Friday, December 26, 2008

New Book Order (And I Mean It This Time)

Several months ago, I posted on a new book order. Due to time constraints and economic uncertainty, that book order was never made. These are interesting times we live in and one has to take a myopic view of his/her day-to-day work, never knowing whether tomorrow will be the day the dreaded pink slip arrives.

But that day is not now. Using birthday money, I made an order last night through Amazon (boy, I'm good with the cheap plugs, eh?):

1. Nature, Design, and Science: The Status of Design in Natural Science - Del Ratzsch
2. Design Paradigms: Case Histories of Error and Judgment in Engineer - Henry Petroski

Order is expected to arrive in January, and when they do, the Library link will be updated.

I hope you had a Merry Christmas, and may 2009 bring happiness and blessings to y'all.

Friday, December 19, 2008

The Challenge of Detecting Design

Mike Gene has an excellent post at The Design Matrix blog. Here's an excerpt:

"The distinction between the mind-like action of designing and the hand-like action of actualizing is key. Conceptualization precedes actualization. Thus, detecting design is much more like detecting another mind than detecting busy hands. In fact, if you did not perceive the mind, the hands would not be detected as designing - they’d be detected as doing. Without making any serious and honest effort to detect the mind-like action of designing, a focus on the hand-like action of actualization will not signal design."


UPDATE 05-Jan-2009: The above link is no longer available.

The "Engineering Hypothesis"

In Chapter 7 of The Design Matrix, Mike Gene introduces his Front-Loaded Evolution hypothesis:

"Since the design of the first cells entailed the propagation of design through reproducing entities, and reproduction entails evolution, a truly intelligent designer would anticipate evolution. ... 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 chose initial states in combination with the way evolution works. ...

"Front-loading, by definition, is about designing the future through the present. It is about imposing some kind of constraint on evolution, or more simply put, it is using evolution to carry out design objectives."

I want to draw your attention to the bold type. "...using evolution to carry out design objectives." What does it mean to "use evolution"?

IMO, this entails engineering-like knowledge. Engineers need to have extensive and detailed knowledge of the materials they are working with along with the relevant mechanisms involved. In FLE, this means the designer requires the same knowledge with regards to the materials of life and evolutionary mechanisms.

FLE implies that the designer utilised this knowledge in the design of the first life form to map out probable outcomes based on how the evolutionary mechanisms would affect the life form and its descendants. However, a caveat is required:

"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 carfully chosen initial states in combination with [evolutionary mechanisms]."
Mike Gene, Chapter 7, The Design Matrix

Now, I shall attempt to expand upon the FLE hypothesis. Thanks to a commenter at Telic Thoughts (TT), I shall call this the "engineering hypothesis" (but I get 100% of the royalties once I trademark it).

In my first TT post, Common Descent & Common Design - An Unexpected Outcome, I wrote how I found it unexpected, yet reasonable, that through the lens of FLE that the differences between common descent and common design evaporate and that common descent would be a design preference for the designer. Using evolutionary mechanisms to do the work through time is using the available energy and materials in an efficient manner. Why re-invent when one can "borrow" from previous designs? This also limits the amount of interventions by the designer to a minimum. To clear any confusion and misunderstanding, common design used in this fashion is different than what is used by human engineers in that it is front-loaded in the first designed life form rather than inserted at various times.

One commenter stated:

"...JJS seems perilously close to admitting he expects no detectable differences between the process in his engineering hypothesis and the process currently accepted by biologists."

There is a big difference. The "engineering hypothesis" implies the currently accepted processes, while valid for accounting for the variation of biological organisms, are not sufficient to start life. Thus, the process in the "engineering hypothesis" differs from the currently accepted process at the beginning of the process.

I should state that this is not a scientific way to detect design in nature, but merely an expansion of an origin of life hypothesis, of which there are many. I hope to be able to expand upon this in future posts, both here and at TT.

Tuesday, December 9, 2008

EE Blog News!

If there's one thing I've learned in life, it is that things change.

Blatant self-promotion warning!!!

I am now a contributing blogger at Telic Thoughts. I've always held TT in high regard, so it is an honour to post there. I plan on writing my first post soon.

I am also experimenting with W*rdPr*ss right now. I will notify everyone if I do decide to move EE. The reason for this potential change? Let's just say time and work are against me and a different location may help.

You may have noticed changes to the sidebar. I get bored easily, and my sidebar appearance is a casualty ;)

I hope to have a new post that is more relevant to EE soon. Stay tuned...

Sunday, December 7, 2008

A Glimpse Of The Future

Just as the analog age is coming to an end and the digitial (HD) age is upon us, along comes football in 3-D! On Thursday, the NFL Network experimented with implementing 3D technology during the Raiders-Chargers game. There were a few hiccups, but overall the reviews were largely positive (LA Times review here).

A few comments:

1. I wonder what it will be like when they work out the bugs?

2. I guess I can hold off that plasma or LCD TV. 3D is the future baby!

3. I bet Dr. Heddle can't wait for this technology to be used for NASCAR!

4. Speaking of other sports in 3D, I can't wait for this to come to hockey!

Friday, December 5, 2008

Dembski Has Dispensed With The EF. Big Deal!

This is a couple of days old, but this comment by Dr. William Dembski at UD has some tickled pink:

I’ve pretty much dispensed with the EF. It suggests that chance, necessity, and design are mutually exclusive. They are not. Straight CSI is clearer as a criterion for design detection.


For me, it's no big deal. I've said EF has had its shortcomings here. And apparently even hard-core ID defender Dave Scott saw it, too.

The asylum is open. Keep it clean.

Sunday, November 30, 2008

Free Time? What's That?? (Oh, And Don't Forget The 2 New Blogs In The Blogroll)

Techne, a new contributer to Telic Thoughts, has an interesting blog called The Teleomechanist. I say interesting loosely because I've only had a chance to skim through it briefly; I need some free time to give it the attention it deserves.

Anyhoo, The Teleomechanist has been added to my blog roll, and it is getting long! I may have to do a re-organisation of my blogroll closet soon (again, need free time which I do not have much of).

Oh, and I also added the Dilbert blog, too. Can't be an engineering blog without it! ;)

UPDATE 02 December 2008: 2nd attempt of re-organising done. I'm probably going to piss off everyone with this, but keep in mind this is not final, especially with all the distractions going on around the house.

Sunday, November 23, 2008

Calling All Engineers Who Want To Be A Part Of Evolution Engineered!

As to be expected when your chosen profession is engineering, work has a tendency to become insanely busy, which it recently has. Couple that with house issues (one of which may make an interesting post, once it becomes resolved) and family life, and I find myself with very little time for posting and/or commenting here at EE.

I am very pleased with how EE has developed during its short existence. There have been several excellent and lively discussions (sometimes too lively!). So much so that I have not had the time to properly investigate some commenters claims.

I have come to the conclusion that EE has become such a sucess that it is too much for one practicing engineer to maintain. Therefore, I am putting out a call for any interested engineers who wish to post here at EE. I don't care if you're on one side or the other; I believe I have more than demonstrated my tolerance for hearing out both sides. I want to hear what engineers think about evolution and ID.

For those interested in writing posts for EE, email me at JJS.PEng@gmail.com

Tuesday, November 11, 2008

Lest We Forget

I apologise for the lateness of this.

This post is dedicated to current and former soldier who fought, and still fight, for the freedom we enjoy.

Thursday, November 6, 2008

I Couldn't Have Say It Any Better...

"...natural selection doesn't "produce" anything. As Darwin himself wrote to his friend Charles Lyell, natural selection preserves certain forms and eliminates others. The real "engine" of change in biology is not natural selection, but rather the "engines of variation" that produce the blizzard of new forms, a few of whom survive and reproduce."
-Allen MacNeill @ TT
IMO, Allen MacNeill is absolutely correct. Natural selection cannot create/design anything. It is merely a filter.

My One (and Hopefully Only) Post on Global Warming

A couple of days ago, author Michael Crichton passed away. He was a gifted storyteller and someone who was not easily swayed by mainstream thinking. I particularly enjoyed reading one of his speeches from 2003 called "Aliens Cause Global Warming". As my salute to Michael Crichton, I present his speech to you for your reading enjoyment.

Saturday, November 1, 2008

Outside the Box, Back in the Blogroll

I once had the blog, Outside the Box (OtB), on my blogroll to the right, but removed it due to lack of updates. I can see now that was a mistake on my part. That is an error that is quickly corrected. OtB has made its return to the EE blogroll (which is getting quite large actually!).

With that done, I found several interesting posts @ OtB regarding the reasons for his belief (parts four and five to come). I encourage you all to read them and post comments, should you feel the need, just keep them clean.

Here are some excerpts I found interesting...

"...the arguments from fine-tuning, no matter how intuitively they point to a Creator, can never prove the existence of God. For me and many others, however, Occam’s razor (the logical construct which says, “All other things being equal, the simplest solution is the best”) leads us to a strong likelihood of a “superintellect” First Cause. The alternate explanations, while plausible, are complex and lack evidence. It is my view that the simplest solution is to credit fine tuning to the hand of the Designer, Planner, and Creator of the universe."
-Cliff Martin, "Reasons: I. Finely-Tuned Cosmos"

"Well, a priori [reasoning from cause to effect] one should expect that the world would be rendered lawful [obedient to law and order] only to the extent that we [human beings] intervene with our ordering intelligence... [But instead we find] in the objective world a high degree of order that we were a priori in no way authorized to expect. This is the ‘miracle’ that is strengthened more and more with the development of our knowledge."
-quote from Albert Einstein as posted by Cliff Martin, "Reasons: II. Ordered Universe"

"Denton uses the term “directed evolution” to help answer the inevitable questions about how complexity of such staggering proportions could ever come to self-organize. Mike Gene suggests another term, which I prefer: front loaded evolution. Both of these theorists have proposed that the incredibly elaborate machinery inside the cell, machinery composed of variously shaped protein molecules specified by RNA blueprints, demand a designer. Not the designer of the Intelligent Design theorists who propose a designer for complex organisms. Rather, the designer of the DNA process which is capable of building such organisms over time through the processes Darwin described."
-Cliff Martin, "Reasons: III. Markers of Intelligence"

It's November, and That Means...

...it's time for post-season football, Canadian style!

Unfortunately, one of my Canadian teams was eliminated today. The University of Saskatchewan Huskies fell to the Simon Fraser Clan (no that is not a typo, there is actually a team named "the Clan") 40-30.

However, the defending Grey Cup champions, the Saskatchewan Roughriders, have clinched home field for the CFL Western Semi-Finals next Saturday against the B.C. Lions. LET'S GO!!! RIDERS!!!

I'm hoping they repeat because my American teams ain't doing squat! Michigan just got eliminated from bowl contention today and the Seahawks are cursed with injuries.

Tuesday, October 28, 2008

In Case You Haven't Noticed...

... I have tried to steer my blog, Evolution Engineered (EE), towards more engineering topics. The posts, Redundancy - A Mark of Design? and WTC7 & ID have been, in my opinion, very successful in terms of providing stimulating and entertaining discussions. I hope to continue this trend in future posts, but I also reserve the right to post on stuff that interest me (call it the blogger's home field advantage).

I hope you continue to enjoy visiting and commenting at EE.

Thursday, October 23, 2008

Information Theory Post at PT

I'd like to think that I have a reputation of being fair to both sides of the ID/evolution debate, giving credit and criticisms where due.

That said, I enjoyed a recent post at Panda's Thumb by PvM entitled "Information Content of DNA" (see my blog roll at the right). I found the post to be interesting and fair. I would have preferred more details (i.e. equations, reference papers) to support the claims made, but I'm sure someone will point me in the right direction.

As some of you know, I believe Information Theory is a key area of interest/research in biology and could help shed light on the ID/evolution debate. The tricky part is determining exactly what constitutes information in biology, something the PT post commented on.

Monday, October 20, 2008

Critical Thinking

From a post at Mike Gene's blog. I particularly like numbers 2 and 4:

"2. understand and define terms (make others define terms, too)

4. question the conclusion: do the facts support it? is there evidence of bias? remember correlation does not equal causation."

Sunday, October 19, 2008

Free Plug For AcademicFreedomBlog

I like the blog AcademicFreedomBlog so much that it is part of my blog roll at the right. Like Tom Gilson at Thinking Christian (another free plug!), I find Dr. Mc's commentary to be even-handed and level-headed.

In the latest post, Baraminology and Pseudoscience, Dr. Mc made some, what I will call, in-your-face comments; direct and brutally honest (IMHO):

"The current classification structure of genus (meaning general) and species (meaning specific) is bankrupt.I don’t think that’s too strong a statement, since after hundreds of years of use a clear definition of what a "species" is has not emerged. Take for instance the coyote ( Canis latrans), the gray wolf (Canis lupus), and the black backed jackal (Canis mesomelas). They are classified as three different species in the genus Canis, yet domesticated dogs of any description are all considered to be the same species (Canis familiaris). The term virtually has no meaning. So why haven’t scientists abandoned this antiquated classification system, developed by an 18th century creationist, in favor of a more precise one? Because fuzzy boundaries serve evolution theory well. If clear boundaries are discovered between classifications of organisms, then that lends support to creationism and undermines evolution. So science is not allowed to advance in that direction! In order to keep baraminology as pseudoscience, we must live with pseudospecies."


I would encourage you to make any comments you feel are necessary over at AcademicFreedomBlog. I am too busy at work to follow the comments at EE (with the exception of this one).

Saturday, September 20, 2008

Paging Dr. Heddle (or Some Other Physicist-Type Person)!

Thanks to a lack of posts that I feel I can competently comment on or are worth commenting on (I blame you UD and AtBC!), I was wandering down one of my favourite site, What You Ought to Know, and watched the episode, Gravity, You Failed Us.

I want to know two things:

1. Explain in layman terms - or maybe undergrad physics terms - what the big deal is with solving for a Three-Body System, and

2. Is there something to this "Electric Universe" thingy?

Feel free to discuss here,

Cooption Confirmed?

I'll just point you to Mike Gene's blog post and you can come back and discuss here.

Friday, September 19, 2008

WTC7 and ID

During the comments of a recent post, it was suggested I look into the collapse of WTC7 from September 11, 2001. A theory going around the web suggested that the collapse was due to a controlled demolition. Not being a big fan of conspiracy theories (which this sounded like one to me), I was skeptical, but I looked into it and found this briefing from the National Institute of Standards and Testing (NIST) dated August 21, 2008. The following is from the linked briefing:

Determining the probable collapse sequence for WTC 7, NIST found that the impact of debris from the collapse of WTC 1 ignited fires on at least 10 floors of WTC 7, and the fires burned out of control on six lower floors. The heat from these uncontrolled fires caused thermal expansion of the steel beams on the lower floors of the east side of WTC 7, damaging the floor framing on multiple floors. Eventually, a girder on Floor 13 lost its connection to a critical interior column that provided support for the long floor spans on the east side of the building. The displaced girder and other local fire-induced damage caused Floor 13 to collapse, beginning a cascade of floor failures down to the fifth floor. Many of these floors had already been at least partially weakened by the fires in the vicinity of the critical column. This collapse of floors left the critical column unsupported over nine stories.

“When this critical column buckled due to lack of floor supports, it was the first domino in the chain,” Sunder explained. “What followed in rapid succession was a progression of structural failures. Failure first occurred all the way to the roof line—involving all three interior columns on the most eastern side of the building. Then, progressing from east to west across WTC 7, all of the columns in the core of the building failed. Finally, the entire façade collapsed.”

The investigation team considered the possibility of other factors playing a role in the collapse of WTC 7, including the possible use of explosives, fires fed by the fuel supply tanks in and under the building, and damage from the falling debris of WTC 1.

The team said that the smallest blast event capable of crippling the critical column would have produced a “sound level of 130 to 140 decibels at a distance of half a mile,” yet no noise this loud was reported by witnesses or recorded on videos.

As for fuel fires, the team found that they could not have been sustained long enough, could not have generated sufficient heat to fail a critical column, and/or would have produced “large amounts of visible smoke” from Floors 5 and 6, which was not observed.

Finally, the report notes that “while debris impact from the collapse of WTC 1 initiated fires in WTC 7, the resulting structural damage had little effect in causing the collapse of WTC 7.”


A chain of probable causes was discovered and laid out in detail by the NIST investigative team. The bottom line: the evidence did NOT point towards controlled demolition.

This parallels the situation of ID: how can we determine if design is a legitimate explanation? At first glance, it may look like design, but peer deeper into the details, and the design may show itself to be an illusion.

Mike Gene has laid out how we may investigate our suspicions in The Design Matrix, but he leaves it at the investigation stage. This is perhaps due in part to ID being "a nascent protoscience".

So let's open the floor for comments. The theme is "By purpose or by accident: how can we tell?"

Welcome to BLOG-O-RAMA-RA-MA!

It is BLOG-O-RAMA-RA-MA time! The rules are simple: how many posts and comments can I do in a 48-hour period?

Remember, it's not just any old blog-o-rama: it's BLOG-O-RAMA-RA-MA!!!

Post Count:
1. WTC7 and ID
2. Cooption Confirmed?
3. Paging Dr. Heddle...

Comment Count:
1. EE (yes, my blog counts too) ;P
2. Thought Provoker
3. Thinking Christian
4. Exiled From GROGGS
5. EE
6. EE
7. EE
8. EE
9. Reasonable Kansans
10. Coincidence Theories
11. EE
12. Reasonable Kansans
13. Reasonable Kansans
14. Coincidence Theories
15. Coincidence Theories
16. EE
17. EE
18. EE
19. Coincidence Theories
20. Coincidence Theories
21. EE

Thursday, September 18, 2008

Paging Dr. Phil (Plait That Is)

Many of you may have noticed a link I have to Dr. Phil Plait's Bad Astronomy site that debunks the Moon Landing Hoax theory quite nicely. Well, I have a bone to pick with Dr. Phil.

It's kil-AW-met-er, not KILL-o-mee-ter. So :P

And those "right-thinking people" who applauded you either don't follow hockey (which means they're not real Canadians) or they're geeks who live in their mother's basement own little world. So double :P

And yes I know I'm just a little bit late in responding to this, but hey, this makes a good "unofficial" start to BLOG-O-RAMA-RA-MA*, eh?

The comments for this post are reserved for humourous verbal smackdowns (but leave yo' mama out of it).

*Just for Dr. Phil, it's pronounced BLAWG-OH-RAHMAH-RAH-MAH

BLOG-O-RAMA-RA-MA This Saturday!!

It's not very often I have time to roam the blogosphere and leave comments here and there. This Saturday (and possibly this weekend) will be one of those times.

So I'm having fun with this. I hereby christen this weekend BLOG-O-RAMA-RA-MA! Tune in for comments galore and maybe even a post or two!

BLOG-O-RAMA-RA-MA! Buy all our playsets and toys!

Side note: I am disabling comment moderation on a trial basis. Your comments should be appearing in real-time now.

UPDATE: It has occured to me that many may ask "What exactly is BLOGORAMARAMA?" I will set up a post listing all the comments I've left behind at various blogs on Saturday night (maybe I'll cheat and start Friday). Any bets I can make 100?

Thursday, September 11, 2008

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.

Monday, September 8, 2008

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.

Wednesday, September 3, 2008

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?

Tuesday, September 2, 2008

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.

Friday, August 29, 2008

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.

Wednesday, August 13, 2008

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)

Monday, August 11, 2008

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.

Sunday, August 3, 2008

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

Friday, August 1, 2008

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

Thursday, July 31, 2008

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

Good Post at Thinking Christian

Tom Gilson @ Thinking Christian has a good post that nicely expresses my views on the subject (with one exception which I expressed in the comment section here).

Get thee to T.C. and read all about it!

:)

Wednesday, July 30, 2008

The Gould Fan Club Speaks!

I kid, of course. The masses (all three of them) have spoken, and the next book I shall read will be Punctuated Equilibrium by the late Stephen Jay Gould, which 2 of the 3 voters selected.

There is still plenty of time to vote on the other poll: What book shall I order:
Endless Forms Most Beautiful - Sean Carroll (2 votes)
Evolution: A Theory In Crisis - Michael Denton (1 vote)
Your Inner Fish - Neil Shubin (0 votes)

Thanks to all three of you for voting. :)

Monday, July 28, 2008

WTF Dembski?!!

There are a couple things on my mind today (other than getting wrapping up details of a project at work). One is on the content of the IC post I'm working on, the second regards the latest antics by Dr. William Dembski.

First, let me say that Dembski is smart and has made significant contributions to the foundation of ID. That said, his behaviour is troubling, bordering on bewildering and asinine.

There are two specific incidents that have left me shaking my head. The first is this post at UD. Two things bother me about it. The first is the picture that goes with the post. There was no need for it as it did not contribute at all to the message other than to denigrate the subject, Olivia Judson. When I first saw it, I said, "WTF Dembski! What were you THINKING?!" I think the answer is self-evident. The second was this "gem" of a quote:

"Could we please dispense with any patronizing nonsense about Darwin being less than the messiah of a materialistic religion that pretends to find its justification in science. If Darwin was not the alpha and omega of evolution, then he was either a knave or a fool or a madman. Darwin did not leave us any other options. He did not intend to. [Hat tip to C. S. Lewis.]"

This is an insult to C.S. Lewis's original argument and doesn't even rank as a third-rate knockoff. All this quote does is to further reinforce opposition opinions that Dembski is fueling the culture wars.

The second incident occurred this morning when Dembski banned one of the most thoughtful commenters at UD, Bob O'H. Bob provided a good balance to the discussions at UD and is one of the reasons I like lurking there. When I first saw the comment, it was another "WTF Dembski?" moment.

As someone who is sympathetic to teleology/design-in-nature standpoint, I am greatly disappointed. We (myself included) are not perfect, but need to be called to accountability. These actions do nothing to further the debate or the ID cause, just to exacerbate tensions that need cooling desperately.

Dr. Dembski, I urge you to re-instate Bob O'H and, at the very least, delete that picture. If this post gets me banned from commenting at UD, so be it. It had to be said.

Thursday, July 24, 2008

New Book Order Soon

Now that I've finished reading 3 out of 5 books from my previous book order and am about to start #4, it's time to start considering a new book order. So let's have some fun, eh?

Poll #1:
My book order thus far consists of:
Information Theory, Evolution, and the Origin of Life - Hubert Yockey
Invention by Design: How Engineers Get From Thought to Thing - Henry Petroski
Nature, Design, and Science: The Status of Design in Natural Science - Del Ratzsch

You get to decide what the fourth book in my order will be from the following options.
1. Endless Forms Most Beautiful - Sean Carroll
2. Evolution: A Theory in Crisis - Michael Denton
3. Your Inner Fish - Neil Shubin

Poll#2:
I have two books left from my previous book order. Which one should I read next?
1. The Edge of Evolution - Michael J. Behe
2. Punctuated Equilibrium - Stephen Jay Gould

Both polls can be found at the top right of this site. I will order/read the books selected by the final poll results.

Have fun!

The Explanatory Continuum

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

All quotes in this post are from Chapter 2 of The Design Matrix.

The Traditional Template

It appears one of Mike Gene’s goals in writing the Design Matrix is to change the current structure of the ID/evolution debate, which he calls the “Traditional Template”.

"…proponents of design look for some feature that cannot possibly be explained by natural causes. Then, once a feature has been proposed, it is argued that only a designer can account for the existence of this feature. (Emphasis mine)

The Traditional Template assigns the non-teleological explanation the default status.

…because this template pushes the design proponent into the position of opposing Darwinian evolution, the design proponent ends up trying to prove a negative.
Proving a negative is notoriously difficult to do for any topic." (Emphasis not mine)

Thus, it would seem that the Traditional Template is a “rigged” debate. Darwinian evolution is presumed “true” and teleologists are left with unenviable task of proving it impossible. The Template is analogous to a defendant having to prove his innocence in a court of law, which is contradictory to our system of law (innocent until proven guilty). Gene implies that it is the job of the proponent (prosecutor) to provide evidence to support his suspicion (charge).

Enter the Explanatory Continuum

How is this done? It starts when the detective first arrives at the scene of the crime. He starts with a hunch and looks for clues to support it and move forward by looking for more incriminating evidence. When enough clues are gathered to get a conviction, an arrest is made. The Design Matrix suggests this is similar to what occurs with the historical sciences, such as evolutionary biology.

Following in the footsteps of the detective analogy, Mike Gene proposes an Explanatory Continuum with the following steps:

1. Impossible
2. Possible*
3. Plausible
4. Probable
5. Fact

Mike Gene suggests that “All investigations must begin with a hunch or suspicion.”, and then grants the possibility of the hunch or suspicion; IOW, all investigations begin at step 2 of the Continuum. This is a radical change from the Traditional Template because all arguments start at the same point in the Continuum. Even though this is a huge step forward (and possibly relief) for teleologists, granting design in nature as a possibility is NOT the end of the investigation.

"Possibilities do not really carry that much weight when trying to account for something that actually happened."

Thus, all suspicions are encouraged to move forward through the Continuum. As defined by Mike Gene, the next step is “plausible”. To move from possible to plausible, some circumstantial evidence needs to be dug up that supports the “suspicion”. Experiments need to be proposed and performed, data collected, and so on. There is work involved to move from the possible to the plausible. But what does it mean that a suspicion is plausible?

"Plausible explanations function to arouse or heighten suspicion but are in need of more evidential support."

IOW, even though our certainty level has increased, more evidence and investigation is required to move forward through the Continuum. The next step forward is “probable”. One moves from plausible to probable as the result of:

"…a vast amount of data that all converge and best make sense in light of the explanation. The probable emerges when it becomes clear to unbiased observers that the explanation is the best way to account for all the relevant data." (Emphasis mine)

Note that “a vast amount of data” is required to move from plausible to probable, which could take years to accumulate, maybe even decades. Also note that the level of fact is approached, but rarely attained. This allows for new and contradictory evidence to be taken into consideration.

Scientific Certainty Revisited

A couple of months ago, I created a post referencing this post at An Evangelical Dialogue on Evolution that listed six meanings for the word evolution and arranged them according to levels of scientific certainty. After reading The Design Matrix, I wondered how these meanings fit into the Explanatory Continuum. So I propose that we take a look at the six meanings of evolution through the lens of the Explanatory Continuum. Please refer to the linked post for a more complete definition of each meaning.

E1. Change over time: I think everyone would agree this would fall into the probable category.

E2. Common ancestry: According to the scientific world and Evangelical Dialogue, this would fall under probable, but why? It would appear that E2 is closer to the boundary of probable and plausible since much of the evidence appears circumstantial and any “hard” evidence either appears to be lacking or is controversial. That said there are two reasons for E2 to be in the probable category: no competing hypothesis and the shear weight of the accumulated circumstantial evidence. Both lend credibility for E2 to be considered probable.

E3. Evolutionary mechanisms: not much controversy here – this falls squarely in the probable category. However, an argument could be made that the mechanisms are well established enough to be considered fact, of which I would have no problem with. After all, the controversy is not whether the mechanisms (gene duplication, genetic shift, etc.) exist, but how they are applied, which brings us to…

E4. Mechanisms (E3) account for (physically) common descent: Charles Darwin argued for the possibility of natural mechanisms to describe the history of life. 150 years later, there is only circumstantial evidence to support Darwin’s hunch. Therefore, E4 falls in the plausible category.

E5. Origin of life (or chemical evolution): This is an interesting category. Circumstantial evidence has come and gone over the years with nothing really sticking. Given Mike’s definition of the Explanatory Continuum, E5 automatically starts at the possibility stage. Is there interesting research occurring in the OOL field? Absolutely. Has the research produced enough circumstantial evidence to proceed forward to the plausible stage? IMO, no.

E6. Evolutionism: This is stuck (and I predict will remain stuck for a long time) in the possible stage. After all, anything’s “possible”.

Summary

Mike Gene’s Explanatory Continuum is a radical shift in the current structure of the evolution/ID debates because it provides more maneuverability and puts the onus on the proponent to provide evidence to prop up his hunch. The “suspicion of design” (a phrase found often throughout The Design Matrix) can be acknowledged while recognizing that evidence is required to progress forward (from possibility to plausibility and from plausibility to probability). So where does that leave ID at this point?

"The debate between teleology and non-teleology is at least 2500 years old and has involved some of history’s greatest thinkers. … But if history spans 2500 years or more, consider the possibility that the non-teleological view has just recently gained the upper hand with more sophisticated versions of the same arguments from old. Teleologists have the potential of evening the playing field somewhat by also reviving their arguments in more sophisticated versions."

Roll up your sleeves, ID; there’s work to be done.

*Note that the Traditional Template falls within steps 1 and 2 of the Explanatory Continuum.

Sources:
Gene, M., The Design Matrix: A Consilience of Clues, 2007
An Evangelical Dialogue on Evolution, “What Does Evolution Mean? A Framework For Christians”

Next post: Irreducible Complexity

Wednesday, July 23, 2008

What You Ought To Know About Autism

I just thought I'd throw this out at ya. Enjoy!

Lessons from the Scablands

Last night, I watched an intriguing episode of NOVA called Mystery of the Megaflood which provided the scientific evidence that the Scablands were formed by a catastrophic flood that was caused by the abrupt (brittle?) failure of an ice dam thousands of years ago. I would encourage everyone to watch this very education and eye-opening show.

Watching Mystery of the Megaflood also made me think of the evolution/ID debates and what lessons can be applied from this:

1. Gradualism is not always the answer. Geology has been dominated by gradualism: geological formations are best explained by erosion via water and/or wind or other mechanism over large periods of time. Catastrophic events were shunned. In fact, when J. Harlen Brentz presented his hypothesis of how the Scablands were formed in 1923, he was ridiculed. However, his hypothesis was later vindicated.

Just as Catastrophism was/is frowned upon by the geological establishment, so is a similar hypothesis frowned upon by the majority of evolutionary biologists: saltationism. Could saltationism be vindicated sometime in the future?

2. A qualifier to point 1 is that Brentz's hypothesis was vindicated due to a large amount of scientific investigation over a period time. Brentz wrote his paper in 1923, his insights were vindicated by the 1950's, and the details were filled in around the 1990's. The point: Catastrophism needed a wealth of scientific experimentation and verification, something that ID is sorely lacking at present. The term "Less talk and more action" seems appropriate.

3. How Brentz's hypothesis was accepted is a great example of how to go through the Explanatory Continuum as proposed by Mike Gene in The Design Matrix: it started as a possibility in 1923 (a remote one); then circumstantial evidence was gathered and the hypothesis progressed to being plausible (1950's); details were filled in such that the hypothesis is now seen as probable (1990's). Note that almost 70 years were needed to progress from possible to plausible to probable. See Chapter 2 of the Design Matrix for more on the Explanatory Continuum.

On an engineering side note, I found the small-scale models presented interesting and educational. However, as any engineer knows, what works at a small scale does not completely translate to a larger scale. This is called "scale effect", and I'd be interested in knowing what scale effects there are in this research.

Monday, July 14, 2008

The Altenberg Sixteen and The EES

Suzan Mazur has been writing on the so-called Altenberg 16 Summit that occured last week. Now she is writing an e-book on the summit, and she has some harsh words regarding the current synthesis (Neo-Darwinian Evolution or NDE) and natural selection:


Evolutionary science is as much about the posturing, salesmanship, stonewalling and bullying that goes on as it is about actual scientific theory. It is a social discourse involving hypotheses of staggering complexity with scientists, recipients of the biggest grants of any intellectuals, assuming the power of politicians while engaged in Animal House pie-throwing and name-calling: "ham-fisted", "looney Marxist hangover", "secular creationist", "philosopher" (a scientist who can’t get grants anymore), "quack", "crackpot". . .

In short, it’s a modern day quest for the holy grail, but with few knights. At a time that calls for scientific vision, scientific inquiry’s been hijacked by an industry of greed, with evolution books hyped like snake oil at a carnival.

Perhaps the most egregious display of commercial dishonesty is next year’s celebration of Charles Darwin’s Origin of Species – the so-called theory of evolution by natural selection, i.e., survival of the fittest, that was foisted on us almost 150 years ago.

Scientists agree that natural selection can occur. But the scientific community has known for some time that natural selection has nothing to do with evolution. ...

I broke the story about the Altenberg affair last March with the assistance of Alastair Thompson and the team at Scoop Media, the independent news agency based in New Zealand. ... But will the A-16 deliver? Will they help rid us of the natural selection "survival of the fittest" mentality that has plagued civilization for a century and a half, and on which Darwinism and neo-Darwinism are based, now that the cat is out of the bag that selection is politics not science? That selection cannot be measured exactly. That it is not the mechanism of evolution. That it is an abstract rusty tool left over from 19th century British imperial exploits.

Or will the A-16 tip-toe around the issue, appease the Darwin industry and protect foundation grants?

-Suzan Mazur


Eeeyikes! Just think what she would have wrote if the topic were creationists!

All kidding aside, there does seem to be, at the very least, a degree of frustration with the role natural selection plays in evolution. Suzan reports that cytogeneticist, Antonio Lima-de-Faria, author of "Evolution Without Selection", "sees any continuance of the natural selection concept as 'compromise'." She also accuses science blogs of "stonewalling" new ideas such as self-organisation:


...one of the stars of the symposium, New York Medical College cell biologist Stuart Newman, hypothesizes that all 35 animal phyla self-organized at the time of the Cambrian explosion (a half billion years ago) without a genetic recipe or selection (hardwiring supposedly followed). Emphasis mine


Allow me to address two items. First, I can see why the science blogs* are bristling at either setting aside or demoting natural selection. Take away NS and all you are left with is one big game of Yahtzee. IOW, evolution without the contingency of NS becomes a framework of chance. If this is true, then I think it's obvious that the new synthesis will be weaker than the one it replaces. What would you prefer: pure chance or chance coupled with contingency?

Second, this could very well be a case of a reporter "glamorising" a simple symposium to sell her article and get her name out there. Take the words of Massimo Pigliucci (HT to Todd Berkebile @ TT):


So, what are the Altenberg 16 going to do in Altenberg next week? ... The agenda is to discuss the current status of evolutionary theory, with a particular emphasis on developments -- some of them under intense debate -- that have occurred since the last version of it has been in put in place back in the 1930s and ‘40s. ...

In the 1930s and ‘40s it became clear that one had to integrate the original Darwinism with the new disciplines of Mendelian and statistical genetics. Such integration occurred through a series of meetings where scientists discussed the status of evolutionary theory, and through the publication of a number of books by people like Theodosius Dobzhansky, Ernst Mayr, George Gaylor Simpson, George Ledyard Stebbins and others. The result was an updated theoretical framework known as the Modern Synthesis (MS). But of course evolutionary biology has further progressed during the last eight decades (unlike, one cannot help but notice, creationism). So for a few years now several evolutionary biologists have suggested that it may be time for another update, call it evolutionary theory 3.0 or, as many of us have begun to refer to it, the Extended Evolutionary Synthesis (EES)**.

A number of authors, including Stephen Gould, Mary Jane West-Eberhard, Eva Jablonka, Stuart Kauffman, Stuart Newman, the above mentioned Gerd Müller, and myself, have published papers and books recently attempting to articulate what an EES might look like, and which elements of the MS will need to be retained, modified or discarded (just like the MS had retained, modified or discarded individual components of the original Darwinism). The goal of the Altenberg workshop is to get some of these people around the same table for three days and trade ideas about these sorts of questions.


So is this a case of tip-toeing to "appease the Darwin industry and protect foundation grants", or is Suzan Mazur exaggerating the outcome of the summit?

The asylum is now open for comments.

HT to Grandma O'Leary @ Post-Darwinist

*I am sure that not all of the science blogs are "stonewalling". This is likely a generalisation on Suzan Mazur's part that isprobably accurate for the majority of the science blogs out there.

**I would encourage everyone to read this pdf file describing the framework for the Extended Evolutionary Synthesis (myself included). After all, this is the potential new synthesis many anticipate will come from meetings like Altenberg. Time will tell whether the EES survives or not.