ID Research, Look to the Example
by Steve PetermannA common complaint about ID is that is has no research program. But what would constitute such a research program? I can think of at least two areas that could qualify, design detection and design dynamics. While ID theorists like Michael Behe, William Dembski, and others have spoken to the issue of design detection, I would like to focus on the area of design dynamics.
In my view while it may be that design detection can be done without appealing to design dynamics, I think it can be a fruitful area that both supports detection and at the same time offers a scientific perspective that can be extremely fruitful and important today. We live in world where the manipulation of genetic material is a real possibility. Mike Gene, Krauze, and Deuce have been addressing this issue here. It is an extremely important issue because of both the potential for benefit but also the threat for disaster.
Who would question the phenomenal success of evolutionary processes in creating remarkable complexity in our world. Somehow those processes have navigated the circuitous path of creating remarkable change without wholesale destruction. While evolution certainly has its "victims" of the process, none the less, it has not imploded the process itself into oblivion. Today such an implosion is a real possibility if arrogance overcomes humility.
So what to do? Genetic engineering offers real possibilities to defeat disease and self create species hopefully toward some noble goal. The benefits may be high but the risks are also high. One moderating factor could be ID research into the design dynamics of "natural" evolution. If, for the sake of argument, it is assumed that there is an intentionality involved in the evolutionary process, how does it work? What are the design processes at work? Why has it been so successful?
Design dynamics is basically the interplay of intelligence and constraint towards some specification. In mission critical applications design dynamics insists on restraint. It recognizes the limitations of foresight and planning and develops contingency plans, bale outs, shut down processes, built in tests, self awareness, environment sensing, feed back loops, etc. While these are engineering factors one would expect similar features in any intelligently designed system. Because of the incredible complexity of biological systems and the far reaching consequences of change, it would behoove genetic engineers to investigate how biotic systems have been designed.
June 8th, 2005 at 8:54 pm
Given my recent critiques in a number of comments, I was hopping that Petermann would provide an actual sample of ID research. That, certainly, is what the title promised. But the example we are to look to turns out to be a promise of future research, with no outline of how such research would be undertaken. The only concrete proposal is that we should "assume that there is an intentionality involved in the evolutionary process", but that is of course what ID purports to prove in the first place.
It remains the case that while ID is a degenerating research program, Darwinism continues as one of the most progressive research programs in science.
Comment by tom_kbel — June 8, 2005 @ 8:54 pm
June 8th, 2005 at 9:09 pm
Tom,
There are plenty of examples of ID research. Meyer's paper, Wells' paper. Some good ones here
Please think before you post a comment.
Comment by Guts — June 8, 2005 @ 9:09 pm
June 8th, 2005 at 9:27 pm
tom_kbel writes that:
I'm not a biologist so maybe I'm not familiar with Darwinian research that employs completely non-intentional causation to produce something fruitful. Can you provide an example of such? Remember the issue is completely non-intentional causation. That means that there is no intentionality employed in that research program. No intentional setting up of constraints, no intentional set up of selection criterion, no biasing towards some specification. Personally I can't even imagine how one would go about formulating that type of research. Please inform me.
Comment by Steve Petermann — June 8, 2005 @ 9:27 pm
June 8th, 2005 at 9:32 pm
This thread was specifially about biological ID research. In a subsequent thread I will detail how ID research has proven to be one of the most fruitful research programs in history.
Comment by Steve Petermann — June 8, 2005 @ 9:32 pm
June 8th, 2005 at 11:48 pm
Guts, Meyers' article was a review article. As such it did not contain emperical research. (It was not even a good review article, in that it neglected large parts of the literature it was purportedly reviewing.) Well's article is more interesting. He presents a hypthesis about spindle microtubules in centrioles. It is (to say the least) not clear how this hypothesis is connected to ID. Further, he has not done any research to test his hypothesis. He does propose two ways to test it, but does not carry out those tests himself. Being generous, I would conclude that we now have one ID generated emperical hypothesis after over 10 years of the ID movement. With luck, it that hypothesis might even be tested before it becomes required by law to teach ID as science in various states of the US. However, the hypothesis does not contradict evolution. Further, evolutionary hypotheses are tested and published on a daily basis.
In the meantime, when someone provides me with a emperical hypothesis that is a clear prediction of ID, not a prediction of Darwinism, and elaborates a means to test it, I will withdraw my claim.
Comment by tom_kbel — June 8, 2005 @ 11:48 pm
June 8th, 2005 at 11:53 pm
Peterman:
So all you need is evidence of an intentionally set up experiment in which no element of the experiment is intentionally set up. When you want to give serious consideration to the evidence for evolution, rather than just retreat behind walls of dogmatism, let me know.
Comment by tom_kbel — June 8, 2005 @ 11:53 pm
June 9th, 2005 at 12:02 am
Tom:
In the paper, he offers a hypothesis derived from the various observations of the literature he cited. So I would say that this is empirical research (although not in the experimental sense).
Its a direct connection between what we observe and what others think is "only an analogy". If it actually is a turbine (like the ones that humans design) it will function as one.
Thats irrelevant. There is plenty of research out there that has never been tested or has yet to be tested. Usually the testing comes from other scientists who follow up the thesis or from the author himself. However, regardless of whether this hypothesis turns out to be true or false, the assertion that there is "no ID research" is clearly false.
Tom:
Actually the hypothesis contradicts several Darwinian assumptions.
That looks to me like a retreat from the claim.
Comment by Guts — June 9, 2005 @ 12:02 am
June 9th, 2005 at 2:41 am
If it is not experimental (including field observations), then it is not emperical. I will make this more explicit. If a proposed theory explains various explanations from a (culled) selection of the literature, but makes no further predictions, it is an ad hoc hypothesis, not an emperical hypothesis. If it can potentially make emperical predictions, but the theorist does not attempt to spell them out; then s/he is indulging in armchair speculation, not science. Only if the emperical predictions are spelt out in sufficient detail to make experimental design possible do we have a scientific hypothesis.
I'm sorry. How does that make it an inference from design. I know some things which are designed and look like turbine blades; but are not turbine blades. Does that refute the design hypothesis with regard to those items? Knifes are designed. Spatula's look like knives. Spatulas do not function as knives. Does it therefore follow, even prima facie, that spatulas are not designed? No? Well in that case the failure of Well's hypothesis would not tend to falsify design theory; or put another way, the success of his prediction would not tend to support it.
It is entirely relevant. For ID to be a progressive scientific research program, it needs to generate detailed testable predictions; and it needs the predictions to be confirmed. Generating a single prediction doesn't cut much mustard; and when that prediction hasn't even been tested it provides absolutely no support for ID as such.
Name the assumptions and spell out how the hypothesis contradicts them.
Why? I clearly spell out conditions under which I would withdraw my claim. Those conditions have not been met; and nor do I expect them to be met. Just because I do not hold my opinions dogmatically is no reason to think I do not really hold them, or that they are unjustified.
Comment by tom_kbel — June 9, 2005 @ 2:41 am
June 9th, 2005 at 3:43 am
Tom:
That seems rather tortured. The definition of "empirical" includes inference from observation, not just experiment. The observation can come from experiments performed by other researchers. The requirement that the reviewer needs to spell out predictions from the hypothesis seems rather ad hoc in and of itself. It is a review, but it's good ID research nonetheless.
Even so though, there are examples of ID research where predictions are spelled out as well.
Spatulas do not look like designed turbines. The design inference doesn't take a piece of something and say that just because that piece is found in a larger designed system, that it is that system. Also, I'm not saying that if Wells hypothesis fails, it means centrioles weren't designed. We are simply using a specific design method (looking for specification) in order to ask scientifically fruitful questions.
We have direct experience of humans designing knives, so even if we are wrong that the knife is not a turbine, it doesn't matter (the knife doesn't look like a turbine anyway). We were simply using the wrong specification. However, we have no experience of anyone designing a centriole. If the centriole looks like a designed turbine (ones that humans make), then the design inference is strong (we have direct experience of an intelligent agent having designed something like it).
Tom, think about the Mars Face fiasco a while back. Pictures of the surface of Mars caught photos of what looked like a human face structure. Here is how one article described the inference to design by many people:
This is what Dembski calls "side information" or independant knowledge of how things work, we use that knowledge to test our inferences about what we think is designed. We have experience of such structures being built by intelligent agents here on earth, and so, if it is an actual face, that strengthens the design inference.
The reason why no one believes that that structure on Mars is designed anymore, is not because we couldn't find a motive, means, method, but because we actually decided to take a closer look. To study it more. To allow the study of it. And of course, we found that it's just a natural landform. Not because it's possible that natural processes can form it, but because it actually wasn't a face at all. There was no specification to hinge a design inference on. The "meaning" conveyed by the complex parts that made up the system (human face) did not exist. The "meaning" here corresponds to function in our example.
The same is being done here. The centriole looks like a turbine (that we design). The hypothesis states, if it actually is a turbine than that strengthens the design inference. If it's not, then it just kinda looked like one and there is no specification to hinge the design inference on (until another hypothesis comes along).
Sure but you need to make the actual hypothesis and predictions first. To say that it isn't ID research because no one has done experimental work with it yet is ridiculous. If the hypothesis is experimentally testable it's because the hypothesis asked a very good and scientifically fruitful question.
The hypothesis is based on a top–>down approach to biology rather than the bottom–>up of Darwinian approaches.
It's rather obvious that you want to define any work that ID proponents have done out of the definition of "research". Thats a sign that you hold to your position dogmatically. At first all you said was "There is no ID research". After I show you a list of good ID research (which consists of the use of ID assumptions and implications to answer some scientific questions, and ask fruitful scientific questions, through use of the primary literature, some hypothesis that make predictions and are even experimentally testable) you come back with all these ad hoc conditions that need to be met in order for it to be called "ID research". By your conditions I can rule out the entire Journal of Theoretical Biology as non-research.
The only thing that is missing from current ID research is experimental work. However, that takes an ID dedicated lab and funding. With the current witch hunt by dogmatic Darwinists under way that even criticises papers they havn't read yet, or films that have nothing to do with Darwinian evolution, you could imagine how much of a challenge this will be.
It is also true that a lot of experimental research papers do support ID regardless of whether the authors agree with intelligent design or not. The data sometimes speaks louder than the current dominant paradigm. Data doesn't give a hoot what you believe. If you can't get a monophyletic tree together showing a universal common ancestor because there was no single universal common ancestor the data will show this whether you are a Darwinist or not. Of course I'm not saying that things are clear cut. My point is that as data that strains the framework of a dominant theory accumulates, it becomes more and more likely that an alternative theory will have more use out of research comming out of the field than the dominant theory.
Comment by Guts — June 9, 2005 @ 3:43 am
June 9th, 2005 at 5:42 am
Assume for a moment that it turns out that centrioles do, in fact, function as turbines. How would this affect any part of Darwinian theory?
As I see it, the ID research program would be to go to a church and sing praises to God.
Meanwhile, some Darwinian in a lab somewhere would determine which gene codes for the construction of the thing, and figure out how that gene evolved to do that coding.
Arms are like levers. Blood vessels are like pipes. Blood is like seawater in salinity, perhaps like microscopic soup in makeup. Skin is like a blanket in some functions. None of those observations suggests any non-Darwinian research path. And, in fact, ID advocates studiously avoid such research. Research shows an evolutionary path for the development of such structures.
Where is there any probative value to "intelligent design?"
Genentech developed an e. coli strain that includes DNA to produce human insulin, for the treatment of diabetes. If "design dynamics" offered any possibility of fruitful research, we already have an engineered life form in Genentech's work which ID advocates could use to demonstrate the ability to determine what is designed from what is not designed. If that methodology worked there, it could be applied somewhere else.
Why is no ID researcher getting off his/her duff to do the demonstration?
We know that ID is sterile science, and that nothing ID advocates have can distinguish between what is designed and what is not. We know no ID advocate is going to test it, because ID will be found not to measure up.
Comment by edarrell — June 9, 2005 @ 5:42 am
June 9th, 2005 at 6:08 am
I don't think any research shows a Darwinian evolutionnary path for the development of any biochemical complex system (especially using Tom's criteria for research). Mostly it's just a lot of comparison of similar amino acid sequences.
I'm not saying that you can't infer evolution from this, but it shows just how much uncertainty there is when employing this kind of evidence. And when it comes to positive ID inferences, there's no need to take the assumption that it evolved in a Darwinian fashion into consideration (the hypothesis in question takes that it can't as axiomatic).
Comment by Guts — June 9, 2005 @ 6:08 am
June 9th, 2005 at 8:41 am
tom wrote:
You've been on this blog long enough to know that there are no anti-evolutionists here. I myself am, to use Mike Gene's term, an IDE, intelligent design evolutionist. The question here is not whether there is evidence for evolution but what causes it. Darwinists claim that there is absolutely no teleology involved. You say there is and has been an enormously fruitful research program which presumably is based on that premise. I'm just asking that you provide an example.
Comment by Steve Petermann — June 9, 2005 @ 8:41 am
June 9th, 2005 at 10:42 am
What "Darwinist" says there is "absolutely no teleology involved" in evolution — other than Richard Dawkins?
What paper, published in a peer-reviewed journal, has ever suggested that?
The rise of Spartina townsendii in the Thames River mudflats, circa 1865, would meet your requirements for an experiment not being "intentionally" set up, wouldn't it?
How about unintentional speciation of flies in the lab?
Comment by edarrell — June 9, 2005 @ 10:42 am
June 10th, 2005 at 11:12 pm
Guts:
Far from ad hoc, it is a direct implication of Imre Lakatos' philosophy of science (as also of Popper's). It is also a strong implication of any Bayesian approach to the philosophy of science as well. It is crucial for a theory to be scientific that it generate novel testable predictions. If it does not, it is (in Lakatos terms) ad hoc. More crucially, it cannot lead to the advance of scientific knowledge. If it makes no testable predictions, it gives no guidance to emperical research. Adherents of such non-scientific views will flounder around randomly without any clear idea of what to research, or (as it will be easier) do no research at all as any such research will have no bearing on the confirmation, or disconfirmation of their theory.
This is illustrated by Meyer's paper. His "hypothesis derived from the various observations of the literature he cited" was that " intelligent design [is] 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". If the ability of ID to generate testable hypothesis as an explanation of lifes complexity is in question, citing the postulate that "ID is the explanation" of a particular instance of lifes complexity provides no support to ID's claim to be science. If the assertion that "Life is designed" generates no testable hypotheses, the assertion that "Marella is designed" does not do so either.
Again, this is entirely false. I have a clear criteria of the difference between science and protoscience; and between (science and protoscience) and non-science. Using that criteria, I hapilly lable OOL research as proto-science even though it has generated thousands of experiments, and still more papers. I hapilly lable freudian psychology as non-science even though it is naturalistic, has generated many experiments and still more observations in its support; and even though Freud (and many Freudian psychologists) have made many valuable observations. I do this because the theory was so constructed as to be not testable. Observations could be fit into its framework, but no possible set of observations could refute the theory as constructed.
I even refuse to give Nic Matzke's excellent article the label of science because, SFAIK, it is not being used by the scientific community to develop testable hypotheses, even though it could be. That article represents a far more detailed literature review than Meyer's, and even though its hypotheses are far more amenable to emperical confirmation or disconfirmation. It is not science because it only represents a (successfull) attempt to refute Behe's argument from IC. Unless it is also part of an ongoing effort of experimental testing, it is not science. (Some of the papers he cites are part of such a process, and are science. And if the experimenters involved in that project take heed of Matzke's article and use it in designing new experiments, it also would be science; but I have no reason to believe that has happened.)
The criteria for science are clear. You must have a core to the research program, which, together with auxilliary hypotheses strongly warrant certain testable conclusions. Those conclusions must be put to the test. The auxilliary hypotheses, and if necessary the core, must then be modified to better fit the observations; with the vital rider that such alterations must increase, and never decrease the testable content of the research program.
When challenged to show that ID is science, I have been reffered to a literature review that makes no testable predictions; and an article which makes testable predictions (but conducts no tests) that are not given warrant by the core and auxilliary hypotheses of the theory. You show as much when you refuse to generalise the "design inference" Wells actually used; and when you refuse to allow that falsifying Well's hypothesis would tend to disconfirm ID theory.
You say there is other ID research out there. Well, maybe. I have not read the entirety of the ID literature. So just quote me an example. Tell me the hypothesis. Show me how the probability of the hypothesis is greater if ID is true (and I won't accept a simple assertion, I shall expect at least an informal derivation). And show me how you would test the hypothesis.
And if you can show me this, I will admit ID to the ranks of proto-science. And when you have shown this repeatedly with thousands of hypotheses, the result of which is to unifiy the auxilliary hypotheses of people committed to ID's core hypothesis; then I will consider ID a science, as will most Darwinian scientists.
And bear in mind, I am not being inconsistent in demanding this. OOL is philosophicaly congenial to me; but I won't call it science, only proto-science- because it shows no tendency to unify auxilliary hypotheses.
You can't even show me the first step. And yet you want ID to be admitted as science without even that first step. Again I ask:
Why should ID be exempted from the standards required of all sciences?
I have yet to recieve an answer.
Comment by tom_kbel — June 10, 2005 @ 11:12 pm
June 11th, 2005 at 7:04 am
I don't really see anything I didn't already address in my last response to you. There is plenty of ID-specific research and I already did list them, Meyer's paper, Wells' paper, and a lot here .
I didn't refuse to show Wells design inference, I made it quite explicit. In fact, from the question you asked concerning Wells paper, it doesn't seem like you even read it yet.
I find it laughable that you are now adding the criteria that I have to calculate a probability of the designer. No other design-detection science has ever done that, it's yet another ad hoc condition you are adding to the definition "research". If you don't believe it's research, it doesn't really matter to me. I don't even care if you don't think it's science. As long as testable hypothesis can be made with ID, such as that it actually guides scientific research, then I have every reason to think that experimental research is inevitable.
Comment by Guts — June 11, 2005 @ 7:04 am
June 13th, 2005 at 8:43 am
If you look at the "ID-specific research" you notice several things.
First, consider the only two examples from peer reviewed scientific literature. You have Meyer's "research" which is in fact a poor quality review article. Review articles, while usefull adjuncts to genuine research, are not themselves scientific research, anymore than are there popular cousins, popular science books. Providing a compact study of current research to make it more accessible to others is not scientific research, whether it is done for other scientists (review articles), students (textbooks), or the general public (popular science books).
You countered this point by suggesting Meyer had made "a hypothesis derived from the various observations of the literature he cited." On rereading the article, I find the hypothesis was simply that ID was the best explanation of the Cambrian Explosion. But that hypothesis is not the derivation of any novel claim, but simply the restatement of his core hypothesis in a particular situation. Simply restating a claim does not make it anymore testable than when you first stated it; so Meyer's paper contributes precisely nothing to expanding emperical research on the basis of the ID hypothesis.
You make much of the fact that he based his hypothesis on the emperical data collected by others. Well congratulations, so also did Aquinas, Locke and Hume (amongst others). "Emperical" is not synonomous with "science". If the emperical basis of ID is to be no more than post hoc retrodictions that "ID explains that very well", then ID ought to be confined to the forums that already teach the theories of Aquinas, Locke and Hume. It should not claim the more rigorous mantle of science if it is not prepared to put in the leg work.
These are points I have raised already. That you see no reason to adress them shows only a commitment to that weakest of conventionalist strategies – simply ignoring critics and contrary evidence.
With regard to Wells' article, again it is clearly not ID based research (as opposed to ID motivated research). Now clearly Wells' (admitedly testable) hypothesis is not based on the ID hypothesis. This is transparent on two grounds. First, his explicit (and sufficient) reasoning that led to his hypothesis is that centrioles look like turbines, therefore they might actually be turbines. If it looks like a duck, it might well be a duck. That is simple, commonsense reasoning that could be, and has been drawn on by Darwinists as easily as by IDists. Nor does the ID hypothesis strengthen the reasoning in any way.
That is shown by simple Bayesian reasoning. You have stated that the failure of Wells' hypothesis would not tend to disconfirm ID at all. (I agree.) But then, the probability of ID being true given that centrioles are not turbines equals the probability that ID is true given that centrioles are turbines. From this in turn it follows that the probability that centrioles are turbines given ID equals the probability that centrioles are turbines given that ID is false. You can't have it both ways. If failure of the prediction does not tend to disconfirm ID, then sucess of the prediction does not tend to confirm it either – the the prediction is epistemically independant of ID, regardless of the motivations of the predictor.
This raises the crucial point, which you laugh of through misunderstanding. You suggest that I am "… now adding the criteria that I have to calculate a probability of the designer." In fact I suggested you "show me how the probability of the hypothesis is greater if ID is true (and I won't accept a simple assertion, I shall expect at least an informal derivation)." That is, I am not asking you to show the probability of the designer, but that the probability of the hypothesis to be tested is greater given that there is a designer, than the probability of the hypothesis given that there is no designer. I did not even ask for a formal derivation. This standard, the misunderstanding of which you reject, is the weakest possible evidentiary relationship between two theories. But apparently, even this weakest standard is to rigorous to be acceptable to ID advocates.
You also suggest Wells' hypothesis is contrary to Darwinism because it is "top down" rather than "bottom up" as (supposedly) is presupposed by Darwinism. I am not entirely sure what you mean by "top down" or "bottom up" – are you contrasting holism with reductionism, or perhaps systems analysis with component analysis? In either case, Darwinism is not committed to a bottom up view (nor to a top down view). You certainly cannot trust Wells on this point, who is known for is misrepresentation of Darwinian theory and evidentiary fact.
Finally, you refer me to a collection of Mikegenes articles. It is intriguing that your best evidence that there is actually an ID research program is, what amounts to, a collection of armchair philosophical musings. I have only read a sample of these essays. What I have found have been attacks against evolution, essays in which admitedly emperically testable conclusions do not have a distinctively ID basis; and essays in which admitedly ID hypotheses do not have emperically testable predictions. They are, in general, no more pertinent than are the Wells and Meyer articles.
I shall take as my sample, the best of those I read, No BR 15. In it Mike reviews some recent research on the high stability against mutation generated by the genetic code. He concludes:
I am not sure that empericaly testable predictions could be (or could not be) derived from this conclusion. Certainly Mike makes no attempt to do so. Consequently, SFAWCT, this essay as it stands is not scientific research, but merely emperically based philosophical speculation.
My concern, however, is that those conclusions cannot be derived from within the ID research program. It is simple enough to demonstrate this point. In the section quoted above, Mike refers to the "reasons" of the designer; and reasons only make sense if you have motives. Consequently, Mike is tacitly appealing to the designers motives, something the ID research program explicitly prohibits as illegitemate.
Without that appeal to motives, and to quite detailed motives, no such derivation can be made. For example, Mike implicitly appeals to a motive of the designer to make the genetic code robust against mutation; and to another motive to allow cross kingdom gene transfers. In making this appeal, he also emphasises that the genetic code may achieve 100% optimization of the maximum possible error restriction for a three basepair codon/twenty amino acid genetic code. But by simply expanding the system to four base pair codons, robustness in the face of mutation could have been quadrupled. Why, then, did the designer not give life four base pair codons? To answer this question, and hence generate a prediction from the ID hypothesis, Mike must now appeal to other motives of the designer which must counter balance the need of stability, and result in some form of balanced optimisation. Absent the details of these other motivations, it is literally impossible to calculate the probability that the designer would use a three base pair system in prefference to a two base pair system; and hence literally impossible to calculate the probability of the three base pair system given the hypothesis of a designer.
This point can be expanded with further examples. Mike cites the conclusion that only one in a million possible genetic codes is as stable, or more stable as the "universal" genetic code against mutation. What he does not mention is that there are somewhere in the order of 2 * 10E16 possible genetic codes using three base pair codons, and twenty amino acids and stop codons. In other words, there are about twenty billion possible genetic codes approximately as robust as the "universal" genetic code. Had the designer desired to, he could have had a seperate genetic code for every genus of organism. In a very obvious refutation of Darwinism, he could have had a different genetic code for chimps, for humans, for gorillas, for gibbons, and so on. (Such a situation would have killed Darwinism dead.)
Of course, Mike has given us a reason why the designer may have preffered to have all one genetic code; but reasons why he may have preffered to have different ones are not hard to find. Facetiously, it would have killed dead the arguments of all those pesky evolutionists for a start. More realistically, a different genetic code between mammals and birds would prevent absolutely the spread of viruses between mammals and birds. No asian flu might well be considered a significant design consideration for a beneficient designer. A different genetic code for chimps and humans would have meant no AIDS virus; again a not insignificant consideration. To determine which hypothesis is actually favoured by a design hypothesis, ie, which of these considerations has more weight for the designer; we need to have a model of the motives of the designer. Indeed, in this example, we also need a model as to which organisms, if any, share a common ancestor. A YEC with the same model of motivations as an OEC could well predict different patterns of distribution of genetic codes.
All of this illustrates very clearly my crucial point. Design could indeed be turned into a scientific theory, in principle. But it can only be done by making detailed auxilliary hypotheses. Without those auxilliary hypotheses, even with the best intentions in the world, no emperical predictions can be made from the theory. This is not rocket science – it is merely a restatement of the Quine/Duhem theorem in a different context.
If you disagree with my assesment of this, or any other of Mike's articles, you are welcome to blog on any particular article; and I will take up the challenge. In the meantime, not even ID advocates can point to any ID research that meets the criteria of emperical testability that I have outlined; criteria that Darwinism accepts and meets continuosly, with new research meeting that criteria being published on, effectively, a daily basis.
In the meantime, this point should be quite clear. I am not imposing ad hoc conditions on ID. I am not ruling out the supernatural beforehand. I am merely expecting ID to comply with the principles of science – principles developed quite independantly of any concern over the C/E debate, and principles which Darwinism, as with all sciences, has no difficulty complying with.
I ask again, WHY SHOULD ID BE EXEMPTED FROM THE RULES OF ALL OTHER SCIENCES?
Tom Curtis
PS: I am unfamiliar with the maths and may have made a mistake calculating the number of possible genetic codes. I would appreciate anyone capable of the maths themselves double checking so that I can correct any error.
Comment by tom_kbel — June 13, 2005 @ 8:43 am
June 14th, 2005 at 9:35 pm
Tom:
This is your opinion, but it's irrelevant.
Sigh, you didn't read the paper. Actually the paper has nothing to do with "the best explanation of the Cambrian Explosion" but with the origin of new forms, including new proteins as well as new organismal forms. His paper discusses the inadequacies and improbabilities associated with various non-design oriented evolutionary mechanisms and suggests that intelligent design as an explanation should be considered.
This is in fact derived from several claims, both new and old (he mentions Axe's new calculations). Even if there were no new claims that he derived this from, it's irrelevant. The fact of the matter is he logically and empirically came to the conclusion that design is the best explanation for the origination of new forms.
No, ID is much more than a collection of information in a review and deriving conclusions from them, which is why I listed many examples of empirical design research.
The Meyer paper is no different from other reviews that set out to elicit more research on a new hypothesis, such as this one:
Once again, examples such as these make your ad hoc conditions and irrelevant criticisms laughable.
The ID hypothesis is indeed strengthened for reasons I already discussed. All you did here was assert that Darwinsits could form that hypothesis also, but thats irrelevant. Besides, no Darwinist has ever tested whether the centriole is actually a functioning turbine. And whether a Darwinist can or cannot is irrelevant as to the implications to ID theory.
Also, Darwinists are notorious for saying "if it looks like a duck, it actually may not be a duck" when it comes to design in Biology.
Bayesian reasoning has nothing to do with this. What are you talking about?
No, you took me out of context here. What I said was that if the specification for "turbine" is false, then we have nothing to hang the design inference on, it may be designed , but there is no empirical reason for saying so since there is no specification. Until another specification comes along.
To illustrate this, let me expand further from my analogy with the mars face. We looked further at the landform and obviously, since it specification "Human Face" failed, it looked just like a random combination of parts. But lets say that we discover another form of life on our planet who's face looks identical to that formation. Now we have a new specification to hinge the design inference on and we realize that the structure was built for them, not for us.
Still, I'm wondering when you are going to start discussing how all of this is not research. None of this is relevant to that question.
Yes I misunderstood , probably because I gave you the benefit of the doubt, since I thought you already read and saw that I gave more than a simple assertion, I was sure you were not asking me for one.
I'm not sure how you can trust a theory that can accomadate both a top down view and a bottom up view simultaneously. Thats like a weather man saying it will rain and it will not rain tomorrow.
There are two sections on that website. One of them consist of some of the best philosohpical essays I've read (concerning the nature of evidence, the nature of science, etc). The other section is empirical in nature, some more so than Wells's testable hypothesis.
Really , which one?
I'm guessing you didn't read any of them. For example, there is a distinctive ID hypothesis that predicts that the degradosome functions as a prong in enolase. Another that proofreading occurs during transcription, etc.
You show how one can derive empirically testable predictions, see below.
You also skipped over a lot of the ones that do make testable predictions and ones where research can be easily derived from derive research from it. For example, his cytosine deamination article where one can say that protein structure may be strongly influenced by the boundaries of the coding sequence. On the C-terminus, you can find TAA-ochre, a TAG-amber, or a TGA-opal, stop codons themselves seem to resist C-T/G-A transitions. Transition of both opal and amber gives ochre which is very resistant to C-T/G-A transition. All of this suggests that C-T transition help stop gene exansion from the C-terminus. When you look at the N-terminus you'll find an ATG that would sometimes transition t ATA. A prediction from this might be at the N-terminus genes will expand as methionine start codons become isoleucines. With this hypothesis in hand one can look at prokaryotes and predict that C-terminal domains would be older than N-terminal domains.
Thats not correct. There is absolutely nothing in ID that prevents one from making a hypothesis based on motive. In fact, this was in fact used in one of my favorite ID hypothesis, that the nitrogenase was used to terraform earth for the purpose of seeding life.
Tom, you just showed how Mike's essay indeed makes testable predictions. So we can draw out an experiment that studies whether a four-based genetic system is actually better than a three-based genetic system when it comes to mutation. My guess is that it's not the amount of letters that go into defining an amino acid but how each nucleotide has a certain probability of being 'hit', and that this probability is different for each nucleotide along the DNA sequence, depends on the surrounding nucleotides, and depends on the mutagen.
The bottom line here, is that you are confusing the non-essential aspect of motive when it comes to making a design inference with a complete denial of it's use in an ID hypothesis. There is nothing illegitimate about using motives in an ID hypohtesis.
There is no reason for a designer to "kill darwinism dead", it's actually quite robust and useful theory that explains many things. To suggest that a designer would integrate hundreds of different genetic codes just to "kill darwinism dead" is the most hilarious thing I have ever heard of.
Well I disagree completely that different codes would eliminate the transmission of diseases from one animal to another, an AIDS virus in a chimp passed to a human might cause damage that results in an even deadlier disease. But this is yet another testable experiment. One can use the "saltational leaps" which could be the result of a single nucleotide difference that makes a new form of virulence that enables a virus to survive in a host that previously could not survive in to suggest that they can.
Of course, I could also test the assertion without bringing motive into the hypothesis. I can perform an experiment, using random mutation and selection, where I can evolve a piece of the genetic code that is just as robust as our present one. Showing that a design hypothesis is superflous. This has not been done for any complex biological system by the Darwinian research programme in the 150 years of it's existence. This is the major impetus (at least as I see it) for the major shift in paradigms.
I have already listed them. At no point in this response have you discussed why this isn't research. There is no reason to blog about this because your points are trivial.
The exact numbers vary according to what particular assumptions are used. For example, if you accept PAM as a better multidimensional measure of amino acid similarity , then the code might literally be the best one.
Comment by Guts — June 14, 2005 @ 9:35 pm
June 15th, 2005 at 7:33 pm
Peterman:
Quite franky, I don't know what "ID evolutionist" means. As the term was invented in part to reject the classification of "ID creationist", and as they users of the term insist (regardless of the intentions of the people who use that term) that by "creationist" is meant what YEC's mean by "creationist"; perhaps the term means what the term "evolutionist" is purported to mean by YEC's, ie, a believer in a metaphysical hypothesis that all of life originated without any intervention of designers, supernatural or otherwise. Or perhaps it is used in the same way as YEC's use the term, "micro evolution" when they say YEC's accept micro evolution as well. Are YEC's ID evolutionists?
Presumably "ID evolutionists" actually believe something in the middle of those two options, but what exactly I do not know. Do you cease being an ID evolutionist if you believe the superkingdoms (Eubacteria; Archeabacteria; and Eukaria) were seperately originated by an intelligent designer? Or if you believe that all modern animal phyla were originated at the base of the Cambrian by direct intervention of a designer? Or if you believe all modern Genuses were orignated by direct intervention of a designer?
As for providing examples of research based on Darwinism – I have already done so in another discussion on this site:
Comment by tom_kbel — June 15, 2005 @ 7:33 pm
June 15th, 2005 at 10:29 pm
Guts:
This is your opinion [that Meyer's article is a poor quality review article], but it's irrelevant.
Far more than just my opinion, it has been well established by a variety of critiques. Of particular interest is the amount of literature that, though purportedly reviewing, he fails to mention:
http://www.pandasthumb.org/pt-archives/000430.html
Sigh, you didn't read the paper. Actually the paper has nothing to do with "the best explanation of the Cambrian Explosion" but with the origin of new forms, including new proteins as well as new organismal forms. His paper discusses the inadequacies and improbabilities associated with various non-design oriented evolutionary mechanisms and suggests that intelligent design as an explanation should be considered.
Have you ever read beyond the title of the paper? The Cambrian is mentioned 50 times in his Meyer's paper, and is his only example of the origin of animal forms. He concludes the paper by saying:
No, ID is much more than a collection of information in a review and deriving conclusions from them, which is why I listed many examples of empirical design research.
The Meyer paper is no different from other reviews that set out to elicit more research on a new hypothesis, such as this one:
Put aside the issue of quality, and the that review paper suggestions are usually more strongly linked to emperical research. It still remains the fact that Meyer's paper is part of a "research program" that has conducted no emperical research, and which has no emperical predictions that are in fact derived from their core hypothesis together with common (and acknowledged) auxilliary hypotheses. IN contrast, Darwinian review papers are (typically) directly connected to such emperical research, research directed at testing emperical predictions that are derived, sometime deductively, but more frequently, by statistical argument or modelling from its core theses together with auxilliary hypotheses that represent consensus opinions, and which are explicitly acknowledged. In controversial areas, some auxilliary hypotheses used are controversial, and are explicitly put to the test – but by doing so they also indirectly put Darwinism to the test. It is this emperical testing that makes Darwinism science.
An analogy to the race track will illustrate the point. Racing is the process of driving cars fast around the track, with the purpose of being the leading car after a certain distance has been covered, or time elapsed. But racing is a team effort. It also includes the activities of the engineers who design the cars, the machinists who produce the parts, and the mechanics who assemble them, and keep them tuned. Without these activities, there is no racing – just grown men sitting in a dust bowl going "BRMMM – BRMM".
BUT, and this is the crucial point, the designing of cars, the machining of parts, and the assembly of cars is not racing unless you put the car on the track and race it. A person who designs an Indy car, and builds it, but keeps it in his garage is not involved in racing. They are merely indulging in an idiosyncratic hobby. Nor are car designers and mechanics involved in racing unless their activity is focussed on producing a car that can be first on the track. If you buy a stock car, have it tuned at the local garage and then head for the track, the car designer and mechanic were not involved in racing. But they are if their design and activity is part of the coordinated effort, designed and necessary to get a car on the track.
In this analogy, theoretical work – the formulating of core hypotheses, and of auxilliary hypotheses, the making of predictions from these – is analogous to designing and building the car. It does not become science unless the car is built, and raced; ie, the experiments are actually conducted. And extending the analogy, the position of ID is that they have designed a car without engine or wheels. Some parts of the Dif that need to rotate are fixed to the chasis; and they want to call this racing before they have any plans to put this car on the track. And to rebut critics that point this out, they point out that Well's has suggested that you can put a stock car on the track as part of the team effort.
Well, I have news for you. That ain't racing; and ID ain't science.
I'm guessing you didn't read any of them. …
You also skipped over a lot of the ones that do make testable predictions and ones where research can be easily derived from derive research from it.
You're guessing that I didn't even read one of them, even though I explicitly review and criticise one of them? Do you actually care about the truth of what you say, or is the only thing that matters to you its rhetorical effect?
Of course I skipped over a lot. That is why I said that "I have only read a sample". Now, if you (or any other contributer) think one of the essays is a particularly good example of ID research, go ahead and blog it. I will not comment on it on this thread, however, for it is already too long.
Thats not correct. There is absolutely nothing in ID that prevents one from making a hypothesis based on motive.
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"
In fact the situation is, while IDists such as Mike are happy to implicitly assume particular motives to derive hypotheses; those assumptions are individual. They are not shared by the ID movement, and do not represent auxilliary hypotheses of the ID "research program". In fact, rather being commited to those assumptions, other IDists feel free to reject them completely when the same assumptions are used to mount a counter argument against ID.
Tom, you just showed how Mike's essay indeed makes testable predictions. So we can draw out an experiment that studies whether a four-based genetic system is actually better than a three-based genetic system when it comes to mutation.
I am fairly certain that Mike would not agree with you in tying the validity of his claims to the falsity of Shannon's theory of information.
The possible robustness of the genetic code in the face of mutation depends largely on the fact that a triplet based code has 64 codons to represent 21 states (20 amino acids, and the lack of an amino acid, ie, a stop codon). A quadruplet based code would have 256 codons to represent the 21 states; almost doubling the redundancy measured in bits, and allowing four codons for every currently distinct codon.
To suggest that a designer would integrate hundreds of different genetic codes just to "kill darwinism dead" is the most hilarious thing I have ever heard of.
You may think it hilarious that a putative designer would want to include irrefutable scientific evidence of his/her existance, but I doubt many ID theorists would agree with you.
Well I disagree completely that different codes would eliminate the transmission of diseases from one animal to another, an AIDS virus in a chimp passed to a human might cause damage that results in an even deadlier disease. But this is yet another testable experiment. One can use the "saltational leaps" which could be the result of a single nucleotide difference that makes a new form of virulence that enables a virus to survive in a host that previously could not survive in to suggest that they can.
Viruses are peices of DNA or RNA coated in proteins which are essential for their transmission. A virus active in a species using one genetic code could not transfer to a species using a different genetic code because, not one codon, or two, but nearly all its genetic sequence would code for different proteins. Suggesting cross infection is likely in this situation is like suggesting that if you replaced at random 90% of the amino acids in the viral proteins with different amino acids, the resulting protein would perform the same function as the original. The only situation in which this is plausible is when just one or two codons differ on rarely used proteins; but with 2 times 10 to the 10th power genetic codes of approximately equal stability to choose from, that is highly unlikely.
Of course, I could also test the assertion without bringing motive into the hypothesis. I can perform an experiment, using random mutation and selection, where I can evolve a piece of the genetic code that is just as robust as our present one. Showing that a design hypothesis is superflous. This has not been done for any complex biological system by the Darwinian research programme in the 150 years of it's existence. This is the major impetus (at least as I see it) for the major shift in paradigms.
So you are convinced Darwinism is false because Darwinists have not done in 150 years in a laboratory something their theory predicts took millions to 100's of millions of years using the entire globe in nature, ie, evolve a genetic code. It is fascinating how dogmatists fasten on the failure to perform unfeasible tests, while ignoring the many feasible tests that could disconfirm Darwinism (but do not) that Darwinists conduct, and report on a continuos basis.
I have already listed them. At no point in this response have you discussed why this isn't research. There is no reason to blog about this because your points are trivial.
Actually, I have laid down several clear criteria of why they are not research; and have defended those criteria from the fact that they follow straightforwardly from the best currently available philosophy of science. Your counter critique has been to say my criteria are ad hoc (they are not, for they follow directly from a clear, independant, and very cogent philosophy of science); to assert falsely and without evidence that Darwinism does not satisfy the criteria I outlined; and to assert that ID is science while failing to provide a cogent responce to any of my critiques of purported examples of research.
You have failed to demonstrate any problem with Lakatos' philosophy of science; and have failed to demonstrate why my criteria do not follow from that philosophy. What is more, you have not even made the attempt. Instead, you wish to assert your own criteria without defence, and without any principled reasons given as to why your criteria can pick out sciences, and exclude clear pseudosciences (such as astrology, for example).
In short, your counterargument has amounted to little more than assertion, coupled with an inability to understand the arguments presented against your position. This inability is again demonstrated by your comment:
The exact number of possible genetic codes using a triplet of nucleotides for codons, and 20 amino acids plus "stop" signals is a simple function of how many ways you can assign 64 codons to 21 results with the requirement that each result has at least one codon assigned. That is a question with a simple mathematical answer in numerical theory.
Your misunderstanding of this question – as also your misunderstanding about viruses, as also your misunderstanding about the effect of a fourth element in the codon, as also your failure to recognise the central place of the Cambrian explosion in Meyer's review article – shows clearly that you do not understand the issues you purport to comment on.
Comment by tom_kbel — June 15, 2005 @ 10:29 pm
June 16th, 2005 at 6:41 pm
I'm going to cut the fat a little (strip out irrelevant he said she said).
Tom:
Wow, did that little pubmed bomb actually get published? LOL. Anyway, those papers that they accuse Meyer of ignoring have been discussed
here. Needless to say, pointing me to a critique by your friends over at Pandas Thumb is not a very convincing argument that the review was of poor quality. Given that they don't like anything that IDers say, even when it has nothing to do with Darwinian evolution. Here is a lesson for you Tom, just because you disagree with it, doesn't mean it's of poor quality.
Of course, there's a reason for that. It's where the emergence of new information is seen, and never again since then. The major point of the paper was how specified complexity could arise in the first place. Which is why his examples did not only include body plans of the cambrian. For example, he discusses the view that one should be able to change all 171 non-active site positions of a protein and still maintain the original function. However, when a small percentage of these are changed, the original function is disrupted. He mentions lysyl oxidase, etc.
Meyer's paper, Wells's paper, and many found here are examples of empirical research, some of which makes predictions derived from their core hypotheses ,many of which include auxilliary hypotheses such as motive.
Well no actually, ID has come out of the "garage" phase. It has published books that spell out several important concepts, and it has published in the primary scientific literature. In your analogy, this is certainly not "racing" yet, but thats ok things are just getting started. There is a lot of designing and tuning up to do. It wouldn't be fun if all the work was already finished. Right now it's in the showroom for all to see, as that cool looking prototype.
You are implying however that no work has been done and that is simply not true. Further more the review I cited doesn't contain any predictions and no experimental work (although it cites many). This is the normal way that science works. These type of reviews are simply there to elicit more research.
Well Mike is already adding to his list which he also blogs as new information comes available. It certainly is a hobby to him, at least for now. But that doesn't make his work any less significant. However, I already discussed very good examples from that list of ID research, and I even derived a hypothesis and prediction from that hypothesis, showing how fruitful ID research really is.
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?
That statement makes absolutely no sense whatsoever.
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. What they measured was, what pattern of amino acids are fine tuned in "coding space" so as to minimize "the impact of mutations and/or mistranslations.". To quote you, your misunderstanding of this paper shows clearly that you do not understand the issues you purport to comment on.
No I think a designer would, and in a lot of ways the designer has, the cell is a veritible machine city. But that has nothing to do with how finch beaks vary, so there is no reason to "kill Darwinism dead" (LOL).
I agree actually. However, what is intriguing is that the ability to transfer code from one species to another lead up to acquired immunity. In this sense we have a testable hypothesis from an ID perspective about the origin and utility of both lateral gene transfer and adaptive immunity and the near universality of the genetic code.
There are no tests, statistical or experimental, that show any biological complex system might have arose through random mutation and selection, much less reported on in a continuous basis. One such test could easily be done for the eubacterial flagellum.
Lets step back and see what we have accomplished.
1. You asserted that ID has done no research. I list examples of exactly the opposite.
2. You come back and add a criteria to the list, ID has done no empirical research. I show that is false, I show that the research I listed is empirical in nature.
3. You come back and add more criteria (even complaining that empirical does not mean scientific), ID has done no experimental research. I show examples of working hypotheses in the literature that have done no experimental research either and yet is still considered amenable to the scientific method. And of course that experimental research is inevitable.
4. You come back and add more criteria, ID for it to be research it must have a heuristic and it must have auxillary hypotheses , you then falsely assert that ID refuses to take motive into account. I show that none of this is true.
Comment by Guts — June 16, 2005 @ 6:41 pm
June 17th, 2005 at 7:44 pm
Needless to say, pointing me to a critique by your friends over at Pandas Thumb is not a very convincing argument that the review was of poor quality. Given that they don't like anything that IDers say, even when it has nothing to do with Darwinian evolution. Here is a lesson for you Tom, just because you disagree with it, doesn't mean it's of poor quality.
And nor does the fact that you agree with it make it good quality. However, I at least, have tried to get beyond that pure subjectivity by pointing to specific failures in Meyer's article. You think those failures don't matter because the ID movement has a responce; but of course, the PT crew has a responce to that responce. Even if it were a brilliant review article, it would not be scientific research until it was part of a research program which made, and tested emperical hypotheses. And, Meyer's article is even worse than that as research because his conclusion, his proposal for emperical testing is just a restatement of the core of the ID research program. If there is a problem relating that core to emperical research, then restating the core in no way contributes to solving that problem.
Of course, there's a reason for that. It's where the emergence of new information is seen, and never again since then. The major point of the paper was how specified complexity could arise in the first place. Which is why his examples did not only include body plans of the cambrian.
The only examples of increase of "specified complexity" he gives are from the Cambrian. Axes research involved the loss of "specified complexity" as a result of multiple simultaneous mutations, and hence is not a gain of "specified complexity". It is certainly not "The Origin of … [a] Higher Taxonomic Category" (to quote from Meyer's title). It is Meyer's opinion (as mentioned in other articles) that the "Cambrian Explosion" is the time when "40 separate major groups of organisms or "phyla" (including all the basic body plans of modern animals) emerged suddenly without clear precursors.". In short, my summary of the conclusion of Meyer's article as being that ID is the best explanation of the Cambrian Explosion, ie, the purported sudden origin of all modern animal forms (and the only origins of higher taxonomic forms he discusses in his paper) was accurate.
Meyer's paper, Wells's paper, and many found here are examples of empirical research, some of which makes predictions derived from their core hypotheses ,many of which include auxilliary hypotheses such as motive.
Once again, Meyer's article draws a conclusion that has few if any consequences for emperical research. (I would say that it in principle cannot have any consequences for emperical research, but that would be tendentious.)
Well's testable conclusions are not predicted by ID with any auxilliary hypotheses. When I have asked you for an inference chain from ID's core hypotheses plus the ID research programs auxilliary hypotheses to Well's conclusion, you have said such a request is absurd. Asked for an alternative form of evidence of the emperical relevance of Well's hypothesis to the ID research program, ie, a Bayesian correlation between the truth of ID and the truth of Well's hypothesis, again you reject the relevance. In short, you have not shown a single reason to thinkg that Well's hypothesis is derived from the ID research program, and hence is relevant to the discussion. The best you can come up with is an apparent incoherence between Well's hypothesis and your misunderstanding of Darwinism. (And, typically, you are even unwilling to clarrify the terms you use in explaining that supposed incoherence.)
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.
You are implying however that no work has been done and that is simply not true. Further more the review I cited doesn't contain any predictions and no experimental work (although it cites many). This is the normal way that science works. These type of reviews are simply there to elicit more research.
What I have been implying all along is that ID has done no scientific research. On other lists I have said explicitly that ID theorists have done work in philosophy of science (for example). (Bad philosophy of science, but philosophy of science, none-the-less.) I also have now doubt that some IDists have done theological research. There is absolutely no doubt that they have done vast quantities of self-publicising. But none of this amounts to scientific research, the point I originally raised. You will of course, at this point, rush of to my original post and point out that the word "scientific" does not appear in it. But I did clearly refer to Lakatos' ideas when I said, "It remains the case that while ID is a degenerating research program, Darwinism continues as one of the most progressive research programs in science." This shows that the question of whether ID was science was uppermost in my mind, as it also shows the ideas of Lakatos about what constituted, and what did not constitute science were foremost in my mind when I made my comments.
Lets step back and see what we have accomplished.
1. You asserted that ID has done no research. I list examples of exactly the opposite.
2. You come back and add a criteria to the list, ID has done no empirical research. I show that is false, I show that the research I listed is empirical in nature.
3. You come back and add more criteria (even complaining that empirical does not mean scientific), ID has done no experimental research. I show examples of working hypotheses in the literature that have done no experimental research either and yet is still considered amenable to the scientific method. And of course that experimental research is inevitable.
4. You come back and add more criteria, ID for it to be research it must have a heuristic and it must have auxillary hypotheses , you then falsely assert that ID refuses to take motive into account. I show that none of this is true.
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.
Specifically, every condition I have mentioned follows directly from Lakatos' theory about the methodology of scientific research programs. Within Lakatos' theory, the conditions I have mentioned are directly implied. That is a point you have not seen fit to challenge (with good reason). But nor have you explicitly challenged the validity of Lakatos' theory; but rather have simply asserted a naive counter theory. In the mean time, you continuosly misrepresent me as making ad hoc conditions; and as having not read articles I clearly have read; and in general, insulted me freely as a substitute for argument.
What I have shown in this thread is that ID does not satisfy the criteria to be considered a scientific research program in Lakatos' theory. But, because of the logical relations between Lakatos' theory and those of Popper and Kuhn; in that case it is not a scientific theory in Popperian or Kuhnian terms either. In short, in terms of the three most widely accepted philosophies of science, and without any invocation of methodological naturalism; ID fails to be a science. Of course, by the criteria of all three philosophies, Darwinism is a science, and a highly successful one (though I have not shown that in this particular discussion).
Finally, to show that Lakatos has been quite central to my thinking about whether ID is a science or not for some time, I refer you to one of my better posts from a discussion list:
http://groups.yahoo.com/group/IntelligentDesignUpdate/message/429
Here is a representative quote:
Comment by tom_kbel — June 17, 2005 @ 7:44 pm
June 17th, 2005 at 10:26 pm
Well Mike is already adding to his list which he also blogs as new information comes available. It certainly is a hobby to him, at least for now. But that doesn't make his work any less significant. However, I already discussed very good examples from that list of ID research, and I even derived a hypothesis and prediction from that hypothesis, showing how fruitful ID research really is.
I am unable to discuss the examples of Mikes research that you give, for, quite frankly, you never bother telling me which ones your refering to. Mike has a well laid out site, and it is quite easy to reference specific articles by number (ie, BR 18, BR 19, BR 20). 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.
(I have noted a consistent pattern in bloggers on this site that they refuse to answer clarrifying questions; refuse to define terms when requested; and cite articles in the vaguest possible manner. If it persists, my conclusion will be that it is a deliberate strategy to evade critique by maintaining a strategically usefull ambiguity about what is being claimed.)
That statement makes absolutely no sense whatsoever.
It is a direct consequence of Shannon's theory that a code that used 256 states to represent 21 states has much greater redundancy, or in other words, a much less tendency for signals to degrade in the face of noise, than does a code with 64 states representing 21 states.
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.
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.
But that has nothing to do with how finch beaks vary, so there is no reason to "kill Darwinism dead" (LOL).
Do you intend here to subscribe to the view that Darwinism is only "micro-evolution"; or are you deliberately misrepresenting the content of Darwinism to avoid acknowledging that you have been caught out saying stupid things? It is difficult to avoid the later conclusion, for surely no-one involved in the debate fails to understand that Darwinism not only incorporates the evolution of finch beaks, but also the evolution of all animals, fungi and plants from single celled eukaryote ancestors, and of course, humans from simian ancestors.
I agree actually. However, what is intriguing is that the ability to transfer code from one species to another lead up to acquired immunity. In this sense we have a testable hypothesis from an ID perspective about the origin and utility of both lateral gene transfer and adaptive immunity and the near universality of the genetic code.
Now you agree? In your previous post you disagreed. Perhaps you should acknowledge that.
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. It also assumes that a putative designer would favour an improved ability to cope with disease at the expense of an increased incidence of types of disease Further, it is dubious as to what extent your emperical postulate is testable. To test it, all you need to show is that incidence and severity of diseases in animals is less as it stands than it would be in a world in which animals had a less capable immune system, but far fewer diseases to which they were vulnerable. That is something which is testable in principle, but it is not feasible to test it.
There are no tests, statistical or experimental, that show any biological complex system might have arose through random mutation and selection, much less reported on in a continuous basis. One such test could easily be done for the eubacterial flagellum.
On the contrary, there are many such tests. One instance is the evidence that the vertebrate eye could arise by RM & NS given only a light sensitive cell as a starting point. Just because you do not like that research does not mean it does not exist.
Again, however, you show your unrealistic expectations for evidence of Darwinism. Do you really think that bacterial flagella could evolve in less that tens of thousands of years such that, Darwinists should have been able to demonstrate its evolution in the laboratory by now? Or perhaps you are merely claiming that Darwinists have not been able to show a potential darwian path for the evolution of the flagella. But in that case, you are wrong, and simply ignoring the evidence never makes it go away.
Comment by tom_kbel — June 17, 2005 @ 10:26 pm
June 18th, 2005 at 12:32 am
Tom:
Where?
What is not empirical about the hypotheses that ID makes?
That makes no sense. The conclusion is the ID research program, that intelligence best explains a wide range of biological phenomenon. Of course it's going to be the same.
The fact that a small percentage of changes to a protein results in a loss of function (and a small percentage in the non-active site no less), shows that there is a large amount of specified information in that protein and Meyers does indeed hypothesize an intelligence for the origin of "information rich" proteins.
That he discusses all these systems would have been obvious if you had actually read the paper:
So in light of this quote, does Meyer's review offer an explanation for more than just body plans?
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?
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?
I'm talking about all of them (in the biotic section).
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?
I don't want to see these type of comments on this board anymore. This blog isn't for you to hurl insults at the other posters. I'm not the only one that has made the observation that you are behaving like an obnoxious "holier than thou" that refuses to admit that he's made a mistake. At the same time, they have engaged you in debate and have very specifically and unambiguously shown why they disagree with you, when all they had to do was shoot your comment down the memory hole.
I wrote:
Tom replied:
"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:
and from a recent discussion:
If you think that a 3 base-pair codon code is less redundant than a 4 base pair codon code and that "expanding the system to four base pair codons, robustness in the face of mutation could have been quadrupled", then your interpretation of the paper doesn't make sense. The paper was not measuring robustness in the face of mutation in terms of the codon length or whether the redundancy varies. How could they? All the possible codes were triplet based and all had the same pattern of redundancy, and yet robustness in the face of mutation varied greatly. If you disagree show me from the paper along with well thought out reasons why you disagree, don't just assert it.
Yes, and it's the latter that is under question. Design theorists don't question that natural selection and random variation occur, in fact, it explains many things. They don't think that Darwinism explains it all. All design theorists find some merit in Darwinian evolution even their rhetoric can seem all encompassing. I'm pretty sure that the designer knew that natural selection and random variation occurs as well. Which is why saying that a designer would want "Darwinism dead" is the most hilarious thing I have ever heard.
I can assure you Tom, it was because of nothing that you said. The reason why I disagreed at first was because I had just read a paper that showed that vesicular stomatitis virus, a virus of mammals, can replicate in insect cells. This came as a surprise to me because what is different from one species to the other is the "preference" of codon usage. For example, there are four codons encoding for Threonine, ACA, ACT, ACG and ACC; however, one species may prefer ACA to encode Threonine whereas the other species may encode Threonine using ACG preferenitally. If you analyze a gene from mouse and compare that with its orthologues in other species you will find out that preference indeed exists. It is possible that for any given two species, the wider the evolution distance, the more different codon usage will be. So if a human virus jumps to an insect, its protein will not be translated very well.
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.
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?
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.
One thing that is feasible to test is if the lateral gene transfer machinery shows patterns that it was intelligently designed, together with the historical patterns of the emergence of aquired immunity, to test whether that shows patterns of intelligent design (whether be through direct intervention or frontloading).
I'm not referring to simplified mathematical models, I'm referring to actual biological experiments and/or a statistical study about the mutations required.
I don't agree that the experiment is not tractable due to timescales. An experiment involving thousands of generations of selective pressure for motility, involving something like this:
Papadopoulos D et. al. Genomic evolution during a 10,000-generation experiment with bacteria.
Proc Natl Acad Sci U S A. 1999 Mar 30;96(7):3807-12.
This should (theoretically) produce a flagellum-like (maybe only somewhat like flagella) IC motile structure that is at least beneficial, if we start with a structure that, as Darwinists say,the flagellum was co-opted from.
Comment by Guts — June 18, 2005 @ 12:32 am
June 18th, 2005 at 10:26 am
Alien Space Station Research
Comment by Irving — June 18, 2005 @ 10:26 am