Open Discussion on "Confirmed Prediction" of ID

I am an equal-opportunity critic.

On the one side, UCD still causes a little "niggle" to go off in the back of my head that tells me something ain't quite right. I may not know how to describe it at this time, but eventually I may. The discussion of the confirmation of UCD from the previous post is one example.

On the other side is a recent post by Patrick at Uncommon Descent entitled "ID-Compatible Predictions: Foresighted Mechanism Identified?".

First the positive. A recent experiment showed that the genes in E.Coli "reacted" to changes in temperature:

"Indeed, upon transition to a higher temperature, many of the genes essential for aerobic respiration were practically turned off.

"To prove that this is not just genetic coincidence ..., the researchers then grew the bacteria in a biologically flipped environment where oxygen levels rose following an increase in temperature. Remarkably, within a few hundred generations the bugs partially adapted to this new regime, and no longer turned off the genes for aerobic respiration when the temperature rose"
-PhysOrg article

To sum up, inactive genes were activated and active genes were rendered inactive due to a change in environment.

Patrick claims this is an example of a prediction he made: foresighted mechanism/front loading. A foresighted mechanism, if identified conclusively, should be considered an objective sign/aspect of design, and thus confirmation of "ID-Compatible Prediction" (side note: dontcha just love the term ID-Compatible?).

Don't misinterpret what I'm saying here. This is NOT conclusive evidence of fore-sighted mechanism/front loading. However, just like the partial confirmation of "junk DNA" having function from the ENCODE project, it is a tantalising first step (Patrick does acknowledge this in the opening of his post regarding junk DNA and other "ID-Compatible predictions").

So what now? It is obvious that further research is required, or as Dr. Heddle so nicely puts it, "Show Me the Experiment[s]!" The prediction needs to be refined and focused.

Also, IMO, too much emphasis was placed on intelligence in Patrick's post when - according to Sal Cordova and others - we do not have a solid definition of intelligence. However, as Sal nicely puts it, design is more tractable and this is where the focus should be on. Objective aspects of design exist (passive design) and can be universally observed. Developing and defining passive design* (or something along those lines) should be the focus.

Bottom line, the experiment is a good start, but much more needs to be done.

The "asylum" is now open.**

*I know I keep dropping hints of this thing called "passive design". I can only say "stay tuned" and "please be patient"; it is coming. :)

**This is just my unique way of opening the floor for comments ;)

Open Discussion on Confirmed Prediction of Common Descent

Dr. David Heddle - no fan of ID and no advocate of evolution - recently posted a comment at Telic Thoughts referring to a confirmed prediction of common descent. I asked him for a source and he kindly directed me to this site which also provided this paper, which described the fusing of two primate chromosones to form 1 human chromosone. This provides strong evidence of common descent, going from 24 primate chromosones to 23 human chromosones.

Being an engineer and not being a biologist/geneticist, some honest questions have come to my mind after reading through the references above:

1. Are the remaining 22 chromosones identical between humans and primates?
2. Are the experiment conditions listed in the paper comparable to "actual" conditions? [I'm still trudging my way through the paper, but I find reading biologist-ese difficult; I require a translator ;) ]

This an open invitation to civil discussion on the above references. Ad hominem comments are not welcome and will be deleted.

Side note: this appears to be along the lines of what Dr. John A. Davison is proposing, that macroevolution occured in the chromosones, not the genes.

It's Like We're in a Detective Novel...

I recently made the comment:

"Your argument is analogous to arriving at an automated assembly plant for cars and stating that the robots "assembled" the cars and there was no need for human engineers when in fact it was human engineers who designed the robots to assemble the cars which were designed by human engineers."

The problem with this analogy is the origins of the robots: it could very well be possible that something else rather than human engineers "designed" the robots or the robots could have always existed. That said, the analogy does do a fairly good job of describing the situation we find ourseleves in. It is like we have entered an "automated" world full of machinery, assembly plants, and factories. So how do we make sense of it all?

A similar analogy was recently put forward by Mike Gene at Telic Thoughts where he more broadly and skillfully illustrates the predicament we find ourselves in:

"Consider some movie where you, the viewer, know that Jones killed Smith, because you watched it happen. Jones, of course, subjectively knows that he killed Smith. The police investigator doesn’t know this, he simply believes that Jones killed Smith because of some clues. The investigator then privately confronts Jones and accuses him of murder. Jones, privately knowing the investigator is correct, simply replies, “There is no evidence and you can’t prove it” and the investigator knows this is true.

Right there, in that scene, we see the difference between evidence and truth. Relying solely on the evidence may very well deliver only a superficial, or even false, understanding of the world."

So let's open up the comments with this: how do we determine whether design is an illustion or not, and perhaps more interesting, should we be making that judgment at all?

Note: I am a supporter for a side-by-side paradigm where those who believe design is an illusion can work productively with those who think design is not an illusion. Both side have interesting things to bring to the table while keeping each other in check.

Friday Funnies

It's tough living with "The Knack"... ;P

The Missing Link in Dr. Kenneth Miller's Rebuttal of Irreducible Complexity

"From an engineering perspective it would make the most sense for evolution to coopt components already available for molecular machines like the flagellum. However, that is not anywhere near enough. Structures like the flagellum bear such a striking similarity to human made machines that one would also expect them to also have a very tight specificity in both the components and the assembly instructions. The components that make up the motor, the bearings, the universal joint, the whip, etc are interdependent on one another not just from the conformal standpoint but also in their dynamic characteristics (i.e. tensile and torsional strength, toughness, torque, rpm, modulus of elasticity, temperature variances, fits and tolerances, and on and on. At least if one was to design such a device there would be hundreds of design decisions to make and exponentially many more ways to foul up than to make it work.

... Then even if all the components were just right, there still has to be tightly controlled assembly processes that are also interdependent. When I think of all the tightly specific mutation sets required for all this, I'm just bewildered how it could come about without an intentionality of some sort."

Steve Petermann commenting at Telic Thoughts

Bingo!

My Library

Just doing some house cleaning, folks. I figure this will make the side bar less tedious to look at. All links are included, where applicable.

Currently in My Library - Design:
Darwin on Trial - Phillip E. Johnson
Darwin Strikes Back - Thomas Woodward
Darwin's Black Box - Michael J. Behe
The Design Matrix: A Consilience of Clues - Mike Gene
The Design Revolution - William A. Dembski
Doubts About Darwin - Thomas Woodward
Mystery of Life's Origin - Charles B. Thaxton, Walter L. Bradley, Roger L. Olson
Nature, Design, and Science: The Status of Design in Natural Science - Del Ratzsch
The Politically Incorrect Guide to Darwinism and Intelligent Design - Jonathan Wells
The Privileged Planet - Guillermo Gonzalez and Jay Richards

Currently in My Library - Engineering:
Design Paradigms: Case Histories of Error and Judgment in Engineering - Henry Petroski
Structures: Or Why Things Don't Fall Down - J.E. Gordon
To Engineer Is Human: The Role of Failure in Successful Design - Henry Petroski

Currently in My Library - Evolution:
The Edge of Evolution - Michael J. Behe
Punctuated Equilibrium - Stephen Jay Gould

Currently in My Library - Christian:
The Abolition of Man - C.S. Lewis
The Case for a Creator - Lee Strobel
The Case for Christ - Lee Strobel
The Case for Faith - Lee Strobel
The Case for the Real Jesus - Lee Strobel
Know Why You Believe - Paul E. Little
Mere Christianity - C.S. Lewis
The Screwtape Letters - C.S. Lewis

Currently in My Library - Fiction:
Animal Farm - George Orwell
Brave New World - Aldous Huxley
The Hobbit - J.R.R. Tolkien
Lord of the Rings Trilogy - J.R.R. Tolkien
The Silmarillion - J.R.R. Tolkien
State of Fear - Michael Crichton

Possible Future Additions to My Library:
1984 - George Orwell
The Chronicles of Narnia series - C.S. Lewis
The Descent of Man - Charles Darwin
Endless Forms Most Beautiful - Sean Carroll
Evolution: A Theory in Crisis - Michael Denton
The Funeral of A Great Myth (from Christian Reflections) - C.S. Lewis
Information Theory, Evolution, and the Origin of Life - Hubert Yockey
Invention by Design: How Engineers Get From Thought to Thing - Henry Petroski
On the Origins of the Species - Charles Darwin
Summer For the Gods: The Scopes Trial and America's Continuing Debate Over Science and Religion - Edward J. Larson
The Trouble With Physics: The Rise of String Theory, The Fall of a Science, and What Comes Next - Lee Smolin
What Darwin Got Wrong (scheduled for 2009 release) - Jerry Fodor and Massimo Piatelli-Palmarini

Nope! No Humility Here!

From the post Mike Lange = Quotation Gold:

As much as I'll be cheering for the Pens, reality says the Red Wings will win the Cup in 6.

D@mn, I'm good!

My Book Order Came In!

Amidst all the chaos, my Amazon order of 5 books came in.

Darwin's Black Box

Punctuated Equilibrium

The Design Matrix

The Edge of Evolution

All interesting books, and you get to vote which one I'll read second because the one I read first was:

Transformers: Devastation!

Quick synopsis: Decepticons rule! Autobots drool!

P.S. Don't forget to vote ;)

EE at One Month - A Look Back

Now that I have some free time while the windows in my home get replaced and the landscapers are tearing up my yard, I think it is a good time to look back on one month of blogging at Evolution Engineered (EE).

It has been an interesting and informative experience. I have been blessed with thoughtful commentators who make very good points. There have been lessons learned, projects started and in-progress, and just a whole lot of fun in between. Where to start?

Lessons Learned

There are two that immediately come to mind.

1. The evolution debates that I have been involved in have yielded surprising results (to me, anyway). I was expecting to debate the merits of the Neo-Darwinian Evolutionary Synthesis (NDES) espoused by Julian Huxley and, more recently, Richard Dawkins.

That didn't happen.

The arguments made by both Paul (from Thinking Christian) and RBH (in Oops, I Did It Again!) did not depend solely on NDES. It was because of this (in part) that I had to take a step back from my debate with RBH to re-assess.

The points made by Paul and RBH, coupled with the Altenberg 16 summit coming up, could very well mean an overhaul of the evolution debate as we (the general public) know it.

2. There are commentators that can keep one honest and help fine-tune one's arguments. I have found that the previously mentioned Paul and Tony Hoffman (in The Expelled Syndrome) fit that role to a T. Commentators like those two mean I will have to be extra dilligent in future posts, which is a good thing.

Of Mud Pies and Proteins - The C.D.F.

EE was created, in part, to serve as a launching point for the Conceptual Design Framework. As all readers can see, it is a work in progress. There are two items I am examining at this point.

1. The Toddler Mud Pie problem. Is this an example of no-design or a low-level design?

2. Proteins - I am assembling an argument of design based on the C.D.F. There is still much to review and ponder on this.

These two items are not the only issues facing the C.D.F. - and yes, I do find it a little humbling that only I have commented on it thus far (is it THAT bad???). I look forward to developing the C.D.F. in the near future.

Reviews, Reviews, Reviews

The review of a chapter in Know Why You Believe by Paul Little was my first ever review. I am looking to get better with future reviews:

1. The Abolition of Man by C.S. Lewis - a planned three-part series, each part dealing with each lecture (Men Without Chests, The Way, and The Abolition of Man).

2. The Privileged Planet by G. Gonzolez and J. Richards - my favourite "ID" book.

Future Project

Three words: universal common descent.

My debate with RBH started with a lingering doubt I had over the "certainty" of UCD. It was like I have doubts about it, but I can't put into words what exactly bothers me about it (scientifically, not theologically).

Then, I ran across an article in TalkOrigins titled 29+ Evidences for Macroevolution: The Scientific Case for Common Descent, by Dr. Douglas Theobald. Here is an article that has been fine-tuned and provides a neat summary for all the scientific evidences for UCD (or CD).

I plan on using my engineering training and knowledge of design* to look at and possibly propose alternative explanations for the evidences provided. It will be a huge task to make my case as robust and "iron-clad" as possible.

Final Remarks

sigh! Blogging is a lot more work than I thought, but the rewards are worth the effort! I look forward to corresponding with current and future commentators, and to constructive criticisms. Thank you all for keeping your stick on the ice!

Note: I am open to have other engineers make posts on this site. If interested, email me at jjs.peng@gmail.com

* Freelurker: I am aware of our previous conversation, but I do believe that engineering design and design in nature have aspects that overlap. If I am out in left field with my points, let me know.

Yoko Ono No Go

Yoko One lost in her bid to block distribution of Expelled. See here, here and here for details (the CTV.ca link is where I first learned about this).

I guess Expelled is coming to Canada after all.