"Searching Large Spaces: Displacement and the No Free Lunch Regress" (March 2005) is a math paper by William Dembski which suggests that the source of assisted searches cannot be explained by stochastic mechanisms:

The No Free Lunch Regress, by demonstrating the incompleteness of stochastic mechanisms to explain assisted searches, fundamentally challenges the materialist dogma that reduces all intelligence to chance and necessity.

One minor quibble with the paper: When one does an assisted search (using hill climbing or genetic algorithms), one does not usually care to find the optimal solution. Instead, the goal is to find the local maximum that can be best achieved given the resources. Thus, the target space can potentially be bigger. Other than this quibble, I think the paper was pretty good.

Update: Dembski has recently written an accessible article titled "In Defense of Intelligent Design."

"Do Centrioles Generate a Polar Ejection Force?" (pdf abstract here) is a paper by Jonathan Wells which speculates that centrioles function like little turbines. One interesting thing about this paper is that its underlying assumption is intelligent design:

Instead of viewing centrioles through the spectacles of molecular reductionism and neo-Darwinism, this hypothesis assumes that they are holistically designed to be turbines. Orthogonally oriented centriolar turbines could generate oscillations in spindle microtubules that resemble the motion produced by a laboratory vortexer.

The full paper is available from Rivista di Biologia.

In the next few days, I will post some papers that I have recently skimmed through that relate to the issue of origins. Thanks to the bio grad student who brought some of these papers to my attention.

"Chance and necessity do not explain the origin of life" (Nov 2004), by J.T. Trevors and D.L. Abel, is a paper that points out the current shortcomings of the idea of abiogenesis. I found this to be an interesting read since a comparsion is made between life (DNA/RNA) and some computer concepts, like operating systems and instruction sets. The paper asks a lot of tough questions:

How did inanimate nature write

(1) the conceptual instructions needed to organize metabolism?

(2) a language/operating system needed to symbolically represent, record and replicate those instructions?

(3) a bijective coding scheme (a one-to-one correspondence of symbol meaning) with planned redundancy so as to reduce noise pollution between triplet codon‘‘block code’’ symbols (‘‘bytes’’) and amino acid symbols?

We could even add a fourth question. How did inanimate nature design and engineer

(4) a cell [Turing machine? (Turing, 1936)] capable of implementing those coded instructions?

The tone of the paper seems to be authoritative rather than cautious. Consider the conclusion:

New approaches to investigating the origin of the genetic code are required. The constraints of historical science are such that the origin of life may never be understood. Selection pressure cannot select nucleotides at the digital programming level where primary structures form. Genomes predetermine the phenotypes which natural selection only secondarily favors. Contentions that offer nothing more than long periods of time offer no mechanism of explanation for the derivation of genetic programming. No new information is provided by such tautologies. The argument simply says it happened. As such, it is nothing more than blind belief. Science must provide rational theoretical mechanism, empirical support, prediction fulfillment, or some combination of these three. If none of these three are available, science should reconsider that molecular evolution of genetic cybernetics is a proven fact and press forward with new research approaches which are not obvious at this time.

If you are a UCI student, you can access the rest of this paper at a UCI computer. Go to the UCI library site, do a search on Cell Biology International, and then go to the November 2004 issue (Volume 28, issue 11). You can also view this from home by establishing a "UCIFull" VPN and then following the same instructions.

I recently received an email from the owner of the Apologia Project web site. He informed me that his site has some video resources relating to intelligent design. Check it out if you are interested.

• Telic Thoughts has a post about causal consciousness.
• Jay Richards at IDTF tackles the question: "Who designed the designer?"
• A mathematician at UCI writes an article for the Daily Pilot, titled "Evolution a good reason to study science." I agree with his assertion that classroom discussions are much better than lectures. Many students would be interested in discussing the issue of origins in a balanced way.
• UCI researchers find that the brain contains certain chemicals, called endocannabinoids, that suppress pain during stressful moments. They are trying to create a new class of pain-killing drugs that builds on this effect. Read the press release at Today at UCI. Perhaps this robustness in the brain was a product of design?

UCBerkeleyNews has an intriguing interview with Nobel Prize winner Charles Townes, a physicist (hat tip: IDTF). Like Fred Brooks (see my previous post), Townes seems to adhere to both evolution and intelligent design. Here is an interesting quote from the interview:

Intelligent design, as one sees it from a scientific point of view, seems to be quite real. This is a very special universe: it's remarkable that it came out just this way. If the laws of physics weren't just the way they are, we couldn't be here at all. The sun couldn't be there, the laws of gravity and nuclear laws and magnetic theory, quantum mechanics, and so on have to be just the way they are for us to be here.

Some scientists argue that "well, there's an enormous number of universes and each one is a little different. This one just happened to turn out right." Well, that's a postulate, and it's a pretty fantastic postulate — it assumes there really are an enormous number of universes and that the laws could be different for each of them. The other possibility is that ours was planned, and that's why it has come out so specially. Now, that design could include evolution perfectly well. It's very clear that there is evolution, and it's important. Evolution is here, and intelligent design is here, and they're both consistent.

I wrote a post about Fred Brook's view on subcreation a couple of days ago. After writing that post, I went to his site again and found a more intriguing lecture, called "The Design of Design". Brooks gave this lecture when he received the 1999 A.M. Turing award. This award is generally regarded as the highest award that a computer scientist can receive; thus, it is often called the "Nobel Prize in Computing." Ninety five percent of the lecture had to do with design methodology in the context of software engineering in a collaborative context. However, his concluding remarks were relevant to the issue of origins. I have transcribed his closing remarks (note that I may have introduced some unintended transcription errors):

I cannot talk about great designers without saying a few words about the great Designer. If you want to see His monument, look around you. I have spent some years working with biochemists in molecular graphics and watched them over the years untangle the structure and function of superoxide dismutase, a little globular protein (called an anti-aging protein) that in every living creature neutralizes the superoxide ions, the products of metabolism which are damaging. Well, superoxide dismuatase is kind of a round globby thing. It has a little crack in it, and the crack is just wide enough that the superoxide ion can get through it down to the active site and no bigger ions can. The charge is distributed on this thing so that it creates a hemispherical electric field that any charged superoxide ion going by is pulled into this crack. Two of these things are bolted together back to back: one scavenging in front, and one scavenging in back. And I can go on and on, and I won’t.

One cannot prove the existence or activity of God by the argument from design, as medieval scholars tried to do. But as a designer with a lifetime of looking, I’m here to testify that what I see in nature all around, from the galaxies down to the molecules, has all the hallmarks of a design and not just a blind process. And I think that any open minded person has to consider that possibility and the evidence for it.

Now you ask, "Well, what about evolution?" I’m comfortable with the processes of mutation and natural selection and so forth. I observe that good programmers don’t write sorts -- they write sort generators. And it seems to me perfectly natural that Jesus Christ when He made all things made mechanisms for making things. So I’m not a seven-day creationist, but I am firmly convinced that what I’m seeing around me is designed.

But surely the hardest problem is the human paradox. I know right from wrong. At least if I see Jack do wrong to John, I know that that’s wrong, even though I may not see it if I’m doing it. And yet, even though I know right, I do wrong. That’s the human paradox. I feel guilt; I want to atone; I desire to worship. Understanding these things is the mystery of design. Well this is neither the time nor the place to go into this marvelous story. But I would conclude by telling you [that] making things [and] doing design is fun. Technology is fun and it is important, and we are proper to devote our energies to it. But the knowledge that matters most is knowing the great Designer who made us and who loves us. Thank you. [Long applause]

As I was perusing an elementary database book ("SQL for Dummies" by Allen Taylor), I came upon an interesting sidenote about database structure. Since life, and particularly the DNA, contains a lot of information, perhaps some database principles can be extracted from biology. Anyways, here is the sidenote:

The value is not in the data, but in the structure

Years ago, some overly clever person calculated that if you reduce human beings to their components of carbon, hydrogen, oxygen, and nitrogen atoms (plus traces of others), they would be worth only 97 cents. However droll this assessment, it's misleading. People aren't composed of mere isolated collections of atoms. Our atoms combine into enzymes, proteins, hormones, and many other substances that would cost millions of dollars per ounce on the pharmaceutical market. The precise structure of these combinations of atoms is what gives them that value. By analogy, database structure makes possible the interpretation of seemingly meaningless data. The structure brings to the surface patterns, trends, and tendencies in the data. Unstructured data - like uncombined atoms - has little or no value.

Commencement ceremonies are taking place this weekend at UCI. Many friends are graduating this year, including some who attended the first iDesign meeting. I watched the ICS graduation this afternoon in the Bren Events Center, and I took several pictures of the event. It was interesting to see the UC seal which prominently bore the motto, "Let there be light." You can see the seal in the first picture below. Hmm... I wonder where they got that phrase from? Anyways, the graduation turned out to be a good event as always. Congratulations to the class of 2005! Come back to UCI when you have a chance and drop by for an iDesign meeting!!

Fred Brooks is well known for his book, The Mythical Man-Month, and for his No Silver Bullet article. That material was required reading in one of my software engineering classes. I made a brief note about man-months in my previous post, and while I was looking through the Internet, I found an interesting article by Brooks. Actually, it was an acceptance lecture for an ACM award. I found a passage on subcreation interesting. Contrast this view of subcreation with the view presented in the TCS article in the previous post. Here's a small excerpt:

Making things has its glories and joys, and they are different from those of the mathematician and of the scientist. Let us reflect together on these in a fundamental way.

The creation account in Genesis 1-2 is marvelously rich and subtle, and it can be read on many levels. I am not myself a seven-day creationist, but I take the account very seriously. It reports that our maker gave humanity seven incredibly splendid "birth-day" gifts. Pondering the list, we see the satisfactions of our deepest longings and the provision of our greatest joys (see Figure 1). Here, I want to focus on the last, the gift of work, of the capability and the call to make things.

J.R.R. Tolkien, author of the epic Lord of the Rings trilogy, spent his life building a rich fantasy world with its own laws, species, languages, and geography. He calls this creativity the gift of subcreation, and he illuminates it in a poem peculiarly relevant to the graphicists' craft [5]:

Although now long estranged,
Man is not wholly lost nor wholly changed,
Dis-graced he may be, yet is not de-throned,
and keeps the rags of lordship once he owned:
Man, Sub-creator, the refracted Light
through whom is splintered from a single White
to many hues, and endlessly combined
in living shapes that move from mind to mind.
Though all the crannies of the world we filled
with Elves and Goblins, though we dared to build
Gods and their houses out of dark and light,
and sowed the seed of dragons—’twas our right
(used or misused). That right has not decayed;
we make still by the law in which we’re made.

Tolkien applies this idea especially to the creation of fantasy, and fantasy worlds; I follow the English writer Dorothy Sayers in applying it to all human making [4].

A little reflection shows us that the power to make things, in imitation of our Maker, is a gift for our sake, not his. As he scornfully reminded the people of Israel, he doesn’t need our creative powers:

“The cattle on a thousand hills are mine; if I were hungry, would I ask you?” [Psalms 50:12].

So we must conclude that the ability and the call to create are given to us to enrich our lives and to enable us to enrich each other.

As I noted in a previous post, Tech Central Station has an interesting article which is critical of intelligent design. The author recycles some standard evolutionist points (like ID == religion, ID's simplicity would stifle the scientific quest, etc.) and then presents what he calls "Scientific Intelligent Design," which he defines as the process of intelligently creating artificial life (using robotics, AI, etc) or augmenting existing life (transhumanism). The article concludes by saying that humans are really the intelligent designers. Let me point out a few things I liked and disliked.

No serious scientist believes the literal Biblical creation account, but many earnest and well-credentialed scientists do believe in Intelligent Design (ID), as a perspective on evolution. And ID, of course, is religiously inspired.

The author begins with an inaccurate overgeneralization of all those who believe in Genesis (for counterexamples, see people like Damadian, Carson, or the late Wilder-Smith). However, the author makes up lost ground with his honest acknowledgement that many scientists hold to ID. There are probably more ID sympathizers in the universities than we will ever know about. If we took a random poll of university professors, I estimate that 20% would at least give ID a fair hearing. The article then makes the inaccurate mapping of evolution => science and ID => religion. Actually, evolutionism (more broadly, naturalism) and ID are two interpretations of the same scientific evidence and both have metaphysical implications. It is simply not good science to automatically rule out design as a possible explanation for life's origin and diversity.

But it's a fallacy to argue that just because one person -- or even all the people of an era -- can't figure out how something works, therefore such mysterious workings are beyond any human comprehension, ever.

So the author is arguing that just because we can't figure out how some evolutionary processes work, that doesn't mean that we will never figure it out; thus, we should never resort to design as an explanation. However, this is a non-sequitur, since design is automatically ruled out from the beginning. An analogy might help. Right next to my computer is a TI-89 calculator. The TI-89 is probably one of the most useful computational tools that a student can have. Suppose I tried to detail the very origin of this calculator, and I constrained myself to non-design explanations. Is it a fallacy to state that a non-design explanation for the origin of a TI-89 is beyond human comprehension, ever? No. Now think of all the biological structures that are more complex and more elegant than a calculator. If after millions of dollars of research money and thousands of GSMM (graduate student man-months), we still cannot figure out the evolutionary pathway to complex biological structures, maybe we should reconsider the framework altogether. By the way, a "man-month" is the amount of work done by one person in one month.

And that's the problem with ID: it's simplistic. To argue that complex biological phenomena are "irreducibly complex" is to abandon the scientific quest.

Actually, many fields implicitly assume design without giving attribution. For example, artificial neural networks are based on a biological proof-of-concept: the brain. One of my professors, who is a evolutionist, once commented about how God must know linear algebra, since the networks in the brain can be modeled with matrix calculations. If some part of a biological structure is mysterious, an implicit assumption in biology is that there is some hidden purpose or functionality in that biological part that is waiting to be discovered. Design assumptions are implicitly made on a daily basis in biology. Thus, design actually furthers the scientific quest.

But whatever the motivations, from all directions, SID ["Scientific Intelligent Design"] is coming. In hardware, it's coming. In software, it's coming. And in wetware -- including the hot-button issue of stem cells from -- it's coming.

So he states that a revolution is coming in areas like AI and cloning. Here is where this article makes an unintended argument for intelligent design. The article acknowledges that human intelligence is used to design artificial life. But artificial life, a term that I am using loosely, is nowhere close to the complexity, power, and efficiency of real life. Robots cannot match the dexterity of your hands or your eyes or your feet.

Recently, I finished a small Matlab project on face recognition for one of my classes. I tried to get Matlab to classify different facial expressions. The project caused me to realize that humans have the innate ability to pick up the slightest facial cues to detect emotions. To test this out, go to a mirror and make a sad face. Then make a neutral face. There is very little difference in those two expressions, yet most humans can discriminate between the two. It is very hard for a computer to have this sort of discriminatory power.

So in remarkably similar fashion to my duck argument, I present another intuitive argument:
1. Actual life (including bugs, ducks, and humans) is currently more efficient, powerful, and complex than artificial life (robots, AI, etc).
2. If X is more efficient, powerful, and complex than Y,then probably more intelligent input went into the formation of X than Y.
3. A significant amount of intelligent input is needed to make artificial life.
4. A more significant amount of intelligent input is needed to make actual life.

Finals is this week! I know that I promised to write a post about the TCS article, but that will have to wait. Dembski has a post about transhumanism here (BTW, he also plugged the iDesign blog a week ago, thanks!). Telic Thoughts also wrote about the issue here.

Hope everyone does well on finals! "Chance favors the prepared mind."

Here is a collection of current news and opinion pieces, in no particular order:

• The Daily Pilot has an opinion piece on the debate over whether or not to teach ID in public schools.
• WorldNetDaily has a news article that details the Smithsonian's backtracking of its sponsorship of the private showing of the Privileged Planet documentary. The National Center for Science Education (a pro-evolution group) has posted a critical review of the Privileged Planet Hypothesis. He Lives has posted a critical review of the NCSE's critical review of the PP Hypothesis. You can view a short web clip of PP.
• Tech Central Station has an interesting article about who the real intelligent designers are. While this article is well-written, there are a couple of fallacies to address, which I will do in my next post.
• UCI engineers create world's fastest method for transmitting information in cell phones and computers. Read the full Today at UCI article.

Let us take a minute to ponder the graphic that is on top of this blog. I have enlarged it here:



This fountain is situated in the physical sciences niche on campus, between Reines Hall and Rowland Hall [lengthy historical sidenote: these buildings were named after two of UCI's Nobel Prize winners who got the award in the same year, making UCI the first public university to win two NPs in separate areas in one year]. This fountain is shaped in such a way that it distributes water into an infinity figure, when you look at it from an aerial perspective. Also notice the two ducks who have decided to take over this pond. I just happened to have a digital camera on me the day I saw this picturesque scene.

Now here comes my intuitive (a.k.a. hand-waving) argument for design:
1. This fountain is elegant and complex.
2. The ducks are more elegant and more complex than the fountain.
3. If X is more elegant and more complex than Y, then X is more likely to be designed than Y.
4. The fountain was likely to be designed.
5. The ducks were more likely to be designed.

Our first iDesign meeting went well today. Thanks to all who showed up. Here are the presentation slides in htm format. A bio student made a good point in the meeting: that a distinction should be made between abiogenesis and Darwinian evolution. Darwin's theory, which assumes that a reproductive organism already exists, mainly attempts to account for the diversity in life. So instead of dichotomizing the different explanatory modes into Darwinian evolution/intelligent design/creationism, perhaps it is better to have the classification of naturalism/intelligent design/creationism. However, I think that it is still okay to label the naturalistic explanation as Darwinism, because most people use these terms interchangeably.



We also had an interesting discussion regarding the nature and very definition of science. Does science == naturalism (or physicalism)? Science is the study of the natural world, but that doesn't mean that we have to automatically reject design as an explanation for the origin of natural structures. Also, another thing we discussed was whether or not ID is testable (or falsifiable).

You can watch a web clip of the Privileged Planet documentary, which makes the case for cosmological ID. Unlocking the Mystery of Life makes the case for biological ID.

If you missed this meeting but are still interested in joining the club, please contact us. We will be planning events for the 2005 fall quarter.

Here is the flyer on campus:

The iDesign blog is now up and running! The plan is to have multiple UCI students/faculty posting on this blog. If you are a UCI student or faculty member who is interested in the issue of origins, please consider joining this brand new club on campus. Send me an email at idesignclub 'at' gmail 'dot' com. I will definitely maintain confidentiality if you request it.

Another note: we need speakers for the 2005-2006 school year. If you know anybody in the UC community who would like to come to an iDesign meeting at UCI to speak on origins, let me know. Also, if you have general suggestions for the club or for this blog, feel free to send them to me.