iDesign @ UCI

Welcome Message To New Students

Interested in Origins?
Join the club.


Mission Statement

FAQ

Organization


MISSION STATEMENT:

iDesign Club at UCI seeks to foster scientific discussions regarding the origins of life and the universe. Theories such as Darwinian evolution, intelligent design, and creationism will be critically analyzed.


FAQ:

Q: WHAT IS THIS CLUB ABOUT?

Origins! We are interested in discussing alternative theories to the origins of biological structures. While the current mainstream theory in academia is Darwinian evolution, we would also like to discuss other viable ideas, such as intelligent design.

Q: WHO CAN BE A MEMBER OF THIS CLUB?

Anybody! Students of Biology, Chemistry, Physics, Mathematics, Computer Science, Engineering, Anthropology, and Philosophy may especially find this club intriguing. However, you do not need to have a science background to be an effective member of this club.

Q: WHEN AND WHERE ARE CLUB MEETINGS?

Please check blog entries for time and place.

Q: WHAT IS THE MEMBERSHIP FEE?

Nothing! There are no membership dues.

Q: IS THIS CLUB BIASED TOWARDS ONE SPECIFIC THEORY OF ORIGINS?

Perhaps. Ponder the name of this club. This club is ideologically the mirror of another club at UCI, the Students for Science and Skepticism. However, our main goal is to give a balanced view of the controversy regarding the origins of life so that students can come to an informed conclusion themselves.

Q: WHAT DOES THE LETTER "i" STAND FOR IN iDESIGN?

Good question -- the answer is intelligent.

Q: WHERE IS THE CLUB CONSTITUTION?

We adhere to the minimum constitution that was provided by the Dean of Students. In the future, we plan to draft a comprehensive constitution and bylaws.

Q: IS iDESIGN AFFILIATED WITH ANY ORGANIZATION?

No. However, we are friends with the IDEA Center


ORGANIZATION:

PRESIDENT:
Arthur
Information and Computer Science

VICE PRESIDENT:
Brian
Biology / English

DIRECTOR:
Andrew
English / Economics



Thursday, July 20, 2006

Compositional Evolution: Some Final Thoughts

I recently finished reading Compositional Evolution, by Richard Watson (which I blogged about previously here and here), and I thought it would be worthwhile to summarize the full results, their limitations, and their relevance to ID. The following gets a little technical and is mostly written for myself, but I've tried to summarize the take-home in layman's terms.

The major claim of the book is that a certain class of search strategies, characterized by combining blocks of genetic data which have been pre-adapted in different environments, is inherently different from standard random-mutation gradualist evolution, and is capable of discovering optima in a complex fitness landscape which gradualism cannot. It does this by traversing the landscape in such a way that the local optima which trap gradualism do not exist.

Compositional Evolution doesn't circumvent the No-Free-Lunch theorems, of course, so this family of search strategies (like all others) is only efficient on a seach space (i.e. cost function) with certain properties. The main requirement is that it be hierarchically decomposable – that is, it must contain groups ("modules") of variables ("genes") which encapsulate internal complexity. The modules are still allowed to have strong dependencies with other modules – i.e. two modules may be interdependent in such a way that a certain configuration of one module may only confer a high fitness value if a certain configuration of another module is also present. This modular structure must be recursive, so that the modules contain modules which contain modules, all the way down.

The basic idea is that these modules can be swapped around until a good combination is found. This module of modules then acts as a new, larger unit of selection and is itself combined randomly with other higher-order modules. In order for evolution to make use of compositional operators, life would need to have (roughly) a hierarchical modular structure. This is a testable claim, and with the amount we know about genetics in e. coli and yeast, it shouldn't be too impractical to look for such modules. Watson himself suggests several areas for research. Of course, this raises questions about what exactly modularity would prove. Is modularity a sign of intelligent engineering, or a way to explain blind evolution? Is lack of modularity a sign of an obviously not designed cludge, or proof that natural selection couldn't overcome the many dependencies to create higher life forms?

The two models of compositional evolution examined in the book are sexual recombination (the random combination of genes from both parents by breaking each genome at certain points, and assembling the pieces into one new genome) and symbiogenesis (the fusing of two symbiotic organisms into one), which Watson describes as the 2 extremes of compositional evolution (symbiogenesis being at the high end because it incorporates all the genetic material from both "parents"). The main issue for all compositional mechanisms is discovering the modules. This is easily done in top-down, designed systems... but can it be done bottom-up, with no prior knowledge of the modules?

With respect to sexual recombination, the answer is "not really". In order for sexual recombination to act in a compositional manner, there are several requirements. First, the parents must be from different niches, or have evolved in somewhat different environments. Otherwise the population converges to the most fit individual without ever discovering regions of higher fitness. Secondly, the number of breakpoints must be constant (that is, not a function of the genome size). Otherwise the overactive recombination is too likely to break up existing good modules from the parents. And third, interdependent ("linked") modules must be adjacent on the chromosome. If they are not, then they are unlikely to travel together during recombination.

Of these, the second and the third are not very biologically plausible. Related genes are often collocated in bacteria but not, ironically, in organisms which reproduce sexually. Watson acknowledges this and postulates that linkage may act compositionally with lateral gene transfer in bacteria and that the important compositional unit in higher organisms is the gene, not groups of genes. The gene-as-compositional-unit comment, however, ignores the fact that his models are built upon hierarchical modularity. It is unclear what benefit a single level of modularity provides over traditional gradualism. Indeed, Watson seems disapointed with the restrictions on recombination and is most proud of his model of symbiogenesis.

Watson's model of symbiogenesis begins with many organisms, each containing only one of the lowest-level modules. Organisms are then randomly tested for the stability (fitness increase) of a join between them. If the join is more fit under a variety of contexts (chosen by comparing them against fully-specified genomes) than both of the "parents", then it is kept, otherwise it is discarded. The unit of selection is entire organisms, and as the algorithm progresses, the correct modules are discovered.

Aside from the fact that symbiotic encapsulation is at best rare and can't account for most of the genetic data, the thing that sounds most fishy to me is that join stability is tested with fully-specified individuals (created by concatenating existing individuals until a full specification is formed). This seems to me like look-ahead not available to evolutionary methods. In fact Watson himself refers to the process as "stochastic lookahead" and justifies it this way:
We want to select for good modules, but what makes a "good module"? A good module is precisely the thing that, when used in assemblies in the future, will produce good assemblies. So, how do we find such an entity? By trying it in a number of assemblies and seeing how it does. (p.261)
The idea, I think, is that joins which are rejected are evolutionary dead ends. Looking ahead to see this allows us to conveniently disregard them before they are actually shown to be unfit. But suppose an ultimately unstable join is so much better in the short run that it eliminates the possibility of an optimal join? It seems to me that a more biologically accurate model would keep joins that are optimal at the time, rather than those which are optimal in some future context.

Posted by Wedge at 10:22 AM | 0 Comments

Tuesday, July 11, 2006

A Typical Day

In cause you're wondering what a typical day is like here at iDesign, it goes a little something like this:



(At least for me anyways; I'm enjoying what's left of my vacation! -- Art) .

Posted by Wedge at 6:38 PM | 2 Comments

Article on the Usefulness of Design vs. Evolutionary Methods

This article by Steve Jurvetson about the usefulness of design vs. evolutionary methods in creating something "really complex" - such as A.I. that exceeds human intelligence - is worth a read, and as a bonus distantly related to the comment thread on my last post.

Particularly interesting is the observation that Microsoft Word is larger than the human genome(!), and this admission:
In fact, biological evolution provides the only "existence proof" that an algorithm can produce complexity transcending that of its antecedents. Biological evolution is so inspiring that engineers have mimicked its operations in areas such as genetic programming, artificial life, and the iterative training of neural networks.
HT: ID the Future

Update: IDTF has posted a response to the above article by a software engineer. It's so good I wish I'd written it myself.

Posted by Wedge at 6:15 PM | 0 Comments

Friday, July 07, 2006

On Evolutionary Explanations

Evolutionists and design theorists often have an extremely different notion of what constitutes "proof" of evolution, and this causes a good deal of confusion. Evolutionists complain that the standard of proof required by design theorists is unreasonably high, and design theorists complain that the proofs of evolution in the literature are not proofs at all. You can guess where I fall on that spectrum.

If you pay close attention, whenever evolutionists are engaged in listing the "proofs" for evolution, they almost exclusively list evidence for common descent. Ask them for the mountain of evidence that necessity and stochastic processes are responsible for making the transitions between the similar forms which they just showed you, and they may draw a few pictures and connect them with arrows, but that is all you are likely to get.

Take this model of the evolutionary origin of the bacterial flagellum. It is long, detailed, and testable. But just what aspects of the model are testable? Precisely the aspects related to homology. The testable claims are about which components may be more ancient that others, which structures may have been intermediate between the Type-III secretory system and the bacterial flagellum, etc. The question of whether natural selection acting on random variation is powerful enough to make the hypothetical transitions is never addressed. Instead it is assumed that proposing intermediates and telling a story about how each might provide an incremental fitness benefit is enough.

I'm not convinced. You see, I'm a computer scientist. I'm used to looking at incredibly complex, interdependent systems at a high level of abstraction and implementing modifications at the very lowest level. There is very rarely a correlation, even in the most well-designed systems, between what changes appear straightforward at a high level of abstraction and what changes are actually straightforward to implement (by "straightforward" I mean changes which do not require a large number of compensatory changes to other parts of the system). There is not enough detail in the above model (or in most evolutionary models) to evaluate whether or not natural selection is sufficiently powerful to get the job done.

This raises an interesting question: How specific does a model have to be to be convincing? That is, how small do the proposed changes have to be to render it likely that natural selection could have filled in the gaps? I don't know of any formal answer to this, but whatever the answer might be it must be able to test natural selection, not merely assert its ability to move between hypothetical intermediate forms described at a high level of abstraction. Ironically, the only people who seem to be interested in doing this sort of thing are design theorists.

Posted by Wedge at 12:19 PM | 5 Comments

Wednesday, July 05, 2006

Man's Brain Rewires Itself

'Rewired brain' revives patient after 19 years

A man in a coma for 19 years has recovered the ability to move and communicate after his brain re-wired itself to compensate for its injuries. This stretches the limits of what the brain was thought capable of doing. The article doesn't say, but I suspect that one of the biggest surprises is seeing this level of neural plasticity in someone so old.

Posted by Wedge at 12:12 PM | 0 Comments


iDESIGN BLOGROLL:

The Design Paradigm
Design Watch
Creation-Evolution Headlines
Telic Thoughts
Uncommon Descent
ID the Future
ID Plus
CreationEvolutionDesign
Evolution News
Dualistic Dissension
ID in the UK
ID Update
Intelligently Sequenced


PRO-DESIGN SITES:

Access Research Network
IDEA Center
UCSD IDEA Club
ISCID


PRO-EVOLUTION SITES:

Panda's Thumb
Talk Origins
Students for Science and Skepticism at UCI
NAS: Science and Creationism


PRO-CREATION SITES:

Answers in Genesis
Institute for Creation Research
A.E. Wilder Smith
Reasons to Believe
Baraminology News
CreationWiki


OTHER INTERESTING SITES:

American Scientific Affiliation
Richard Sternberg


ANTEATER LINKS:

University of California, Irvine
New University
Irvine Review
School of Biological Sciences
School of Medicine
School of Physical Sciences
Donald Bren School of Information and Computer Science
Henry Samueli School of Engineering
UCI Athletics
UCI Alumni Association


BLOG ARCHIVES:

June 2005
July 2005
August 2005
September 2005
October 2005
November 2005
December 2005
January 2006
February 2006
March 2006
April 2006
May 2006
June 2006
July 2006
August 2006
September 2006
December 2006
January 2007
February 2007
April 2007

Copyright © iDesign at UCI 2005. The views presented in this web site are our own. By using this site, you signify that iDesign at UCI is not liable for anything. Site maintained by Arthur Asuncion. Template last modified June 15, 2005.

Powered by Blogger