Is this indeed demonstrable, or will we always be able to insert our favorite cure-all– natural selection, fairies– into an ill-defined gap?

Isn’t that the only hope for ID? That our knowledge will leave us gaps for it to hide in? ID does not give us any tools to determine if a gap is intrinsic or caused by incomplete knowledge. In other words, ID cannot even compete with ‘we don’t know’, let alone natural selection which is a clearly defined mechanism and which has been shown to match what is needed for complex specified information to arise.

The use of terms like code, program etc all may give the impression that there is some intelligence required. Take the concept of control science such as feedback loop, integral feedback loop, all suggest the need for some ‘controller’. So let’s go back into time where the heart was seen as a pump, does this mean that the heart requires a designer beyond the natural processes of chance and regularity found in evolutionary science? Or more recent, the bacterial flagellum, which is compared to an ‘engine’, does this make the flagellum ‘designed’? What if science, as it has done, provides plausible pathways for its origin and evolution? So far ID proponents have been quick to reject such scenarios as ‘just-so-stories’… If ID proponents object to ‘just so stories’ I am sure they reject ID’s ‘just not-so stories’?

The origin and evolution of the genetic code is a very interesting area and much has been learned.

So where did the switch from “teleomatic causation to teleonomic causation in biological organisms” take place?

Does the genetic code assign similar codons to similar amino acids because of chemical interactions between them? Unlike adaptive explanations, which can only explain the relative positions of amino acids in the code, stereochemical explanations could tie codon assignments to absolute, verifiable rules. However, modern translation encodes amino acid sequences without direct codon/amino acid interaction. If there is a relationship between RNA sequences with intrinsic affinity for amino acids and the modern genetic code, we must therefore explain a historical transition in which direct interactions were abandoned.

Tests of a stereochemical genetic code, Rob Knight, Laura Landweber and Michael Yarus Department of Molecular, Cellular and Developmental Biology
University of Colorado

Researchers have found a strong affinity between the triplets that code for a particular amino-acid and the amino-acid itself. This suggests that originally the protein sequences may have been templated directly from the bases and that the tRNA transcription processes evolved later.

This was originally shown for arginine and more recently for additional aminoacids

Far be it from me to disagree with either W. V. Quine or Ernst Mayr, but Darwin didn’t show that teleology doesn ‘t exist; he merely proposed a mechanism for evolution which doesn’t require it.

Excellent observation. Which is why evolution and religion need not be at odds after all.

There are data that indicate that the genetic code had a chemical (or steroechemical) basis - that in fact the amino acid-codon correspondence we see today isn’t entirely arbitrary.

Indeed, the work by various research on the genetic code has shown that there is a combination of ‘regularity’, ‘chance’ and ’selection’ which played their roles in the origin and evolution of the code. People such as Freeland, Knight, Landweber.

Someone should point out that ID does NOT say that the design had to be of supernatural origin, as Macneill falsely claims above. He made the same bogus claim in comments at telicthoughts on their post about the ID course.

Falsely??? Come on, first of all the writings of ID advocates show that it’s all about the supernatural, secondly logically ID insists on the supernatural, by eliminating natural processes and calling that which is left intelligent design. It may not be directly self evident that ID insists on the supernatural but I believe a strong case exists that logically and empirically ID is all about the supernatural.

It seems that Harold has some issues with MacNeill and I hope that we can discuss these issues in a more polite manner?

You compare its pattern of information to that which is known to be “arbitrary” when intelligent agents code for function and adaptation. Already, when Darwinists try to engage in simulations they find that they cannot escape their own creative act of design.

That by itself is a logically speaking very poor response. If the argument is that natural processes such as regularity and chance cannot explain something and experiments show that this is wrong, then suggesting that the experimenter is somehow the causal factor misses the point. All that is needed is variation and selection which can be shown to be sufficient for the evolution of information (real information) in the genome.

You also seem to conflate the concept of information as used by Dembski, and as used by science when it comes to the genome (Shannon) and semantic information. All that is requireed for information is for the data to be non-uniformly distributed. The genetic code and its evolution has been quite extensively studied and contrary to ID, it has presented us with some excellent knowledge as to what may have happened (remember, science is tentative). Your objections to code, and natural selection seem to be mostly semantic and philosophical not scientific. For instance one can define quite rigorously natural selection and study it in nature. So how do scientists explain the evolution of the genetic code? While certainly many parts are lacking in supporting evidence, it’s remarkable that science is slowly teasing apart a likely scenario. Just check out the work by Knight, Landweber or Freelkand who have tested experimentally the various hypotheses. Just because we may not be able to understand how science may test for such hypotheses does not make science unable to do so.
Art raises some good questions as to ID arguments when it comes to for instance the genetic code. I do not believe that there is a foundation to be found in ID’s foundational claims for the origin of the genetic code. On the one hand, the argument is that since ACTG have no chemical affinity that there are not regular forces guiding the genetic code (and wrongly so but that’s another topic), thus rejecting natural processes. Assume that this argument were correct, why should this give any credibility to design? Why would design use ACTG? Such a claim seems arbitrary and in fact unanswerable by ID’s own claims that design says nothing about the designer and thus lacking means, motives and opportunity, and not to mention ‘hard evidence’ ID remains unable to formulate predictions or hypotheses relevant to its own foundational claims.

I also agree that intelligent agency that is not emperically determinable is of no interest to science. Our claim, of course, is that it is unambiguously identifiable; and most of the ID project is devoted to making that rigorous.

How is ID unambiguously identifiable and are you suggesting that rigor is so far lacking in ID’s claims? I would agree, starting with the flawed eliminative approach combined with false positives, making the ID inference useless.
I agree that there are cases where design is detectable, science does it all the time but such inferences are not based on ID’s methods but rather on extending our knowledge of regularity and chance processes to establish means, motives and opportunities.

Sal points to the displacement theorem, whatever that may be, but until this theorem can be shown to be relevant to evolution, such claims are meaningless. Dembski’s ‘conservation of information’ arguments, his displacement claims only serve to strengthen the conclusions that ID is about the supernatural. As far as a turing machine, your claims lack in rigor. In fact, as has been pointed out to you before, Turing machines are quite simple, at least conceptually. In fact, as Edis has argued, regularity and chance may indeed form a completeness solution, resolving that Godel paradox, used by some to argue against evolution. Biological function and genetic code are correlated yes. So what?

Hi. One I think the link died for “other papers”. I hope you get to reference Albert Voie’s paper too!

See:
Biological function and the genetic code are interdependent

You hit the nail on the head:

in any program a certain degree of non-determinism is needed for information content

Absolutely right. An furthermore, not just the program, but also the machine on which the program runs, namely, a Turing Machine, must be made of materials that allow for indeterminism. A “probable Turing Machine” is an oxymoron. The OOL disproven via “proof by contradiction” not “argument from ignorance”.

As I like to point out, the information content of a Shakespearean poem is independent of the chemistry of the ink and paper conveying the poem. In similar manner, Turing Machines (whether they appear on Intel micro-processors made of silicon or cells made of DNA and amino acids) have an independence from the chemistry on which the Turing Machine is implemented. The chemistry must allow a VERY large degree of indeterminism for the Turing Machine to exist, and therefore, because of that fact, chemistry can not also be the cause of the Turing Machine!!!! Abel’s paper mentions that chance and necessity do not explain Turing Machines.

The question then arises, whether natural selection acting on a replicator can make a Turing Machine. The Displacement Theorem cast serious doubt on that. A computer factory is more complicated (more improbable) than a computer itself. The same would hold true for natural selection making a Turing Machine, it is more likely raw chance will succeed than natural selection, but that’s not saying much!

In general, salient teleological features of material objects have an independence from the material substrate on which they reside. In general then, materialistic explanations are catergorically inappropriate to explain non-material features (such as telelogical features). What is useful however, in the case of OOL and Turing machines, is that the improbability of the Turing Machine and the amount of non-material information content is mathematically measurable and thus subject to scientific inquiry.

Salvador

I also agree that intelligent agency that is not emperically determinable is of no interest to science. Our claim, of course, is that it is unambiguously identifiable; and most of the ID project is devoted to making that rigorous.

Art G– I’ll follow your links.

“Hoyle’s theory of an intelligent universe is probably one of them.”

Again, this sentence carries with it the implication that the “intelligence” that ID theory purports to identify is woven into the natural laws of the universe itself. If that is the case, then ID would also qualify as “natural” in the same way as all other processes that follow “natural laws.”

However, there is no branch of natural science (including biology) in which more than a tiny minority of regular practictioners believe that there is incontrovertable, empirical evidence supporting the contention that “natural laws” include some kind of “intelligent agency.” Furthermore, as I have pointed out in an earlier post, it is not at all clear that even if such an “intelligent agency” (call it “entelechy” as Max Dreisch did) did exist that its actions would produce any difference as far as natural processes are concerned. Indeed, if such an “intelligent agency” does exist, its activities are so subtle that they cannot be distinguished from “non-intelligent” causative forces, at least at the level of empirical analysis (including statistical analysis). As many have pointed out, if the situation were otherwise (i.e. if the action of such an “intelligent agency” were unambiguously identifiable using standard experimental design and statistical analysis, the first person to publish the results of such an unambiguous identification would instantly become more famous than Newton, Darwin, and Einstein among the scientific community and the general public. So far, it hasn’t happened, although nothing says it’s impossible (improbability is something else again).

You said:

“I don’t think I’ve heard this particular argument from the ID side; unless perhaps I’m not understanding you. Why should a completely arbitrary code support ID more than otherwise?”

My argument:

“ID proponents hold up codes of human origins as examples of systems that are also arbitrary, and claim that this feature is diagnostic of design. They use this analogy to buttress the claim that the genetic code is a product of design.”

Here is a sampling of excerpts that contain the idea:
From http://www.arn.org/docs/meyer/sm_dnaotherdesigns.htm:

“To see the distinction between order and information, compare the sequence “ABABABABAB ABAB” to the sequence “Time and tide wait for no man.” The first sequence is repetitive and ordered, but not complex or informative. Systems that are characterized by both specificity and complexity (what information theorists call “specified complexity”) have “information content.” Since such systems have the qualitative feature of aperiodicity or complexity, they are qualitatively distinguishable from systems characterized by simple periodic order. Thus, attempts to explain the origin of order have no relevance to discussions of the origin of information content. Significantly, the nucleotide sequences in the coding regions of DNA have, by all accounts, a high information content–that is, they are both highly specified and complex, just like meaningful English sentences or functional lines of code in computer software.

Yet the information contained in an English sentence or computer software does not derive from the chemistry of the ink or the physics of magnetism, but from a source extrinsic to physics and chemistry altogether. Indeed, in both cases, the message transcends the properties of the medium. The information in DNA also transcends the properties of its material medium. Because chemical bonds do not determine the arrangement of nucleotide bases, the nucleotides can assume a vast array of possible sequences and thereby express many different biochemical messages.

If the properties of matter (i.e., the medium) do not suffice to explain the origin of information, what does? Our experience with information-intensive systems (especially codes and languages) indicates that such systems always come from an intelligent source–i.e., from mental or personal agents, not chance or material necessity.”

From http://www.gnmagazine.org/issues/gn58/tinycode.htm:

“If the information in the book was spoken aloud, written in chalk or electronically reproduced in a computer, the information does not suffer qualitatively from the means of transporting it. “In fact the content of the message,” says professor Phillip Johnson, “is independent of the physical makeup of the medium” (Defeating Darwinism by Opening Minds, 1997, p. 71).
The same principle is found in the genetic code. The DNA molecule carries the genetic language, but the language itself is independent of its carrier. The same genetic information can be written in a book, stored in a compact disk or sent over the Internet, and yet the quality or content of the message has not changed by changing the means of conveying it.”

Finally (this is but a sampling – the theme can be found in the various ID-inspired lesson plans that have been the subject of much debate), from http://www.nyackcollege.edu/bible/Chan_Intelligent_Design_as_Apologetic_Argument.doc :

“What, then, is the origin of this genetic information encoded in DNA? Is there any chance that it arose gradually over time? Did laws of attraction between the C, T, G and A bases help bring about their present arrangement? ID theorists Stephen Meyer and Walter Bradley have shown that there is as little reason to believe the nucleotides have self-organizing properties as there is to believe the letters on this page were drawn together by the chemistry of the ink.37 Unlike the hardware components of the bacterial flagellum, the software in DNA is essentially a language.38 As in the case of English letters and words, the sequence of nucleotide bases is a closed system of symbols, whose meaning is confined to the internal coding system. In the English language, the combination of the letters CAT represents an animal with four legs that catches mice. In DNA, the nucleotide combination CAT represents the amino acid Histidine. There is no intrinsic linkage of CAT to either the four-legged animal or to Histidine; they are merely system-specific symbols.
Where does this leave us as far as origins are concerned? Our uniform experience seems to suggest that internal coding systems are producible only by intelligence. “

I think the theme I allude to comes thru loud and clear in these items.

Finally (for now), you asked:

“Or are you arguing that the patterns in genetic codes are not conditionally independent and thus probably the result of deterministic natural laws?”

That’s what the data tell us.

ID proponents hold up codes of human origins as examples of systems that are also arbitrary, and claim that this feature is diagnostic of design. They use this analogy to buttress the claim that the genetic code is a product of design.

I don’t think I’ve heard this particular argument from the ID side; unless perhaps I’m not understanding you. Why should a completely arbitrary code support ID more than otherwise? Or are you arguing that the patterns in genetic codes are not conditionally independent and thus probably the result of deterministic natural laws?

And as to the question of supernatural versus natural causes, if the source of “intelligent design” is not supernatural, then it is natural, yes?

Those would seem to be the two possibilities, if natural/supernatural is a valid dichotomy for potential causes. There are various possible scenarios for “natural” intelligent design; Hoyle’s theory of an intelligent universe is probably one of them.

But ID doesn’t claim either that intelligence in question is not supernatural or that it is, in some way, reducible to the laws of physics and chemistry. We don’t believe we have enough empirical information to posit either way on that question.*

Some have suggested that intelligent/non-intelligent is a far more useful dichotomy in analyzing causes. Perhaps this is something like Mayr’s teleonomic/teleomatic differentiation.

For after all, in the history of science “supernatural” seems to have been more of a slur cast upon whichever theory is unpopular at a time and pretty much devoid of any real meaning. What method would you have of distinguishing natural and supernatural causes in empirical science?

*[although, if you want to define natural causes as those which have empirically observable effects, then by definition the “designer” of ID theory is natural, whatever other properties it may have.]

Art G