Wednesday, June 26, 2013

Black-box “optimization” is merely sampling

[Edit: The replacement is here at last. There have been many visits to this page since I retracted the post. I apologize to those who have been waiting.]

The main points of this post were correct, but the math contained some errors. I am working on a replacement.

Dembski’s perennial misconception of fitness

DiEb has begun a response to the latest morph of the creationist model of “search” (Dembski, Ewert, and Marks, “A General Theory of Information Cost Incurred by Successful Search” [pdf]). Here, slightly modified, is a rather general comment I made.

In the conventional “no free lunch” analytic framework, the objective (cost, fitness) function is a component of the problem. Dembski, Ewert, and Marks turn the objective function into an “oracle” that is part of the problem-solver itself. This model is inappropriate to most, if not all, of the evolutionary computations they purport to have analyzed.

Back in the 1990’s, Dembski committed himself to the misconception that Richard Dawkins’ Weasel program uses the fitness function in order to “hit the target.” Various people have tried, with no apparent success, to explain to him that one of the offspring in each generation survives because it is the most fit. The so-called target is nothing but the fittest individual.

To put it simply, the fitness function comes first. The “target” is defined in terms of the fitness function. Dembski gets this backwards. He believes that the target comes first, and that the fitness function is defined in terms of the target.

Dembski and Marks carry this to extreme in “Life's Conservation Law.” They claim that biological targets exist implicitly in nature, and that if Darwinian evolution “hits” them, then fitness functions necessarily have guided evolution. A remarkable aspect of this claim is that they treat fitness functions, which are abstractions appearing in mathematical models of evolution, as though they really exist.

The “search for a search” is another abstraction that they reify. A probability measure on the sample space is a mathematical abstraction. They merely assert that a search practitioner, in selecting a search, searches the uncountably infinite set of probability measures. To that I say, “Give me a physical description of the process.”

Thursday, June 6, 2013

Open access to Biological Information: New Perspectives

I previously raised an eyebrow at an editor of Springer’s “Intelligent Systems Reference Library,” in which the creationist volume Biological Information: New Perspectives (eds. Robert J. Marks II, Michael J. Behe, William A. Dembski, Bruce L. Gordon, and John C. Sanford) was scheduled to appear. The proceedings of the secret scientific symposium of scientists and “scientists”…

In the spring of 2011 a diverse group of scientists gathered at Cornell University with an eye on the major new principles that might be required to unravel the problem of biological information. These scientists included experts in information theory, computer science, numerical simulation, thermodynamics, evolutionary theory, whole organism biology, developmental biology, molecular biology, genetics, physics, biophysics, mathematics, and linguistics. Original scientific research was presented and discussed at this symposium, which was then written up, and constitute most of the twenty-four peer-edited papers in this volume.
… (did I mention science?) that took place at, but not under the auspices of, Cornell University have migrated to World Scientific. You can read the volume online, free of charge.

The big surprise is that “Section Four: Biological Information and Self-Organizational Complexity Theory” comprises two dissenting papers, one by Stuart Kauffman (whose views on many things are similar to my own), and the other by Bruce H. Weber. Although editor Gordon is none too clear on the matter in his introduction to the section, it appears that Kauffman and Weber actually contributed to a previous secret meeting, the proceedings of which were never published.

Their involvement in this project traces back to a 2007 conference I organized in Boston under the auspices of the Discovery Institute’s Center for Science and Culture. The conference commemorated the famous 1967 Wistar Symposium on “Mathematical Challenges to the Neo-Darwinian Interpretation of Evolution.” [...] The general perception among the participants in the Boston symposium, as with the participants in the Cornell University conference giving rise to this compendium, is that the mathematical and biological challenges posed to the modern evolutionary synthesis (neo-Darwinism) have not been resolved, but actually have grown more acute as our knowledge of molecular biology, cell biology, developmental biology, and genetics has exploded.
Gee, that sounds like “these guys are on our side.” But here’s the second half of Weber’s abstract:
Presently, however, there is ferment in the Darwinian Research Tradition as new knowledge from molecular and developmental biology, together with the deployment of complex systems dynamics, suggests that an expanded and extended evolutionary synthesis is possible, one that could be particularly robust in explaining the emergence of evolutionary novelties and even of life itself. Critics of Darwinism need to address such theoretical advances and not just respond to earlier versions of the research tradition.
So Gordon contradicts Weber while trying to paint him as an ally. He makes a fine point of the inadequacy of the “modern evolutionary synthesis (neo-Darwinism),” which is hardly where Darwinian evolutionary theory stands today. Kauffman highlights in his abstract the essential reason that the information measures of Dembski and Marks go nowhere in biology.
Biological evolution rests on both quantum random and classical non-random natural selection and whole-part interactions that render the sample space of adjacent biological possibilities unknowable.
I’ve heard him put it more simply: We don’t know the phase space. This means that it is impossible to assign probabilities to evolutionary trajectories. And taking logarithms of probabilities is how Dembski and Marks get information.

I wrote “scientists and ‘scientists’” above because only two of the five editors are scientists, and because engineers, computer scientists, and mathematicians have contributed heavily.

Unsurprisingly, about half of the “new perspectives” are variations on old themes of why evolution doesn’t work. John C. Sanford, a young-earth creationist who believes that genomes have been going to hell in a handbasket since the Fall of Man, authored seven of the papers and one of the section introductions. Dembski, Marks, MontaƱez and Ewert continue to bash evolutionary computation, including artificial life.

Jonathan Wells shocks us by reporting, “Not Junk After All: Non-Protein-Coding DNA Carries Extensive Biological Information.” Other papers show that the genetic code is fine-tuned, and furthermore that DNA sequences and computer code look much alike, with appropriate visualization. I’m sure there are other sensations to be found on closer inspection of the volume.

Sunday, February 17, 2013

Oppose the Scientific Education and Academic Freedom Act

The Common Education Committee of the Oklahoma House of Representatives will consider House Bill 1674 on Tuesday, February 19 at 10:30 a.m. Here I make it easy for Oklahomans who use a mail application to contact the committee members. Those of you who contacted the Senate Education Committee regarding the Oklahoma Science Education Act (Senate Bill 758) can quickly modify your note to apply to HB 1674. (Do please oppose SB 758, which has not yet been scheduled for consideration.)

The National Center for Science Education has provided background information on both the Senate and the House bills. The Oklahomans for Excellence in Science Education have analyzed HB 1674 [PDF].

My characterization of how the bills are related: SB 758 is essentially HB 1674 stripped of motivation, indications of legislative intent, examples of "scientific controversy," and the requirement that students learn what is in the curriculum. The author of HB 1674, Rep. Gus Blackwell, has in fact become a coauthor of SB 758.

House Common Education Committee

Clicking on a link below creates an email note that begins with a personalized salutation, e.g., "Dear Representative Coody." You need only paste in the rest of the note, and then send it. (Contact Rep. Blackwell only if you live in District 61.) Please be brief and respectful. Include your full name and street address.

HT: Oklahomans for Excellence in Science Education.

Dennis CaseyVice

Wednesday, February 6, 2013

Oppose the Oklahoma Science Education Act

Oklahoma’s Senate Education Committee will consider yet another “science education” bill introduced by Senator Josh Brecheen. Below, I make it easy to contact members of the committee. You can learn about the history of Senator Brecheen and the ancestry of Senate Bill 758 here. The Oklahomans for Excellence in Science Education provide an analysis, "Why SB 758 by Brecheen is a Bad Bill."

Synopsis of SB 758

The science curriculum addresses "scientific controversies." All school boards and administrators must

  1. try to help teachers find effective ways to teach about scientific controversies;
  2. try to encourage science students not only to engage in traditional learning, but also to "respond appropriately and respectfully to differences of opinion about controversial issues;" and
  3. permit teachers to instruct pupils in "scientific strengths and scientific weaknesses of existing scientific theories covered in the course being taught."
This has nothing to do with promotion of religion, non-religion, etc.


The phrases "scientific controversies" and "scientific strengths and scientific weaknesses of existing scientific theories covered in the course" appear in adjacent sentences, but the bill actually does not connect the two. The restriction in scope of "strengths and weaknesses" does not apply to "scientific controversies." Thus a teacher might regard "intelligent design vs. Darwinism" as a scientific controversy, even though intelligent design is not a theory covered in the course. There is no "scientific" qualifier of the "controversial issues" on which students have "differences of opinion." A teacher might feel compelled to allow debate after a student brings up creationism.

The bill neither defines nor identifies "scientific controversies," but asserts that the science curriculum already addresses them, and requires that administrators help teachers present them effectively. This shrewdly establishes that teaching effectiveness is an issue. Administrators may evaluate teachers on their handling of "scientific controversies," as well as their moderation of student debate. Thus administrators have the power to identify controversies that an effective teacher should address, and also the power to specify that effective teaching of them requires presentation of certain "strengths and weaknesses" of theories.

Teachers are free to impose nonstandard "strengths and weaknesses" instruction on students, even in cases where administrators do not recommend it. Although a principal might respond legitimately by assigning a low performance rating to a teacher, the legal risk in doing so would be high. Then again, the teacher might also place the local school district at risk of lawsuit. If enacted, the bill would put some school administrators between rocks and hard places.

The guts of the bill

The five paragraphs of Section 2 contain the substance of the bill. I have quoted them here, and added emphasis.

A. The State Board of Education, school district boards of education, school district superintendents and school principals shall endeavor to create an environment within public school districts that encourages students to explore scientific questions, learn about scientific evidence, develop critical thinking skills and respond appropriately and respectfully to differences of opinion about controversial issues.
Start by requiring public schools to do what they already are required to do, and in fact do. Then indicate that civil debate of "controversial issues" belongs in science class. The omission of scientific here must be intentional, as repetitiously as it is used elsewhere.
B. The State Board of Education, school district boards of education, school district superintendents and school principals shall endeavor to assist teachers to find effective ways to present the science curriculum as it addresses scientific controversies. Teachers shall be permitted to help students understand, analyze, critique and review in an objective manner the scientific strengths and scientific weaknesses of existing scientific theories covered in the course being taught.
Posit that the curriculum already addresses "scientific controversies," without making it clear what they are. Open up opportunity for school boards and administrators to change instruction top-down, and for individual teachers to make radical changes at the classroom level.
C. Neither the State Board of Education, nor any school district board of education, school district superintendent or school principal shall prohibit any teacher in a public school district in this state from helping students understand, analyze, critique and review in an objective manner the scientific strengths and weaknesses of existing scientific theories covered in the course being taught.
"This means you!"
D. This section only protects the teaching of scientific information and shall not be construed to promote any religious or non-religious doctrine, promote discrimination for or against a particular set of religious beliefs or non-beliefs or promote discrimination for or against religion or non-religion.
"Ignore that creationist behind the curtain. We are the mighty Legislature!"
E. By no later than the start of the 2013-2014 school year, the State Department of Education shall notify school district boards of education and school district superintendents of public schools in the state of the provisions of this act. Each school district board of education and school district superintendent shall notify all employees within the school district of the provisions of this act.

"Glad tidings to all — nurses, cooks, and janitors!"

Senate Education Committee

Clicking on one of the links below creates an email note that begins with a personalized salutation, e.g., "Dear Senator Ford." (Contact Senator Brecheen only if you live in his district.) You need only paste in the rest of the note, and then send it. Please be brief and respectful. Include your full name and street address.

Thanks to Oklahomans for Excellence in Science Education for supplying the contact information.

Gary StanislawskiVice