DNA as Digital Technology

_{Barry Arrington
November 19, 2011

Intelligent Design

1}_{Categories
Intelligent Design}

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Which Bible thumping ID nutbag wrote the following:

There is a sense, therefore, in which the three-dimensional coiled shape of a protein is determined by the one-dimensional sequence of code symbols in the DNA…. The whole translation, from strictly sequential DNA ROM [read-only memory] to precisely invariant three-dimensional protein shape, is a remarkable feat of digital information technology.

Comments

Petrushka, A hypothesis regarding a transition might sound like this: X variation occurred. It conferred Y benefit, and was selected. Q variation occurred. It was neutral, but then combined through drift with R variation, which conferred Z benefit, which was selected. If no one can even string a few of those together, then it's not even hypothetical. It's conceptual. Like when I imagine the flying car of the future without knowing how to build one. That's what I mean when I say that no one has ever described a significant evolutionary change in specific evolutionary terms. It's reasonable to allow that there are constraints (time) on what we're able to observe. But if no one can even hypothesize one or even part of one then it's still at square one, the "Gee, what if?" step. That there are thousands of papers and not a single concrete example or even established possibility says as much as no papers at all. First it's an "umbrella" theory supported by lots of hypotheses. But then the most important hypothesis - the one that establishes the core principle of how organisms evolve to adapt over time - isn't even incorrect, it's missing entirely.ScottAndrews2_{November 21, 2011
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Petrushka: <blockquoteIf you can anticipate the utility of coding sequences or new molecules, you can make a fortune in pharmaceuticals. If that is what you want. However I say there are already existing remedies for most ills- nature-made remedies, meaning we do not need pharaceuticals.Joseph_{November 21, 2011
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By the way, you have posted a quotation in such a way that it looks like I am the author. I disputed the characterization of pathways as smooth.Petrushka_{November 21, 2011
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The landscape metaphor was invented sixty or seventy years ago. Thousands of papers have been published on the concepts of ridges and networks. It's an active field of research. I can't even imagine what you mean by claiming there is no hypothesis. It's the single most important hypothesis in biology. Everything in evolution depends on species having diverged as a result of known types of genetic change. Not all known changes are small. there are whole genome duplications, gene duplications, transpositions, horizontal gene transfer and such, but they are known, observable and widely studied.Petrushka_{November 21, 2011
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Petrushka,
We have very good reasons for hypothesizing a smooth incremental path.
My point is that no one has hypothesized one. How does this get a pass from idea to cornerstone of biology without even a hypothesis?ScottAndrews2_{November 21, 2011
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Not true. If somone hears something for the first time it is a safe bet they would have to have it explained to them.
You'll have to explain that to me. I've not heard that statement before. If you can anticipate the utility of coding sequences or new molecules, you can make a fortune in pharmaceuticals. The industry is currently spending upwards of a billion dollars to develop a single molecule using directed evolution.Petrushka_{November 21, 2011
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One of the characteristics of human language is that new statements can be understood.
Not true. If somone hears something for the first time it is a safe bet they would have to have it explained to them.
One of the characteristics of DNA is that the meaning of new sequences cannot be anticipated.
How do you know that? One of the characteristics of all anti-IDists is to just say anything.Joseph_{November 21, 2011
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One of the characteristics of human language is that new statements can be understood. One of the characteristics of DNA is that the meaning of new sequences cannot be anticipated.Petrushka_{November 21, 2011
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Petrushka:
Of course common descent is compatible with common design. Direct creation is compatible with design. What could possibly be incompatible?
If there weren't any similarities that would count against a common design. And if living organisms were reducible to matter and energy that would count against design, ie be incompatible with design. Geez this has only been common knowledge for decades- where have you been?Joseph_{November 21, 2011
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Petrushka:
What does matter is observed mechanisms of change.
True, yet there isn't anything we can extrapolate from those observed mechanisms that supports universal common descent. Why doesn't that count against the theory of evolution?
Fecundity and selection are an agency.
The ONLY "selection" is ARTIFICIAL selection. Natural selection is an oxymoron as nature does NOT select. IOW your alleged "agency" require that which needs explaining in the first place and not only that has never been observed to construct new, useful multi-part systems.Joseph_{November 21, 2011
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My point is that a system of controls, the function of which cannot be predicted, is not a language in the ordinary sense of the therm, nor can it support design, except through fecundity and selection.Petrushka_{November 21, 2011
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P: Again, you are putting up a strawman. ES is pointing our the significance of meaningfulness of code, and its context of things that put it to work in communication systems. And the reason why small changes in a code context can make for big differences in outcome is because there is a system of meaning that takes the switch as prescriptive information for a train of pre-loaded actions. THAT overall system is what has to be explained, not the small shift. As well, the basic fact that relatively small but big enough random changes --i.e. they jump far enough on a Hamming distance space metric -- typically cause chaos, i.e. destroy function, shows the presence of islands of function as a typical behaviour of information-rich functional systems. A simple example of this is how fairly small injections of random changes reduce text to chaos. KFkairosfocus_{November 21, 2011
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Hold on a minute. What equivocation are you talking about? I see no valid methodological reason to disallow design as a possible explanation. Unless we commits to materialism a priori, we should agree that it is a valid assumption. In the case of life as best explained by design we are talking about design which is, for want of a better word, outperforms human or animal design capabilities. In what I said there was no restriction. I was only using analogies from what we know. Spontaneous self-organisation of systems (not to be confused with self-ordering such as crystallisation) that involves hierarchical formally describable relationships between components (such as those that exist in a living cell) has never been observed. Not to see that is not to see the woods for the trees.Eugene S_{November 21, 2011
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Petruska: you know that in current discourse, the incrementalism in view is that of the neo-Darwinian synthesis, which still dominates the field, whatever supplements may be admitted. And you know full well -- having been repeatedly told [and given links] -- that the entire design theory project would collapse if just one clear and credible case of 500 - 1,000 or more bits of functionally specific complex information would be shown to have occurred by chance plus mechanical necessity without intelligent intervention. Your attempt to imply "unfalsifiable" is a willfully distorted strawman put up in the face of abundant and accessible evidence, and so plainly points to an attitude problem. Please, do better than that. KFkairosfocus_{November 21, 2011
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You are engaging in equivocation. You start by asserting that the DNA code is a language, then attempt to restrict DNA to what human languages can do. The problem is that one cannot read it for meaning because one cannot know in advance the consequences of small changes. There is no meaning independent of the consequences. The consequences may be deterministic, but that does not make them predictable. Design requires that materials have predictable attributes (consider engineering concepts of strength, cost, weight, etc.) There are multi-billion dollar industries that would be quite different if one could predict the utility of small changes in molecules. Pharmaceutical makers would not have to make millions of molecules and sieve them for function, then sieve them again for safety.Petrushka_{November 21, 2011
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If there was common ancestry, the actual evidence does not support Darwin’s incrementalism.
Darwin's view of incrementalism is irrelevant, because he had no knowledge of genetic mechanisms. What does matter is observed mechanisms of change. Of course common descent is compatible with common design. Direct creation is compatible with design. What could possibly be incompatible?Petrushka_{November 21, 2011
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BTW, I agree with Chaitin regarding the possibility of small program differences leading to large output differences (whereby a "delta" in genotype is amplified at the phenotype level). So body plans being different may not always be a consequence of direct intelligent input. It all depends and we need quantitative assessments to distinguish one from the other in practice.Eugene S_{November 21, 2011
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Thinking aloud... Meaning should come first. DNA is what it is not because it has this particular sequence of molecules but because this sequence has a meaning. Imagine for a moment that such claims as those by Yockey turn out to be true. Do you really think that a monkey typing something from Shakespeare by chance means it? A language is a means of communication between entities that are either intelligent agents themselves (human or aminal languages) or those designed by intelligence (computer languages). If intelligence is reducible to chemistry & physics, then you get an infinite regress. So we either say 'yes' to an infinite regress or suppose that intelligence is not reducible to them (i.e. it may or may not be embodied).Eugene S_{November 21, 2011
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F/N: Further to all this, "fecundity" plus "selection" are precisely NOT intelligent agents, they are proposed as blind processes -- the opposite of agency. Why do you insist on a confusion of language?kairosfocus_{November 20, 2011
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PS: And if you wish to test this, simply produce a case where blind chance plus mechanical necessity acting without intelligent control or guidance, produce 500+ bits of functionally specific complex info. The infinite monkeys article observes, on random document generation:
One computer program run by Dan Oliver of Scottsdale, Arizona, according to an article in The New Yorker, came up with a result on August 4, 2004: After the group had worked for 42,162,500,000 billion billion monkey-years, one of the "monkeys" typed, “VALENTINE. Cease toIdor:eFLP0FRjWK78aXzVOwm)-‘;8.t" The first 19 letters of this sequence can be found in "The Two Gentlemen of Verona". Other teams have reproduced 18 characters from "Timon of Athens", 17 from "Troilus and Cressida", and 16 from "Richard II".[21] A website entitled The Monkey Shakespeare Simulator, launched on July 1, 2003, contained a Java applet that simulates a large population of monkeys typing randomly, with the stated intention of seeing how long it takes the virtual monkeys to produce a complete Shakespearean play from beginning to end. For example, it produced this partial line from Henry IV, Part 2, reporting that it took "2,737,850 million billion billion billion monkey-years" to reach 24 matching characters: RUMOUR. Open your ears; 9r"5j5&?OWTY Z0d...
kairosfocus_{November 20, 2011
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P:
What could be done to test the hypothesis that ~~an unspecified agent having unspecified abilities did unspecified things at unspecified times~~ [there are empircally tested, well warranted signs that point reliably to design as causal factor]
See the strawman caricature, insistently repeated in the teeth of corrections over and over again? What does that tell us about your underlying attitude? I suggest, to start afresh on a sounder footing, you work your way through the discussions here, here and here, for starters. Let me clip the introduction section for the first, from NWE:
Intelligent design (ID) is the view that it is possible to infer from empirical evidence 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" [1] Intelligent design cannot be inferred from complexity alone, since complex patterns often happen by chance. ID focuses on just those sorts of complex patterns that in human experience are produced by a mind that conceives and executes a plan. According to adherents, intelligent design can be detected in the natural laws and structure of the cosmos; it also can be detected in at least some features of living things. Greater clarity on the topic may be gained from a discussion of what ID is not considered to be by its leading theorists. Intelligent design generally is not defined the same as creationism, with proponents maintaining that ID relies on scientific evidence rather than on Scripture or religious doctrines. ID makes no claims about biblical chronology, and technically a person does not have to believe in God to infer intelligent design in nature. As a theory, ID also does not specify the identity or nature of the designer, so it is not the same as natural theology, which reasons from nature to the existence and attributes of God. ID does not claim that all species of living things were created in their present forms, and it does not claim to provide a complete account of the history of the universe or of living things. ID also is not considered by its theorists to be an "argument from ignorance"; that is, intelligent design is not to be inferred simply on the basis that the cause of something is unknown (any more than a person accused of willful intent can be convicted without evidence). According to various adherents, ID does not claim that design must be optimal; something may be intelligently designed even if it is flawed (as are many objects made by humans). ID may be considered to consist only of the minimal assertion that it is possible to infer from empirical evidence that some features of the natural world are best explained by an intelligent agent. It conflicts with views claiming that there is no real design in the cosmos (e.g., materialistic philosophy) or in living things (e.g., Darwinian evolution) or that design, though real, is undetectable (e.g., some forms of theistic evolution).
In short, design theory is that scientific discipline that studies empirical signs of design, and in applying the findings to certain features of the natural world finds in these, tested and reliable signs that point to cause by a process of design. In addition, analyses like the infinite monkeys analysis point out that the other source of high contingency in our observed world, chance, is maximally implausible as a credible source of the relevant features, such as digital code in DNA, for first cell based life and for novel main body plans, and other features up to and including the evident fine tuning of the cosmos we inhabit. So we have direct empirical basis on warrant by inference to best, empirically tested explanation, and we have analytical warrant on the search capacity of the observed solar system and cosmos. (And FYI, in the expression Chance variation + differential reproductive success and culling out --> descent with modification, the culling out SUBTRACTS info, it does not ad it, it is only the chance variation that is the source for any possibility of novelty.) That that empirical evidence warrants such an inference is an achievement by itself, whatever else we may wish to know about the source of such design. That which we may not know for now, does not warrant rejection or dismissal of what we can know on reasonable warrant comparable to that which is a commonplace in scientific studies of the past. So, kindly cease and desist from erecting strawmen and knocking them over. After this, if you resort to the same strawman caricature, you will plainly be willfully persisting in misrepresentation in the teeth of relevant correction. GEM of TKIkairosfocus_{November 20, 2011
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P:
but common descent requires the transitions to be incremental
See the "it MUST have been like that" rather than, on evidence this is what was the case? One assertion to substantiate another, do you not see the circle of argument? There is but one definite fact about the world of the deep past, however deep is was: fossil life is the only directly evident life from the time beyond prehistory. The evidence, as Gould et al have admitted and as the Cambrian fossils plainly say [cf the Meyer PBSW paper . . . which passed proper peer review by renowned scientists], is, sudden appearance of diverse forms [top down at that], stasis of body plans, disappearance or continuity into the modern era. If there was common ancestry, the actual evidence does not support Darwin's incrementalism. And, common descent is compatible with common design, e.g. by frontloading or even episodic engineering [try using viri as vehicles for directed mutations], etc. The issue is that the dominant mechanism proposed cuts clean across the actual directly relevant evidence. And if we go for more indirect evidence, the protein domains also fit in with islands of function. As does the very nature of complex digital code. But, some will insist, this is the way it MUST have been . . . Darwinian a priorism . . . GEM of TKIkairosfocus_{November 20, 2011
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I don't think anyone thinks the landscape is smooth, but common descent requires the transitions to be incremental. That's why there's always been the debate over missing links.Petrushka_{November 20, 2011
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We have very good reasons for hypothesizing a smooth incremental path.
The trouble is that you can't hypothesize that as a general concept. Someone has to actually hypothesize a smooth incremental path. Why hasn't anyone?ScottAndrews2_{November 20, 2011
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And, there is no good reason to accept that a smooth incremental path exists from first life through the body plans, starting with the major characteristics of both protein fold domains and the fossil record. KF
We have very good reasons for hypothesizing a smooth incremental path. We have the fossil record, and now we are developing genomic data that supports a nested hierarchy. I won't assert it's a done deal, but it's the way to bet. Just about everything done in evolutionary biology is done to test this hypothesis. What could be done to test the hypothesis that an unspecified agent having unspecified abilities did unspecified things at unspecified times?Petrushka_{November 20, 2011
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It reminds me of an old bumper sticker - "I'm fat, you're ugly. I can lose weight." There's nothing logically wrong with ID. There's just unanswered questions. The combined fantasy of abiogenesis followed by darwinian evolution is fallacious at face value. No one should take it seriously. Unanswered questions can be answered. Reason-defying logical absurdities stay in the pseudo-academic spin cycle of crazy stories and vague speculation forever.ScottAndrews2_{November 20, 2011
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Petrushka,
Simply asserting that an invisible agent having no attributes did some unspecified something at unspecified times and places
First, you're embellishing because your sentence didn't have enough unknowns in it. So take out the unspecified time and place. They aren't specified, but we have a ballpark idea. Second, ID doesn't mention invisible. Take that out. Third, how could it not have attributes? Again, you're just being colorful to make it sound more absurd. What about microwaves as a candidate? Or fermentation? Obviously you're not limiting your candidates known to produce macroevolutionary diversification, or else you wouldn't have included variation, selection, and drift. I get it, you're begging the question again. You'll just re-assert it in every post. There is no more reason to attribute biological diversity to variation, selection, and drift than to microwaves or fermentation. If there were, biology books wouldn't be full of finch beaks and bacterial loss of function. If variation and selection are like throwing the pieces of a blender in box and shaking it, drift is like taking the pieces of lots of blenders and putting them in a bigger box and shaking it. What it shares in common with RM+NS is that there is no significant transformation which can be specifically described in terms of it. This is where you typically point to phylogenetic trees and fossil transitions which cannot and do not provide evidence of diversification by selection or drift. There is no observed mechanism to compare design against. We propose someone did it, we just don't know how. You propose it happened all by itself, you just don't know how. The first leaves unanswered questions, which is fine because that's what science is for. The second is a vacuous non-explanation, because it posits absolutely anything that anyone can think of was long as it wasn't intelligent. Monkeys on rafts.ScottAndrews2_{November 20, 2011
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P, The problem -- as has been pointed out repeatedly -- is we do not have the resources of ATOMS and TIME in the observed cosmos to do the calculation for novel body plans. And, there is no good reason to accept that a smooth incremental path exists from first life through the body plans, starting with the major characteristics of both protein fold domains and the fossil record. KFkairosfocus_{November 20, 2011
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Fecundity and selection are an agency. You can easily demonstrate with software that this is an intelligent agency capable of computing any possible string. This is not just my opinion. It comes from Hubert Yockey. The difference between selection and the Designer is that selection can be studied through selective breeding, through directed evolution and through modelling in software; the Designer is imaginary. Worse than imaginary, because it has no identity, no attributes, no capabilities or limitations, no observed instances of action. It is not a candidate for the source of variation in living things because it doesn't even have any imagined existence.Petrushka_{November 20, 2011
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A candidate would be an observed agent or phenomenon. So far the only observed phenomenon is variation and selection (including drift).
What do you mean by observed agent? Why not just an agent? Besides, agency is the only observed source of functional digital code. That's how it should have looked.M. Holcumbrink_{November 20, 2011
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