding the theorem to comprehending the truth of the proof results from a relatively small set of messages, even among the set of all proofs.

Now, what is the probability that of a randomly generated bitstring N bits long can be decrypted (or creatively recrypted) into one of these proofs using a decryption algorithm with Kolmogorov complexity less than N/4?

What, then, is the problem with claiming that specified complexity is a reliable empirical marker of intelligence? The problem isn't that establishing specified complexity assumes the form of an eliminative argument. Nor is the problem that specified complexity fails to identify a causal story. Instead, the problem is that specified complexity is supposed to miscarry by counterexample. In particular, the Darwinian mechanism is supposed to purchase specified complexity apart from a designing intelligence. But does it? [from here]

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