The final prediction listed in this appendix relates directly to the research work done by Doug Axe in the BioLogic Institute. The argument is that the arrangement of amino acids in functional molecules like proteins should be rare, that . . . → Read More: ID Prediction #12]]> “The functional sequences of amino acids within amino acid ¬sequence space should be extremely rare rather than common.”

The final prediction listed in this appendix relates directly to the research work done by Doug Axe in the BioLogic Institute. The argument is that the arrangement of amino acids in functional molecules like proteins should be rare, that is, the protein’s function is very sensitive to changes in the amino acid sequence. The inference is that it could not have been achieved by chance mutations of individual amino acids and therefore could only have been arranged by an intelligent designer. Axe has reported on a significant amount of work that shows the arrangement of amino acids is indeed highly tuned and specific to its function.
The question is not whether such a sequence is rare, but whether this truly reflects the work of an intelligent agent rather than natural selection operating on a large population of possibilities. The ID claim builds on Dembski’s explanatory filter and relies on probability calculations to show that no random event could achieve such a configuration in the lifespan of the universe.
However, the great difficulty of all probability calculations for living molecules is that neither the intermediate steps nor the process mechanisms are adequately known to calculate a trustworthy probability. The history of biochemistry has been that transformations from one state to another that seem incredibly improbable, turn out to be highly probable when we understand the details of the process. One example of that was discussed in a previous post, namely the antibody example. The transition from a state of a population of identical pre-B cells to a state of highly specified complex B cells with high affinity to relevant antigens would be calculated to have impossible odds of occurring if we knew nothing about the mechanisms driving that transition. Now that the details have been elucidated over the last few decades, we see how random rearrangement processes and natural selection make that transition highly probable.
I would suggest that all of Meyer’s probability calculations in this book, as well as any others relating to the development of biomolecules, suffer from this deficiency. A proper probability calculation requires detailed knowledge of the initial state and the process by which the system moves to the next state. It must also reflect the size of the population of the initial state. Instead, Meyer makes calculations of the type that assume the initial state is a set of disconnected nucleotides which then inexplicably and randomly assemble themselves into a functional protein. It is no wonder the result is impossibly low. Nature doesn’t work that way. Most origin of life researchers are not looking for evidence of the incredibly improbable event. Rather, they seek the understanding of the precursor populations that could predictably migrate to the next step. At the present time, no one knows enough about the intermediate steps to either claim understanding of such evolution or of claiming that such evolution could not have occurred.
Axe may well find that the sequences are rare with respect to sensitivity to changes in individual amino acids but that still doesn’t give us much information about the probability of its evolution. Larger scale mixing, matching, and borrowing of sections of amino acids are known to occur in many processes that form proteins. This means that the opportunity space for generating new proteins is enormous, making it extremely difficult to ascertain what actually happened in the evolutionary past. But it makes it even more difficult to show that such evolutionary changes couldn’t have happened. In light of current evolutionary thought of how proteins evolved, one might even predict that many, if not most, amino acid sequences in proteins are rare. They were unlikely to have evolved by changes in one amino acid at a time. This prediction does not seem to be fruitful in elucidating a unique prediction of ID.

This prediction deals with the issue of “bad design.” The ID concept . . . → Read More: ID Prediction #10]]> “If an intelligent (and benevolent) agent designed life, then studies of putatively bad designs in life-such as the vertebrate retina and virulent bacteria-should reveal either (a) reasons for the designs that show a hidden functional logic or (b) evidence of decay of originally good designs.”

This prediction deals with the issue of “bad design.” The ID concept has spawned many discussions on both sides of how an intelligent designer might or might not carry out a design. As mentioned repeatedly in these posts and comments, I believe that ID is non-scientific precisely because the proposed intelligent agent is not amenable to independent scientific observation to understand how it can effect a design. These discussions are therefore, in my opinion, quite worthless except to generate speculative arguments. What constitutes a truly bad design? How does one define bad design? How do we know what an indeterminate intelligent agent would or would not do? We simply don’t know.

Meyer speculates that such an agent would never do a truly bad design. Therefore there must be a reason for everything. Hence, what we think is bad, will be found to have some secret beneficial function. He hedges his bets and admits that perhaps a bad design could occur if a design point were originally good but decayed to a bad state. Why an intelligent agent wouldn’t be able or willing to prevent or avoid that is not at all clear.

In any case, I find this path to be a fruitless direction. Nothing will be gained by discussing what kinds of designs are good or bad with respect to an intelligent designer that we cannot study.

This is a prediction that is indeed in sharp contrast to that predicted by evolutionary development. The issue seems to be the degree . . . → Read More: ID Prediction #9]]> “The fossil record, in particular, should show evidence of dis¬crete infusions of information into the biosphere at episodic intervals as well as a top-down, rather than bottom-up, pattern of appearance of new fossil forms.”

This is a prediction that is indeed in sharp contrast to that predicted by evolutionary development. The issue seems to be the degree of increase in information. Though Meyer does not concur, the scientific community in general recognizes that DNA information can increase during the reproduction process. Various mechanisms like gene duplication or a wide variety of mechanisms for DNA insertion increase the total amount of DNA information. These may be detrimental, neutral, or beneficial. The detrimental ones hinder or prevent further reproduction, ending that particular implementation. The others may persist and become specified in the sense of carrying out particular functions. The degree of change of information is typically limited to that which can be reached from an existing organism. We do not yet fully comprehend the range of genetic changes that can occur in this way. Mutations in complex organisms like primates are more likely to be large scale changes in segments of DNA instead of point mutations of nucleotides. Rather dramatic and significant physiological changes are therefore expected and have been observed and documented.

But what Meyer points out is that his proposed indeterminate intelligent designer is not limited by incremental changes to the existing organism. There could, in theory, be far more dramatic changes in DNA information content than that achieved by descent with modification. Such an event has never been observed and doesn’t meet Meyer’s criteria for historical causal analysis. Nor do we know why an intelligent designer would choose to make such large changes as opposed to small incremental ones.

Showing evidence for such large scale changes is quite a challenge. Without a specific mechanism to predict when and where and what type of large scale changes we might expect, we have little guidance. On one hand, if the intelligent designer truly operated at its caprice, then one would expect very little correlation or sequence in the fossil record. There is no reason why the genetic tree should have any coherence at all. If, however, that intelligent designer just wanted to tweak things a bit, perhaps being impatient with the time it was taking evolution to make progress, we might see smaller changes. But those would be hard to distinguish from the extent of changes that can occur in natural reproduction.

What we do know is that there is a truly amazing degree of coherence and correlation in the connection of all living organisms. Some DNA segments are common among virtually all forms of cellular life, with changes consistent with common descent. No major discontinuities have been discovered, meaning that any influence of an intelligent designer as opposed to normal reproduction would be minor.

This is another prediction that would shake up the scientific world if it were confirmed. Yet, even this does not have a clear connection to an intelligent designer in the sense that such a designer would be compelled to operate in this way. The debate would continue.

Again, Meyer shows a degree of knowledge about what the proposed intelligent designer would or would not do. Such knowledge is not accessible to or testable by the scientific community in general. In this case, Meyer . . . → Read More: ID Prediction #8]]> “If a designing intelligence acted discretely in the history of life, the various subdisciplines of biology should show evidence of polyphyly.”

Again, Meyer shows a degree of knowledge about what the proposed intelligent designer would or would not do. Such knowledge is not accessible to or testable by the scientific community in general. In this case, Meyer suggests that the designing intelligence would have designed life on earth through several different originating species and not one common ancestral source, though it’s not clear why. Polyphyly could also conceivably be due to abiogenesis being more probable than we currently think, a possibility that cannot yet be ruled out.

It is interesting to speculate what would constitute evidence of polyphily. Would a major discontinuity in the fossil time sequence suffice? Or would it require finding life based on different amino acids than the 20 used in terrestrial life? Or life with a different chirality of biomolecules? Or life based on a different set of nucleotides than the 4 that comprise all known life that has been discovered so far? Meyer states “Since intelligent agents have the freedom to combine modular elements and subsystems in unique ways from a variety of information sources, we should expect phylogenetic analyses of diverse systems and molecules to generate some conflicting trees.” In other words, does he mean that if we cannot resolve conflicts in putting together a phylogenetic tree, we have evidence of polyphyly? It may be true that a polyphyletic system would have multiple discontinuities in its tree of life, but proving that conflicts are due to polyphyly wouldn’t be that simple.

In any case, it is noteworthy that not even a hint of polyphyly has been discovered so far. If polyphyly ever is proven, it would indeed be a major change in understanding of life on earth. It would not necessarily strengthen the case of ID since there is no necessary relationship between the two.

This prediction essentially involves experimental confirmation of the hypotheses proposed by Jonathan Wells of the role of centrioles in cell division. Meyer quotes from . . . → Read More: ID Prediction #6]]> “Sophisticated imaging techniques will reveal nanomachines (turbines) in centrioles that play a role in cell division. Other evidence will show that malfunctions in the regulation of these machines are responsible for chromosomal damage.”

This prediction essentially involves experimental confirmation of the hypotheses proposed by Jonathan Wells of the role of centrioles in cell division. Meyer quotes from an abstract that Wells wrote for a scientific article. “Instead of viewing centrioles through the spectacles of molecular reductionism and neo-Darwinism, this hypothesis assumes that they are holistically designed to be turbines… What if centrioles really are tiny turbines? This is much easier to conceive if we adopt a holistic rather than reductionistic approach, and if we regard centrioles as designed structures rather than accidental by-products of neo-Darwinian evolution.”

What is the significance of turbines in centrioles playing a role in cell division? What does it mean to “play a role?” This prediction is not very specific. Nor is it clear how “playing a role in cell division” is connected to the claims of ID.

It seems that the argument relates to the origin of the idea. Wells writes that a holistic, or system-based, approach, in contrast to a reductionistic approach, leads one to seek a functional role for centrioles. Let us suppose that this is confirmed, however that might be accomplished. To what extent would this confirm or deny the validity of the claims of ID. It would indeed confirm a prediction that was developed by someone who was working from the ID paradigm. But before this confirms the validity of the paradigm, it must also be shown that the result is a unique consequence of the claims of ID. Is a role of centrioles in cell division a repudiation of alternative explanations? Is it a necessary and unique implication of ID?

In favor of the ID perspective, a positive result of this type can show how ID-based thinking may lead to some fruitful results. It is not clear that those results can only be the effect of ID processes. Unless the prediction is a differentiating prediction that can occur only if the ID paradigm is correct, the success of the prediction will again fail to settle any arguments.

A common feature . . . → Read More: ID Prediction #5]]> “Investigation of the logic of regulatory and information¬-processing systems in cells will reveal the use of design strategies and logic that mirrors (though possibly exceeds in complexity) those used in systems designed by engineers. Cell biologists will find regulatory systems that function in accord with a logic that can be expressed as an algorithm.”

A common feature of ID literature is the discussion of analogies between human-designed systems and biological systems. Indeed, the similarities are remarkable in many ways. This prediction foresees more of the same. It follows from the claim that just as complex specified information in non-biological systems is always the result of an intelligent agent such as humans, then complex specified information in the biological system is also the result of an intelligent agent. The obvious corollary is that the design strategy and logic embedded in that information is very similar.

The term “mirror” isn’t defined by Meyer and it isn’t clear how closely the two systems need to match in order to either verify or negate the prediction. What if 90% of the strategies are mirrored? 80%? What if a design strategy is found that isn’t mirrored? Is that enough to negate the prediction? Who’s the arbiter to determine what a design strategy is?

The reference to algorithms is puzzling. Is the implication that only systems that are the product of an intelligent agent can function in accord with a logic that can be expressed in an algorithm? How is this a useful prediction of ID?

It seems that this is a prediction that will be true, no matter whether ID is true or not.

This is the experimental biochemistry version of the computer simulation prediction (see #2). Meyer discusses in some degree of detail how origin-of-life researchers strive to demonstrate experimentally how replicase functions can arise from various RNA-world . . . → Read More: ID Prediction #4]]> “Informational accounting will reveal that any improvements in replicase function in ribozymes are the result of active informa¬tion supplied by ribozyme engineers.”

This is the experimental biochemistry version of the computer simulation prediction (see #2). Meyer discusses in some degree of detail how origin-of-life researchers strive to demonstrate experimentally how replicase functions can arise from various RNA-world molecules such as ribozymes. His complaint is that any progress claimed to demonstrate development of new function is actually the result of information actively supplied by the biochemists setting up the experiment.

The challenge seems to be a natural extension of the basic claim Meyer is making, namely that all complex specified information is the result of the action of an intelligent agent. Yet, the challenge may be a catch-22. Experimental verification of even a small part of an evolutionary process requires researchers to set up the environment in such a way as to obtain results in about eight orders of magnitude faster time than might have happened in evolution. This necessarily involves some artificial influence of the starting points or the environmental conditions. The rules of informational accounting are sufficiently vague that separating the active information required to set up the experiment from active information unfairly generating the target information is to some degree in the eye of the beholder. Once again, the prediction might be met but few will change their mind about ID as a result.