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This is a post in responce to a conversation at Telic Thoughts.
I am posting it here as a record as my last few posts at Telic Thoughts have been deleted without comment.
Tom Curtis
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GUTS wrote:
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That he discusses all these systems would have been obvious if you had actually read the paper:
If not, as this review has argued, could the emergence of novel information-rich genes, proteins, cell types and body plans have resulted from actual design, rather than a purposeless process that merely mimics the powers of a designing intelligence?
So in light of this quote, does Meyer’s review offer an explanation for more than just body plans?
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It seems very convenient for you to quote Meyer out of context. However, the quoted sentence is a conditional, from which you have left out the antecedent. And if we included that antecedent, the quote reads like this:
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Does neo-Darwinism or any other purely materialistic model of morphogenesis account
for the origin of the genetic and other forms of CSI necessary to produce novel
organismal form? If not, as this review has argued, could the emergence of novel
information-rich genes, proteins, cell types and body plans have resulted from actual
design, rather than a purposeless process that merely mimics the powers of a designing
intelligence?
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So clearly, even here, Meyer is primarilly concerned with the origin of novel body plans - and the only examples of such origin that he provides are those that form the Cambrian Explosion. He is only concerned with novel genes, proteins and cell types as they ar required for the generation of novel body forms.
This whole line of discussion began because you said, despite my claim to the contrary, that I had not read Meyer's article. You claimed this because I wrote that, "On rereading the article, I find the hypothesis was simply that ID was the best explanation of the Cambrian Explosion." Well, let's look at Meyer summarises his conclusion:
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An experience-based analysis of the causal powers of various explanatory hypotheses
suggests purposive or intelligent design as a causally adequate--and perhaps the most
causally adequate--explanation for the origin of the complex specified information
required to build the Cambrian animals and the novel forms they represent.
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But, of course, the Cambrian Explosion was just the apparently sudden origin of those "novel forms"; and hence also of any genetic alterations or novel proteins needed to generate those forms. Are you now going to suggest that Meyer has not read his own paper? In fact, the reason I summarised Meyer's paper as I did is because I had quoted this very sentence in my preceding post; but having given the full conclusion, you conclude from my abbreviated summary of it that I had not read the paper.
I will not pursue this line of discussion further. I find it highly amusing that you are affronted that I suggest that bloggers on this site may place rhetorical considerations above the desire for truth, while at the same time you make repeated suggestions from which it is an immediate inference that I am a liar. This follows a consistent pattern of hypocrisy on this blog. You all are happy to repeatedly suggest that rhetoric rather than truth is the guiding basis of ID critics comments, as, for example, when they refer to Intelligent Design Creationism. But should an equivalent suggestion be made about bloggers here, that WILL be grounds for censorship.
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Mike’s better papers do at least potentially lead to emperical hypotheses; but to do so they invoke auxilliary hypotheses that are not part of the ID research program.
Now you are being disingenuous. The only auxilliary hypothesis that you mentioned that an ID hypothesis must have is motive. You then falsely asserted that ID regards questions of motive as illegitimate. And yet, motive is a question that Dembski himself described as being part of an ID research program. Do you retract your statement?
That is your reading of what has happened, and clearly I disagree with it. Part of the basis of your reading is the (insulting) inference that you continually make that because I mention conditions for the first time, I am making those conditions up as I go along. From my perspective, those conditions were implicit in what I originally said, and I am merely clarrifying for someone who is evidentally unable to make the appropriate inferences.
How can you blame me, you don’t even know when to admit that you are wrong about something. For example, you say that Mike takes motive into account but that this is not part of Dembski’s ID research program. I show you the opposite, but then you assert it again in your response to me. Does that sound like someone who is being rational about this subject?
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I can blame you because you are obviously making no effort to understand my arguments. Your total butchery of my "knife/spatula" analogy showed you didn't even remotely comprehend it. You apparently can't understand why it is a necessary condition for a hypothesis to predict an observation that p(O|H) > p(O). I have repeatedly mentioned the importance of Lakatos' philosophy in other comments on this site, and yet you did not even imagine for a moment that that might mean my criteria had some connection with that philosophy (despite it being obvious that they do); nor even that I might have some knowledge on a subject on which I was so keen to comment.
As to not knowing how to admit I am wrong, I have an obvious character flaw. You see, I don't admit I am wrong until someone can provide me with convincing evidence that I am. (Sometimes that someone is myself.) But far from showing me evidence that I am wrong, you have yet to show you understand my argument. You ignore foundational principles in the philosophy of science, and when asked for clarrifying comments, retreat into obscurity. For example, when asked what you meant by "top down" you refused to answer, instead just making a rhetorical sally. (I can think of three definitions of top down processes or reasoning, two of which Darwinism is entirely compatible with.) When asked to narrow your discussion to one paper at a time so that we can get down to brass tacks, you refuse. When asked from which article you draw your information for discussing C and N terminal domains, you respond "all of them". What all 20+ of Mike's articles discuss C and N terminal domains? When asked about the three specific articles that refer to cytosine deamination you are considering when discussing C and N terminal domains (none of which discuss C or N terminal domains), you respond, "If you don’t understand the material, then how could claim that there are no empirical hypothesis and no research that can be derived from them? Not even in principle?" Two comments are in order about that responce. First, when Joy claims that there is absolutely no Darwinian research, that Darwinism is entirely unemperical, you do not expect her to have read and rebutted all of the tens of thousand of peer reviewed research articles (not to mention published books) purporting to have found just such emperical evidence. And second, I do not claim universal knowledge. If you present me a particular paper claiming to be scientific research, I will read it and discuss it. Given such a paper, I can follow back on areas I am not clear on, and gain the knowledge necessary to understand the paper; and have promised to so discuss any papers you present one at a time for my consideration. In the meantime, you want me to consider as scientific research papers that you will not discuss in detail, and whose author is on record as saying they are not scientific research, but a mere hobby. Mike was thrilled that I might consider his efforts a nascent proto-science; but you want me to consider them without further discussion to be a full fledged research project.
Moreover, it is untrue that I have not responded to your comments about Dembski and motives. Here is what you said:
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So Dembski was wrong when he said: “Nevertheless, taken strictly as a scientific theory, intelligent design refuses to speculate about the nature of this designing intelligence”?
You misread this. That has nothing to do with whether one can speculate about the motive of a designing intelligence. Such speculation cannot be known scientifically (which is why he says in a “strict scientific” sense), and the theory itself is not committed to any such speculation (i.e. whether the designer is God or some other form of intelligent agency, or even benevolent). Maybe in the future , as the theory is more fully worked out, it will be. In fact, directly after that paragraph, Dembski goes on to speculate about the motive of a designer when it comes to sub-optimal design (with respect to compromise).
But more specifically and relevant to this discussion, in chapter 6 of No Free Lunch, a chapter called Design as a Scientific Research Programme incidently, Dembski identifies one of the questions to consider as the “Intentionality Problem” , which is all about motivation for a particular design. Does that sound to you like ID regards these type of questions as illegitimate?
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and my responce:
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Mike’s better papers do at least potentially lead to emperical hypotheses; but to do so they invoke auxilliary hypotheses that are not part of the ID research program. All that shows is that if ID got down to business; made specific predictions about the age of the earth, and common descent, and about the motives of, and techniques used by the designer; well then ID would be a scientific research program. (Or at least it would be if the ID theorists did not take the conventionalist strategy used by YECs to avoid acknowledgement of refutations.) Of course, I have never denied that.
That is the point of the Dembski quote. Mike can invoke motives or ages of the Earth or whatever he likes to make predictions; but those predictions are not part of the ID research program because they are not part of the “protective belt of auxilliary hypotheses” (Lakatos) which all ID researchers accept as part of the research program. By refusing to commit to the auxilliary hypotheses that are needed to make emperical predictions, ID preserves itself from falsification as a research program, but only at the expense of not being scientific.
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However, you may wish me to answer point by point, something I am more than happy to do. To start, Dembski does not discuss motives in the next paragraph. Rather, he says:
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No real designer attempts optimality in the sense of attaining perfect design. Indeed, there is no such thing as perfect design. Real designers strive for constrained optimization, which is something completely different. As Henry Petroski, an engineer and historian at Duke, aptly remarks in Invention by Design: "All design involves conflicting objectives and hence compromise, and the best designs will always be those that come up with the best compromise."[1] Constrained optimization is the art of compromise between conflicting objectives.
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Clearly he takes himself to be discussing general constraints of rationality rather then specific motives. As such, he is wrong to charge Gould with ignoring this point. Further, Dembski goes on to say, "Not knowing the objectives of the designer, Gould is in no position to say whether the designer has come up with a faulty compromise among those objectives." But this is only a valid objection if discussion of motives is precluded from the start. If the development auxiliary hypotheses about the motives of a designer is a legitemate part of a scientific research program (something Dembski denies in this article, even if he wishes to affirm it later), then a critics speculations about possible motives of the designer become as legitimate a part of science as are the speculations made within the research program. The proper responce is to either show a flaw in the critics argument, or to accept that the critic has shown that a certain motive is not possessed by the designer. Responding as Dembski does that the critics speculations necessarily means they are indulging in philosophical or religious argument is either dishonest rhetoric, or means that your own potential speculations about the designers motives philosophical or religous, and therefore NOT part of the scientific research program.
However, refering to the article linked as the "intentionality problem" (I don't possess "No Free Lunch"), Demsbski clearly does lay down as a future activity the possibility of determining the designers intentions. Several points need to be made about this. First, as a future activity, that means that no such speculations are currently part of the ID research program. In consequence, Mike's speculations are not part of the ID research program because they are not agreed to, as auxilliary hypotheses, by all, or even most ID theorists - or at least, they will not publicly commit to those motives. Second, as pointed out above, this claim is inconsistent with Dembski's rebutall of Gould; a rebutal that Dembski has not retracted or withdrawn from publication. Thus, the situation seems to be that Dembski is claiming that ID is a scientific research program because at some unnamed future time ID theorists might start to expand on auxilliary hypotheses regarding motives of the designer; but that any speculation by critics about motives of the designer is necessarilly an illegitimate dragging of theology into the discussion. Thus Dembski preserves the maximum of unfalsifiability along with a minimum of content. So while my original claim that ID forbids discussing motives may be too strong; the ID position on motives is still inconsistent with it being a scientific research program.
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Those three articles are the only articles in which he discusses cytosine deamination, SFAIK, and there connection to your emperical test is obscure, to say the least. Could you please reference specific articles; point out the claims in those articles on which you base your conclusion; and then lay out how your conclusion follows from those claims. Otherwise I am unable to respond to your claims on the simple basis that they are not cogently presented – ie, I do not know what you are talking about.
If you don’t understand the material, then how could claim that there are no empirical hypothesis and no research that can be derived from them? Not even in principle? Why do you assert such things as if they are fact when you don’t take the the time to read and evaluate and understand lists of research when they are given to you?
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It's very simple, really. First, I do not claim universal competence, ie, to be a "know it all" in your offensive phrase. I will, however, make the effort to understand any particular claim that anyone is prepared to put forward and discuss. I am not, on the other hand, going to waste time discussing the claims of someone who will not even specify the paper which is the basis of his claim. IMO, such refusal to get specific about the details shows the person does not understand the basis of their claim, and is merely wildly asserting what they want to be true.
On the other hand, when you have good principled reasons to believe something, you do not have to have examined every possible counterexample in order to assert it. You implicitly accept this principle. You do not expect Joy to have examined every published paper on Darwinism before she asserts that Darwinism is rationalistic rather than empericist; and do not chide her because she doesn't "take the time to read and evaluate and understand lists of research given to" her. The contrast is that while she does not have principled reasons for her belief that Darwinism is rationalistic, I do have principled reasons for believing there is no ID based scientific research (as opposed to ID motivated scientific research). With regard to your list, that principled reason starts with the fact that the author of the papers listed regards those papers as a hobby, and as not being scientific research. In fact, he appears to regard them as I do, as explorations of ideas that might be turned into scientific research given time and effort (and given the acceptance of key auxilliary hypotheses). But given that view, it is not justified to say that ID has a research program on the basis of these papers. Indeed, if it were appropriate to say ID has a research program on the basis of some short, anonymous, papers published on the net without any peer review; then we would also have to say that YECreationism, cDK and geocentrism also have scientific research programs. At least their internet published "research" is not anonymous.
More importantly, I have principled reasons to think ID cannot generate a scientific research program in its current form. This follows directly from the Quine-Duhem thesis, that any thesis can be made compatible with any observation with sufficient ad hoc hypotheses; and the fact that ID has not commited to any auxilliary hypotheses. That refusal to commit means that every possible observation can be predicted from ID given auxilliary hypotheses concocted for that prediction (but not otherwise adhered to). Alternatively, it means that given only those theses that constitute the ID program, no emperical predictions can be made. That the ID movement has no interest in becoming a science (as opposed to being called a science) is made obvious by the fact that even after 10 years, they are unprepared to commit to even such well confirmed facts as the age of the Earth, or the common descent of all eutherians, or all birds, or all angiosperms as auxilliary hypotheses in order to actually make testable predictions.
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I wrote:
Actually , you misunderstood the paper. In the paper, all of the possible codes have the same redundancy, so this is not what they were measuring when they refer to robustness against mutation.
Tom replied:
No, in the paper they only consider codes which use triplets of nucleotides as codons. Naturally they all have the same average redundancy. But they do not have the same redundancy, and hence robustness against mutation as would a four nucleotide codon code.
“Same average redundancy” makes no sense, redundancy in the paper means the assignment of multiple codons to a single amino acid, all the possible codes contain exactly the same pattern of redundancy, hence this is not part of the robustness that they are looking at. You can see this from this quote from the paper:
We further retain both the pattern of redundancy and the position of ‘‘stop’’ codons found in the canonical genetic code. Although redundancy patterns vary in secondarily derived nonstandard codes, their relevance to the evolution of the canonical code is unclear.
and from a recent discussion:
Defining a set of possible codes. For most Monte Carlo analyses of the adaptive code, ‘possible
codes’ are defined as those which maintain the pattern of synonymous coding (i.e. redundancy) found
within the standard genetic code. This conservative restriction controls for possible biochemical
restrictions on code variation, and biases analysis against a false positive result for the adaptive
hypothesis (see text for detailed discussion).(2003) S.J. Freeland, T. Wu and N. Keulmann, Origins of Life and Evolution of the Biosphere 33: 457-477.
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You appear to be right about these studies using the same redundancy pattern as the standard genetic code, a fact I had not picked up in reading previous reports of this research. This does not alter my point about 4 base pair codons. With four base pairs, each current codon could be represented by four other codons. This means the average number of mutations required to change an amino acid would be higher, ie, the 4 bp codon system is on average more robust than the 3 bp system. It also follows that the most robust 4 bp system would be more robust than the three bp system.
That the range of codes generated was restricted to the current redundancy pattern changes slightly my view of this research. Contrary to Freeland et al., 2003 (and the equivalent claim in Freeland et al., 2000); testing only codes with equivalent redundancy patterns does not bias against a false positive for the adaptive result. Freeland et al. (2000) explain their claim:
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More importantly, if our restrictions underestimate possible code variation, then they actually bias our analysis against the adaptive hypothesis: most variation in redundancy (especially individual codon reassignments) would reduce the remarkable symmetry of the canonical code, leading to an increased error value. For example, a code in which individual codons are randomly reassigned produces a sample of one million variant codes with a mean error value (
Dmean) between 23% (p 5 1, w 5 1) and 33% (p 5 1, w 5 5) higher than the mean of a sample produced by our method. Given these considerations, in asking whether the arrangement of amino acid assignments within the canonical code is adaptive, retaining the synonymous codon block structure for all variants represents the best compromise.
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This is correct, and means that the proportion of genetic codes better than the standard code is less for the full range of possible codes than for the range of redundancy preserving codes. But, the number of possible 3 bp codes is "several orders of magnitude" higher than the number of redundancy preserving codes. Consequently Freeland et al.'s methodology under estimates the absolute number of such more optimal codes. This is explained by Gilis et al. (2001):
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Our results confirm and specify those of Freeland and Hurst [22]: the genetic code seems structured so as to minimize the consequences of translation errors on the three-dimensional structure and stability of the coded proteins. We have shown that, using the cost function gmutate which best reflects the roles of various amino acids in protein structures, and taking amino-acid frequencies into account, about 2 out of 109 random codes do better than the natural code. But we have to keep in mind that there exist 20! ≈ 2 × 1018 possible codes preserving the codon block structure, which means that we can expect about 109 better codes overall [47]. Moreover, if the codon block structure is not preserved [46], the number of possible codes is larger by orders of magnitude, and therefore the number of codes better than the natural one will certainly be much larger.
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(Note that I had underestimated the number of possible 3 bp genetic codes.)
Further, the failure to base the estimate of optimality on all possible 3 base codes is made worse by the fact that the optimality patterns being measured may be in part a product of the genetic code itself. This is easily illustrated by considering Gilis et al.'s measure of optimality taking into account amino acid frequencies. Given two potential amino acids at a particular loci that have equivalent effect in the protein, the proportions of the amino acid will be a function of the number of codons that code for each amino acid. If one is coded for by two codons, and the other by only one; then two thirds of amino acids at that loci will be of the first type, and only one third of the second simply in virtue of the number of nucleotide sequences that represent each amino acid. (This will not be exactly true because of different mutation rates, but the point is still valid.) M Di Guilio (J Theor Biol. 2001 Jan 21;208(2):141-4) argues that the PAM 74-100 matrix used by Freeland is similliarly tautologous. If he is right, it does not mean the studies are not indicative, but that they are not definitive - a problem made worse by the failure to use alternate redundancy patterns. (I have not read his article, and may not be able to assess its validity should I do so.)
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Now you agree? In your previous post you disagreed. Perhaps you should acknowledge that.
I can assure you Tom, it was because of nothing that you said. [...]
However, I realized that this might not be the same case for species with very different genetic codes, and I agree that it’s extremely unlikely and may not even be possible, especially since bacterial viruses can’t infect humans. You see, unlike you, I am able to rationally think through these type of things, and regardless of whether I have to agree with someone that I am arguing with, I can be reasonable. It’s not hard, you should try it.
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I note your pointless insult. It is also an insult that is directly contradicted by the facts. The only reason you thought about the possibility of alternate genetic codes immunizing against cross species viral transfers is because I thought about it without coaching, and pointed it out to you. That you later overcame your own confusion which led to your rejecting my obvious point does not show you to have greater capacity to think about these things rationally. On the contrary, it shows that uncoached I was able to think the consequences through clearly, but that even when the consequence had been pointed out to you, you still laboured under irrelevant confusions. In fact, you continue to be confused on the topic, as illustrated by your next claim:
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Besides, the reason why you brought it up was because you thought that motive was an illegitimate question in the ID movement, thats not true. And why would the designer use anything but the best code in all of it’s/hers/his designs?
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As I pointed out, there are numerous genetic codes that are in the same ball park of quality, or better than the standard code. Using Gilis et al.'s estimate that the code is 1 in a billion amongst the restricted set of identical redundancy block codes, they estimate that there are still approx. 2 billion possible genetic codes that are equal to or better than the standard code. As they point out, this number would be significantly larger if you considered all possible triple bp codes. Freeland et al.'s (2000) claim that the standard genetic code may be the best only applies in the case when the code follows a particular path of evolution. That is, if a particular factor was important in the codes evolution, given a random starting point it is unlikely that a better code could have evolved. But as better codes in pure engineering terms (ie, without regard to method of origin) are known to exist, that is hardly relevant. So the question then becomes, why did the designer choose to use a code of which 2% of codes are better (ie, 98% optimality by Freeland's measure)? And why only one amongst several billion codes of equivalent or better optimality; when using more would have ensured against many of the world's deadliest diseases?
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Now, however, you have an emperical postulate from an ID perspective. It is, however, not a part of an ID research program because your postulate assumes common descent; something which the ID research program refuses to make a commitment on.
For now. Maybe in the future ID will become more restricted and thus this hypothesis can be incorporated in the larger ID research program. What matters though, is that the ID hypothesis can do fruitful empirical research, make predictions from that research, and that more research can be derived from it.
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No. If ID incorporates the hypothesis of common descent as a recognised auxilliary hypothesis; and if it also incorporated a hypothesis that one motive of the designer was to maximise the robustness of the genetic code against point mutation; then an article such as Mike's would represent an emperical prediction by ID. At that stage, ID could correctly be called a nascent proto-science (a phrase Mike seems quite taken with). And then, if scientists (whether favourable to, or opposed to ID) conducted experiments to test that hypothesis, then ID would have a research program; and would graduate to being a proto science. But to call ID science on that possible future fulfillment of these conditions is nonsense. It is not science until it delivers the goods. Evolution did not become science with Erasmus Darwin, or even with Le Chevalier de Lamarck - because their musing did not, and could not deliver emperical goods. It only became a science when Charles Darwin backed up his ideas with clear auxilliary hypotheses, clear predictions from those hypotheses, and 15 years of successfull emperical research based on that hypothesis. Once again, there is no reason why ID should escape the standards of every other science.
However, there is a reason I only said that ID as pursued by Mike "MIGHT be a nascent proto science". The fact is that the ID movement refuses to hammer out the auxilliary hypotheses necessary to make that progress. They refuse to do so, what is more, for religious reasons because any attempt to clarify auxilliary hypotheses would result in an unbridgable divide between YE and OE ID theorists, as also between theistic and merely agnostic ID theists. Even Mike's efforts only "might be" because he does not insist that ID must pursue this path to become a science (from what little I have read). On the contrary, he criticises ID critics for calling ID religious when they point out exactly this failing in ID, and its religious basis. In doing so he tacitly defends the "wedge movements" tactical, and religious compromise on scientific standards. And by defending that compromise, he helps to ensure it will not end - ie, that ID will never have a chance to be born as a proto-science.
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