A Positive, Testable Case for Intelligent Design - Evolution News & Views

Evolution News and Views (ENV) provides original reporting and analysis about the debate over intelligent design and evolution, including breaking news about scientific research.

Evolution News and Views
Intelligent Design NEWS
 

A Positive, Testable Case for Intelligent Design

ID is testable cover story.jpg

In 2009, I discussed a paper in BioEssays titled "MicroRNAs and metazoan macroevolution: insights into canalization, complexity, and the Cambrian explosion" which stated that "elucidating the materialistic basis of the Cambrian explosion has become more elusive, not less, the more we know about the event itself, and cannot be explained away by coupling extinction of intermediates with long stretches of geologic time, despite the contrary claims of some modern neo-Darwinists." At that time, I noted that "[t]he authors give no indication that they themselves support intelligent design (ID), and it seems they are still hopeful for a 'materialistic' explanation for the Cambrian explosion." Recently I was directed to an article by one of the paper's authors, Mark McPeek, a professor of biology at Dartmouth College, where Dr. McPeek makes it clear that he is in fact not an ID-proponent. Dr. McPeek notes that he is a theist, and he's entitled to his theistic evolutionary views. But I felt it was worth responding to some of his criticisms of ID since they reflect common misunderstandings of the theory of intelligent design.

The passage in question is where he states:

What makes something science is not merely having hypotheses. Science is having hypotheses and then testing them. The Intelligent Design hypothesis is untestable by science, exactly because we can never empirically know or understand the actions of God or any other Intelligent Designer. This in no way negates the validity of the hypothesis. It simply means that this hypothesis is outside the purview of science, because science can only support or refute hypotheses that are empirically testable, and this is not one of them.

Dr. McPeek's article goes wrong where he says: "The Intelligent Design hypothesis is untestable by science, exactly because we can never empirically know or understand the actions of God or any other Intelligent Designer." Let's take God out of the equation here so Dr. McPeek's statement now says: "The Intelligent Design hypothesis is untestable by science, exactly because we can never empirically know or understand the actions of ... any ... Intelligent Designer." That statement is incorrect.

It's quite a simple exercise to know and understand the actions of humans, who happen to be intelligent designers. For example, by studying the actions of humans in the world around us we can construct a variety of testable predictions about intelligent design.

The theory of intelligent design begins with observations of how intelligent agents act when designing things. By observing human intelligent agents, there is actually quite a bit we can learn know and understand about the actions of intelligent designers. Here are some observations:

Table 1. Ways Designers Act When Designing (Observations):
(1) Intelligent agents think with an "end goal" in mind, allowing them to solve complex problems by taking many parts and arranging them in intricate patterns that perform a specific function (e.g. complex and specified information):

"Agents can arrange matter with distant goals in mind. In their use of language, they routinely 'find' highly isolated and improbable functional sequences amid vast spaces of combinatorial possibilities." (Meyer, 2004 a)

"[W]e have repeated experience of rational and conscious agents-in particular ourselves-generating or causing increases in complex specified information, both in the form of sequence-specific lines of code and in the form of hierarchically arranged systems of parts. ... Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source from a mind or personal agent." (Meyer, 2004 b))

(2) Intelligent agents can rapidly infuse large amounts of information into systems:

"Intelligent design provides a sufficient causal explanation for the origin of large amounts of information, since we have considerable experience of intelligent agents generating informational configurations of matter." (Meyer, 2003.)

"We know from experience that intelligent agents often conceive of plans prior to the material instantiation of the systems that conform to the plans--that is, the intelligent design of a blueprint often precedes the assembly of parts in accord with a blueprint or preconceived design plan." (Meyer, 2003.)

(3) Intelligent agents re-use functional components that work over and over in different systems (e.g., wheels for cars and airplanes):

"An intelligent cause may reuse or redeploy the same module in different systems, without there necessarily being any material or physical connection between those systems. Even more simply, intelligent causes can generate identical patterns independently." (Nelson and Wells, 2003.)
(4) Intelligent agents typically create functional things (although we may sometimes think something is functionless, not realizing its true function):

"Since non-coding regions do not produce proteins, Darwinian biologists have been dismissing them for decades as random evolutionary noise or 'junk DNA.' From an ID perspective, however, it is extremely unlikely that an organism would expend its resources on preserving and transmitting so much 'junk.'" (Wells, 2004.)

So by observing human intelligent agents, there is a lot we can know and understand about intelligent designers. These observations can then be converted into hypotheses and predictions about what we should find if an object was designed. This makes intelligent design a scientific theory capable of generating testable predictions, as seen in Table 2 below:

Table 2. Predictions of Design (Hypothesis):

(1) Natural structures will be found that contain many parts arranged in intricate patterns that perform a specific function (e.g. complex and specified information).
(2) Forms containing large amounts of novel information will appear in the fossil record suddenly and without similar precursors.
(3) Convergence will occur routinely. That is, genes and other functional parts will be re-used in different and unrelated organisms.
(4) Much so-called "junk DNA" will turn out to perform valuable functions.

Dr. McPeek says, "Science is having hypotheses and then testing them." There's nothing wrong with that statement. He goes on to say that "science can only support or refute hypotheses that are empirically testable." There's nothing wrong with that statement either. The problem is when he says that ID "is not" such a testable hypothesis. But as seen in the quote above, this accusation is made right after Dr. McPeek made his inaccurate statement that we can "never empirically know or understand the actions of ... any ... Intelligent Designer." On the contrary, if we can empirically know and understand the actions of intelligent agents, then we can make testable predictions about what we should find if intelligent causation was at work.

That's exactly what ID proponents do. And the predictions of ID can be put to the test, as discussed in Table 3:

Table 3. Examining the Evidence (Experiment and Conclusion):

(1) Language-based codes can be revealed by seeking to understand the workings of genetics and inheritance. High levels of specified complexity and irreducibly complexity are detected in biological systems through theoretical analysis, computer simulations and calculations (Behe & Snoke, 2004; Dembski 1998b; Axe et al. 2008; Axe, 2010a; Axe, 2010b; Dembski and Marks 2009a; Dembski and Marks 2009b; Ewert et al. 2009; Ewert et al. 2010; Chiu et al. 2002; Durston et al. 2007; Abel and Trevors, 2006; Voie 2006), "reverse engineering" (e.g. knockout experiments) (Minnich and Meyer, 2004; McIntosh 2009a; McIntosh 2009b) or mutational sensitivity tests (Axe, 2000; Axe, 2004; Gauger et al. 2010).
(2) The fossil record shows that species often appear abruptly without similar precursors. (Meyer, 2004; Lonnig, 2004; McIntosh 2009b)
(3) Similar parts are commonly found in widely different organisms. Many genes and functional parts not distributed in a manner predicted by ancestry, and are often found in clearly unrelated organisms. (Davison, 2005; Nelson & Wells, 2003; Lönnig, 2004; Sherman 2007)
(4) There have been numerous discoveries of functionality for "junk-DNA." Examples include recently discovered surprised functionality in some pseudogenes, microRNAs, introns, LINE and ALU elements. (Sternberg, 2002, Sternberg and Shapiro, 2005; McIntosh, 2009a)

Finally, in a later section of his article, Dr. McPeek writes: "if God's hand were accepted as the scientific explanation for some complexity of nature, scientific inquiry into that complexity -- by definition -- stops." Again, nothing could be further from the truth. Below are about a dozen or so examples of areas where ID is helping science to generate new scientific knowledge and open up new avenues of research. Each example includes citations to mainstream scientific articles and publications by ID proponents that discuss this research:

  • ID directs research which has detected high levels of complex and specified information in biology in the form of fine-tuning of protein sequences. This has practical implications not just for explaining biological origins but also for engineering enzymes and anticipating / fighting the future evolution of diseases. (See Axe, 2004; Axe, 2000; Axe, 2010 ba)
  • ID predicts that scientists will find instances of fine-tuning of the laws and constants of physics to allow for life, leading to a variety of fine-tuning arguments, including the Galactic Habitable Zone. This has huge implications for proper cosmological models of the universe, hints at proper avenues for successful "theories of everything" which must accommodate fine-tuning, and other implications for theoretical physics. (See Gonzalez 2001; Halsmer, 2009.)
  • ID has helped scientists to understand intelligence as a scientifically studyable cause of biological complexity, and to understand the types of information it generates. (See Meyer, 2004b; Dembski, 1998b; McIntosh, 2009a.)
  • ID has led to both experimental and theoretical research into how limitations on the ability of Darwinian evolution to evolve traits that require multiple mutations to function. This of course has practical implications for fighting problems like antibiotic resistance or engineering bacteria. (See Behe & Snoke, 2004; Gauger et al. 2010).
  • ID implies that there are limits to the information-generative powers of Darwinian searches, leading to the finding that the search abilities of Darwinian processes are limited, which has practical implications for the viability of using genetic algorithms to solve problems. This particular example is relevant because Dr. McPeek cites the evolution of anti-biotic resistance, antiviral drug resistance, and insecticide resistance as his prime examples of the utility of Darwinian evolution. Ironically, one of the primary the ways that scientists combat such forms of resistance is based upon the premise that there are LIMITS to the amount that organisms can evolve. If biological realities like limits to evolution did not exist, it would be pointless for medical doctors to try to combat antibiotic resistance or antiviral drug resistance, because evolution could always produce an adaptation such that the target organism would become resistant without incurring a fitness cost. So ID's predictions about the existence of limits to evolution is what helps combat antibiotic, antiviral and pesticide resistance--not knowledge of Darwinian evolution. (See: Dembski and Marks 2009a; Dembski and Marks, 2009b; Ewert et al. 2009; Ewert et al. 2010; Axe et al. 2008.; Axe 2010a; Axe 2010b; Meyer 2004b; McIntosh 2009a; and many others.)
  • ID thinking has helped scientists properly measure functional biological information, leading to concepts like complex and specified information or functional sequence complexity. This allows us to better quantify complexity and understand what features are, or are not, within the reach of Darwinian evolution. (See, for example, Meyer, 2004b; Durston et al. 2007; Chiu and Thomas 2002.)
  • ID has caused scientists to investigate computer-like properties of DNA and the genome in the hopes of better understanding genetics and the origin of biological systems. (See Sternberg, 2008; Voie, 2006; Abel & Trevors, 2006.)
  • ID serves as a paradigm for biology which helps scientists reverse engineer molecular machines like the bacterial flagellum to understand their function like machines, and to understand how the machine-like properties of life allow biological systems to function. (See for example Minnich and Meyer, 2004); McIntosh, 2009a.)
  • ID causes scientists to view cellular components as "designed structures rather than accidental by-products of neo-Darwinian evolution," allowing scientists to propose testable hypotheses about causes of cancer. (See Wells, 2005.)
  • ID leads to the view of life as being front-loaded with information such that it is designed to evolve, expecting (and now finding!) previously unanticipated "out of place" genes in various taxa. (See, for example, Sherman, 2007; de Roos, 2005; de Roos, 2007; de Roos, 2006.)
  • ID explains the cause of the widespread feature of extreme degrees of "convergent evolution," including convergent genetic evolution. (See Lönnig, 2004; Nelson, & Wells, 2003; Davison, 2005.)
  • ID explains causes of explosions of biodiversity (as well as mass extinction) in the history of life. (See Lönnig, 2004; Meyer, 2004b; Meyer et al., 2003.)
  • ID has quite naturally directed scientists to predict function for junk-DNA, leading to various types of research seeking function for non-coding "junk"-DNA, allowing us to understand development and cellular biology. (See Wells, 2004; McIntosh, 2009a); Seaman and Sanford, 2009.)

While it seems clear that Dr. McPeek's criticisms of ID are based upon severe misunderstandings of the theory, don't expect him to admit he's wrong. Dr. McPeek holds a prestigious position at an Ivy League school where he pursues research related to evolutionary biology. If Thomas Kuhn's ideas hold any merit, he's not likely to admit the veracity of a new, competing paradigm of biology. Also, his article makes it clear he's capitulated to the NOMA construct which pretends that, as he puts it, "science can only be mute on these issues, since we cannot empirically test the existence, actions or methods of God." While we might not be able to scientifically identify the designer as God, we can certainly find signs of intelligent action in nature.

Dr. McPeek might feel that it is impossible to scientifically test for the prior action of an intelligent agent, but a lot of other scientists disagree with him. Many of their peer-reviewed scientific publications are cited among the references below.

References cited:

Douglas D. Axe, "Extreme Functional Sensitivity to Conservative Amino Acid Changes on Enzyme Exteriors," Journal of Molecular Biology, Vol. 301:585-595 (2000).

Douglas D. Axe, "Estimating the Prevalence of Protein Sequences Adopting Functional Enzyme Folds," Journal of Molecular Biology, 1-21 (2004).

Douglas D. Axe, Brendan W. Dixon, Philip Lu, "Stylus: A System for Evolutionary Experimentation Based on a Protein/Proteome Model with Non-Arbitrary Functional Constraints," PLoS One, Vol. 3(6):e2246 (June 2008).

a. Douglas D. Axe, "The Case Against a Darwinian Origin of Protein Folds," Bio-Complexity, Vol. 2010).

b. Douglas D. Axe, "The Limits of Complex Adaptation: An Analysis Based on a Simple Model of Structured Bacterial Populations," BIO-Complexity, Vol. 2010(4):1-10.

Michael J. Behe & David W. Snoke, "Simulating Evolution by Gene Duplication of Protein Features That Require Multiple Amino Acid Residues," Protein Science, Vol. 13:2651-2664 (2004).

Chiu, David K.Y., and Lui, Thomas W.H., "Integrated Use of Multiple Interdependent Patterns for Biomolecular Sequence Analysis," International Journal of Fuzzy Systems, Vol. 4(3):766-775 (September, 2002).

John A. Davison, "A Prescribed Evolutionary Hypothesis," Rivista di Biologia/Biology Forum, Vol. 98: 155-166. (2005).

a. William Dembski, "Intelligent Science and Design," First Things, Vol. 86:21-27 (October 1998).

b. W.A. Dembski, The Design Inference: Eliminating Chance through Small Probabilities (Cambridge University Press, 1998).

a. William A. Dembski and Robert J. Marks II, "Conservation of Information in Search: Measuring the Cost of Success," IEEE Transactions on Systems, Man and Cybernetics A, Systems & Humans, Vol. 39 (5):1051-1061 (September, 2009).

b. William A. Dembski, and Robert J. Marks II, "Bernoulli's Principle of Insufficient Reason and Conservation of Information in Computer Search," Proceedings of the 2009 IEEE International Conference on Systems, Man, and Cybernetics San Antonio, TX, USA, 2647-2652 (October 2009).

Kirk K. Durston, David K. Y. Chiu, David L. Abel, Jack T. Trevors, "Measuring the functional sequence complexity of proteins," Theoretical Biology and Medical Modelling, Vol. 4:47 (2007).

Winston Ewert, William A. Dembski, and Robert J. Marks II, "Evolutionary Synthesis of Nand Logic: Dissecting a Digital Organism," Proceedings of the 2009 IEEE International Conference on Systems, Man, and Cybernetics San Antonio, TX, USA, 3047-3053 (October 2009).

Winston Ewert, George Montanez, William A. Dembski, Robert J. Marks II, "Efficient Per Query Information Extraction from a Hamming Oracle," Proceedings of the the 42nd Meeting of the Southeastern Symposium on System Theory, IEEE, University of Texas at Tyler, March 7-9, 2010, pp.290-297.

Ann K Gauger, Stephanie Ebnet, Pamela F Fahey, Ralph Seelke, "Reductive Evolution Can Prevent Populations from Taking Simple Adaptive Paths to High Fitness," BIO-Complexity, Vol. 2010.

Guillermo Gonzalez et al., "Refuges for Life in a Hostile Universe," Scientific American (October, 2001).

D. Halsmer et al., "The Coherence of an Engineered World," International Journal of Design & Nature and Ecodynamics , Vol. 4 (1):47-65 (2009).

Wolf-Ekkehard Lonnig, "Dynamic genomes, morphological stasis, and the origin of irreducible complexity," in Dynamical Genetics pp. 101-119 (Valerio Parisi, Valeria De Fonzo, and Filippo Aluffi-Pentini eds., 2004).

Casey Luskin, "Human Origins and Intelligent Design," Progress in Complexity and Design, (Vol 4.1, November, 2005).

Stephen C. Meyer, Marcus Ross, Paul Nelson & Paul Chien, "The Cambrian Explosion: Biology's Big Bang," in Darwinism, Design, and Public Education (John A. Campbell and Stephen C. Meyer eds., Michigan State University Press, 2003).

a. Stephen C. Meyer, "The Cambrian Information Explosion," in Debating Design (edited by Michael Ruse and William Dembski; Cambridge University Press 2004).

b. Stephen C. Meyer, "The origin of biological information and the higher taxonomic categories," Proceedings of the Biological Society of Washington, Vol. 117(2):213-239 (2004).

a. A.C. McIntosh, "Information and Entropy -- Top-Down or Bottom-Up Development in Living Systems?," International Journal of Design & Nature and Ecodynamics, Vol. 4(4):351-385 (2009).

b. A.C. McIntosh, "Evidence of Design in Bird Feathers and Avian Respiration," International Journal of Design & Nature and Ecodynamics, Vol. 4(2): 154-169 (2009).

Scott A. Minnich & Stephen C. Meyer, "Genetic analysis of coordinate flagellar and type III regulatory circuits in pathogenic bacteria," in Proceedings of the Second International Conference on Design & Nature, Rhodes Greece (M.W. Collins & C.A. Brebbia eds., 2004).

Paul Nelson and Jonathan Wells, "Homology in Biology," in Darwinism, Design, and Public Education, (Michigan State University Press, 2003).

Albert D. G. de Roos, "Origins of introns based on the definition of exon modules and their conserved interfaces," Bioinformatics, Vol. 21(1):2-9 (2005).

Albert D. G. de Roos, "Conserved intron positions in ancient protein modules," Biology Direct, Vol. 2:7 (2007).

Albert D. G. de Roos, "The Origin of the Eukaryotic Cell Based on Conservation of Existing Interfaces," Artificial Life, Vol. 12:513-523 (2006).

Josiah D. Seaman and John C. Sanford, "Skittle: A 2-Dimensional Genome Visualization Tool," BMC Informatics, Vol. 10:451 (2009).

Michael Sherman, "Universal Genome in the Origin of Metazoa: Thoughts About Evolution," Cell Cycle, Vol. 6(15):1873-1877 (August 1, 2007).

Richard Sternberg and James A. Shapiro, "How Repeated Retroelements format genome function," Cytogenetic and Genome Research, Vol. 110: 108-116 (2005).

Richard v. Sternberg, "On the Roles of Repetitive DNA Elements in the Context of a Unified Genomic- Epigenetic System," Annals of the New York Academy of Sciences, Vol. 981: 154-188 (2002).

Richard v. Sternberg, "DNA Codes and Information: Formal Structures and Relational Causes," Acta Biotheoretica, Vol. 56(3):205-232 (September, 2008).

J.T. Trevors and D.L. Abel, "Chance and necessity do not explain the origin of life," Cell Biology International, Vol. 28: 729-739 (2004).

J. T. Trevors and D. Abel, "Self-organization vs. self-ordering events in life-origin models," Physics of Life Reviews, Vol. 3: 211--228 (2006).

Oyvind Albert Voie, "Biological function and the genetic code are interdependent," Chaos, Solitons and Fractals, Vol. 28:1000--1004 (2006).

Jonathan Wells, "Using Intelligent Design Theory to Guide Scientific Research" Progress in Complexity, Information, and Design (Vol. 3.1.2, November 2004).

Jonathan Wells, "Do Centrioles Generate a Polar Ejection Force?," Rivista di Biologia / Biology Forum, Vol. 98:71-96 (2005).


40 Comments

Dear Reed,

Thanks for submitting your comment. I can’t help but note that your comment appears to be trying to deflect the issue. My article here offers detailed arguments for a positive, testable case for intelligent design (ID), and in response to your first comment I explained why Theobald’s paper does not demonstrate universal common ancestry. You wrote back disputing my use of the term “null hypothesis.” I’ll respond to your criticism in short order, but one thing is quite clear: You didn’t reply to most of what I said about Theobald’s paper, nor have you responded to any of my arguments regarding the positive, testable case for design. My article is a discussion of a larger issue of a positive case for design, but your comments about whether Theobald used a “null hypothesis” have no impact on my arguments.

Let’s talk a little bit about null hypotheses. Regarding Theobald’s use of a null hypothesis, you write:
He used Bayesian statistical methods to compare two hypotheses and thus does not have a null hypothesis. Null hypotheses are used in frequentist statistical methods developed by RA Fisher, whom you probably know was a founder of both modern statistics and evolutionary genetics. It is simply impossible for anyone to accurately describe Theobald's work as having a null hypothesis.
I'm sure I'm nowhere near the expert in Bayesian statistics that you are, but I did study RA Fisher's work in grad school. His work on randomness had a strong influence on the methods used in paleomagnetic studies to determine whether a true remanent magnetic field was present in a set of samples, or whether we were looking at randomized data, or something else.

But you are raising red herring after red herring here to deflect from the core issue. In fact, your admission that Theobald “used Bayesian statistical methods to compare two hypotheses” essentially concedes my primary point. My argument is that if you are advocating hypothesis A and compare it to hypothesis B—but hypothesis B is a preposterous hypothesis—then it’s not impressive if hypothesis A comes out looking like the winner. So whether we call hypothesis B a “null hypothesis” or if we use your words to say Theobald “compared two hypotheses,” my point remains the same: Theobald tested universal common ancestry for similar but widespread gene sequences against the entirely preposterous hypothesis that those genes convergently arrived at the same sequence by sheer chance. The fact that universal common ancestry came out looking good in this comparison is a trivial point.

The triviality of Theobald’s conclusion is especially noteworthy given that he ignored the mechanism of common design, which is perfectly capable of generating similar genetic sequences in different organisms. Theobald’s paper refuted chance convergence, not common design. Thus, your original comment that “Dr. Theobald tested the hypotheses of universal common descent against uncommon descent and found that common descent was significantly better supported by the data” is completely irrelevant, and trivial, if you want to get involved in a debate over intelligent design.

Additionally, I don’t think it’s unfair to characterize Theobald’s method as using a “null hypothesis.” You admit that he “compared two hypotheses.” When one tests a hypothesis against a null hypothesis, one is comparing two hypotheses. Perhaps Theobald didn’t use RA Fisher’s statistical techniques, but I never claimed that’s what he did. After all, one can refute a null hypothesis without delving into Fisherian statistics. For example, after I learned about Fisher’s work while finishing my master’s degree in paleomagnetism, I went to law school where I learned that null hypotheses are often used in legal arguments, especially in criminal law. This is despite the fact that the criminal prosecutions don’t typically (if ever) use Fisherian statistical analyses to make their case. I’m loathe to quote Wikipedia, but it rightly notes that “In most legal systems, the presumption that a defendant is innocent (‘until proven guilty’) can be interpreted as saying that his or her innocence is the null hypothesis.” In that sense, using a null hypothesis is not unlike comparing two hypotheses, and doesn’t require using Fisherian statistical analysis. So I don’t find my characterization of Theobald using a null hypothesis to be inaccurate.

After all, Theobald himself notes that his method was to compare universal common ancestry to “competing multiple-ancestry hypotheses"--the notion that sheer chance convergence generated the similar DNA sequences we observe. It sure seems to me like he's using that as a null hypothesis. In fact, the authorities Eugenie Koonin and Yuri Wolf critique Theobald in the journal Biology Direct by observing that he uses a "general null hypothesis of independent ancestry" (emphasis added) This passage from Theobald's paper makes me think they are correct:
Sequence similarity is an empirical observation, whereas the conclusion of homology is a hypothesis proposed to explain the similarity. Statistically significant sequence similarity can arise from factors other than common ancestry, such as convergent evolution due to selection, structural constraints on sequence identity, mutation bias, chance, or artifact manufacture. For these reasons, a skeptic who rejects the common ancestry of all life might nevertheless accept that universally conserved proteins have similar sequences and are "homologous" in the original pre-Darwinian sense of the term (homology here being similarity of structure due to ''fidelity to archetype''). Consequently, it would be advantageous to have a method that is able to objectively quantify the support from sequence data for common-ancestry versus.
My response to your prior comment, by the way, cited other biologists who sharply critiqued Theobald’s results as trivial for the same reasons I have given here. You didn't reply to this authority, but I find it worth repeating:
Cogniscenti cringed when they saw the Theobald paper, knowing that "it is trivial". It is trivial because the straw man that Theobald attacks in a text largely formulated in convoluted legalese, is that significant sequence similarity might arise by chance as opposed to descent with modification. Ignoring the strength of the universality of the genetic code and the commonality of central intermediary metabolism among cells as evidence, Theobald construed a non-issue that the referees of his paper, whoever they may have been, found convincing and novel (!).

(Comments by William Martin of the University of Duesseldorf in review of Eugene V. Koonin and Yuri I. Wolf, "The common ancestry of life," Biology Direct, Vol. 5:64 (2010).)
In any case, whether we call it a ‘null hypothesis’ or ‘comparing two competing hypotheses’ is quibbling about words. I’m sure you’re quite knowledgeable about this subject, but your attempt to bring into this conversation what William Martin calls the “convoluted legalese” bioinformatics statistical analysis is a red herring that doesn’t change the fact that Theobald tested universal common ancestry by comparing it to the preposterous hypothesis that similar genes acquired their similar sequences entirely by chance.

Finally, you challenged me to provide a Bayesian statistical model for testing ID which would take “several months” to develop. You write: “If you really believe this, then it should be possible to express a positive model that can be plugged into a Bayes-factor analysis.” Your challenge raises another red herring.

I do believe ID is testable, but I don’t need to create a Bayesian model to show that. In fact, the whole purpose of my article was to present a valid method for testing predictions made by the theory of intelligent design. You didn’t respond to my argument but instead challenged me to use another method to test ID using Bayesian analysis. Perhaps there are 50 different potential methods to test ID. My purpose was to show one valid method of testing positive predictions of ID, and your comments did not refute that method.

Since your comments seem to raise red herring after red herring, this makes me wonder if you actually have any strong counter-arguments to my article. If you want to develop a Bayesian model to test ID, feel free. That’s not material to my argument here, which presents another legitimate way for testing ID.

That said, I think this is an area where more ID proponents can and should do more work. With the crushing numbers of papers out there struggling to resolve conflicts between alleged phylogenetic trees, the argument for common descent is falling into disarray, and I think this is an area where a lot of work could be contributed from an ID-based paradigm. Thanks again for writing.

Sincerely,

Casey

In response to krissmith777, you’ve repeated a lot of common but very dangerous evolution-of-the-gaps logic here, so this will take a little time to unpack. But I recommend that you read Marc Hoffman’s good comment as a starting point because it will help you understand why many genetic algorithms don’t represent true Darwinian evolution.

I would also encourage you to be willing to truly seek the facts here and not be bullied into neo-Darwinian thinking by the “gaps” arguments of evolutionists.

Thus, you first stated:

Are you implying that mutation is a designed process? So when we see "selection" creating something new, we see intelligent programming involved--i.e. the systems are intelligently designed to evolve. Casey...(or to be more polite) Mr. Luskin, when you say "designed to evolve," this looks like a case of moving the goal posts.

I reply: There's no moving of the goal posts here because in this case, these genetic algorithms were not accurately modeling biological evolution. So I'm not conceding that Darwinian evolution can do interesting things in biology because these programs don't really model truly Darwinian evolution. Sorry if I didn't make that clear earlier.

The problem with these genetic algorithms is that they don’t model truly Darwinian evolution. Read some of the work by Dembski and Marks I’ve cited in my main post here. Their research, for example, found that evolutionary simulations like Avida use “active information” to aid the search. Part of what that means in practice is that the types of “mutations” that are allowed by the program really aren’t random mutations but rather the program is designed to swap in and out fully-functional logic commands. It only takes a few commands in the right order to evolve the target function. So this is very different from biological evolution in that their simulation of evolution pre-programs types of mutations that are designed to easily confer a benefit on the digital organism. Dembski and Marks call this active stair-step information. So these digital organisms were designed to evolve. It does not model biological reality.

You asked: “Realizing that some ID proponents accept "common decent" of humans from others in the animal kingdom, why do even the ID proponents that accept common decent tend to reject the idea of fossils with intermediate features between different species (I.e., the transitional fossils)?”

I reply: I’m not aware of pro-common descent ID proponents like Michael Behe challenging intermediate fossils. Paleontology is not really his game. As for me, I’m a scientific skeptic of common descent but I accept that there are some fossils with intermediate features. For example, I think that the horse sequence shows some intermediate fossils. But from the beginning to the end of the horse sequence, I think it shows little more than microevolution. So it’s not demonstrating that fundamentally new types of organisms can evolve.

You asked: “Assuming that "complexity" is interchangeable with "design." On what basis should one accept the premise that complexity means something did not evolve by natural process?”

I reply: Well, where in your experience does technological complexity come from? If it only comes from intelligence and not from unguided natural causes, then why assume that biological complexity arose from unguided natural causes?

You wrote: “He admits that just because something is complex, or even irreducible for that matter meaning it couldn't have evolved ‘directly,’ we cannot rule out that the path may have been ‘indirect.’ But notice that he ends up dismissing that option because he deems the ‘likelihood’ really low without giving evidence. -- He may not have known this, but he hit on something: Indirect evolution can/does happen.”

I reply: You’re really changing the subject here but I addressed this very topic in a recent article here on ENV: “ Michael Behe's Critics Misunderstand Irreducible Complexity and Make Darwinian Evolution Unfalsifiable” So my first challenge to you is: please give an example of indirect evolution producing something interesting or else this is nothing more than wishful speculation.

My second point is to reiterate that mere possibility does not mean scientific plausibility. I explain this in the post I just cited:

Behe's view doesn't require absolute falsification. His view is that a direct Darwinian pathway is effectively falsified by the presence of irreducible complexity, not absolutely falsified. Perhaps indirect routes are possible (in the same way that anything is possible), but possible does not mean plausible, or likely.

This has been Behe's point all along: the inability to achieve 100% refutation of a wildly speculative indirect evolutionary scenario does not mean that irreducible complexity is invalid. To argue such is to hold irreducible complexity to an unreasonably high standard. To the contrary, the fact that evolutionists are forced to respond to Behe with such tenuous and speculative stories of indirect evolution shows the strength of the argument for irreducible complexity. Behe makes this precise point in Science and Evidence for Design in the Universe, Proceedings of the Wethersfield Institute:

[O]ne needs to relax Darwin's criterion from this: "If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down." to something like this:

If a complex organ exists which seems very unlikely to have been produced by numerous, successive, slight modifications, and if no experiments have shown that it or comparable structures can be so produced, then maybe we are barking up the wrong tree. So, LET'S BREAK SOME RULES!

Of course people will differ on the point at which they decide to break rules. But at least with the realistic criterion there could be evidence against the unfalsifiable. At least then people like Doolittle and Miller would run a risk when they cite an experiment that shows the opposite of what they had thought. At least then science would have a way to escape from the rut of unfalsifiability and think new thoughts.

(Michael Behe, "Answering Scientific Criticisms of Intelligent Design," Science and Evidence for Design in the Universe, Proceedings of the Wethersfield Institute, Vol 9:146-147 (Ignatius Press, 2000).)

[…]

That that critics refuse to accept falsification it also means that critics are placing Darwinian evolution in an effectively unfalsifiable position, where no level of complexity can falsify it. Proponents of Darwinism are effectively arguing that if an explanation is merely possible, then it defeats counter-arguments. As David Abel writes, this is an unhealthy state for science:

Mere possibility is not an adequate basis for asserting scientific plausibility. A precisely defined universal bound is needed beyond which the assertion of plausibility, particularly in life-origin models, can be considered operationally falsified. ... But at some point our reluctance to exclude any possibility becomes stultifying to operational science. Falsification is critical to narrowing down the list of serious possibilities. Almost all hypotheses are possible. Few of them wind up being helpful and scientific ally productive. Just because a hypothesis is possible should not grant that hypothesis scientific respectability. More attention to the concept of "infeasibility" has been suggested. Millions of dollars in astrobiology grant money have been wasted on scenarios that are possible, but plausibly bankrupt. The question for scientific methodology should not be, "Is this scenario possible?" The question should be, "Is this possibility a plausible scientific hypothesis?" One chance in 10200 is theoretically possible, but given maximum cosmic probabilistic resources, such a possibility is hardly plausible. With funding resources rapidly drying up, science needs a foundational principle by which to falsify a myriad of theoretical possibilities that are not worthy of serious scientific consideration and modeling.

(David L. Abel, "The Universal Plausibility Metric (UPM) & Principle (UPP)," Theoretical Biology and Medical Modelling, Vol. 6:27 (Dec. 3, 2009).)

…[Critics] might have had a point if indirect evolutionary pathways had been demonstrated to actually be plausible scientific arguments. But that's the problem with the claim that multiple parts can come together from different systems to spontaneously form complex multipart systems: such explanations aren't scientifically plausible. They do not defeat counter-arguments to Darwinian evolution like irreducible complexity.

The critics need to remember David Abel's words that "[m]ere possibility is not an adequate basis for asserting scientific plausibility." Boudry, Blancke and Braekman confuse mere possibility with scientific plausibility. They can't claim to have explained the evolutionary origin of irreducible complexity when their "explanation" is in fact little more than wishful thinking and wild speculation.

So I would say the same to you: can you provide examples which show that indirect evolutionary pathways are plausible scientific arguments?

You asked: “Why do you arrive to the conclusion that natural forces cannot produce complexity? No one here is saying that complexity has to "evolve directly."”

I reply: I’m talking about both direct and indirect pathways. If you want to know why I say this, then you should read Darwin’s Black Box en toto because Behe makes a pretty compelling case. Additionally, I wrote a lengthy review last year of the inability of unguided evolutionary mechanisms to explain the origin of new genetic information. If you wish, you can read that article here.

You wrote: “And even if Darwinian evolution were to turn out to be wrong, why would design even follow?... Again, on what basis does "complexity" equal "design?”

I reply: I appreciate your comments Kris but if this is the quality of questions I’m getting then it’s clear that ID-critics have very little to offer. The entire point of my article here was to show that ID makes testable positive predictions and does not merely rely upon refuting Darwinian evolution.

To reiterate some of our knowledge which shows why specified complexity leads to design:

"Agents can arrange matter with distant goals in mind. In their use of language, they routinely 'find' highly isolated and improbable functional sequences amid vast spaces of combinatorial possibilities." (Meyer, 2004 a)

"[W]e have repeated experience of rational and conscious agents-in particular ourselves-generating or causing increases in complex specified information, both in the form of sequence-specific lines of code and in the form of hierarchically arranged systems of parts. ... Our experience-based knowledge of information-flow confirms that systems with large amounts of specified complexity (especially codes and languages) invariably originate from an intelligent source from a mind or personal agent." (Meyer, 2004 b))

You wrote: “There is an old biologists proverb that says, ‘Evolution is smarter than you.’”

I reply: Actually it was Thomas H. Huxley who said that “science commits suicide when it adopts a creed.” So what you are saying sounds like “evolution of the gaps” thinking which assumes that any gap in our knowledge will one day be solved by evolutionary explanation. I reject gaps thinking of all forms and I try to explain things based upon what we do know, not what we don’t know. So you seem to assume that evolution always has a pathway. I’m not willing to make any such assumptions.

Keep in mind that contrary to the rhetoric of guys like Donald Prothero, ID’s arguments haven’t been overturned. In 2008, Behe's would-be critics tried to refute him in the journal Genetics, but found that to obtain only two specific mutations via Darwinian evolution “for humans with a much smaller effective population size, this type of change would take > 100 million years.” The critics admitted this was “very unlikely to occur on a reasonable timescale.”[1] In other words, there is too much complex and specified information in many proteins and enzymes to be generated in humans by neo-Darwinian processes on a reasonable evolutionary timescale.

Thanks and I hope this helps. And by the way, please call me Casey : )

Sincerely,

Casey

[1] Rick Durrett and Deena Schmidt, "Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution," Genetics, Vol. 180: 1501--1509 (November 2008).

Dear Robert Camp,

You wrote: “To suggest that a designer of such magnitude is compelled by the natural laws he himself created to conserve particular stretches of DNA over great swaths of the evolutionary tree isn't just a breach of judgement, it flies in the face of common sense...”

I reply: I’m not arguing that has to always be the case. But there are constraints of physics and chemistry and so observing conserved sequences should not refute design. But since you feel that conservation points strongly to Darwinian processes, then what do you make of the fact that much basic cellular machinery or key biological components can be functionally analogous, but at the sequence level often not conserved, and in some cases even not homologous? I could give multiple examples, here are a few:

Michael Syvanen, "Recent emergence of the modern genetic code: a proposal,” Trends in Genetics, Vol. 18(5):245-248 (May, 2002): “These considerations further undermine the need to postulate the existence of a ‘last common ancestor’; a simpler model would be that multiple lineages gave rise to life today.”

Todd H. Oakley and Clifford W. Cunningham, "Molecular phylogenetic evidence for the independent evolutionary origin of an arthropod compound eye," Proceedings of the National Academy of Sciences USA, Vol. 99(3):1426-1430 (Feb. 5, 2002): This article explains why the phylogenetic data requires that either two unlikely evolutionary hypotheses are true: either extremely similar compound arthropod eyes evolved multiple times independently in an example of extreme convergent evolution, or eyes were lost in large numbers of species.

Leipe et al., “Did DNA replication evolve twice independently?” Nucleic Acids Research, Vol. 27(17): 3389-3401 (1999): This article discusses how DNA is central to life but finds it surprising that various different types of organisms use very different enzymes to replicate DNA. It suggests that the machinery allowing DNA replication must have evolved twice.

Desmond et al., "On the last common ancestor and early evolution of eukaryotes: reconstructing the history of mitochondrial ribosomes," Research in Microbiology, Vol. 162(1):53-7 (January, 2011): "mitochondrial ribosomes appear to have undergone a very dynamic evolutionary history in the different eukaryotic lineages, involving the loss of different sets of ribosomal protein-coding genes, their transfer to the host genome, as well as the acquisition of many novel components. This chaotic history for a such fundamental cellular machinery is puzzling, especially when compared to cytosolic, bacterial or chloroplastic ribosomes, which are much more stable. Intriguingly, archaeal ribosomes also show a very dynamic nature, with multiple independent losses among lineages."

W. F. Doolittle, “Phylogenetic Classification and the Universal Tree,” Science, Vol. 284:2124-2128 (June 25, 1999): “Molecular phylogenists will have failed to find the ‘true tree,’ not because their methods are inadequate or because they have chosen the wrong genes, but because the history of life cannot properly be represented as a tree.”

So we don’t see broad conservation in all cases, and the data often doesn’t fit what evolutionary “common sense,” as you put it, would tell us.

Additionally, as I previously wrote in response to you, gene sequences often don’t fit into a tree-like pattern. So the data is not nearly as simplistic a case for evolution as you describe it to be.

You wrote: "especially since in such a case the more obvious and parsimonious explanation for a theist would appear to be a god who designed evolution to work exactly as the data show"

I reply: This is amusing because I usually don’t give much credence to people who refuse to capitalize “God” to preach at me about how “god” ought to operate.

In any case, if you want to bring theology into the discussion that’s your choice. I’m arguing based upon science. If you want to bring theology into the discussion, I can think of all kinds of great theological reasons why God might not use neo-Darwinian processes—but that’s not a topic for this thread because today we’re talking about science. My case for design is based upon science, not theology.

You asked: “If your inference to the designer is based upon analogy with human agency then don't you agree that in order to follow through on testing the inference you'll have to, at some point, eliminate humans as a possible candidate designing agent?”

I reply: You think ID is focused on studying designers but you should read kuartus4’s great comment. ID is about detecting design, not identifying the designer. We can detect intelligent design because we understand how intelligent agents operate. So your question exposes that you do not understand what ID is all about.

Thanks and I hope this helps to clear some things up.

Casey

In response to Olorin, Olorin writes that "The point of the Tittaalik example is not the accuracy of the prediction, but rather that Neil Shubin made a prediction concerning a specific type of fossil at a particular location at a definite date, and then went out and tested it."

Actually, I think that this misses part of my main point. My point was that I'm not sure that evolution actually made any clear prediction here because once we discovered tetrapod tracks from 397 mya, the supposed "prediction" that we should find fish-to-tetrapod intermediates around 375 million years ago is nullified.

So this is an odd case where people thought evolution predicted X, and X was found and touted as a "confirmed prediction" of evolution. But then later it was realized that evolution actually didn't predict X. So what does evolution predict here? As I said, your guess is as good as mine.

Despite evolution's lack of clear predictions in some areas, I am trying to lay out concrete testable predictions of ID. Let's now turn back to this:

You then challenged me "to show a similar specific prediction about a particular detailed situation that can be tested for the presence vel non of 'design.'"

I find it extremely ironic that you claim I "sidestepped the issue" since the entire purpose of my article is to answer the exact question you just posed. My article gives 4 testable predictions of ID. The presence of high levels of complex and specified information is ONLY produced by intelligent agency. That is a testable prediction that can establish an intelligent agent was at work.

You also said "please remember that a 'prediction' must occur in advance of the event that tests it".

I reply: I guess your standard doesn't apply to Darwin (and many other scientific theories) because most of the Origin of Species was written to explain pre-existing data.

In any case, I'm happy to allow your standard to apply to ID, because the predictions of ID that I cited DO predict data that we're testing for in the future. For example, if you read the links I've mentioned then you would have seen that ID predicted function for junk-DNA long before such function was discovered. Likewise, Dembski's work predicted high CSI in proteins before Axe discovered astronomically high CSI in proteins in his 2000 and 2004 research papers. Other studies have found similarly high CSI in biological systems.

So ID is predicting data in advance. The dozen or so areas I cited where ID is helping to advance scientific knowledge helps to flesh this out.

Thanks and I hope this helps.

Sincerely,

Casey

@Casey Luskin

You say,

Regarding (1) and (3), genetic algorithms, which are artifacts designed by humans, can have these qualities. And as much of the work by Dembski and Marks (cited in my article) shows, when genetic algorithms evolve into something "new," because intelligence was required to program the evolution.

I'm a bit confused. Are you implying that mutation is a designed process?

So when we see "selection" creating something new, we see intelligent programming involved--i.e. the systems are intelligently designed to evolve.

Casey...(or to be more polite) Mr. Luskin, when you say "designed to evolve," this looks like a case of moving the goal posts. But this begs a question: Let me just say first that I do not consider Intelligent Design as being necessarily the same as Creationism, and I realize that several proponents do accept Common Decent. That said, I must ask: Realizing that some ID proponents accept "common decent" of humans from others in the animal kingdom, why do even the ID proponents that accept common decent tend to reject the idea of fossils with intermediate features between different species (I.e., the transitional fossils)? I ask this because it's an inconsistency that has really intrigued me since I started to try reading Darwin's Black Box a few years ago, that being since Michael Behe accepts common decent. Whether living things are "designed to evolve" is true, or whether Darwinian evolution by natural selection is true, the fossil record would still be come out essentially the same.[1]

Arguably, the ability to reproduce is more complex than any technology we've created. That means that biological organisms are more complex than any human technology. But if human technology is designed, what does that say about biological organisms...?

Assuming that "complexity" is interchangeable with "design." On what basis should one accept the premise that complexity means something did not evolve by natural process? Even Michael Behe says in his book:

Even if a system is irreducibly complex/b>one can not definitely rule out the possibility of an indirect, circuitous route. As the complexity of an interacting system increases, though, the likelihood of such an indirect route drops precipitously. (Michael Behe: Darwin's Black Box, page 40 )

He admits that just because something is complex, or even irreducible for that matter meaning it couldn't have evolved "directly," we cannot rule out that the path may have been "indirect." But notice that he ends up dismissing that option because he deems the "likelihood" really low without giving evidence. -- He may not have known this, but he hit on something: Indirect evolution can/does happen.

But I admit I digress a bit.

Back to the main point here: Why do you arrive to the conclusion that natural forces cannot produce complexity? No one here is saying that complexity has to "evolve directly." There is no path. And even if Darwinian evolution were to turn out to be wrong, why would design even follow?[2]

But if human technology is designed, what does that say about biological organisms...?

There is an old biologists proverb that says, "Evolution is smarter than you." Again, on what basis does "complexity" equal "design?"

_______________________________
[1] As a reference, see Evolution: What the Fossils Say and Why it Matters, by Donald R. Prothero.

[2] The invalidation of one theory in no way implies that the competing hypothesis is true; both in fact may be wrong. Even if Darwin was wrong about the mechanism of evolution, that doesn't indicate that natural forces are not responsible.

Mr Luskin continues to sidestep the issue.

The point of the Tittaalik example is not the accuracy of the prediction, but rather that Neil Shubin made a prediction concerning a specific type of fossil at a particular location at a definite date, and then went out and tested it. It could have been wrong. The point is that it was testable, and was in fact tested by its proponent.

My question to Mr Luskin is to show a similar specific prediction about a particular detailed situation that can be tested for the presence vel non of "design." What outcome would demonstrate the presence of design, what alternative outcome would not?

I'm having trouble coming up with an example, because I think that none exist. Mr Luskin believes they do. That's why I'm asking him to produce one.

And please remember that a "prediction" must occur in advance of the event that tests it, not afterward. Explaining the past is easy; predicting the future is harder.

In response to Krisssmith777's three differences between human artifacts and living creatures pertaining to Darwinian evolution:

> Living creatures are subject to natural selection; human artifacts are not.
> Living creatures reproduce; human artifacts do not.
> Living artifacts mutate by natural means; human artifacts do not.

My first inclination is to say, and please forgive the bluntness of this, so what? What bearing does environment have on whether something is designed or not? However, I'll bite and attempt to address each one of these criteria.

1. The assertion that living creatures are subject to natural selection, and human artifacts are not is not entirely true. To illustrate this, we need not look any further than free market economics 101. A free market economy, whether in a small town, a large city, a state, or the nation as a whole, is an engineered thing. And, as we have all seen with various products or services, survival of the fittest (natural selection) does tend to assert itself in an economy. Take for example the dueling videotape formats back in the 70s and 80s. BetaMax and VHS were both competing for dominance in the marketplace. Both had advantages over one another in the areas of picture quality and recording time. But only one made it out on top: VHS. In this case, the marketplace selected VHS, leaving BetaMax all but extinct. So while Krissmith777 was undoubtedly thinking of natural selection in terms of nature, the concept does exist in other ecosystems, operating on human artifacts (In case you don't think Betamax is an artifact, try to find one in your local Wal-Mart).

2. The assertion that only living creatures reproduce while human artifacts do not is also not entirely true. Starting as far back as 1949, computer scientists were dreaming of what a self-replicating virtual "organism" might look like. Today, we see the fruits of their theories realized with over 100,000 varieties of computer viruses, worms, trojans, and other malware that can infect the ecosystem of the computer, many of which self-replicate. Many of these digital pathogens are designed to mutate to evade detection by the digital immune system of various anti-malware vendors. (A very interesting read can be had here: http://www.infoplease.com/ipa/A0872842.html ).

Funny thing about computer viruses: if we were to gaze into an environment where evolution would theoretically take place at a very accelerated pace, it would be in the virtual world of computer code, and in particular, computer viruses. Allow me to explain: suppose that a computer virus appears "in the wild" and begins to "infect" computer systems worldwide. Antivirus (AV) vendors rush to build a signature-based immunity for the virus to prevent further infection, and to repair damage. Later on, we see more "variants," or mutations of the same virus appear, different enough from the original as to elude the detection by the then current antivirus signature files. AV vendors catch up and release signature files to detect the new varient. Then, all of a sudden, a brand new virus appears in the wild, again evading detection by AV software. The AV vendors again catch up to stop the spread of infection.

What has happened here? Are we seeing Darwinian evolution in action? Are we seeing mutations in computer code that creates variations of the same virus (microevolution) and brand new forms of viruses (macroevolution)? At first, it would appear so. But each mutated virus has been programmed to evade detection by mutating, and there is only so far that it can mutate. To get the "jumps" of macroevolution, a malware designer must create a new virus. That's how new viruses appear "in the wild." We never see brand new specimens appear by evolving from other code. If that were the case, we wouldn't be seeing malware programmers getting jail sentences. They could always blame digital Darwin!

3. The last assertion that living artifacts mutate by natural means and human artifacts do not is also not entirely accurate. For even inside the computer, we see natural processes and materials at work, and "mutations" can occur with a surge in electricity. Unfortunately, we don't see "beneficial" mutations; only ones that trash your data and corrupt your hard drive. And as I have shown above, computer viruses, when programmed to (read: designed to), will mutate to avoid detection.

I like the comments.
I would encourage opening more of the articles to comments.

Hi, I believe you asked about design intervention.
I dont think that ID theory is about that. ID theory is about DESIGN DETECTION not DESIGN IMPLEMENTATION. ID doesnt pretend to know how the designer did it or how he intervened,ID is simply about constructing a reliable model for recognizing design where ever it is found.
If that is not what you meant, then please ignore this comment.

You're right that this has gotten too long, so I'll skip to the crux. Nearly all of your points depend upon assumptions that are illegitimately folded into the premises of the argument.

You wrote: "Common design easily explains biological similarity that does not fit into a nested hierarchy, because designers re-use parts that work but are not obligated to do so in a manner that is consistent with a nested hierarchy." But even this seemingly innocuous comment depends upon hasty assumptions about putative designers operating as humans would.

In the case of an inference to natural non-human agency this is a small problem in that it puts the cart before the horse and naively assumes the horse is walking backwards. But in the case of an inference to a transcendental designer of cosmoses it's an enormous error in reason. To suggest that a designer of such magnitude is compelled by the natural laws he himself created to conserve particular stretches of DNA over great swaths of the evolutionary tree isn't just a breach of judgement, it flies in the face of common sense (especially since in such a case the more obvious and parsimonious explanation for a theist would appear to be a god who designed evolution to work exactly as the data show).

But this is what happens when you extend analogical rationale far beyond that which it will support. ID is full of, if not based upon, unwarranted assumptions drawn from this faulty logic. I won't repeat myself so I'll simply ask you this,

- If your inference to the designer is based upon analogy with human agency then don't you agree that in order to follow through on testing the inference you'll have to, at some point, eliminate humans as a possible candidate designing agent?
- If so, don't you have to do this by establishing that something has happened in the purported design process that is beyond the capacity of humans?
- And if so again, doesn't this mean that evidence other than analogical reasoning is required to demonstrate the veracity of the inference?

I don't know how you achieve this without some evidence as to the methods or motives of the designer. The continued disavowal of this requirement remains, in my opinion, the foundational thin ice upon which virtually all of ID rests.

Thanks for the opportunity to comment.

Dear All,

Allow me to highlight a few issues here. If they repeat anything already articulated in this interesting discussion, please accept my apologies.

1. humans are not the only intelligence readily available to experiment with. How about apes and other animals? It is known e.g. that ants/termites/bees exhibit so-called swarm intelligence that is also testable.

2. ID is simple and it appeals to me. On the contrary, Darwinian macroevolution has become an overburdened theory, which is a clear indication it has seen its better days. The only really hard argument for ID as it now stands, is that of Stuart Kauffman and his antichaos theory. He argues that biosystems have an ability to spontaneously organise themselves (and this is observable). Strikingly, from the computer science perspective, swarm intelligence based search algorithms allow for huge speed-ups in terms of execution times. This can offer a massive discount in terms of bounds on bio- complexity waiting times. I am wrestling myself with this argument. I am confident in ID though.

3. In relation to ID, we should not confuse two things: one is ID as a scientific (!) theory, and quite another is its religious implications. ID does not contradict with religion but it is a scientific theory and goes the other way around, by making inferences based on the observable. In my opinion, revelation is not contrary, but "orthogonal" to it.


Mr. Luskin, you seem to have not understood Dr. Theobald's paper at all. You describe it as having a "null hypothesis," but this is factually wrong. He used Bayesian statistical methods to compare two hypotheses and thus does not have a null hypothesis. Null hypotheses are used in frequentist statistical methods developed by RA Fisher, whom you probably know was a founder of both modern statistics and evolutionary genetics. It is simply impossible for anyone to accurately describe Theobald's work as having a null hypothesis. (Note many have made this mistake as well, including Drs. Martin and Koonin, whom you mention.)

As far as answering my challenge, I don't care about articles that try to disprove evolution in an attempt to support ID (a negative test). That doesn't answer the challenge. In order to produce an analysis to go along with Dr. Theobald's, you (or another DI fellow) need to produce a positive model for designer intervention in molecular data. E.g. if the hand of God operates, what is the "P(molecular data | common designer)". You claim ID is testable and scientific. If you really believe this, then it should be possible to express a positive model that can be plugged into a Bayes-factor analysis. I can think of a few ideas, but if I make the model and it fails you may see my work as a strawman. Thus I leave it up to the ID people to do this.

On advantage of using Bayes factors is that the exact nature of the common designer can be integrated over. So all the possibilities that the DI likes to throw out can be explicitly included. So whether Hanuman, God, Jesus, God, the Holy Ghost, God, Richard Dawkins, God, Moses, God, Uranus, God, Thor, God, Prof. X, or God is the true common designer (or a mixture of the ones above), they all can be included in the model. (Of course, you may prefer to use a Dirac delta function for your prior.)

I understand that the comments of this blog are not a good forum to conduct sophisticated science. (I think Dr. Theobald spent over a year working on his calculations.) I understand your background is not in statistics, so feel free to contact some of your math-trained fellows like Drs. Dembski and Berlinski and put together a model, and get back to me. In fact, if they are not able to help you, I'll be happy to shepherd your descent into biological modeling. Once the design of the model is complete, I can then get with Dr. Theobald, and we can compare that model to his, then publish the results jointly on your site and PT sometime in several months time.

If you don't want to work with me, I can recommend an expert in Bayesian analysis of molecular data whom I believe would be extremely interested in extending Dr. Theobald's analysis to "common designer" models.

So what do you think? Are you game?

Dear Robert Camp,

Thanks for the lengthy reply but we seem to be going in circles now. I’m going to thus only respond to certain comments you made to keep it shorter.

You wrote regarding SETI:

“SETI is a hypothesis that is currently being tested. It has been explicitly configured to be testable by taking the example of human agency (the kinds of technology humans use, the kinds of signals we create and the purposes thereof) and using it as a model. SETI is therefore constrained in its experimental design to be able to find extraterrestrials that are much enough like humans that they can be detected.”

I agree with you. And the same goes for detecting design in biology. ID seeks to detect a designer at work who is enough like humans that they can be detected. (If you’re a JudeoChristian theist, this is no theological problem since humans said to have been created in the image of God and thus share certain mental / psyche similarities with God.) But theology isn't necessary here: ID detects intelligent agents that are intelligent in a way that’s enough like humans that those agents can be detected. So I’ll gladly accept your rebuttal here because it acknowledges that ID can detect a designer that's enough like humans to be detected. And since humans are intelligent, if the designer is intelligent, then we can detect the such intelligent design.

You wrote regarding prediction 2: “What you feel is immaterial to the issue under discussion. What matter is what the current scientific consensus has to say about the subject. Couching your prediction as if this consensus doesn't exist amounts to assuming that which you wish to demonstrate.”

I reply: That's a semantic rebuttal, not a substantive one. ID is in the business of challenging the consensus, so the fact that something is the consensus doesn't make it infallible. If the consensus was by definition unchallengeable then science could never progress. That's the danger with Darwin-of-the-gaps thinking: it seeks to insulate the Darwinian consensus from scientific challenge.

And scientific challenge--not "feeling"--is exactly what I'm talking about. Given that I, and many other ID proponents, have written extensively on the inability of Darwinian evolution to explain abrupt appearance of new life-forms, this is not just a "feeling" but a strong scientific argument that needs to be dealt with. So if you wish to respond, please respond to the scientific arguments at links like:

Punctuated Equilibrium and Patterns from the Fossil Record
Or
The Cambrian Explosion: Biology’s Big Bang

In fact, given that my post started by noting that Dr. McPeek admitted that "elucidating the materialistic basis of the Cambrian explosion has become more elusive, not less, the more we know about the event itself, and cannot be explained away by coupling extinction of intermediates with long stretches of geologic time, despite the contrary claims of some modern neo-Darwinists,” I think I am justified in my skepticism of the "consensus" here.

You write: “Common descent "explains" the data by discovering inherent properties and patterns (i.e., the nested hierarchy) and connecting cause and effect in observable, testable ways.”

I reply: That’s correct that common descent seeks to find a nested hierarchical pattern. The problem is that a nested hierarchy is decidedly NOT what we are finding. As an article in New Scientist titled, "Why Darwin was wrong about the tree of life," states:

“For a long time the holy grail was to build a tree of life,” says Eric Bapteste, an evolutionary biologist at the Pierre and Marie Curie University in Paris, France. A few years ago it looked as though the grail was within reach. But today the project lies in tatters, torn to pieces by an onslaught of negative evidence. Many biologists now argue that the tree concept is obsolete and needs to be discarded. “We have no evidence at all that the tree of life is a reality,” says Bapteste. That bombshell has even persuaded some that our fundamental view of biology needs to change.

According to the article, the basic problem is that one DNA sequence would yield one tree, while another sequence would yield a different tree:

The problems began in the early 1990s when it became possible to sequence actual bacterial and archaeal genes rather than just RNA. Everybody expected these DNA sequences to confirm the RNA tree, and sometimes they did but, crucially, sometimes they did not. RNA, for example, might suggest that species A was more closely related to species B than species C, but a tree made from DNA would suggest the reverse.”

For the record, that’s the opposite of a nested hierarchy.

The article discusses various proposals among evolutionary scientists to resolve these incongruities, largely entailing ad hoc appeals to a process called lateral gene transfer (LGT), where bacteria swap genes, thereby muddying any phylogenetic signal. Yet this article observed that conflicts between trees occurs even among higher branches of the tree of life where such gene swapping is not observed to take place, stating: "More fundamentally, recent research suggests that the evolution of animals and plants isn't exactly tree-like either."

Among these higher branches, the article found that “The problem was that different genes told contradictory evolutionary stories.” This led one scientist to admit that even among these relationships of higher organisms, “We’ve just annihilated the tree of life.”

In my view, this sort of data provides a proper test of common descent, and shows that much data is running counter to the nested hierarchy predicted by common descent.

You wrote: “Common design does not explain the data.”

I reply: Sure it does. Designers are not constrained to be required to always use a nested hierarchy. So ID predicts that we'll find some data that might be force-fit into a nested hierarchy but a lot of data that won't. So if the data points to a non-nested model of life, such as orchard model of life, then design best explains the data. We can test for a nested hierarchy, which means we can test for an orchard model.

You ask: “But why would a creator of biological novelty be constrained such that re-use of resources would be necessary?”

I reply: Because the designer is designing organisms to live in our universe, and our universe has certain physical constraints.

You write: “’Common design’ may be many things, but it is certainly not an explanation for the data.”

I reply: Repetition and emphasis does not make it so. Common design easily explains biological similarity that does not fit into a nested hierarchy, because designers re-use parts that work but are not obligated to do so in a manner that is consistent with a nested hierarchy.

You write: “I will simply say again that you do not, and cannot, know anything about the disposition of supernatural design until you know something of the designer.”

I reply: If you know the designer is intelligent then it shares a property that humans have, so by studying humans we can learn something about the designer. This holds true if the designer is natural or supernatural. The rest of your comment basically keeps saying the same thing so I’m going to stop here because I’ve pretty clearly answered your basic argument. Thanks.

Casey

Daniel Brown wants to remind us of the big picture, and I think that he has done this—but not in the way he intended. For example, look at how he described evolution:

evoloution [sic]
who: no need
what:descent with modification
When/Where: wherever there are living organisms
Why: Invitable [sic] outcome of living organisms

This is the sort of simplistic evolutionary thinking which refuses to actually test whether the data fits the theory.

Sure, Darwinian selection will operate in a system where there is variation, replication, and differential survival. But that’s a mathematical truism which does NOT in any way imply that complex machinelike structures (which underlie all of biology) are capable of evolving in a step-by-step fashion that is wholly blind to future needs.

Remember that Darwin himself said “If it could be demonstrated that any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down.” Darwin didn’t know of any such structures but clearly, in principle at least, there can be structures which cannot be built by a Darwinian process. So the fact that selection takes place under certain conditions is a trivial observation when dealing with complex features that are beyond the reach of Darwinian selection. We must not assume that structures are simple enough to be generated by an unguided process like Darwinian selection.

For example, Darwin assumed that the cell was like a primitive blob of protoplasm that could easily evolve new biological functions. In Darwin’s Black Box, Michael Behe explains, "To Darwin, then, as to every other scientist of the time, the cell was a black box. ... The question of how life works was not one that Darwin or his contemporaries could answer."

Modern technology has allowed biochemists to open Darwin's black box, revealing a micro-world of mind-boggling complexity. Even leading proponents of evolution have acknowledged this complexity. Past U.S. National Academy of Sciences President Bruce Alberts (who is ANTI-ID) has described this complexity in the journal Cell as an elaborate factory: "The entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines.” (Bruce Alberts, "The Cell as a Collection of Protein Machines: Preparing the Next Generation of Molecular Biologists," Cell, Vol. 92:291 (February 8, 1998).)

But could such integrated complexity evolve in a stepwise, Darwinian fashion? Behe recalls that in Origin of Species, Darwin admitted that if "any complex organ existed which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down." According to Behe, "by opening the ultimate black box, the cell," modern biochemistry "has pushed Darwin's theory to the limit."

The simplest cell requires hundreds of genes, numerous complex biological machines and biochemical pathways, and a fully functional genetic code in order to survive. Darwinian evolution - blind natural selection acting on random mutations - has failed to provide Darwinian explanations for how basic cellular biochemistry might have evolved. Five years after Behe published Darwin's Black Box, biochemist Franklin Harold stated an Oxford University Press monograph that "there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.” (Franklin M. Harold, The Way of the Cell: Molecules, Organisms and the Order of Life, p. 205 (Oxford University Press, 2001).)

We must not simply assume that there are sufficient probabilistic resources to generate the complex features we observe, but test whether there are sufficient probabilistic resources. Many of the research papers I cited in this article investigate these questions, such as: Axe, 2000; Axe, 2004; Axe et al., 2008; Axe, 2010a. Axe, 2010b; Behe & Snoke, 2004; Gauger et al. 2010.

Finally, Daniel Brown likes to attack ID through outlandish rhetoric that misrepresents the theory. This might make one feel good, but it is not a valid form of argument. Here are a couple places where he wrongly describes ID:

- He says that ID's explanatory powers isto what extent is unkown [sic]”

Actually ID proponents are carefully testing the powers of Darwinian processes vs. intelligent causes. You might wish to read some of the papers I cited to get an idea of ID research and thinking on this question: Axe, 2000; Axe, 2004; Axe et al., 2008; Axe, 2010a. Axe, 2010b; Behe & Snoke, 2004; Dembski, 1998; Dembski & Marks, 2009a; Dembski & Marks, 2009b; Ewert et al. 2009; Ewert et al. 2010; Gauger et al. 2010.

- Daniel Brown also frames ID as saying “Wherever you cant prove evolution has occured or if it is generally accepted evolution has occured, say evidence is not good enough”

Again, this statement is refuted by my entire article, which shows that ID makes positive predictions that are testable and does not depend merely on refuting evolution. His assertion about ID is nothing more than that—a mere assertion—and it is not a response to my article since my article refutes that very assertion.

Thanks.

Sincerely,

Casey

My response to Olorin's first comment was 1449 words long. Thus, in response to Olorin's latet rejoinder, I'm pretty sure I had a lot more to say than merely "quibble" that his dates are off. It sounds like Olorin is trying to deflect from the issue here. Olorin, if you actually did read my comment, then you obviously missed the point.

If you read my full article "Evolutionary Biologists Are Unaware of Their Own Arguments: Reappraising Nature's Prized 'Gem,' Tiktaalik," you will learn that multiple top evolutionary biologists made the specific prediction that a transitional form between fish and tetrapods would be found in rocks 380-363 million years old. When Tiktaalik was found from about 375 mya, they touted it as a confirmed "prediction" of neo-Darwinian evolution.

But now we know that tetrapods existed at least as early as 397 million years ago. So this "prediction" of neo-Darwinian evolution has fallen apart, and if there is a predicted time period for transitional forms between fish and tetrapods, Tiktaalik is over 20 million years off.

Given that what was once called a "prediction" of neo-Darwinism really turned to not be a prediction, I'm not sure what evolution really predicts here. But I do know this much: this isn't just a quibble over a small change in dates. As Nature editor Henry Gee put it, the existence of tetrapods at 397 million years ago means "an enormous evolutionary void has opened beneath our feet." That sounds like a bad state of affairs for the evidence for neo-Darwinian evolution.

So next time a Darwin lobbyist boasts that an evolutionary "prediction" has been fulfilled, remember the failure of predictions regarding Tiktaalik.

Olorin ends with an attack on "testability of ID hypotheses." Well, my post laid out 4 testable predictions that I believe ID makes. So I think I more than answered your request.

p.s. KrisSmith777 tried to help Olorin out by noting 3 differences between human artifacts and biological organisms:

1. Living creatures are subject to natural selection; human artifacts are not.
2. Living creatures reproduce; human artifacts do not.
3. Living artifacts mutate by natural means; human artifacts do not.

Regarding (1) and (3), genetic algorithms, which are artifacts designed by humans, can have these qualities. And as much of the work by Dembski and Marks (cited in my article) shows, when genetic algorithms evolve into something "new," because intelligence was required to program the evolution. So when we see "selection" creating something new, we see intelligent programming involved--i.e. the systems are intelligently designed to evolve.

That said, quality 2 stands out and it intrigues me. I'm not aware of a human machine that can reproduce itself. Arguably, the ability to reproduce is more complex than any technology we've created. That means that biological organisms are more complex than any human technology. But if human technology is designed, what does that say about biological organisms...?

If anything, I think these examples point to design in biological organisms!

Thanks again for these interesting comments!

Sincerely,

Casey

Billy Cee complains that there isn’t “an actual ‘theory’” of ID “anywhere.” Well, let’s take the U.S. National Academy of Science’s definition of “theory” and see if ID meets it:

Theory: In science, a well-substantiated explanation of some aspect of the natural world that can incorporate facts, laws, and tested hypotheses. The contention that evolution should be taught as "theory, not as fact" confuses the common use of these words through the accumulation of evidence. Rather, theories are the end points of science. They are understandings that develop from extensive observation, experimentation, and creative reflection. They incorporate a large body of scientific facts, laws, tested hypotheses, and logical inferences."

(Science and Creationism: A View from the National Academy of Sciences, p. 2 (National Academy Press, 1999).)

Well, from my post, I think ID more than meets this definition of theory.

ID incorporates many facts such as the facts we know about the origin of information in DNA, the abrupt appearance of groups in the fossil record, re-usage of common genetic components in diverse organisms, function for noncoding DNA, etc.
ID incorporates laws, such as the law of conversation of information, discussed in some of the articles I cited (see for example Dembski & Marks, 2009a)
ID incorporates tested hypotheses, such as the four hypotheses and predictions I mentioned in Table 2.

Additionally, many of the citations show that the conclusion of ID is the result of extensive observation, experimentation, and creative reflection, as well as logical inferences. In fact, we infer ID by first observing the types of information produced by intelligent agents when they act, and then performing experimental tests on natural systems to determine if they hold such information.

So if Billy Cee wants a theory of ID, by the standards of the U.S. National Academy of Sciences, I think he’s got one.

Thanks for the comment.

Sincerely,

Casey

@Casey Luskin

Olorin told you that there are ways that living organisms differ from human artifacts.. You then challenged him by saying, "If you are correct, then why don't you give an actual example?" I'll give you some examples myself:

1. Living creatures are subject to natural selection; human artifacts are not.

2. Living creatures reproduce; human artifacts do not.

3. Living artifacts mutate by natural means; human artifacts do not.

Darwinian evolution needs all three of these; human artifacts are not capable of any of them.

---Just my two cents.

I have never seen an actual "theory" anywhere, but the VERY FIRST THING YOU SEE ON THE ID website is:

"The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection."

I'm surprised no one seems to notice the White Elephant in the ID living room: A Lion chasing down the slowest Zerbra ISN'T "unintelligent" or undirected!!

So That whole piece by C. Luskin is pretty much moot. There is no reason to replace Darwin, just update it.

BillyCee

Mr Luskin quibbles that Olorin's predicted dates for tetrapod evolution may be off by a few percent. So let us ask Mr Luskin what dates ID predicts for the emergence of tetrapods, and how he would establish that tetrapods arose by design, rather than by evolution?

Again, the question was testability of ID hypotheses.

Nicely written article, Casey. Not being a scientist, please excuse my layman's perspective on this, but I feel that I must post some comments. It seems to me that the whole debate between ID and Darwin revolves around common sense, or the rejection thereof. I'll explain:

1. Various scientific disciplines exist to detect if something is randomly produced, or if some other agent acted upon normally random materials in such a way as to bring forth ordered information. For example, a star-studded singer whose name I dare not "share" once believed that Mount Rushmore was a naturally occurring phenomenon. Of course, we all laughed. It's quite obvious that the contours, features, and structures on the mountain are quite the work of an artist. How could anyone actually think that this landmark wasn't intelligently created? But, beginning more than a century and a half earlier, the first of the faces carved into the man-made sculpture lived and breathed, carving out a new way of live, a new land of self-governance and freedom. Mr. Washington quite closely resembled the left-most face on the mountain of today, and yet, everything he was, everything that he did, and everything that he became was, as we are told, a mere accident. How is it that a simple likeness carved out of stone is, by common sense, seen to be created by an intelligent and skilled artist, but the much more elegant original, infinitely more complex and vastly superior, was not?

2. Archaeologists routinely distinguish between human designed artifacts such as arrowheads vs. stray stones, often without much debate. Why are confirmed arrowheads not seen as something created naturally, instead of human craftmanship?

3. Why is the modern supercomputer, with its ability to compute upwards of 92 trillion operations/second, seen as a model of hardware and software engineering, and the human brain, capable of upwards of 38 thousand trillion operations/second (in a MUCH smaller space), seen as originating by chance? According to InsideHPC.com, the government has given researchers millions of dollars to REVERSE ENGINEER the brain's computational abilities. Reverse engineering would seem to imply an engineer (see the article here: http://insidehpc.com/2009/03/12/even-supercomputers-not-yet-close-to-the-raw-power-of-human-brain ).

It's just common sense. If something appears designed, performs as designed, then perhaps it is designed. This raises, what I feel, is the centerpiece of the whole argument: people don't have a problem with seeing design in a system; they may, however, have a problem with the identity of the Designer. Richard Dawkins even admitted as much in "Expelled" when he stated that he saw the possibility of the existence of the Judeo-Christian God as being a, "...VERY unpleasant prospect..."

Whenever the claim that intelligent design is indicated in nature I like to remind people of the big picture, namely the who what when where and why.

evoloution
who: no need
what:descent with modification
When/Where: wherever there are living organisms
Why: Invitable outcome of living organisms

ID
who: dont know, all that is known is that it is intelligent and designs things but to what extent is unkown, also there may be between 1 and infinity of them.
what:Intelligent designer changes existing organisms/ poofs new organisms into existance/ takes existing creatures from another dimensions and puts them on earth
when/where: Wherever you cant prove evolution has occured or if it is generally accepted evolution has occured, say evidence is not good enough
Why: Whim of the intelligent designer? It was bored? Its boss made it work on it?

What can ID show from this?

As a simple example in the biochemical realm, consider molecules that might take thousands of years to develop in nature because the combination of conditions that would produce them are rare. So just create them in the controlled conditions of a lab.

Creating molecules in the lab that ordinarily take thousands of years to develop in nature bypasses the very mechanisms that need to be tested. Your approach assumes that the path nature takes will achieve the results you expect.

You grant that the combination of conditions is rare. But isn’t that the question that needs to be answered? How rare are those combinations and is there sufficient time for nature to search for and find those combinations?

The multi-generational, multi-year bacteria tests suggest that there are limits to what evolution can accomplish in the time available.

C.L. - "He gives every indication that he intends to include all forms of intelligent causation, and that includes humans."

I already noted two "indications" to the contrary. I don't believe I'm reading anything into his statement, especially since the meaning you take from it is particularly simplistic. I don't know of anyone who would deny that we can know and understand the actions of humans.

But I admit I don't know for certain what McPeek's intent was. That, of course, is the difficulty with identifying Intelligent Design.

"SETI, for example, is seeking to detect evidence of nonhuman intelligent designers who are extraterrestrials. Since we understand how intelligent agents act by studying humans, there’s no in principle barrier to detecting the action of other intelligent agents, even if they aren’t human."

You cite the example of SETI as a response to my comment that analogizing from human design to unknown designers, "whether they are supernatural or natural," is unwarranted. But SETI stands as evidence for my point, not against.

SETI is a hypothesis that is currently being tested. It has been explicitly configured to be testable by taking the example of human agency (the kinds of technology humans use, the kinds of signals we create and the purposes thereof) and using it as a model. SETI is therefore constrained in its experimental design to be able to find extraterrestrials that are much enough like humans that they can be detected.

The point is, then, that what we know of human design is helpful in detecting either other human design, or something similar enough that a model of human design provides a useful template.

As I said in my previous post, ID theorists could emulate this approach and have a testable hypothesis, but only if they were willing to similarly constrain their model. And as your "whether they are supernatural or..." clearly indicates, that is counter to ID purposes.

"So you've conceded that my first set of observations and predictions about ID help us to reliably distinguish between ID and material processes. Even if my other predictions aren't useful to you, you seem to concede that ID does make at least some useful predictions."

Not some - one. Your first observation is the only one I conceded (and is, I think, the only salient diagnostic of design). But the existence of intent or an "end goal" is less a theoretical prediction than it is the result of a winnowing of alternatives (like your other "predictions") which can be eliminated on the basis of being uninformative regarding a choice between inference to natural or supernatural processes (because they could be characteristic of either).

"As for prediction 2, I feel that the abrupt appearance of complex biological features is unexplained by neo-Darwinian evolution (including auxiliary hypotheses like punc eq or evo devo) so like prediction 1, it too refutes neo-Darwinian evolution.

What you feel is immaterial to the issue under discussion. What matter is what the current scientific consensus has to say about the subject. Couching your prediction as if this consensus doesn't exist amounts to assuming that which you wish to demonstrate.

With predictions 2, 3, and 4 revealed as inadequate, your argument that ID is a positive research program rests upon #1. And l submit that the only way to know anything about the intent or purpose behind some putative design is to know something of the designer - a stipulation ID proponents continue to dismiss as inessential.

"Thus, the next time you hear that neo-Darwinism explains why tetrapods share a similar bone structure in their limbs, realize that an equally good explanation is common design. Can neo-Darwinian common descent explain this data? Sure. But so can ID. Such data is not powerful evidence for descent over design."

Of course it is. The reason for this is the nature of what we call an "explanation." Common descent "explains" the data by discovering inherent properties and patterns (i.e., the nested heirarchy) and connecting cause and effect in observable, testable ways. An explanation elucidates the "how" and the "why" of the subject of investigation. Common design does not explain the data. It does not inform our understanding of how these events occurred, or why the data demonstrate particular systems of order or arrangement.

Common design, in fact, depends upon assumptions which cannot be known, (e.g., a designer is just as likely to re-use design elements as natural processes would be). But why would a creator of biological novelty be constrained such that re-use of resources would be necessary? I know of no reason a supernatural designer might be so limited, and neither do you. It may be true, but that is the kind of assumption that depends directly upon knowledge of the designer (purposes, abilities etc.), something, once again, that ID proponents disavow.

"Common design" may be many things, but it is certainly not an explanation for the data.

But each prediction is what we would expect from a designer regardless of whether they are natural or supernatural"

Let's see.

"Regarding prediction (1), designers generate complex systems that require goal directed processes. This would hold true whether the designer is natural or supernatural."

Designers also generate simple systems. Designers also sometimes generate design for which the intent, the goal, is obscure. These concerns do not inform the choice between purposive and non-purposive agency and are thus irrelevant.

As to what "holds true" for supernatural designers, I will simply say again that you do not, and cannot, know anything about the disposition of supernatural design until you know something of the designer. To extrapolate from what we know of natural (human) agency is illogical and presumptuous.

"Regarding prediction (2), when designers generate such complex systems they appear in the historical record abruptly, fully formed. This would hold true whether the designer is natural or supernatural."

You have no idea that this would be the case, for either natural or supernatural designers, until you know of the intent behind the design.

"Regarding prediction (3), perhaps a supernatural designer is not always obligated to re-use the same exact parts. But the designer of our universe chose to make a universe that has regular operating laws that operate throughout the cosmos. Thus, any designer that is designing structures for use within our universe will face certain physical constraints."

Once again, you are folding numerous unjustified assumptions into your argument. Not until you tell me which designer you're talking about, what you know of him/her/it and how you know it, these complaints are irrelevant.

"In fact, there are constraints in any natural environment so if a designer is building different organisms to exist in the same natural environment then perhaps it makes sense that a designer would re-use parts which are good at meeting those constraints."

And does this mean that if I can produce examples of apparent re-use of resources (common design) in organisms for which the environments are very different, if not impertinent, you will concede the point?

"Regarding prediction 4, designers generate systems and parts with functions. This would hold true whether the designer is natural or supernatural."

Well, this is a truism, and as such is utterly unrevealing. Anything that we know to be designed must perform a function, if only by virtue of being a representation of the designer's intent.

"Robert Camp then writes: "Unless and until you can present some evidence as to the existence and intent of the designer in question, there is no testable hypothesis to which predictions can be logically or empirically connected."

I reply: In fact, presenting evidence of the prior action of an intelligent designer is exactly what I've done. We must understand how historical sciences work."

I don't wish to seem ungrateful, and in fact I appreciate that you have opened up this forum to comments, but I'd appreciate if you would respond to what I've written and not what you've misread. I said nothing about "presenting evidence of the prior action of an intelligent designer," a completely uncircumscribed notion. I said "evidence as to the existence and intent of the designer in question, a very different requirement.

"ID is a historical science, meaning it employs the principle of uniformitarianism, which holds that the present is the key to the past. ID investigations thus begin with observations about how intelligent agents operate and then proceed to convert those observations into positive predictions of what scientists should find in nature if intelligent design was involved in the origin of a given natural object."

One cannot employ the principle of uniformitarianism when one has no observation or data to support the inference at issue. There is plenty of historical support for inference to human agency. There is no warrant for inference to any intelligent agency other than human. We don't have observations about intelligent agents. We have observations about humans. Until it can be demonstrated evidentially that those observations can be transferred to some putative other intelligent agent it cannot be assumed that there is anything about human agency that applies comprehensively to all possible intelligent agents.

Suggesting otherwise is about as explicit an assumption of one's conclusion as there can be.

"So just because we can’t directly observe Pangaea in the present doesn’t mean we can’t use the methods of historical sciences to piece together clues and demonstrate that it existed in the past."

Of course not, because we're not positing unevidenced and untestable non-natural processes. And those mechanisms we are positing can be demonstrated to be directly related to the effects we see.

"Likewise, by observing present-day actions of human intelligence, we can find that the methods used by intelligent agents explain much of the data we see in biology. We can infer the existence of the designer by finding evidence of the types of information and patterns which in our experience derive from intelligence. So I've presented much evidence of a designer."

No, by observing present-day action of humans we can find that the methods used explain much of the data we see in anthropology and archeology. Unless you're talking about artificial selection and genetic manipulation, human agency doesn't offer any explanation for the development and descent of life on earth.

And yes, you can infer a designer by finding evidence that matches information and patterns from your experience, but only the designer of your experience. Going beyond that to analogically intuiting a designer of life and universes may be fine as religion, or rhetoric, but it is not logical and it is in no way scientific.

"But humans are intelligent. So by studying human artifacts we’re studying how intelligent agents operate."

Yes, we're studying how human intelligent agents operate. You cannot know that anything about human agency is applicable to an entirely unknown intelligent agency without some information as to the unknown agent.

"This allows us to detect the prior action of other intelligent agents, whether they were human or not."

It simply does not allow such a thing (unless, as discussed previously, one is attempting to detect a model of human agency). The above is posed as a counterargument, but it is not. It is just a restatement of your assumptions.

These attempts to conflate human and non-natural design are understandable, and unlike some of my compatriots on the anti-ID side, I believe they are sincere. But they are badly flawed. Until you can demonstrate how and why our experience with human design can logically be employed as representative of all putative design, you have only beliefs masquerading as empirical illations.

Until you know something of the existence, capacity and responsibility of your proposed designer, you cannot identify (I)ntelligent (D)esign.

Does Dr. McPeek explain why he believes that, if God ... then scientific inquiry ceases ... or anything empirical about the process would be unknowable?

He seems to take a "punctuated" leap here from science to the metaphysical. For fun, let's suppose the futurists quoted in the recent TIME article on "The Singularity" are correct in forecasting that the human brain will be reverse engineered by the mid-2020s. If they are right, then wouldn't we see something (many things in fact) significant about the engineering of the brain (or even trace something of the workings of an Engineer)?

To Mr. Feheley, ID infers a design, and by extension suggests a Designer. Christians have skins in the game, but so should any non-materialist.

Dear Dr. Cartwright,

Thanks for joining in here and citing Douglas Theobald’s paper on common descent. In fact I discussed this paper at length in some prior articles here at ENV, two of which are here and here.

In response to your comment:

First, I must note that intelligent design is not necessarily incompatible with common ancestry. So even if Theobald’s test is correct, I'm not sure how it would refute ID.

But Theobald is looking to demonstrate full-blown neo-Darwinian common ancestry where all gene sequences are the result of an unguided process of descent with modification. Thus my second point is that if we consider common design as an alternative to common descent, his paper does not demonstrate common descent is a better explanation.

Theobald's paper tested common ancestry against the null hypothesis that genes in different organism arrived at similar sequences by chance. So if his hypothesis demonstrates that common ancestry, as you put it, "found that common descent was significantly better supported by the data" best explains the data, then he did so by comparing it only to sheer chance. His null hypothesis wasn't mere "uncommon descent" but more like 'uncommon descent without the possibility of intelligent design.'

But there are other explanations for similar gene sequences besides neo-Darwinian common ancestry and sheer chance which Theobald ignores.

For example, Theobald's test ignores the possibility of common design. Common design is at least as good an explanation for functional genetic similarities as common descent. Why is this? It's simple. As I explain in my post, Paul Nelson and Jonathan Wells observe, "An intelligent cause may reuse or redeploy the same module in different systems, without there necessarily being any material or physical connection between those systems. Even more simply, intelligent causes can generate identical patterns independently."

Likewise, in their book Intelligent Design Uncensored, William Dembski and Jonathan Witt include a lucid discussion of why mere functional biological similarities do not demonstrate the superiority of common descent over common design:

"According to this argument, the Darwinian principle of common ancestry predicts such common features, vindicating the theory of evolution. One problem with this line of argument is that people recognized common features long before Darwin, and they attributed them to common design. Just as we find certain features cropping up again and again in the realm of human technology (e.g., wheels and axles on wagons, buggies and cars) so too we can expect an intelligent designer to reuse good design ideas in a variety of situations where they work."

(William Dembski and Jonathan Witt, Intelligent Design Uncensored: An Easy-to-Understand Guide to the Controversy, p. 85 (InterVarsity Press, 2010).)

So functional genetic similarity can be explained by common descent, but also by common design. They both explain how similar functional genetic sequences can appear. As noted in my prior post, ID is not necessarily incompatible with common ancestry, but common design is an equally good explanation for why two taxa can have highly similar functional genetic sequences. After all, designers regularly re-use parts, programs, or components that work in different designs. As another example, engineers use wheels on both cars and airplanes, or technology designers put keyboards on both computers and cell-phones. Or software designers will re-use subroutines in different software programs. So common design can explain this data equally well.

But Theobald ignores this possibility. As I will discuss further at the end, it seems to me that Dr. Theobald was not really interested in testing universal common ancestry.

Second, there’s a lot of data that common descent does not explain. As I explain here, there’s much anomalous data that does not fit with the predictions of common descent. For example:

(1) Phylogeny and biogeography don't always agree.
(2) Phylogeny and paleontology don't always agree.
(3) Transitional fossils are often missing (or the "predicted" transitional fossils fall apart on closer inspection).
(4) Hierarchical classifications often fail.
(5) "Homologous" structures often have different developmental pathways or different structures often have "homologous" developmental pathways.
(6) Morphological and molecular phylogenies are often incongruent.
(7) Molecule-based phylogenies often sharply contradict one-another.


Regarding item 7 in the list, it is extremely common that molecule-based trees contradict one-another. As I explain in a recent article here, molecular systematists have their epicycles (like horizontal gene transfer) to try to explain this data. But that does not change the fact that genetic similarity is constantly appearing in places unpredicted by common descent. In my view, this sort of data provides a proper test of common descent, and shows that much data is running counter to the nested hierarchy predicted by common descent.

In closing, I’m fine if you want to cite Theobald’s paper:

(1) If the paper is valid, I'm not sure it woudl necessarily refute ID.

(2) The paper tests common ancestry against the wrong null hypothesis and does not acknowledge the possibility that similar genetic sequences were generated by common design.

(3) The paper only tests genes which are ubiquitously found throughout the diverse domains of life, and does not acknowledge that there are many gene sequences that don’t fit a nice neat nested hierarchy. Thus, genetic similarity is constantly being discovered in places not predicted by common descent, causing molecular trees to conflict with one-another. So I think that the paper tests universal common descent in the wrong way, but when tested in the right way the tree of life hypothesis fails.

Thus, perhaps the reason that New Scientist observed that one study found that "[t]he problem was that different genes told contradictory evolutionary stories" is because the genes have wholly different stories to tell, namely stories that indicate that all organisms are not genetically related. For those open-minded enough to consider it, common design is a viable alternative to common descent.

You finally asked: "Care to propose a specific model of ID that can be statistically tested using the same methods and data?"

I reply: Be careful what you wish for! Actually Theobald’s paper shows precisely how neo-Darwinian evolutionists are NOT INTERESTED in actually testing common descent. So if you are asking me to test my hypothesis like Theobald tests his, then I refuse to do so because Theobald used such a preposterous null hypothesis that he did NOT offer anything close to a reasonable test of his model.

If you don't believe me, consider comments of a reviewer of a critique of Theobald's paper by Eugenie Koonin and Yuri Wolf:

Cogniscenti cringed when they saw the Theobald paper, knowing that "it is trivial". It is trivial because the straw man that Theobald attacks in a text largely formulated in convoluted legalese, is that significant sequence similarity might arise by chance as opposed to descent with modification. Ignoring the strength of the universality of the genetic code and the commonality of central intermediary metabolism among cells as evidence, Theobald construed a non-issue that the referees of his paper, whoever they may have been, found convincing and novel (!).


(Comments by William Martin of the University of Duesseldorf in review of Eugene V Koonin and Yuri I Wolf, "The common ancestry of life," Biology Direct, Vol. 5:64 (2010).)

You wrote: "If ID is empirically testable, and DNA sequences are the product of ID, then it should be possible to define a statistical model by which to compare the hand of God versus evolution."

I reply: I made it quite explicit that we could not scientifically claim that to detect the "hand of God" as I wrote "While we might not be able to scientifically identify the designer as God, we can certainly find signs of intelligent action in nature."

But when framed properly, I’m happy to accept your challenge. Many of the papers I cited in this post provide exactly what you request. See, especially, some of the work of Michael Behe and Doug Axe testing the sufficiency of neo-Darwinian processes to explain the origin of rare functional gene sequences. Some of the relevant work includes: Axe, 2000; Axe, 2004; Axe et al., 2008; Axe, 2010a. Axe, 2010b; Behe & Snoke, 2004; Dembski, 1998; Dembski & Marks, 2009a; Dembski & Marks, 2009b; Ewert et al. 2009; Ewert et al. 2010; Gauger et al. 2010. Thanks.

But I must make one final note: Koonin and Wolf wrote in response to Theobald that "A formal demonstration of the Universal Common Ancestry hypothesis has not been achieved and is unlikely to be feasible in principle." (Eugene V Koonin and Yuri I Wolf, "The common ancestry of life," Biology Direct, Vol. 5:64 (2010).)

So if you're wanting a robust test for ID, then you might not want ID to be tested like common descent, because some experts feel that a formal test of universal common ancestry is not possible.

Thanks again for writing.

Sincerely,

Casey

In response to Robert Camp, he takes a very bold tone, stating: "There is a reason McPeek used the words 'any other' and capitalized the first letters of 'Intelligent Designer.' He was very clearly distinguishing untestable (non-natural) agency from that which you go on to discuss: human design."

I reply: I’m not sure you’re correct. You are reading an interpretation into Dr. McPeek's argument which is not apparent from the text. I simply took Dr. McPeek’s words at face value and when he says "we can never empirically know or understand the actions of God or any other Intelligent Designer" then I take that to mean exactly what he said: "we can we can never empirically know or understand the actions of God or any other Intelligent Designer." The words "any other Intelligent Designer" make it clear that he’s intends his point to be taken very broadly--applying to "any other Intelligent Designer." He gives every indication that he intends to include all forms of intelligent causation, and that includes humans.

So again, you are reading words into Dr. McPeek's argument that simply aren’t there. He made a very broad statement that we can never empirically detect the action an "any" intelligence, and I was just taking his words at face value.

But let's say for the sake of argument you're correct in your interpretation of Dr. McPeek's words. If you are correct, then that simply means that you and Dr. McPeek are conceding that we can detect the action of human intelligent agents. But if we can study and learn how to detect the prior action of intelligent agents by studying humans, then there’s no reason we can’t detect the action of other intelligent agents, whether they are supernatural or natural designers, God or humans. Or at least, as I will show, you have not given me any reason to conclude that we can only detect the prior action of human intelligence and not non-human intelligence.

You wrote: "there is simply no analogical warrant for extending this information to putative intelligent agents for which we lack evidence establishing either existence, capacity or responsibility."

I reply: That’s not correct at all. SETI, for example, is seeking to detect evidence of nonhuman intelligent designers who are extraterrestrials. Since we understand how intelligent agents act by studying humans, there’s no in principle barrier to detecting the action of other intelligent agents, even if they aren’t human. They key principle is that they are intelligent, not that they are human. If they’re intelligent, then they share a property that we have (intelligence), a property we can study and understand, and a property whose effects we can reliably detect in nature.

Forgive the double or triple negatives here, but you have not at all established that we cannot detect non-human intelligence. And the existence of SETI shows that some serious scientists disagree with you.

You write: "Unfortunately, your Table 1 does little to illuminate the matter. Only your first observation succeeds in presenting a distinguishing characteristic of human design (intent, or 'end goal'). As natural processes are demonstrably capable of producing your next three observations they are at best non-diagnostic of design, and at worst an example of assuming the conclusion at issue."

I reply: I'm glad that you conceded that with regards to the presence of high levels of CSI and irreducibly complex machines, ID and neo-Darwinian evolution make mutually exclusive predictions which are useful for helping us to discriminate between design and descent.

So you've conceded that my first set of observations and predictions about ID help us to reliably distinguish between ID and material processes. Even if my other predictions aren't useful to you, you seem to concede that ID does make at least some useful predictions.

But in fact I believe that ID's other predictions I listed (#s 2, 3 and 4) are entirely useful and help show that ID is a scientific theory. As I will show, your criticisms of those predictions do not hold up.

As for prediction 2, I feel that the abrupt appearance of complex biological features is unexplained by neo-Darwinian evolution (including auxiliary hypotheses like punc eq or evo devo) so like prediction 1, it too refutes neo-Darwinian evolution.

But I agree with you regarding predictions 3 and 4 that neo-Darwinian causes can explain much (though not all, as in the case of extreme convergent similarity) of this data. If you see this as a weakness of ID then you have missed the point of my entire post. My post was titled "A Positive, Testable Case for Intelligent Design," which means that my argument for design is not predicated upon merely refuting neo-Darwinian evolution. ID is not merely a negative argument against evolution. The case for design is positive and ID makes predictions that stand on their own without considering what other theories may or may not predict.

Thus, the next time you hear that neo-Darwinism explains why tetrapods share a similar bone structure in their limbs, realize that an equally good explanation is common design. Can neo-Darwinian common descent explain this data? Sure. But so can ID. Such data is not powerful evidence for descent over design.

And in fact there are many instances where we see high levels of similarity appearing in places not predicted by common descent. Neo-Darwinians call this “convergent” evolution but at some point we have to admit that the many examples of extreme convergent evolution (including genetic convergent evolution) are far better explained by common design than common descent.

As for prediction 4, perhaps neo-Darwinism is not refuted by the discovery of function for non-coding DNA or vestigial organs. But that’s small consolation given that the now-refuted junk-DNA mindset was born and bred out of the neo-Darwinian paradigm. If some rogue biologists had the courage to study function for junk-DNA that's great, but it was not because of the neo-Darwinian paradigm but rather in spite of it.

In fact, there is clear evidence that neo-Darwinian thinking hindered scientists from discovering function for noncoding “junk” DNA. A 2003 article in Science is any indication, then it seems that the neo-Darwinian paradigm did indeed impose a taboo on research into function for junk-DNA. As the article stated:

Although catchy, the term 'junk DNA' for many years repelled mainstream researchers from studying noncoding DNA. Who, except a small number of genomic clochards, would like to dig through genomic garbage? However, in science as in normal life, there are some clochards who, at the risk of being ridiculed, explore unpopular territories. Because of them, the view of junk DNA, especially repetitive elements, began to change in the early 1990s. Now, more and more biologists regard repetitive elements as a genomic treasure."

(Wojciech Makalowski, "Not Junk After All," Science, Vol. 300(5623):1246-1247 (May 23, 2003).)

How much clearer could it be? This 2003 article acknowledges that "the term 'junk DNA' for many years repelled mainstream researchers from studying noncoding DNA" and further notes that those biologists who did study function for "junk-DNA" faced "the risk of being ridiculed." (emphases added) In science, where reputation is so important, it's much easier to shift one's research focus to where the money, the momentum, and the praise flow freely -- not where research is "repelled" and "ridiculed."

In fact, even some of the evolutionary biologists who risked "ridicule" to seek function for junk-DNA have lamented how their paradigm has stifled research into junk-DNA. Also in 2003, John Mattick, an evolutionist biologist who is a standout because of his research seeking function for junk-DNA, stated in Scientific American the following striking comment:

Yet the introns within genes and the long stretches of intergenic DNA between genes, Mattick says, “were immediately assumed to be evolutionary junk.” That assumption was too hasty. … "I think this will come to be a classic story of orthodoxy derailing objective analysis of the facts, in this case for a quarter of a century," Mattick says. "The failure to recognize the full implications of this--particularly the possibility that the intervening noncoding sequences may be transmitting parallel information in the form of RNA molecules--may well go down as one of the biggest mistakes in the history of molecular biology."

(John S. Mattick quoted in W. Wayt Gibbs, "The Unseen Genome, Gems Among the Junk," Scientific American (November, 2003).)

Again, the fact that the existence of mass function for noncoding DNA doesn’t necessarily refute neo-Darwinism is small consolation when so many biologists—under the basis of evolutionary thinking—wrongly predicted that noncoding DNA would be functionless junk.

So no one is assuming conclusions here, we’re making predictions that naturally flow out of our understanding of how intelligent agents operate. If you don’t believe me, consider the fact that long before evidence of function for noncoding DNA started pouring in, ID proponents had long been prediction function for 'junk' DNA. Please see here for some documentation.

Robert Camp then wrote: "Table 2 suffers from similar problems (especially the part about assuming conclusions in your premises), except now you are now also ascribing to your putative intelligence concerns (e.g. reuse of resources) that are important only to natural, limited designers."

I reply: You still have not explained how I am assuming any conclusions in my premises. I fail to see how that criticism applies.

But each prediction is what we would expect from a designer regardless of whether they are natural or supernatural.

Regarding prediction (1), designers generate complex systems that require goal directed processes. This would hold true whether the designer is natural or supernatural.

Regarding prediction (2), when designers generate such complex systems they appear in the historical record abruptly, fully formed. This would hold true whether the designer is natural or supernatural.

Regarding prediction (3), perhaps a supernatural designer is not always obligated to re-use the same exact parts. But the designer of our universe chose to make a universe that has regular operating laws that operate throughout the cosmos. Thus, any designer that is designing structures for use within our universe will face certain physical constraints. In fact, there are constraints in any natural environment so if a designer is building different organisms to exist in the same natural environment then perhaps it makes sense that a designer would re-use parts which are good at meeting those constraints. So I don't think your objection holds up here, for this point would hold true whether the designer is natural or supernatural.

Regarding prediction 4, designers generate systems and parts with functions. This would hold true whether the designer is natural or supernatural.

So I see no reason why my arguments must apply only to human intelligent designers. They seem to hold to intelligent agents generally, whether human or not.

Robert Camp then writes: "Unless and until you can present some evidence as to the existence and intent of the designer in question, there is no testable hypothesis to which predictions can be logically or empirically connected."

I reply: In fact, presenting evidence of the prior action of an intelligent designer is exactly what I've done. We must understand how historical sciences work.

ID is a historical science, meaning it employs the principle of uniformitarianism, which holds that the present is the key to the past. ID investigations thus begin with observations about how intelligent agents operate and then proceed to convert those observations into positive predictions of what scientists should find in nature if intelligent design was involved in the origin of a given natural object.

This is much how other historical sciences operate. I’m a HUGE supporter of the theory of plate tectonics. But we can’t go back in time and directly observe that Pangaea existed. But we can observe that plates are moving today, and we can find tell-tale signs that if you rewind plate movements (and look at other clues), the continents fit together as a single giant landmass.

So just because we can’t directly observe Pangaea in the present doesn’t mean we can’t use the methods of historical sciences to piece together clues and demonstrate that it existed in the past.

Likewise, by observing present-day actions of human intelligence, we can find that the methods used by intelligent agents explain much of the data we see in biology. We can infer the existence of the designer by finding evidence of the types of information and patterns which in our experience derive from intelligence. So I've presented much evidence of a designer.

As a final note, many critics of ID mistakenly believe that the theory is focused upon studying the designer, alleging that it specifically invokes supernatural forces or a deity. But ID is not focused on studying the actual intelligent cause responsible for life. Instead, ID studies objects in nature, attempting to determine if natural objects bear an informational signature indicating that an intelligent cause was involved in their origin. As William Dembski explains:

“Intelligent design is the science that studies signs of intelligence. Note that a sign is not the thing signified. … As a scientific research program, intelligent design investigates the effects of intelligence, not intelligence as such.”

(William Dembski, The Design Revolution, pg. 33 (InterVarsity Press, 2004).)

Similarly, Michael Behe explains that we can detect design even if we don’t know anything about the identity or nature of the designer:

"The conclusion that something was designed can be made quite independently of knowledge of the designer. As a matter of procedure, the design must first be apprehended before there can be any further question about the designer. The inference to design can be held with all the firmness that is possible in this world, without knowing anything about the designer."

(Michael Behe, Darwin's Black Box: The Biochemical Challenge to Evolution, pg. 197 (Free Press, 1996).)

Behe even goes so far as to suggest that “[i]ntelligent design does not require a candidate for the role of the designer.” Thus, as a scientific theory, ID does not focus on studying the actual intelligent designer, but simply studies objects in nature to determine if they bear the signs of intelligent design.

Robert Camp finally wrote: "The analogy with human design is logically flawed. We can identify human artifacts because we are familiar with humans - not the other way around."

I reply: But humans are intelligent. So by studying human artifacts we’re studying how intelligent agents operate. This allows us to detect the prior action of other intelligent agents, whether they were human or not. Your argument has not established that we can't detect the prior action of non-human agents, provided they are intelligent like us.

In response to Olorin, Olorin first stated: "We can find many ways in which living organisms differ from human artifacts, yet this does not falsify the design hypothesis, either."

I reply: If you are correct, then why don't you give an actual example?

In fact, I raised potential differences between living organisms and human artifacts that could in principle falsify the design hypothesis. For example, I noted that human artifacts are designed for a function or purpose. If structures in living organisms have no function or purpose, then arguably they did not arrive at that state through design. Don't take my word for it, take the words of people like Richard Dawkins, Michael Shermer, Francis Collins, Ken Miller, and many others who have all argued that "junk DNA" or "vestigial organs" ought to falsify ID.

Here's just one example from Ken Miller:

"the human genome is littered with pseudogenes, gene fragments, ‘orphaned’ genes, ‘junk’ DNA, and so many repeated copies of pointless DNA sequences that it cannot be attributed to anything that resembles intelligent design."

(Kenneth R. Miller, "Life’s Grand Design," Technology Review, pp. 25-32 (February/March, 1994).)

So Miller is right on his logic, but he's wrong on the facts, because since 1994 we've discovered that these types of DNA are in fact not "pointless" but in many cases serve vital functions for the cell. So Miller laid out a legitimate test for ID, and ID turns out to have passed that test.

Olorin follows up by stating: "For example, evolution framed a hypothesis that fish transitioned to tetrapods about 350-4000Mya. A team of paleontologists froze their socks off for several years and found Tiktaalk. Hypothesis tested."

I reply: Olorin got his dates a little off--the claimed predicted dates for a fish-to-tetrapod intermediate are actually more like 380-360 million years ago. As Tiktaalik's website states:

"Common sense tells us that the transitional form must have arisen 380-363 million years ago. ... In order to find our transitional fossil, we'll need to find rocks that are between 380 and 363 million years old."

Likewise Jerry Coyne writes that "[Neil] Shubin predicted that if transitional forms existed, their fossils would be found in strata around 375 million years old."

But did evolution really predict this? If it did, then their prediction has fallen apart.

Olorin obviously hasn't been following recent developments on this topic of whether the fossil record really predicts that we’ll find fish-to-tetrapod transitions around 380-360 million years ago. As I document at "Evolutionary Biologists Are Unaware of Their Own Arguments: Reappraising Nature's Prized 'Gem,' Tiktaalik," evolutionary biologists did predict that a transition would be found in rocks about 375 million years old. Jerry Coyne even boasts that what’s "marvelous is that [Tiktaalik's] discovery was not only anticipated, but predicted to occur in rocks of a certain age and in a certain place."

You can read my documentation of all their predictions here, and I would kindly ask that you read that post before you comment further on this topic.

But there's a major problem for evolutionists who boast about this confirmed 'prediction'. The problem is that in early 2010, TRUE tetrapod tracks, with digits, were reported from rocks aged about 397 million years. This means that if there's any evolutionary prediction, it's that transitions between fish and tetrapods ought to be found before 397 million years. But Tiktaalik is about 20 million years too late to fit that "prediction."

Consider how Nature reported on these tracks:

The fish-tetrapod transition was thus seemingly quite well documented. There was a consensus that the divergence between some elpistostegalians (such as Tiktaalik or Panderichthys) and tetrapods might have occurred during the Givetian, 391-385 Myr ago. Coeval with the earliest fossil tetrapods, trackways dating to the Late Devonian were evidence for their ability to walk or crawl on shores.


Now, however, Nied?wiedzki et al. lob a grenade into that picture. They report the stunning discovery of tetrapod trackways with distinct digit imprints from Zache?mie, Poland, that are unambiguously dated to the lowermost Eifelian (397 Myr ago). This site (an old quarry) has yielded a dozen trackways made by several individuals that ranged from about 0.5 to 2.5 metres in total length, and numerous isolated footprints found on fragments of scree. The tracks predate the oldest tetrapod skeletal remains by 18 Myr and, more surprisingly, the earliest elpistostegalian fishes by about 10 Myr.

(Philippe Janvier & Gaël Clément, "Muddy tetrapod origins," Nature 463:40-41 (January 7, 2010).)

Or as a Nature news article put it:

The oldest known tracks of a four-limbed land animal could rewrite part of vertebrate evolution. Some prints, showing individual digits, were found in limestone slabs unearthed in a quarry near Zache?mie, Poland, dated to about 395 million years ago -- more than 18 million years before tetrapods were thought to have evolved.


The tracks suggest that the animals that made them were up to 2.5 metres long and had a footpad up to 26 centimetres wide, although most prints were about 15 centimetres wide, reports a team of Polish and Swedish scientists in Nature this week. This would mean that large, land-roaming tetrapods would have coexisted for 10 million years with the elpistostegids -- including Tiktaalik roseae, which lived 375 million years ago -- a group thought to mark the transition from fish to land-roaming animals.

("Discovery pushes back date of first four-legged animal")

A few--though only a few--evolutionists also acknowledged these 397 million year old tetrapod tracks meant the collapse of the "prediction" that a transitional form between fish and tetrapods would be found from rocks aged 375 million years.

In a striking quote, Nature editor Henry Gee quietly acknowledged on his Nature blog that the early tetrapod tracks "means that the neatly gift-wrapped correlation between stratigraphy and phylogeny, in which elpistostegids represent a transitional form in the swift evolution of tetrapods in the mid-Frasnian, is a cruel illusion. If -- as the Polish footprints show -- tetrapods already existed in the Eifelian, then an enormous evolutionary void has opened beneath our feet..."

Again, if there's any evolutionary prediction, it's that transitions between fish and tetrapods ought to be found before 397 million years. But as Gee says, no such fossils exist and these trakcs leave "an enormous evolutionary void. Tiktaalik doesn't fill that void because it's at least 20 million years too late.

So does evolution really predict that we'll find a transitional form between 380 and 363 million years ago? I don’t think so. What does evolution really predict here? Your guess is as good as mine. But given that we have evidence of true tetrapods from 397 million years ago, I don't think it's really so clear that evolution "predicts" we'll find transitional forms between fish and tetrapods nearly 20 million years AFTER tetrapods already existed.

Olorin also wrote "Evolution predicts that, if humans and apes had a common ancestor, a couple of chromosomes either separated in apes or fused in hominids."

I'm not sure how strong this prediction is. If we hadn't found evidence of a fused chromosome, would that refute neo-Darwinian evolution? No. Evolutionists would just claim that the fused telomeres and extra centromere were deleted, removing any evidence of fusion. For a discussion of how this really doesn't provide strong evidence for neo-Darwinian evolution, please see here.

But let's be charitable and say that perhaps neo-Darwinian evolution did predict the fusion evidence. OK fine. ID isn't incompatible with common ancestry, so even if the fusion evidence clearly shows common ancestry between humans and apes (which it doesn't), then it's not clear why that would refute ID. I also cited numerous confirmed predictions of ID, which aren't negated by a confirmed prediction of evolution.

Olorin asks: "how would Mr Luskin determine that the wolf and the Tasmanian devil were designed together, for example?"

I reply: No one is every claiming one can "determine" with 100% certainty these questions. If you hold ID to such a standard then you are holding ID to a standard that no scientific theory is held to. But we can test predictions. Examples of extreme convergent evolution that cannot be neo-Darwinian processes and is expected under ID. That data points towards the design hypothesis.

Finally, Olorin asked "if ID can generate hypotheses that can be tested by experiment and by field work, why have ID investigators not done so? Since ID claims to follow the scientific method, one might think this would be the first item of business."

I reply: I'm not sure if you read my article here but it cites dozens of peer-reviewed papers which reflect much experimental and field work done by ID proponents which backs these predictions. Olorin's demand has already been met.

In response to "Olof," he wrote: "The first problem I see with this article is point number one, about a designer having an end goal in mind. Who says that a goal was set or has been achieved in nature? This is a common misconception by people who reject evolution in thinking that evolution is heading in a direction towards a 'goal'."

I reply: Of course you are correct that neo-Darwinian evolution is not goal-directed. I fully understand that. Many leading theorists have made this point clear. As E.O. Wilson states:

"[L]ife has diversified on Earth autonomously without any kind of external guidance. Evolution in a pure Darwinian world has no goal or purpose: the exclusive driving force is random mutations sorted out by natural selection from one generation to the next."


(Edward O. Wilson, "Intelligent Evolution: The consequences of Charles Darwin's 'one long argument'," Harvard Magazine (November-December, 2005).)

But to claim that nothing in nature is the result of a goal-directed process is to assume the truth of the neo-Darwinian argument. I’m interested testing these questions, not assuming what the right answer is.

In that regard, the reason I reject neo-Darwinian evolution isn't because I mistakenly think evolution is heading towards a goal. The reason I reject neo-Darwinian evolution neo-Darwinian evolution is not a goal directed process, but the complex machine-like structures we observe in biology require a goal directed process in order to originate.

Stephen C. Meyer explains that the inability of natural selection to work towards any goal is exactly what makes it impotent as a sufficient cause for the complexity of life:

"Natural selection lacks foresight. What natural selection lacks, intelligent selection--purposive or goal-directed design--provides. Rational agents can arrange both matter and symbols with distant goals in mind. In using language, the human mind routinely “finds” or generates highly improbable linguistic sequences to convey an intended or preconceived idea. In the process of thought, functional objectives precede and constrain the selection of words, sounds and symbols to generate functional (and indeed meaningful) sequences from among a vast ensemble of meaningless alternative combinations of sound or symbol. Similarly, the construction of complex technological objects and products, such as bridges, circuit boards, engines and software, result from the application of goal-directed constraints (Polanyi 1967, 1968). Indeed, in all functionally integrated complex systems where the cause is known by experience or observation, design engineers or other intelligent agents applied boundary constraints to limit possibilities in order to produce improbable forms, sequences or structures. Rational agents have repeatedly demonstrated the capacity to constrain the possible to actualize improbable but initially unrealized future functions. Repeated experience affirms that intelligent agents (minds) uniquely possess such causal powers.


Analysis of the problem of the origin of biological information, therefore, exposes a deficiency in the causal powers of natural selection that corresponds precisely to powers that agents are uniquely known to possess. Intelligent agents have foresight. Such agents can select functional goals before they exist. They can devise or select material means to accomplish those ends from among an array of possibilities and then actualize those goals in accord with a preconceived design plan or set of functional requirements. Rational agents can constrain combinatorial space with distant outcomes in mind. The causal powers that natural selection lacks--almost by definition--are associated with the attributes of consciousness and rationality--with purposive intelligence. Thus, by invoking design to explain the origin of new biological information, contemporary design theorists are not positing an arbitrary explanatory element unmotivated by a consideration of the evidence. Instead, they are positing an entity possessing precisely the attributes and causal powers that the phenomenon in question requires as a condition of its production and explanation."


(Stephen C. Meyer, "The origin of biological information and the higher taxonomic categories," Proceedings of the Biological Society of Washington, Vol. 117(2):213-239 (2004) (internal citations removed).)

Biology is built upon information, language-based code, and machines--all entities that require a goal directed process to originate. Intelligent design is a goal directed process which can explain this data.

In response to "Jerry Feheley," he stated: "What I don't understand is how Intelligent Design (because it is there) in any ways proves the existence of say the Christian God who gave us the bible, the ten commandments, his son Jesus, the holy spirit etc."

I reply: I'm not sure if you are trying to critique ID or not, but ID doesn't claim to address those issues. As my post states: “While we might not be able to scientifically identify the designer as God, we can certainly find signs of intelligent action in nature.”

I have no doubt that Intelligent Design is evident in the workings of the Universe from the Big Bang through the creation of life in all its forms. I respect all religions in their quest to understand the Universe and this most amazing life.

What I don't understand is how Intelligent Design (because it is there) in any ways proves the existence of say the Christian God who gave us the bible, the ten commandments, his son Jesus, the holy spirit etc.

It seems to me that Intelligent Design is something the Universe itself miraculously and mysteriously does before our very eyes. We can see the magnificent wondrous designs unfolding as the Universe does them. The Universe itself has majestically figured out the unknowable. The Universe itself deserves our respect, admiration, appreciation and awe. The Universe has created us.

This says to me the Universe itself is God.

The difficulty atheists and neo-Darwinists seem two have is two-fold. They cannot rationalize the condition we currently live in (disease, genetic abnormalities, war, hatred, etc.) with the concept of an extremely wise creator. Not hard to understand, as most people cannot. And it is not for lack of information. The second reason is that most people do not want to be accountable to any kind of higher being. They have grown up in a sea of subtle, distorted teachings that make the Creator look like a vindictive egomaniac or aloof and sadistic. There is a very good reason why the world is the mess that it is, and it is not entirely from poor human management. The Bible gives clear answers, and it is not traditional creationism. They may not be scientifically provable, but there is more than sufficient circumstantial proof to convince even the most hard-headed critic. Certainly more than Darwinism claims. And with what is at stake, you cannot afford not to investigate.

The first problem I see with this article is point number one, about a designer having an end goal in mind. Who says that a goal was set or has been achieved in nature? This is a common misconception by people who reject evolution in thinking that evolution is heading in a direction towards a "goal".

Prof. McPeek means something different than Mr Luskin by “testability.” Mr Luskin can list similarities to human design all he likes, but this is not testing. We can find many ways in which living organisms differ from human artifacts, yet this does not falsify the design hypothesis, either.

For example, evolution framed a hypothesis that fish transitioned to tetrapods about 350-4000Mya. A team of paleontologists froze their socks off for several years and found Tiktaalk. Hypothesis tested. Evolution predicts that, if humans and apes had a common ancestor, a couple of chromosomes either separated in apes or fused in hominids. Bingo.

ID cites “convergent traits” as evidence for design. So how would Mr Luskin determine that the wolf and the Tasmanian devil were designed together, for example? How would ID test whether the ostrich and the moa reused the same parts, and, if so, which parts?

Finally, if ID can generate hypotheses that can be tested by experiment and by field work, why have ID investigators not done so? Since ID claims to follow the scientific method, one might think this would be the first item of business.

Another annoying soundbite is the one that ID is a 'science stopper'. I don't see how the premise that unexplained complex biological features are designed is any more of a science stopper than the one that they must have formed by random mutation and natural selection. They're both interpretations that can be applied to all cases, and are similarly final.

The only thing going for the latter, if you accept the premise that only physical causes are allowable in science, is that it *is* a physical cause.

Even on that questionable premise, it's completely illogical to say, because it *would* be more scientific (on the aforesaid premise) *were* it the explanation, then it is the preferred explanation-- regardless of the evidence for it.

"you can't test a million-year evolutionary sequence in the lab either."
Actually science and engineering can and do test things in ways that take a long time to happen in nature. For example, the ASTM standards for Accelerated Weathering Tests at http://www.astm.org/Standards/D4799.htm relate to ways of speeding up the effects of natural processes.
As a simple example in the biochemical realm, consider molecules that might take thousands of years to develop in nature because the combination of conditions that would produce them are rare. So just create them in the controlled conditions of a lab.
Then create some other molecules in the lab that would take comparably long to occur in nature. And combine them to synthesize molecules dependent on these predecessors.
Voila! Science has just created in a few hours something that is dependent on possibly independent rare occurrences that might never have been spatially close enough together for their results to interact.
But that's just the prelude. Since science can speed things up so much in this fashion, how is it that science has not yet been able to create life in the laboratory?

"Let's take God out of the equation here so Dr. McPeek's statement now says: "The Intelligent Design hypothesis is untestable by science, exactly because we can never empirically know or understand the actions of ... any ... Intelligent Designer." That statement is incorrect."

No, it's not. There is a reason McPeek used the words "any other' and capitalized the first letters of "Intelligent Designer." He was very clearly distinguishing untestable (non-natural) agency from that which you go on to discuss: human design.

There is no question that we can, and do, know a great deal about the acts and artifacts of human agency. But there is simply no analogical warrant for extending this information to putative intelligent agents for which we lack evidence establishing either existence, capacity or responsibility.

Unfortunately, your Table 1 does little to illuminate the matter. Only your first observation succeeds in presenting a distinguishing characteristic of human design (intent, or "end goal"). As natural processes are demonstrably capable of producing your next three observations they are at best non-diagnostic of design, and at worst an example of assuming the conclusion at issue.

Table 2 suffers from similar problems (especially the part about assuming conclusions in your premises), except now you are now also ascribing to your putative intelligence concerns (e.g. reuse of resources) that are important only to natural, limited designers. Unless it is your intent to argue that humans (the only intelligence with which we are familiar) are the Intelligent Designers to be identified by your predictions, this aspect of your argument, must be considered a non sequitur.

The deficiencies of Table 2 leave Table 3 irrelevant.

Your presentation of ID research relies upon misapprehensions and misapplications of logic. Unless and until you can present some evidence as to the existence and intent of the designer in question, there is no testable hypothesis to which predictions can be logically or empirically connected.

The analogy with human design is logically flawed. We can identify human artifacts because we are familiar with humans - not the other way around.

The theory of evolution is just an extension of the spontaneous generation of life theories from the 1700's.

As you recall Dr. Theobald tested the hypotheses of universal common descent against uncommon descent and found that common descent was significantly better supported by the data.

Care to propose a specific model of ID that can be statistically tested using the same methods and data? If ID is empirically testable, and DNA sequences are the product of ID, then it should be possible to define a statistical model by which to compare the hand of God versus evolution.

This is the ultimate test. Any takers?

Thanks again for yet another GREAT blog post, Casey! I enjoyed reading this.

Your blogs, literature-reviews and insights are very much appreciated.

J

When someone claims that a particular scientific hypothesis is not testable, it's not always clear to me what that person means by that statement.

Some seem to imply that the only way to test a hypothesis is in the laboratory. I recall Eugenie Scott's saying that you can't put God in a test tube. Well, you can't test a million-year evolutionary sequence in the lab either.

The events that led to evolution or intelligent design occurred a long time ago. Stephen Meyer recalls Darwin's method of testing historical hypotheses. We should propose causes of past effects that we know by our universal and common experience produce those same effects today. The only known cause of the complex, specified structures that are observed in living things is intelligent agency.

Now it may be that unguided nature can accomplish what intelligent agency can accomplish but how can science demonstrate that? If there has been a demonstration that the kind of complexity observed in living things can come about without intelligent agency, I am unaware of such demonstrations.

Evolutionary algorithms have been offered up as demonstrations of the ability of natural processes to achieve the complexity observed in nature. David Berlinski does not accept that. He says that evolutionary algorithms that work are non-Darwinian, and Darwinian algorithms do not work.

Based on what has been demonstrated so far it seems to me that intelligent agency is the “winner”.