A Challenge

Lately, I've found myself quoting and referring to The Design Matrix to answer questions from critics of front-loaded evolution (FLE). A lot of frustration could be avoided if the book was actually read and any references could be quickly looked up by both advocates and critics.

I also want to thank the critics here at EE by name.

Freelurker
Dave R.
Art Hunt
Tony Hoffman

I hold you to a high standard that I've found most critics of my TT posts do not possess.
(Please let me know if you don't want your name in this post and I'll remove ASAP).

In the spirit of a challenge given to me first by Dave R., I wish to issue a challenge to all critics who have NOT read The Design Matrix (DM). If you read DM, I'll read a book of your choice.

Deal?

UPDATE 22-Jan-2009: I have one stipulation: the proposed book should be of comparable price with DM (currently just under $20 at Amazon). And kudos to Dave for taking me up on my challenge. I knew you'd be first! :)

Cooption Confirmed?

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

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

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