Even though I use search in an engineering context for my job, I recognized none of the terms used. Sure enough, all of the terms of art were coined by Dembski et al and if you do a Google search on “information conservation” or “software oracle” you find the rest of the computer science and engineering community is completely ignoring this supposedly groundbreaking work in the area of search. If you think search is not important, think Google. The footnotes for each of these terms refer to papers written by Dembski. Then when you looked at who cited these papers it’s the same people! It’s this kind of self-plagiarism that got Ward Churchill fired from the University of Colorado. While Churchill didn’t footnote his self-citations I seriously doubt most people would do what I did, running down the footnotes and searching for (often less than 10) citations in Google Scholar. The reason why many of us are so strident about peer review with ID is we get the sense that they are way too insular and don’t interact enough with the wider academic community. The result is the same paper gets published over and over again. This paper is no exception.

The thesis of the paper embodies a false dichotomy.

Algorithms that conduct even moderately sized searches require external assistance to be successful. When such an algorithm produces apparently impressive results, conservation of information [1-3], including the No Free Lunch Theorem [4-11], dictates we are faced with one of two possibilities. The first is that the search problem under consideration is not as difficult as it first appears. At times, the problems solved by seemingly complex algorithms can appear extremely difficult whereas a closer inspection reveals the search is relatively simple and, from a random query or exhaustive search perspective, has a larger probability of success than implicitly supposed. The other alternative, for difficult problems, is that active information has been inserted in the search program to increase the chances of success. 1

1 Formally, active information is defined as -log2(p/q) where p is the probability of success for an unassisted search and q is the probability of success for an assisted search. Informally, it is the amount of information added to the search that improves the probability of success over the baseline search.

Search is affected by more than the two factors of a trivial search or so-called active information. Computational complexity gives a way to judge search algorithms. In essence, the computational complexity of the algorithm tells us how fast it runs. This is expressed by so-called Big O notation. A linear search is O(n) and a binary search is O(log n). But that’s not the end of it. Search algorithms also need to have to be matched to a search space. Order log n search algorithms need the search space to be sorted or hashed. Think how long your Google search would take if it literally had to search every web page out there. In short, the search algorithm needs to fit the search space in order to be efficient.

Thus, the question in front of us is whether genetic algorithms can efficiently search for optimal protein binding. That’s what ev looked at. It showed that, yes, genetic algorithms do search such spaces efficiently and furthermore it disproved Dembski’s so-called law of conservation of information as the very paper cited by Dembski et al showed that information increased. But Dembski et al claim that the information increase came from some “help” given to the algorithm. Let’s see if that really is the case and go ad fontes (to the source code).

Here’s how the algorithm chooses between bugs.

/* begin module ev.score */
Static double score(w, width, creature, x, e)
wmatrix *w;
long width;
uchar *creature;
long x;
everything *e;
{
/* Evaluate the w matrix placed on the genome at position x.
Note: x+1 is the first base touched by the w matrix. That is, x is
the zero of the w, and the first base of the w is at x+1.
Note that the score function does not imply how the recognition
occurs. That is done by the recognize function. */
double realval = 0.0; /* the value of the site evaluated by w */
long integerval; /* the value of the site evaluated by w */
long l; /* index to w matrix */

if (!e->noise) {
integerval = 0;
for (l = 0; l matrix[P_getbits_UB(creature, l + x, 1, 3) - (long)a]
[l];
return integerval;
}
e->noise = false;
/* */
}

/* end module ev.score version = 2.50; (@ of ev 1988 oct 6 */

/*writeln(output,'in evaluate, bug: ',bug:1);*/
/* translate the recognizer gene into the w matrix */
translate(e, bug, 1L, &w);
/* scan the genome */
WITH = &e->p.creature[bug-1];
FORLIM = e->precalc.endscang;
for (x = 0; x p.width, WITH->genome, x, e);
if (P_getbits_UB(e->p.sitelocations, x - 1, 0, 3) != recognized)
m++;
}
/* record the results */
e->p.rank[bug-1][(long)bugid] = bug; /* identify the bug */
e->p.rank[bug-1][(long)mistakes] = m;
/*;writeln(output, 'bug ',bug:1, ' makes ',m:1,' mistakes');*/
}

Note how the perceptron is not part of the algorithm itself. It’s just a fitness function for the (fairly pedestrian) genetic algorithm which counts binding mistakes and does selection based on bugs that have fewer binding mistakes surviving more often than those who don’t. There was a special rule for ties that Dembski objected to in 2001. There are parameters in the code which turn that rule off. No “information” was added to the algorithm itself. Rather, when Dembski et al claim that the so-called Hamming Oracle and the perceptron add information they are in effect saying the fitness function adds information and not the genetic algorithm used by ev.

The success of ev is largely due to active information introduced by the Hamming oracle and from the perceptron structure. It is not due to the evolutionary algorithm used to perform the search. Indeed, other algorithms are shown to mine active information more efficiently from the knowledge sources provided by ev [13].

The question that should be asked is does the fitness function used in ev accurately model protein binding and does protein binding affect evolutionary fitness? If it does, then Dembski et al have just proven that natural selection adds active information along with disproving the conservation of information!

I’ll close with a description of the perceptron so that the reader can determine whether or not protein binding really is accurately modeled. Again note when Dembski made a comment on the code and the date of the paper we are discussing here. Perhaps the biologists here could comment on that more relevant question.

A population of evolving creatures is modelled. Each creature
consists of a genome made of the 4 bases. All creatures have a
certain number of binding sites, and the recognizer for the sites
is encoded by a gene in each genome. The genomes are completely
random at first. The recognizer of each creature is translated
from the gene form to a perceptron-like weight matrix. This matrix
is scanned across the genome. The number of mistakes made is
counted. There are two kinds of mistake:

how many times the recognizer misses a real site

and

What does this rule mean? It means that in a duel it is possible for two
bugs to have a tie. This is not an unreasonable result, and it frequently
happens in the natural world! What does removing the rule mean? It means
that the bugs will duel to the death, even if it is an arbitrary death!
Clearly this cannot affect the overall evolution, but it might slow things
down. Indeed it is interesting because it is often the case that in
fights the combatants are not killed.

There were three things that stood out with the R2K data:

1. There were too many pairs of even and odd numbers in the crosstabs. If a percentage of a male respondent was even then so was the female and the same was the case for an odd number. The odds that this would happen by random is 10^228. That’s right. 1 followed by 228 zeroes.

2. The variance between the weekly samples was too small. (9.947). A chi-squared distribution showed the odds of this happening via regular polling is 1 in 10^16.

3. There was insufficient week to week variation that was zero. There are too many times that the week-to-week variance was plus or minus one but not zero. This last one I want to focus on because it shows how our innate sense of what is “random” fails us.

First, let’s look at how Gallup’s tracking poll varies from week to week:

Now R2K’s weekly variance:

Note the “narrowness” of the R2K versus Gallup distribution. Now on to the psychology of trying to pretend to be random. On the TV series Numbers one episode showed how spatial distributions are too uniform to be random. The criminal in the story was trying to look like the crimes were in random locations but his human psychology betrayed him. There is an analogous issue here. See this 1960 study on generating a “random” sequence. What we do like the Numbers example is we have insufficient runs and clustering. It looks like 0100110110110101 and not like 1111100101111100000. We sense the repeated 1s and 0s don’t look “random” enough when in reality real random sequences act like that. Having the same approval or disapproval numbers between weeks doesn’t feel right so instead a small change one way or the other wrongly feels random. The same goes for large week-to-week jumps. Rigorous mathematical analysis shows, however, it’s not.

Intelligent Design uses the same “gut feel” rather than calculated statistics. They complain that the evolutionary process cannot be random. In the process of doing their “folk science” they make some very basic statistical mistakes.

Note Nick Matzke’s critique of Behe’s statistics of the odds of drug resistant malaria in Edge of Evolution:

Here again, Behe just assumes this. He gives no reasons in his book for why two binding sites would have to evolve *at once* anywhere in actual real-life evolution, which is the only reason you would multiply 10^20 by 10^20 to get 10^40 required organisms. In real life, evolution would most commonly evolve one binding site for one function, then the complex would sit around doing its function for awhile, and then occasionally another protein would evolve binding for some other function, or for improving the current function. It’s called exaptation — change of function in evolution — and it has been absolutely fundamental in evolutionary theory ever since Darwin.

The mistake is the assumption that the two random gene changes are statistically independent when they are not. The other “gut feel” that’s done by Intelligent Design proponents is that intelligent agency and “randomness” are mutually exclusive categories. As we see from the behavior of intelligent agents above not only is randomness not the antithesis of this, it’s required. We cannot rely on our flawed instincts. We have to do the math.

An Origins Parable

Over the years, there has been a great deal of blood spilled, or at least ink spilled, over the creation science and origins debates. What follows is an “intelligently designed” attempt to illustrate the differences between various positions on origins, using a somewhat humorous but generally accurate parable. This is presented in the form of position statements on the fictitious but highly controversial “embryology versus Bible” debate.

BACKGROUND

The science of embryology says that a baby is formed through natural processes, starting with the “conception” when a sperm cell joins with an egg cell. These two cells join their DNA and subdivide into multiple cells, which becomes a fetus. Over time, the fetus grows in size through cellular division, and various biological structures gradually develop into distinctive body parts. After approximately nine months, a normal pregnancy will come to full term, and the baby is born.

By contrast, the Bible declares that babies are made by God. Psalm 139:13-14 (NIV) declares, “For you created my inmost being; you knit me together in my mother’s womb. I praise you because I am fearfully and wonderfully made; your works are wonderful, I know that full well.” Also, “Thus saith the Lord, thy redeemer, and he that formed thee from the womb, I am the Lord that maketh all things” (Isaiah 44:24); and “Did not he that made me in the womb make him? and did not one fashion us in the womb?” (Job 31:15).

Does God create babies, or are they formed through gradual biological processes? The following statements outline various theological positions in this controversy.

ATHEISM / MATERIALISM

Babies are formed through purely natural processes of biological development. These processes can be studied and examined scientifically, and follow regular patterns of natural cause and effect. There is no reason to think that a divine being or miraculous intervention are required in order to help this process along. Physical matter is all there is, and nature is quite capable of getting the job done without the action of a god or gods.

NEW ATHEISM

Same as above, and anyone who still believes God is involved in the process of human birth is either a lunatic, an idiot, or both.

YOUNG EMBRYO CONCEPTIONISM (YEC) with APPEARANCE OF AGE and CATASTROPHISM

The godless embryologists tell us that babies are formed through naturalistic processes in the absence of God. This is known as “materialism”. They also mistakenly believe that babies are formed gradually over a process of many months, which is based on their naturalistic assumption of “uniformitarianism” – the belief that processes of biological development only take place uniformly and gradually. Yet they have no explanation for all the complex interactions that lead to the development of the various systems in our bodies.

Holy scripture, on the other hand, declares that God knits us together in our mother’s womb, and that He is the creator and maker of our physical bodies as well as our souls. Who are we to believe, human scientists with limited and incomplete knowledge, or God who knows all things and has declared Himself to be our Maker?

Since God is all-powerful, there is no reason to believe that He needed all those months and laborious activity in order to create a human body. Whereas secular, anti-Christian science declares that it takes nine months for a baby to form, the Christian assumption of “catastophism” says that things don’t have to necessarily happen slowly over long periods of time, but can actually develop quickly through a rapid succession of stages. New research indicates that babies may actually be formed in about ten seconds through a rapid process of development, not the nine months as generally assumed by materialistic scientists. All the presumed length of time and gradual steps of development over months of time, including the detailed history implanted in the memory of the mother, sonagram pictures, and doctor’s office records, actually just indicate an appearance of age and not actual age. God creates babies in ten seconds and implants a supernatural soul just before their eventual birth, but due to the effects of “appearance of age” it merely seems like it has taken place over a long period of time.

OLD EMBRYO CONCEPTIONISM (OEC)

The science of embryology is generally correct with respect to the physical sequence of the creation of babies, including the time of development from conception to birth, and the processes of fertilization, implantation, and gradual biological development. Yet science cannot explain exactly how the body of a fetus develops new body parts and internal organs, the development of the complexities of the eye, the circulatory and immune systems, etc. All they can do is presume that nature is capable of doing these things in the absence of God, without providing any sort of complete explanation.

Scripture provides the answer to these problems that continue to stump materialistic scientists. It says that God forms us in our mother’s womb, but it also says that God “fashions” us, using language similar to the working of an artisan, such as a potter. A potter uses raw materials such as clay and the spinning motion of a potter’s wheel, yet he imparts intelligent action at various points in order to shape the clay. In the same way, naturalistic forces and materials by themselves are unable to account for all the amazing complexity of the human body. God intercedes at various points during the process of fetal development in order to miraculously create elements of bodily function, yet in between times, He allows the natural process of biological development to proceed in normal fashion. Most notably is the injection of the human soul, which is an act of divine fiat and cannot be explained in naturalistic terms.

INTELLIGENT DESIGN (ID)

The intricate processes and systems in the human body are amazingly complex and cannot be accounted for in terms of materialistic assumptions. Systems such as the human eye, DNA, immune system, etc., have surprising levels of complexity and specificity which are best viewed in terms of information theory, using Shannon’s theorems. The degree of complex specified information (CSI) present in DNA and many other biological structures and systems are best explained as a designed system that originated from some intelligent source, rather than through a series of random, chance events.

Intelligent design is a scientific claim about design being evidenced by the information content, not a theological or philosophical claim. ID makes no claims as to the identity of the “intelligent designer” — it might have been from a God or gods, an alien, or possibly an intelligent stork that is capable of producing these designed features within an otherwise natural process. ID also makes no statement as to the length of fetal development — it could be ten seconds or nine months, but that conclusion is beyond the kind of scientific assertion that ID is able to make.

THEISTIC EMBRYOLOGY (TE)

The science of embryology is very well developed and has a great deal of accurate knowledge of bodily processes inherent in the development and birth of a child. While science cannot (and perhaps never will) have complete knowledge of every detailed step in this developmental process, the general conclusion that human fetal development occurs through essentially natural processes seems to be an inescapable conclusion based on the evidence at hand. There is no reason to assume that supernatural miracles are necessary in order to progress a fetus from one stage of development to another, and science continues to fill in gaps in our limited human knowledge as to the details of this process.

However, science is limited to studying only the natural, “secondary” causes and effects, and has nothing whatsoever to say about the presence or absence of a divine Creator. The belief in a divine Creator is a theological position, which is entirely justified based on the evidence, but which can neither be conclusively proven nor disproven by science. Among the evidences that point to a divine creator is the very fact that something exists rather than nothing, and the fact that life bears evidence of a beginning and progress toward a final end, rather than an eternal self-existence. As theists, we absolutely believe that God is the Creator and sustainer of all things, including fetal development, and that He is the “primary cause” of all things. The fact that He chooses to create human bodies through a progression of apparently natural, secondary causes is not surprising, because that is how all of nature appears to work from a scientific point of view.

Theistic Embryologists differ over the degree or manner of God’s involvement in fetal development. Some believe that God’s providence is universally and completely present within and through all things at all times, so that the development of a fetus is simultaneously the work of Providence (primary cause) and natural processes (secondary causes). Others prefer a view known as “front-loading” or “fully gifted conception”, which holds that God only needed to create the initial blueprint of how cells can fertilize, reproduce, and develop. After that, no more interventions or miraculous acts are required to progress the fetus through its development. TEs also differ on whether the soul is a supernatural creation that is implanted into the physical human body, or whether the soul is an emergent property of humankind.

Dr. Scott went out of her way to distinguish between religion and science. Surprisingly (to me), she from the outset made room for religion. When asked explicitly about her religious faith later in the Q&A, she distanced herself from the question and claimed that it had no place in this forum. This was a talk about science education and not about her private religious beliefs. It seemed clear to me that the questioner was pushing for a “Darwinian evolution leads to atheism” type position and Dr. Scott refused to go there. The talk was sponsored in part by a new student group at CSU, Leaders in Free Thought (LIFT), who were probably disappointed with all of this. I was glad to see it and it clearly set the tone of the rest of the talk. Given this I could have seen a local ASA chapter (not yet existent) or our CSU Christian Faculty Network help sponsor this talk.

Interestingly, during the panel discussion this thread was continued. The question of religious belief came up again and all of the panelists were quick to say that education about evolution had nothing necessarily to do with religious belief. One panelist was a self-admitted religious person but from a non-Christian perspective. During the panel Q&A a couple of apparent evangelical questioners asked about how the teachers handled or should handle students who were convinced young-earth creationists (YEC) or intelligent design (ID) advocates. Somewhat shocking to me, all agreed that the issue was not whether the students agreed with what they were being taught, but whether they understood the material. Frankly, I was pleased to hear this and was glad that public school educators respected the private opinions of their students and their families. Their goal was to teach science (at least the content side–there was a significant emphasis on the importance of teaching scientific methodology) as what scientists currently think.

There was a certain inconsistency, however, and I attempted to raise this in the Q&A time. I’m not sure I was clear, because the responses were somewhat generic. Both Dr. Scott’s talk and the panel began with a reference to surveys that indicated that most Americans don’t accept evolution and that this indicated a failure of American science education. The inconsistency that I see is that “accepting evolution” doesn’t seem to be the goal of science education if all that is important is that students understand what scientists think. Thus, the framing of the question is critical here. Is the question “Do you accept evolution?” or “Do you understand evolution?” The only answer I got was that in polls the framing of the question is critical.

I’d be curious about what ASAers think about this issue. Is the goal of science education (at least the content side) merely knowing what scientists think or is it accepting it as true (within the limitations that all scientific knowledge has a certain tentativity to it)? At what point in the science education or science practice process does the requirement that scientists accept the conclusions of science kick in? Granting of the Ph.D.? Granting of tenure? Peer review? Obviously, the answers differ depending on the institution and the nature of the research journal.

The title of Dr. Scott’s lecture was “Not Over After Dover” and was a review of the various court rulings forbidding the teaching of creationism and intelligent design in the public school. While in general I am not very sympathetic with demarcationist arguments and I’m not at all convinced that the current views of separation of church and state are the right interpretation of the Constitution, I was nearly in total agreement with the scientific arguments presented (critical of YEC and ID). Her clear definition of evolution, her distinction between common ancestry and various mechanisms of evolution, and her rebuttals of Dembski and Behe were all things that I agreed with and have used in my own presentations. In general, I would call NCBE a friend of ASA.

I had two pieces of advice for Dr. Scott.

1. That she recognize that the search for and recognition of intelligent agents is scientific. After all, her background is physical anthropology. Anthropology, archaeology, the search for extraterrestrial intelligence (SETI), forensics, etc. are all scientific. Social and human sciences all deal with intelligent agents. Admit it, and then explain why ID is different. When I mentioned this, her response was positive. Her explanation had to do with the identity and scientific accessibility of the designer. We recognize ID because we are familiar with designers that design similar things. All the disciplines mentioned follow that pattern. I think this is close to what Randy Isaac is getting at in his review of  Meyer’s Signature in the Cell (most recent post in that series). God as designer is unlike any designer we know. Not only is his handiwork designed, he upholds and controls the very substances things are made of, the laws that govern it all, and any evolutionary history that may have led to their being.

2. That she appeal to evangelical supporters of evolution (ASA, Francis Collins, Denis Lamoureux, B.B. Warfield, John Stott, perhaps Tim Keller, etc.). Appeal to Roman Catholic or even mainline Protestant thinkers, doesn’t really help convince an evangelical. The evangelical needs to see fellow evangelicals that they trust in order to move ahead here. Appeal to Catholic or possibly theologically liberal theologians does no good. Even appeal to ASA, Collins, Lamoureaux, and others willing to “give up” a historical Adam and Eve or a historical Fall will not be accepted. While I’m not questioning anyone’s evangelicalism in saying this, it is largely the case that once you have given up a historical Adam and Eve that many (maybe most) evangelicals will suggest that you have moved significantly in the direction toward the theological liberal. The fact that there are examples of thinkers on this issue who don’t do this (Warfield, Stott, Keller, myself, etc.) will enable some to accept evolution. Dr. Scott agreed with my assessment here but pointed out that her motivation was primarily to show that accepting evolution was not inherently atheistic. In other words, it was part of her setting the context that being pro-evolution is not to be anti-religious.