During our meeting yesterday, someone asked whether any peer-reviewed work exists that supports intelligent design. I think that the ID community still has a lot of work to do in this regard. I mentioned some pieces that are either friendly to the notion of design or skeptical of blind evolutionary processes. Here are the links to those pieces that I mentioned:

• "The Design Inference: Eliminating Chance Through Small Probabilities." William Dembski. Cambridge Studies in Probability, Induction and Decision Theory, 1998.
• "Chance and necessity do not explain the origin of life." Trevors J, Abel D. Cell Biology Int., 2004.
• "The origin of biological information and the higher taxonomic categories." Proceedings of the Biological Society of Washington, 2004. This paper was subsequently recalled and the editor of the journal, Richard Sternberg, got into trouble.
• I also mentioned an article that attempts to refute Michael Behe's notion of irreducible complexity: "Evolution of Hormone-Receptor Complexity by Molecular Exploitation." Bridgham J, Carrol S, Thornton J. Science, 7 April 2006. This study prompted an editorial in Science: "Reducible Complexity" by Chris Adami. The existence of these works suggests that irreducible complexity is a scientific idea that is falsifiable. Here is Michael Behe's response and here is Paul Nelson's response to that Science article..

Along with the New University, the Daily Pilot wrote an article about iDesign's "Colloquium on Origins" event a couple weeks ago. It is more focused towards the perspective of the faculty who represented evolution.

That article is also in the news section of the Physical Sciences web site.

This afternoon, I was able to attend a talk by Marvin Minsky, who is one of the fathers of artificial intelligence (AI). Minsky's topic was on the nature of intelligence and its implications for AI. Minsky made some interesting points:

• He argued that it is better for AI researchers to focus on endowing computers with intelligence rather than working on areas like robotics or rule-based systems.
• Minsky suggested that "consciousness" does not really exist as a unit and that "consciousness" is simply a collection of many different processes in the brain that can eventually be figured out. I do not agree with Minskey on this point.
• He also suggested that genetic algorithms are mediocre and that the process of evolution is not smart by nature. When discussing the circuitry and organization in the brain, Minsky said that evolution will stoop to any level to get things done.
• Minsky also argued that the concept of "interior grounding" (which suggests that knowledge can be innately gained) is superior to the concept of "grounding in experience" (knowledge gained through contact with the outer world). He suggested that "interior grounding" can explain the innate Chomsky grammars in humans.

Minsky's talk was very interesting, and I'm glad that he came to UCI.

One can view the complexity of the brain (and the mystery of consciousness) through the evolutionary lens and through the lens of intelligent design. In my opinion, the design lens seems to give a more coherent and satisfying picture.

The screening of the documentary was great! It was a much smaller group than the colloquium, but it allowed for an interesting hour-long discussion time at the end. Professors and students came and some made some interesting criticisms and comments about intelligent design. Thanks to all who came!

If you wish to watch "Unlocking The Mystery Of Life" online, you may do so here (Real Player required).

"Unlocking The Mystery Of Life" is tonight! It is at 6:00 PM in Howard Schneiderman Lecture Hall (HSLH 100). Please plan to arrive early, because walking to HSLH 100 could take 15 minutes. Please consult the map.

For help or more information, please call Andrew at (714) 624-7335. HSLH 100 is right next to the B.C. Caverns restaurant and close to the Science Library as well. Hope to see you there!

iDesign @ UCI is proud to present the following documentary about biological intelligent design:

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Title: Unlocking The Mystery Of Life: The Scientific Case For Intelligent Design

Date: Thursday, May 25, 2006

Time: 6:00 PM

Location: Howard Schneiderman Lecture Hall (HSLH 100)

Admission: Free (but parking is $7)

Running Time: 1 hour

Who is Invited: Everyone

Preview of Documentary: Here

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Back Cover Description of Documentary:

In 1859, Charles Darwin published, "On the Origin of Species." In it, he argued that all of life on earth was the product of undirected natural processes. Time, chance, and natural selection.

Since Darwin, biologists have relied on such processes to account for the origin of living things. Yet today, this approach is being challenged as never before.

"Unlocking the Mystery of Life" tells the story of contemporary scientists who are advancing a powerful but controversial idea -- the theory of intelligent design.

Using state-of-the-art computer animation, "Unlocking the Mystery of Life" transports you into the interior of the living cell to explore systems and machines that bear the unmistakable hallmarks of design. Rotary motors that spin at 100,000 rpm. A biological information processing system more powerful than any computer network. And, a thread-like molecule that stores instructions to build the essential components of every living organism on earth.

This compelling documentary examines an idea with the power to revolutionize our understanding of life...and to unlock the mystery of its origin.

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Map for Visitors:

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I highly encourage everybody who is interested to come! This event is free and open to the public. Even if you have watched this documentary before, the experience will be different on a big screen. It was actually this documentary that kindled my own interest in intelligent design. Everybody is invited!

Pick up this week's New University newspaper -- the paper did a great job of covering our "Colloquium on Origins: Evolution & Intelligent Design" event last Wednesday. Here is a link to the article, titled "Evolution or Intelligent Design?" Here are some relevant clips from the article:

By consisting of presentations from both the intelligent design and evolutionary perspective, a discussion panel and a Q-and-A session, the colloquium successfully demonstrated an effective way to further the understanding of both origin theories, “allowing students to hear balanced presentations of intelligent design and Darwinian evolution from experts on both sides,” Asuncion said.

...

However, what can be said for sure is that the colloquium was an excellent way for the UCI campus to address the debate between evolution and intelligent design.

Last Saturday's Undergraduate Research Symposium, themed "Let There Be Light," was a great event. Here is coverage from the New University. I was amazed at some of the posters and presentations made by my fellow undergraduate students. Congratulations to all who participated!

I attended Biola University's "Intelligent Design Under Fire" event last Friday. The main issues that were brought up were irreducible complexity, the rules of science, and consensus in scientific circles. I was able to greet Dr. Michael Behe (author of "Darwin's Black Box") after the event. I also wanted to greet Antony Flew (the famous former athiest), but he left before I could get to him. In any case, it was an interesting and civil discussion.

The main point that resonated throughout the audience was that if scientists could publish scientific arguments against Behe's notion of irreducible complexity (e.g. "reducible complexity"), then Behe should also be given the privilege of making his scientific case for irreducible complexity in the prestigious science journals.

The "Colloquium on Origins: Evolution & Intelligent Design" event last Wednesday was a great success. A sizeable crowd of 250-300 people, consisting of students, faculty, and guests, filled Social Science Lecture Hall and eagerly listened to presentations on intelligent design & evolution. To complement Wedge's great report, here is my brief report of what took place:

• Dr. Paul Nelson gave a 30 minute presentation on the Cambrian Explosion. He mainly questioned how the various animal body plans could have been produced by the undirected forces of natural selection and mutation.
• Dr. Ralph Seelke gave a 30 minute presentation on the capabilities and limitations of producing new functionality in bacteria. His main point was that it is almost impossible to experimentally demonstrate the evolution of a new function in bacteria when multiple independent mutations are needed for that new function.
• Dr. Walter Fitch gave a 15 minute presentation which basically focused on the ways of knowing and the different positions that one can take in the origins debate. His main argument was that if intelligent design were true, then the human body should have been designed better to avoid disease and malady.
• Then there was a full panel discussion with the distinguished faculty (Dr. Walter Fitch, Dr. Timothy Bradley, Dr. Gregory Weiss) and the ID speakers (Dr. Paul Nelson, Dr. Ralph Seelke). Dr. Bradley's main points were that God and evolution should be separate issues and that it is important to find a natural mechanism for the origin of life. Dr. Weiss and Dr. Nelson engaged in friendly sparring over the issue of the origin of RNA.
• Finally, there was an hour-long Q-&-A session for the audience.

In summary, many people greatly enjoyed the event, although some did suggest that more time should be given to each speaker. Maybe next time, we could start an hour earlier or even do an all-day conference! I commend all the participants for maintaining a professional and cordial spirit throughout the event. I believe that the students got a better understanding of the arguments for intelligent design.

iDesign would like to thank:

• Dr. Paul Nelson & Dr. Ralph Seelke for visiting the campus
• Dr. Walter Fitch, Dr. Tim Bradley, and Dr. Greg Weiss for participating in the event
• DOS, ASUCI, the New University, and the Irvine Review
• The student clubs that allowed us to make announcements of this event in their meetings
• Gil Dodgen for announcing this event on the Uncommon Descent blog and Gary Robbins for announcing this event on his sciencedude blog
• Family, friends, and God
• Anybody else that we have neglected to mention

A few days ago I attended a lecture about the protein-degredation mechanism in cells. It's pretty complicated, but basically this is what happens: an enzyme complex called a ubiquitin ligase recognizes proteins that should be degraded and attaches a chain of ubiquitin moledules to it. This chain of ubiquitin is then recognized by a special protein structure which chews up the marked protein, releasing the amino acids.

A certain class of ubiquitin ligases is roughly U-shaped, with the ubiquitin on one end and a domain to bind the target protein on the other. Binding the target brings it close enough to the opposite arm to ubiquinate it. The ubiquitin ligase needs to be able to recognize many different proteins, and it is able to do this simply by switching out the protein (called an F-box adapter) at the binding end of the "U".

One of the slides illustrating this showed several ubiquitin ligases, each with a different F-box adapter represented by geometric shapes, and the proteins that particular adapter could ubiquinate. As I was looking at that slide, I had a strange moment of recognition: I've seen that before, I thought. Holy Crap! Is that a design pattern? Yes, it is. It turns out that ubiquitin ligase implements the strategy design pattern, made famous in computer science by the book Design Patterns.

Wednesday night's colloquium went very well (Congratulations, Art!). It was civil, academic, and very scientifically oriented – thanks in large part to Ralph Seelke's fantastic talk, which was essentially a presentation of experimental results. Just being able to frame the debate in those terms is a huge win for ID. Some scattered thoughts (I've included all the questions I should have asked, but didn't think to):

1. In the panel discussion, both sides accused the other's experiments of not accurately representing the real world: Paul Nelson described the current state of ribozyme engineering (the attempt to create self-replicating RNA) as requiring too much intelligent guidance to accurately model evolution. Likewise, Gregory Weiss accused Seelke's e-coli evolution experiments of ignoring the cooperation and interactions among organisms in the real world, which make possible evolutionary changes that would be difficult otherwise. I think the issue of whose experiments better represent the real world is going to be a crucial one.

2. Seelke stated he was unimpressed with the current state of bacterial evolution experiments, because the bacteria generally evolve quickly at first and then plateu. Does anyone know of experiments where this is not the case (i.e., in which the bacteria continue to improve gradually over the whole course of the experiment)?

3. It seems to me that Seelke presented strong evidence against the theory that gene duplication can play any sort of significant role in evolution. Here is an outline of his results:
   
   He found that e-coli could easily restore function to a mutated gene if only one mutation was needed to do so. If two mutations were required, however, functionality was not restored in his experiments (a few billion bacteria over a few thousand generations). In fact, one strain actually deleted the non-functional gene(!).
   
   The point is not that such a mutation is strictly impossible. The probability of any one mutation is about one in a billion (no problem), the probability of the right two acruing is one in a billion billion. There are populations of bacteria on the earth with the probabilistic resources to overcome this. However, they are racing against the clock because while that gene is non-functional, it will be under selective pressure for removal. Furthermore, this is just too slow. The earth isn't old enough for any higher organism with a longer life cycle to wait around a billion billion generations everytime it needs a new gene.
   
   This is a big problem, since one of the major vehicles of evolutionary change in higher organisms is supposedly gene duplication, in which an essential gene is duplicated, and the second copy is then free to evolve an additional function without killing the cell. In the event that that gene requires more than one mutatation to evolve novel function, it likely will never aquire it.
   
   Can anyone cite evidence for widespread gene duplication as a vehicle for major evolutionary change? I'd appreciate experimental results, but evidence from homology would be interesting too.

4. One of the standard responses to how evolution overcomes irreducible complexity is co-option: that is, existing structures in the cell take on new function, thereby eliminating the need to build that function from the ground up. This is a potential way around Seelke's results – natural selection doesn't need to create a novel, selectively advantageous gene all at once, because it can take an existing gene and adapt it for new function in an incremental manner. I'm not an expert, but I don't think that the evidence from homology supports cooption on the massive scale this response predicts.

5. Gregory Weiss claimed during the faculty panel that RNA is, contrary to Paul Nelson's assertions, a pretty stable molecule. Can anyone point me to resources that verify/falsify this? Specifically I'd like to know how long it lasts in solution, its melting temperature, etc. compared to the same figures for DNA.

6. Paul Nelson's sparring with Gregory Weiss over self-replicating RNA was really interesting. Last time I checked, we had only succeeded in creating RNA that could duplicate a short region of itself. Apparently the field is doing much better than that, though I wasn't able to tell from the comments exactly what researchers can and can't do

7. Paul Nelson made some remarks on the problems of prebiotic RNA synthesis that bear noting. Besides the fact that ribozyme engineering assumes that RNA already exists (because there is no convincing mechanism for pre-biotic RNA synthesis), there is the question of concentration. The fundamental unit of life is the cell because maintaining high concentrations of particular substances is critical for self-replication and every other life process. The problem for origin-of-life research is not just to create self-replicating RNA but to explain how it could have been present in sufficient concentration to actually do any replicating.

In case you need directions or other help in coming to the "Colloquium on Origins: Evolution & Intelligent Design" event, please contact Andrew at (714) 624-7335.

See you there!

An interesting article in the April 27 issue of Nature reports that scientists have succeeded in teaching Starlings to recognize recursive acoustic patterns, giving them an edge over freshman computer science majors. The ability to understand recursion was previously thought to be unique to humans. If you're on a university network, you can access the full text of the paper here, and a more readable summary of the findings here.

Here is a PDF version of this advertisement. You can also see this ad in this week's New University.

FOR IMMEDIATE RELEASE

Student Club Will Host Intelligent Design & Evolution Colloquium at UC Irvine

(University of California, Irvine, May 8) -- Experts will present arguments for biological intelligent design at "Colloquium on Origins: Evolution & Intelligent Design" on Wednesday, May 10th at 7:00 P.M. in Social Science Lecture Hall 100. Following the presentations, a distinguished UC Irvine faculty panel will critique the arguments made.

Dr. Paul Nelson, a philosopher of biology and a nationally-known proponent of intelligent design, will discuss the role that natural selection plays in explaining the complexity of animal phyla, and the possibilities that intelligent design brings to the table. Dr. Ralph Seelke, a biology professor at the University of Wisconsin-Superior who has performed extensive research on experimental evolution, will discuss the capabilities and limitations of evolution in producing new functionality in bacteria.

The distinguished UC Irvine faculty panel will include Dr. Walter Fitch, professor of ecology and evolutionary biology and National Academy of Science member, Dr. Timothy Bradley, professor of ecology and evolutionary biology and fellow of the American Association for the Advancement of Science, and Dr. Gregory Weiss, assistant professor of chemistry, molecular biology, and biochemistry. Faculty panelists will share their thoughts and critiques of the presentations made by Nelson and Seelke. Following the panel discussion, there will be a question-and-answer session open to the audience.

This event is sponsored by iDesign@UCI, a student organization on campus which seeks to foster friendly discussions on origins-related issues. This event is open to the general public and admission is free.

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On May 16-17, there will be an International Symposium on LifeChips at the Beckman Center of the National Academies. This event is sponsored by the Henry Samueli School of Engineering. The event sounds interesting but it also looks to be a little expensive for students. In any case, those who are interested in the intersection of engineering and the life sciences might enjoy this event.

Physorg has a good article about the bat's amazing ability to catch prey (HT: Design Watch). As mentioned before, the bat's navigational system may actually be a good example of isomorphic instantiation. Here's a clip of the article:

"The bat keeps the compass direction to the target a constant, but it changes its flight direction at the same time," says Ghose. "So, when the bat chases an insect, if the insect is initially located to the northwest, the bat maneuvers to always keep the target to the northwest while closing distance.

"This strategy is called parallel navigation after the parallel nature of the bearing lines. Interestingly, in the late 1940s engineers working on the problem of how to program guided missiles to hit their targets implemented a similar strategy."

This entry marks iDesign blog's 100th post. Thanks to all my fellow bloggers, and thanks to all the readers!

If you have any comments or suggestions about this blog, feel free to leave a comment or send an email to idesignclub 'at' gmail 'dot' com.

Here is an interesting article in Nature: Proteome survey reveals modularity of the yeast cell machinery (HT: CEH). In order to read this article, you would need to use the UCIfull VPN.

Modularity is one of the enduring principles in software engineering. If we find evidence for elegant modular architectures in life, can we conclude that life was engineered too?

I recently wrote an article detailing several tips for academic success -- it's in the current issue of the Irvine Review. These tips may be of interest to those who still have midterms.

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1. Find A Reason To Excel

It is important to have a reason to excel in college, since one must be willing to sacrifice time in order to succeed academically. One reason is that higher academic performance usually opens doors to better careers. Don’t read the rest of this article without introspectively identifying a motivating reason.

2. Don’t Work & Don’t Party

Try not to let a mundane job take time away from college studies. In the long run, it would be more advantageous to excel academically during college and get a high-paying job once one finishes with a degree.

I realize that a majority of students need to work during the quarter due to financial constraints. In this case, seek to minimize other time-consuming activities, like unnecessary social events, relationships, parties, and video games. In order to do well in college, one needs to devote plenty of time to studying.

3. Ask Many Questions

If a concept is confusing, do not hesitate to ask a question in class. It is better to resolve each ambiguous point during class than to have a pile of confusing material to study right before an exam. If a set of questions builds up, it would be wise to visit the professor’s office hour or a discussion section in order to ask these questions.

In order to ask good questions, it is important to learn to think critically. Not every claim that an instructor may make is necessarily true. One must learn to analyze the reasoning behind each claim. Critical analysis and a skeptical eye will help one to gain a richer understanding of the material.

4. Prepare Rather Than Procrastinate

Keep track of the course schedule. Knowledge of each exam date and homework deadline will help one to manage time properly. It is also important to keep up with course readings in order to be fully prepared for the exam. And if possible, finish each project, essay, and homework assignment a day before it is due.

5. Make Personal Study Guides For Exams

Since tests comprise the bulk of the grade in many courses, it is crucial to cram hard before every exam. I would suggest devoting at least one full day of studying for each major midterm or final. I recommend making a checklist of necessary concepts to know for the exam.

When reading through all the notes, slides, handouts, homework solutions, and relevant book chapters, it is important to look out for concepts and formulas that absolutely must be memorized. Write these essential formulas and concepts down on a separate sheet of paper. Focus entirely on this sheet when the exam time draws near.

6. Think Strategically

It is important to keep track of the percentage values of each assignment and exam in order to know how to allocate one’s time. Also, it may be wise to invoke the pass/no-pass option when one is performing poorly in a class.

7. Learn to Communicate

Verbal and written communication skills are important assets to have in college. For essay tests, it is important to be able to develop cogent argumentation. There are many ways to develop one’s communication skills. For instance, if one wants to develop the skill of writing, then I would suggest that one contact the Editor of the Irvine Review and apply for a Staff Writer position.

8. Hang Out With The Right People In The Right Places

If one hangs out with people who care about excelling in college, one will also probably care about excelling in college too. It is good to utilize peer pressure to one’s academic advantage. It may be beneficial to join study groups or tutoring services like LARC. Also, one should identify places on campus which are good for studying and places which are terrible for studying. Avoid the latter place as much as possible.

9. Engage In Research & Apply For Scholarships

Getting involved in academic research is probably the single most effective way to enhance one’s academic career as an undergraduate. Research opens many doors in the academic world and is looked upon favorably by employers. Consider visiting the Undergraduate Research Opportunities Program (UROP) here at UCI.

Scholarships are available at the national, university, school, and departmental levels. One should try to apply for all the scholarships for which one is eligible. A scholarship not only assists in paying for tuition but also greatly enhances one’s resume. Consider visiting the Scholarship Opportunities Program here at UCI.

10. Maintain A Balance

Take college very seriously, but don’t take it too seriously. There is much more to life than academics. It is important to balance one’s time between work and relaxation in order to prevent getting burned out. Don’t take more classes than what is feasible -- 16 units is an ideal load.

Also, it is crucial not to get too stressed out if one receives a poor grade. Just attempt to do better the next time around.

Conclusion

Succeeding in college has little to do with how innately smart one may be. Rather, the amount of success is directly correlated to the amount of time that one devotes to college. One only needs a motivating reason and the mental endurance to make it all the way through.

On a lighter note: The Great Debate

My personal favorite:
Stephen J. Gould: None. The bulb jumped into the socket when no one was looking. Gradually.

(HT: Uncommon Descent)