New Moderation Policy

Due to recent events, I've had to change EE's Comment Moderation Policy. Up until now, all comments were posted real-time and without moderation. Now, all comments go through moderation and if I find that the insults go too far, then I reject the comment and ask that the comment be re-posted without the insults.

I apologise for the inconvenience. I hope to have an open door policy again in the near future.

Redundancy - A Mark of Design?

Staying up until 3am does have its upsides. I stumbled upon an excellent NOVA episode in the wee hours of Sunday morning called "Building on Ground Zero". The program went through both the ASCE and NIST investigations into the collapse of the Twin Towers (WTC1 and WTC2). Both reports came to similar conclusions (impact and explosion of airplane coupled with weakening of steel trusses by fire brought the Twin Towers down), but attributed different mechanisms (pancake floor collapse as opposed to truss connection pulling columns inward causing fracture).

"Building on Ground Zero also focused on a design feature used frequently by structural engineers called redundancy. In structural engineering, redundancy generally means multiple load paths. The ultimate goal of a structural engineer is to safely transmit the loads to the ground. This is usually done by focusing on a primary load path. But what happens when the primary load path is compromised? If the load cannot safely get to the ground, then the equilibrium of the structure is shot and collapse (in part or in whole) occurs. If a structure is said to be redundant, then there are multiple loads paths. Redundancy is also a means to prevent progressive collapse where the failure of a single member causes the failure or collapse of the structure (in part or as a whole). In part, it was the redundancy of Twin Towers' structural design that allowed them to remain standing despite multiple columns being severed, thus allowing several hundred occupants the ability to escape.

So can redundancy in a natural object point towards design? Possibly. Taking the Mike Gene approach, let's grant that a redundant feature in a natural object is possibly the outcome of a purposeful design. In order to progress to plausibility, I propose one of the things that needs to be looked at is the context of the redundancy (i.e. does the redundancy serve a purpose?). Redundancy without meaning or context points more towards a "Myopic Tinkerer" than a "Rational Engineer".

However, there is an interesting flip side to this: I don't believe the designer of WTC1 and 2 intentionally incorporated redundancy for the events of 9/11.* This would mean that redundancy was an accidental outcome rather than purposely used for the case that several columns at a certain point would be missing. So where does this fit in to the "design paradigm" and it is possible to even know if the redundancy was purposely designed or not?

The asylum is now open. Let the comments commence!

*The tubular structure of WTC1 and 2 were designed to resist wind and earthquake loads, as well as the impact of a Boeing 707. I don't believe that the impact studies looked at the possibility that the 707 would take out several columns at a certain elevation, but I could be wrong.

It Is Official: Football Season Is Upon Us!

With the NFL regular season about to kickoff on Thursday, I hereby declared the season of football officially open. Any given weekend, I now have up to four teams to follow from the NFL, NCAA, CFL (Canadian Football League) and CIS (Canadian Interuniversity Sport - not the OTHER CIS).

I am pumped about my 7-2, 1st place Riders, and am looking forward to the second-half of the CFL season.

I am pumped about the prospects of my NFL team, the Seattle Seahawks. Loudest stadium in the league, an experienced and speedy defense, and Matt Hasselbeck at the reigns means high expectations. I'm always nervous about those 10am PT starts, though, and of course, the Hawks play in Buffalo on Sunday 10am.

My college teams are enigmas.

Each year, I never quite know how the University of Saskatchewan Huskies are going to do, but they're usually near the top of the Canada West conference. A 25-0 stomping of the U of Calgary Dinos was a good start!

And then there's the Michigan Wolverines. New coach, new system, no players. Could be a long year. A bowl game would be an awesome year (how's that for reduced expectations, eh?) But that loss to Utah last weekend was painful.

Oh well, my pro teams will keep me interested.

Comments open: Are you pumped about football returning?

Blog Posts That Interest Me (For One Reason Or Another)

As you may (or may not) have noticed, I have quite a few blogs listed at the right. Following what they all have to say can be quite the task. Here are some posts from the listed blogs that have caught my eye for one reason or another:

JFS Special: Eleven things you may not know about food irradiation - Junkfood Science

This blog is a personal favourite and the comprehensive post on food irradiation is one of the reasons why. Sandy Szwarc is level-headed yet not afraid to push back at the scare-mongerers.

Is evolution theory important in medical research, or not? - I'm From Missouri

I'm not a fan of the name-calling (on both sides), but this topic really needs to be looked at more closely (cue the comment flood!).

An interesting comment quoting Jerry Coyne:

"To some extent these excesses are not Mindell’s fault, for, if truth be told, evolution hasn’t yielded many practical or commercial benefits. Yes, bacteria evolve drug resistance, and yes, we must take countermeasures, but beyond that there is not much to say. Evolution cannot help us predict what new vaccines to manufacture because microbes evolve unpredictably."

Lying to Advance a Cause - Telic Thoughts
Bio Prof: "It Is OK to Use Some Inaccuracies Temporarily" to Sell Evolution - Darwinian Fundamentalism

I really hope this is only one man's opinion on teaching evolution.

UPDATE (03-Sept-2008): This is an awesome comment by Thought Provoker at TT. It's also entertaining to read his responses to this Coturnix fellow.

Why I'm not a Behe fan, Part I, Why I'm not a Behe fan, Part IIA: the malaria scam, Behe botches basic probability...how likely is that?, Why I'm not a Behe fan, Part IIB: abusing genetics - Quintessence of Dust

Me thinks Dr. Matheson is not a Michael Behe fan. Seriously, I have to read EoE and re-read these posts to get some proper perspective.

Please fire U.S. gymnastics coach and poor sport Martha Karolyi - Coincidence Theories

The U.S. got beat by 13-years olds. Neener! Neener! Nee! Ner!

Slavery Revisited: the lesson of John Newton - He Lives

An excellent post on one aspect of Christianity. A good lesson to all that once you accept Jesus, you do not magically become perfect.

Consider this an open thread to discuss any topic of interest.

I Like My Solar System Rare, Please!

I have enjoyed my nice little break/vacation from the biological ID/evolution debates*. But I have poked my head in at several sites (including EE) out of curiosity.

A post at Telic Thoughts entitled The Uniqueness of Our Solar System caught my eye (HT: Bradford). Referencing a blog post and an online article, the post goes on to say:

"Paradigms change with time. The one advancing the belief that we inhabit a not very special solar system having an ordinary star is being challenged.

Intelligent Design has a cosmological component. If life arising is an unusual event in our universe, the formation of solar systems, with planets having earth-like conditions, might be rarer still."

A couple of not-so random thoughts:

1. When looking for a level-headed argument, I usually head over to Dr. David Heddle's blog, He Lives. It is interesting to note that while he does not think much of biological ID, he does fully support cosmological ID**. So let me do an experiment. When mentioning biological ID or IC, I get a huge response.

UPDATE (03-Sept-2008): So let me throw this out at you:"Cosmological ID is science". I am curious what the response will be. (Note: While Dr. Heddle is sympathetic towards Cosmological ID and says it is on more firm scientific ground than Biological ID, he never explicitly stated that it is science. - HT: freelurker)

UPDATE 2 (03-Sept-2008): It's always best to get it from the source (thanks Dr. Heddle).

2. I have always been intrigued by the stark differences in the various solar systems, but I have never come across a comprehensive listing of these extrasolar systems. I would like to see the following in such a listing: parent star spectral type and mass, planetary mass and diametre***, orbit details (eccentricity, closest distance to star, furthest distance to star, etc.), and comparison (both tabular and graphical) to our solar system.

*Let's face it: family, work, and my lawn will always take priority over EE. I could probably add barbecuing, football and hockey.
** To save you time, Dr. Heddle's cosmological ID posts are here, here, here, here, here, here, and probably more before 2005.
*** One must include diametre along with mass since Newton's equation for gravitational force comes into play for determining the likelihood of life - simple or complex - on these planets.

For Your Entertainment...

I am not one to fall for or to espouse conspiracy theories. In fact, I think Oswald acted alone.

That said, there is a book available from amazon.uk.co called The Darwin Conspiracy by Roy Davies. From the book site, here is the synopsis:

"Charles Darwin has been hailed as the greatest scientist of the 19th century for his discovery of the secrets of evolution. Today, the impact of his work is still felt throughout the world.

But did Darwin really come up with the idea of evolution himself or did he take it from a young researcher trying to impress him?

The Darwin Conspiracy examines how Darwin struggled for years in scientific dead-ends until he was presented with the solution to the greatest scientific puzzle of his day by a naïve naturalist collecting beetles in a tropical jungle.

So began the conspiracy by which eminent scientists promoted the ideas of Darwin ahead of those of Alfred Russel Wallace in order to achieve ever-lasting fame for their greatest friend.

Using extensive research about contemporary shipping time tables and Darwin's own correspondence, the author challenges the commonly-held belief that Darwin scored a scientific breakthrough when in reality he used another man's insights for his own benefit, and committed one of the greatest scientific crimes in history.

The Darwin Conspiracy is a true story about deceit and deception and stands as an outstanding metaphor for the idea of survival of the fittest."

Based on the site, a review (see below) and a portion of the book provided, it would appear that The Darwin Conspiracy is an overview of previous research into the history of Darwin's research. I would find this interesting to see how Darwin fits in with other research done by Lamarck, Blythe and Wallace (among others).

As for the "conspiracy" charge, there may or may not be something to it. Let's grant for the moment that the upper-class Darwin was favoured over the lower-class Wallace. That Darwin was favoured over Wallace doesn't surprise me either since it is almost "natural" that the upper class will support one of their own over someone "below" them. From this alone, I don't see an active conspiracy.

For fun, let's pretend Darwin did "plagiarise" Wallace. Would this affect the science of evolution? I say no, but Darwin being the academic equivalent of common thief kind of puts a damper on Darwin Day celebrations, eh?

(HT to David Tyler @ ARN)

Peer Review .. Plus Other Notes

Last week, two full years after I submitted my Master's thesis for publication, my paper was submitted to the ASCE Journal of Structural Engineering. That means I will be facing the dreaded PEER REVIEW soon! I have to say that defending my thesis was one of the most humbling experiences I have ever had, so I am NOT looking forward to this. This will probably reinforce my decision to NOT go for my Ph.D.!

In other news...

I think I should make Bilbo my agent. I get a review of The Design Matrix posted at Telic Thoughts and EE becomes THE place to comment! It almost makes me want to place ads at the asylum, but I don't think I'm ready to be a "blog whore" yet. ;) Thanks to all the new (and old) commenters. Your views and comments are respected and appreciated.

I have posted 4 reviews of The Design Matrix, and I find it interesting that the only post that has NO comments is on the Explanatory Continuum. Does this mean we're ready to discard the Traditional Template and enter a new phase of the age-old debate?

Thank you all for voting on the poll. Evolution: A Theory in Crisis won over Endless Forms Most Beautiful by a mere two votes. OK, I'll admit, one of those votes was mine, so technically Denton's book won by 1 vote.

That said, I am in a little bit of a bind. I find myself wanting to either take a break from reading evo/ID books, or just setting aside Punctuated Equilibrium and Edge of Evolution for something I am more currently interested in reading.

ID Research Themes

This is the fourth in a series of posts regarding themes in Darwin’s Black Box and The Design Matrix.

"The vast majority of scientists do not view Intelligent Design as science and I happen to agree with them. ... At best, Intelligent Design may only be a nascent proto-science..."
Mike Gene, Introduction, The Design Matrix

Interesting start to a post entitled "ID Research Themes", eh? However, it would appear that Gene switches gears from his introductory comments later on:

"Actually, the concept of design can be useful as a research guide. Several years ago, while reading some scientific articles describing the proofreading process of protein synthesis, it occurred to me that an important step of information flow appeared to lack proofreading. Already aware that the process of making DNA and protein synthesis was proofread, I wondered about transcription, the process of making RNA. I could not recall ever hearing anything about proofreading being associated with RNA polymerase activity ... It struck me that this was a great opportunity to use the hypothesis of design. Since the terminal step in information transfer (mRNA to protein) is proofread, could I use [ID] to infer that the earlier step in the information transfer (DNA to RNA) was likewise proofread? Yes.

... With this hypothesis in hand, I could go into a lab and design experiments to discover whether proofreading does indeed occur during transcription. ... If I had, in fact, performed these experiments, my prediction would have been borne out. A literature search I performed after coming up with this hypothesis provided support that there is good evidence that RNA polymerase can proofread. Thus, the suspicion of design was able to direct a line of thinking that not only could generate research, but could also uncover truths and further understanding of our biological world." (Emphasis mine)
"Mike Gene, Chapter 4, The Design Matrix*

Impressive, but Mike just keeps on giving. In Chapter 10, Mike Gene lists several testable hypotheses he developed from each of the four criteria within the Design Matrix (links provided where provided):

Rationality:
1. transcriptional proofreading (from Chapter 4)
2. lagging strand synthesis
3. use of cytosine as part of the DNA molecule

Discontinuity:
4. investigating the bacterial flagellum (here too)
5. investigating the eukaryotic flagellum

Analogy:
6. degradosome (an earlier hypothesis here)
7. use of nano-wheels in the cell

Foresight:
8. assisted in developing the hypothesis of front-loading evolution

There you go! Eight (8) working design hypotheses!

To the teleologist, go! Develop your own hypotheses (or use Mike's) and design your own experiments.

To the non-teleologist, please drop your argument about ID not being able to develop a viable research programme. Mike Gene has shown that it is an empty argument

*See link to #1 if you object to this prediction.

Source:
Gene, M., The Design Matrix: A Consilience of Clues, 2007
http://www.idthink.net/

Next: Engineering Thinking in Darwin's Black Box and The Design Matrix

The Design Matrix Revealed

This is the third in a series of posts regarding themes in Darwin’s Black Box and The Design Matrix.

All quotes in this post are from Chapter 10 of The Design Matrix.

The Design Matrix

Mike Gene’s book, The Design Matrix, is an interesting and enjoyable read which culminates in Chapter 10 where the Design Matrix (DM), a method to gauge the degree of design in a natural object, is described in detail.

The DM has four separate criteria for scoring*:

1. Analogy (A): The more similarities of biotic features to features known to be designed (engineered), the stronger the analogy.

2. Discontinuity (D): Non-teleological processes cannot explain biotic feature. When A is coupled with D, the design suspicion is strengthened.

3. Rationality (R): Does the biotic feature display function and “purpose”? IOW, would a competent engineer design it that way?

4. Foresight (F): Are there aspects to the biotic feature(s) that point towards thinking forward rather than immediate success? (Engineer with foresight vs. myopic tinkerer)

“The Design Matrix … works by taking the scoring along each criterion and fusing them together as a whole… In this way, the four criteria are treated independently as possible, yielding their own respective score. Then, the scores are simply averaged to give a final score…”

Each criterion is given a score by the user that ranges from -5 to +5 where a positive score leans towards a suspicion of design while a negative score suggests no design. For example, if the evidence either way is “strong”, then +/- 5 is scored; if moderate, +/- 3; if modest, +/-1. Zero represents a thoroughly ambiguous situation. Once all four criteria are scored, their average is taken: sum of A, D, R, and F divided by 4. The final score suggests whether a suspicion of design is warranted or not.

Mike Gene goes through several examples. While I’ll leave it to the reader to sift through the details, here is how Mike scored various objects, both natural and human designed (A, D, R, F, final score):

Pseudogene: -5, -5, -5, -3, -4.5
PCP Pathway: +1, -5, -4, 0, -2
Eye: +3, -3, +2, -2, 0
Genetic Code:+4, +2, +4, +2, +3
Book: +5, +5, +4, +3, +4.25
Car: +5, +5, +4, +4, +4.5

Thus, according to Mike’s scoring, the genetic code demonstrates a moderate suspicion of design, the pseudogene and the PCP pathway lean towards non-teleological explanations, and the eye is ambiguous. It should also be noted that the scores are subject to change should new evidence come forth.

Strengths and Weaknesses

“Again, we must be clear that the scoring is not objective. The Design Matrix is not intended to be a scientific instrument, …”

As I have surmised in previous posts, the DM is not an objective measure of design in nature. So what use does it have? Let’s look at its strengths to help us define its use.

“Combining the scores … happens to eliminate one of the most popular arguments against design – ‘god of the gaps.’ A Discontinuity score, by itself, is quite vulnerable to this complaint. But if the Discontinuity score is combined with three lines of positive indicators of design, the “gaps” complaint no longer applies.”

“Within the Matrix design is not inferred simply because there is a lack of evidence that something evolved. Instead, such considerations are simply one piece of the puzzle, where Discontinuity, combined with Analogy, Foresight, and Rationality give us a broader perspective with which to reach a tentative conclusion.”

With the DM, Mike Gene combines scores from four (mostly) independent lines of evidence into a single score that suggests whether teleological processes (design) should be suspected or not. This means that the negative evidence of IC can be augmented by positive evidence from A, R, and F, thus strengthening the design suspicion. However, the opposite can be true: a lack of positive evidence from A, R, and F weakens the suspicion of design raised by the negative evidence of IC.

The second strength of the DM is it forces each user to put their reasoning for scoring out in the open. Willy-nilly scoring won’t cut it. Each score has to be supported evidence. As in court cases, the more evidence, the stronger the case. Also, independent scoring from a separate user of the DM can point out both strengths and weaknesses in the original scoring.

Summary

“If you, the reader, still find yourself wanting independent evidence of a designer and needing some part of evolution to be disproved, you will have been disappointed.”

While the DM is not an objective measure of design in natural object, it can be a useful tool, helping to provide direction to those who wish to “follow the Rabbit**”. Suspicions of design can be strengthened and thus a direction for future research and experiments can be made clearer.


*These descriptions are brief. For a more detailed description, read Chapters 8 and 9 of The Design Matrix.
**The Rabbit and Duck theme is a favourite of Mike’s. It has its origins from this drawing, suggesting two people can look at the same thing yet see two different things. Mike defined the Rabbit as those who see design in nature and the Duck as those who see nature caused by non-teleological mechanisms.

Source:
Gene, M., The Design Matrix: A Consilience of Clues, 2007

Next: ID Research Themes

Irreducible Complexity

This is the second in a series of posts regarding themes in Darwin’s Black Box and The Design Matrix.

Behe Starts a Furor

“By irreducibly complex I mean a single system composed of several well-matched, interacting parts that contribute to the basic function, wherein the removal of any one of the parts causes the system to effectively cease function.”
Michael Behe, Chapter 2, Darwin’s Black Box

In 1996, Dr. Michael Behe provided in his book, Darwin’s Black Box (DBB), this simple definition for a simple, yet potentially powerful concept – irreducible complexity (IC). In the subsequent years, an academic war of words broke out which beckoned the question: why the furor? Surely the above definition alone couldn’t have started the maelstrom of criticisms that began soon after it was published?

Let me propose that much of the hullaballoo (did I really just write hullaballoo???) is due to Behe’s application of IC, which amounts to IC = evolution impossible. To clarify Behe’s argument, while it is impossible for a direct evolutionary pathway to produce an IC system, it is possible for indirect evolutionary pathways to do so. However, when he scanned the scientific literature, Behe noted that there was no paper describing the indirect routes in significant detail.

The Traditional Template Invoked

The concept IC as defined by Michael Behe is simple, brilliant and stands as a potential marker of design. To provide backup, Behe eloquently presented several cases of IC systems (cilia, flagellum, blood clotting, etc.). He also anticipated most of the criticisms directed towards his thesis and answered them fairly adequately. However, Behe became entangled within the Tradition Template of the debate the moment he presented a negative argument (IC = evolution impossible), and even though Behe attempts to make a positive argument for design in Chapters 8 through 11, the negative argument dominates DBB. In my opinion, this tactic has halted the concept of IC in its tracks before teleologists could take it for a proper test drive. By arguing an impossibility, Behe unwittingly assumed the “traditional role” of the dissenter.

Accordingly, Behe’s critics were more than willing to assume their “traditional role” to demonstrate that it is possible for DE to produce IC systems. Kenneth Miller, a biologist at Brown University, is generally credited with proposing the best argument against Behe’s application of IC: cooption* - the parts of an IC system were coopted from parts of other precursor systems. With cooption, Miller showed it was possible for evolutionary mechanisms to develop IC systems (Note I said possible, not plausible nor probable). Since Behe is arguing it is impossible for evolution to produce an IC system, all Miller had to do was show it was merely possible. Thus it would appear that the Traditional Template has given a seemingly crushing blow to IC**.

Hopping Down the Bunny Trail

Enter Mike Gene. In his book, The Design Matrix (DM), Gene takes IC for a test drive within the Explanatory Continuum.

First, Gene pointed out that cooption was “really the only evolutionary explanation that has the potential to explain the origin of an [IC] system.” Second, he recognised a flaw in the cooption argument:

“The most basic problem with the conventional use of [cooption] is its complete reliance on chance.”
Mike Gene, Chapter 8, The Design Matrix

Third, Gene made the cooption explanation plausible by incorporating his working front-loaded evolution*** (FLE) hypothesis.

Mike Gene then applied the brakes and headed back to the starting line. He granted that cooption is possible, thus avoids getting entangled in the Traditional. Gene then investigated what independent evidence is needed to progress it to plausible.

If cooption was to be a viable explanation, it must be gradual. Then Mike Gene pointed out that to construct an IC system through gradual cooption, “the previous existence of simpler precursors and multiplied functions” should be abundant. If these precursors are missing, then the IC system can be said to consist of “system-dependent parts”.

“A system-dependent part would be something that does not exist or function apart from the context of the machine.”
Mike Gene, Chapter 8, The Design Matrix

With this, Mike Gene laid the framework for one of four criteria in his Design Matrix (more on this in the next post). This, coupled with FLE, has advanced IC from Behe’s simple yet powerful concept to a possible marker of design. Thanks to Mike Gene, IC has new life.

Sources:
Behe, M., Darwin’s Black Box: The Biochemical Challenge to Evolution, 2006
Gene, M., The Design Matrix: A Consilience of Clues, 2007

*Even if I am wrong and Miller did not originally come up with cooption, he is at least credited with being the “front-man” for the argument against IC = evolution impossible.
**There are many other critiques of Behe and IC; one of the more extensive (and honest) ones comes from Thornhill and Ussery, “A Classification of Possible Routs in Darwinian Evolution.” from Journal of Theoretical Biology in 2000. A summary of their findings can be found in Chapter 8 of The Design Matrix
*** “Front-loading is the investment of a significant amount of information at the initial stage of evolution (the first life forms) whereby this information shapes and constrains subsequent evolution through its dissipation. This is not to say that every aspect of evolution is pre-programmed and determined. It merely means that life was built to evolve with tendencies as a consequence of carefully chosen initial states in combination with the way evolution works.” Mike Gene, Chapter 7, The Design Matrix

Next post: The Design Matrix Revealed