A De Novo Gene: Unlikely and Very Unlikely

faded glory: The distinction between intelligence, law, and chance is over two thousand years old, beginning with Plato's "Laws." If you can think of another kind of cause, you will be the first. So, it's a perfectly reasonable assumption to bring to any dialogue. Science assumes many things less certain than that. ----"As to brains and mind, I very much like the expression that ‘the mind is what the brain does’. Brains are an organ, a object, and mind is a process, the operation of the organ." There is no empirical evidence for, or any logical reason to believe, the assertion that the mind is a "process." Quite the contrary, if the mind is anything, it is a faculty, just as is the brain is an organ. In any case, the point is that the Darwinist cannot discuss the two terms "mind" and "brain" while using the word "natural" in any meaningful way, except of course by claiming that mind "is" the brain or else that it is grounded in the brain, which is another way of saying that it isn't a mind at all. - "This is not an accurate representation of my views. I very much conceive of the universal nature of various patterns in nature. This is because I see the human mind as no more than an integral part of all of nature, rather than something natural imbued with some special powers ‘from the outside’." How, then, do you explain the origin of the design in an ancient hunter's spear? Where did the design come from and how did it happen? You are trying to conflate the cause of wind, rain, and erosion, with the cause of intentional action. That is what happens when you characterize all these kinds of causes as "natural." ---"If any, it is the dualists who struggle with conceiving of this unity. Universe, mind, matter, law and chance are all parts of nature, and as far as anyone can demonstrate there are no two kinds of intelligence, but just various types and degrees of a single phenomenon. As for ’supernatural’, I don’t think it means anything else but an imaginary explanation for the unknown – an empty label." In that case, perhaps you could serve yourself and your colleagues by defining the word, "natural," because no one knows what the Darwinist means when he uses that term. While you may not agree with our definition of "natural," you clearly know what it is. StephenB

StephenB: "When ID advocates use the term “natural,” in a scientific sense, they are talking about “natural causes,” such as law and chance, as opposed to non-natural causes, such as intelligent agency." - Stephen, I am not convinced of this dichotomy between law & chance on the one hand, and intelligence on the other hand. The nature of intelligence is still obscure, and I don't think it is has been demonstrated at all that intelligence has another component other than law & chance in some form. Moreover, how do you deal with things like spiders building webs, or termites building colonies? Is there no intelligence there or are these things not natural? What about dogs? Are dogs unintelligent or non-natural? This distinction is fraught with problems. My view is that intelligence comes in degrees, and at the lower end of the scale it is almost indistiguishable from what you would call 'natural', whereas at the higher end of the scale it looks rather different from law & chance. Yet, its nature (pun intended) remains unresolved, and assertng that anything more is involved than law & chance is a metaphysical claim that has been debated for millenia without any concrete results whatsoever. StephenB: "Under those circumstances, the term’s meaning is precise enough to use as part of the rational discourse. On the other hand, when anti-ID partisans enter the arena, they look for ways to muddy the debate waters by ignoring ID’s scientific definition of “natural” and use their own formulation, which has never been defined. At best, they play on the dichotomy between “natural” and “supernatural,” even though they have never explained the meaning of one in the context of the other. That is why they don’t know what to do with words such as, “mind” or “brain.” For them, both faculties would have to be “in nature,” whatever that means, so there cannot be any substantial difference between the two." - As I explained, the terms' meaning is not at all clear because the suggested dichotomy may not actually exist. As to brains and mind, I very much like the expression that 'the mind is what the brain does'. Brains are an organ, a object, and mind is a process, the operation of the organ. There is no empirical evidence, but plenty of metaphysical speculation, to demonstrate that anything more is involved. StephenB: "Further, and more importantly, they cannot conceive of the universal nature of the origins of various patterns in nature. If a human “mind” designs something and leaves evidence of complex-specified information, that is, for Darwinists, a natural event. Yet, if a “supernatural” mind, or for that matter, a Divine mind, designs a universe, leaving that same texture of complex-specified information, it is, for them, a supernatural event, which means, we are told, that we cannot compare the similarity between the patterns coming from the two kinds of intelligent agents because one is supernatural and the other is natural. That is the kind of illogical nonsense they give us. Calling it “methodological naturalism,” doesn’t make it any less illogical." - This is not an accurate representation of my views. I very much conceive of the universal nature of various patterns in nature. This is because I see the human mind as no more than an integral part of all of nature, rather than something natural imbued with some special powers 'from the outside'. If any, it is the dualists who struggle with conceiving of this unity. Universe, mind, matter, law and chance are all parts of nature, and as far as anyone can demonstrate there are no two kinds of intelligence, but just various types and degrees of a single phenomenon. As for 'supernatural', I don't think it means anything else but an imaginary explanation for the unknown - an empty label. fG faded_Glory

Jerry:

You keep trying this non sequitur approach of yours.

So, then, you believe that ID would be equally furthered by yet another closet analysis of the kind you describe (a study conducted and interpretable within orthodox evolutionary biology, but privately reinterpreted employing ID's conceptual framework), and by an ID researcher making an prediction that follows directly and necessarily from ID's conceptual framework, one that would not follow from orthodox evolutionary theory, testing that prediction by means of a well designed study, and finding that the prediction was confirmed. There is nothing particularly more powerful or dispositive about the second approach relative to the first. Right? Voice Coil

Jerry, I too enjoyed that article. My only complaint - it was too short. I wasn't in the slightest bit tired of reading it. Upright BiPed

Jerry, that's a good article by Frank Tipler. Clearly, he get's it. I have had a parallel experience on this site. Just as Tipler's adversaries have to deny the laws of mathematics and physics to make their case, my adversaries have had to deny the laws of causality to make their case. You will probably recognize William Lane Craig's popularized version of the foundational argument. [A] Anything that begins to exist, must have a cause, [B] the universe began to exist, therefore,[C] the universe had a cause. That point is even less controversial that Tipler's and his isn't really controversial at all. Nevertheless, Darwinists come to this site and say either that [A] is not necessarily true, and, when refuted, change course and then declare that it is trivial and circular, which of course, it isn't. Even Hume and Kant, the two skeptics that led the way to our current malaise, and who, in many respects, provided the intellectual justfication for Darwin's general theory of evolution, admitted openly that no rational person would ever declare that something could come into existence without a cause. Yet Darwinists come here regularly to challenge the point. Thus, you are debating science with folks who don't even accept the law of causality, one of the vital metaphysical foundations for science. When you finally pin them down with facts that lead to an intelligent cause, they simply deny that any such cause is necessary. When you finally pin them down with facts that show the statistical impossibility that naturalistic forces can create information, they begin to argue on behalf of common descent, which, as you know, is not even in dispute for most ID advocates. Or, they just go through the same old routine that something can come from nothing, failing to realize that if that was the case, science, rationality, and even reasoned discourse couldn't exist. There is no way to argue against that kind of irrationality except to point it out from time to time. StephenB

StephenB, others, I posted something the other day on the Gravity thread which should be a separate thread but which I believe got buried by the host of other comments posted, It is by Frank Tipler and truth in science http://pajamasmedia.com/blog/orwellian-nightmare-science-is-whatever-the-party-says-it-is/?print=1 Given the anti science objections to ID on this thread it would be appropriate to what has been discussed here. jerry

:That’s not enough. You need studies that an ID scientist would do that a non ID scientist wouldn’t do: those driven by predictions that arise from ID. As you say, “occasionally design some different studies.” That is the only activity that can provide dispositive scientific justification for preferring an ID explanation over others.: Got to give you credit for persistence. You keep trying this non sequitur approach of yours. First, there have been some studies already done in this vein. Studies that examine the limits of novel protein formation are such studies. Dembski and Marks work are also such studies. Also every study which maps a genome is an ID study even though nearly all of the ones done are by people who would deny they are doing an ID study. ID has limited resources to do research by design of the academy. If someone said they were doing a study based on testing ID not only would they not get the study approved, but they would be ostracized by the science community. Just leave it that ID studies are being done all the time but are not identified as such. Behe wrote a book called the Edge of Evolution and in it he shows how research already done can be used to support ID. So right now the best ID research is being done in the biology labs around the world in universities and big government labs. I think it kinda neat that all these anti ID people are carrying ID's bags. By the way we have been down these arbitrary illogical objections before several times so it is easy to point out the irrelevancy of your comments. You must get them from a template published on the internet some place which hasn't been updated to make better sense. The current scientific establishment is scared to death of ID. They feign ennui about ID but let it come up and they go ape s__t about it. If it was a nothing area, they would generally ignore it or even provide some funds to disprove it. But because they know of no way to disprove it, they try to oppress it. And they really goes nuts when they see their own research used to support ID. But in truth every research project they do must support ID which I find kind of ironic. So when you make these objections we know what it is about. But keep trying, you may get somewhere some day. jerry

I have to apologize. I got it exactly backwards at @35. I said, "When ID advocates use the term “natural,” in a scientific sense, they are talking about “natural causes” as opposed to “non-natural” causes, such as law or chance. Under those circumstances, the term’s meaning is precise enough to use as part of the rational discourse." That, of course, is spectacularly wrong. What I should have said it this: When ID advocates use the term "natural," in a scientific sense, they are talking about "natural causes," such as law and chance, as opposed to non-natural causes, such as intelligent agency. Under those circumstances, the term’s meaning is precise enough to use as part of the rational discourse. On the other hand, when anti-ID partisans enter the arena, they look for ways to muddy the debate waters by ignoring ID’s scientific definition of “natural” and use their own formulation, which has never been defined. At best, they play on the dichotomy between “natural” and “supernatural,” even though they have never explained the meaning of one in the context of the other. That is why they don’t know what to do with words such as, “mind” or “brain.” For them, both faculties would have to be “in nature,” whatever that means, so there cannot be any substantial difference between the two. Further, and more importantly, they cannot conceive of the universal nature of the origins of various patterns in nature. If a human “mind” designs something and leaves evidence of complex-specified information, that is, for Darwinists, a natural event. Yet, if a “supernatural” mind, or for that matter, a Divine mind, designs a universe, leaving that same texture of complex-specified information, it is, for them, a supernatural event, which means, we are told, that we cannot compare the similarity between the patterns coming from the two kinds of intelligent agents because one is supernatural and the other is natural. That is the kind of illogical nonsense they give us. Calling it “methodological naturalism,” doesn’t make it any less illogical. That is why I, for one, ask them to use the word “natural,” only with reference to undirected evolution or with respect to that which was not caused by an intelligent agent. Of course, they continually refuse to do that because such a discipline would lend itself to the very kind of clarity they seek to avoid. StephenB

Jerry:

But there is no study that a non ID scientist would do that an ID scientist wouldn’t do.

That's not enough. You need studies that an ID scientist would do that a non ID scientist wouldn't do: those driven by predictions that arise from ID. As you say, "occasionally design some different studies." That is the only activity that can provide dispositive scientific justification for preferring an ID explanation over others. Voice Coil

StephenB, I did not see your comment till I wrote mine. Have to go off to a Christmas concert in 5 minutes. Come back here later in the day because I posted something a couple days ago that got buried in the mass of comments that is very interesting and appropriate for its own thread. jerry

Faded Glory, It is nice to see your stripes haven't changed. There is no contradiction in what I have said unless you and the rest of us here want to use the term unnatural to include events in our world that include the operation of intelligence. Most would not want to do this. It so happens that natural and unnatural may not be exhaustive as the use of our grammar would normally indicate. Are the operations of an intelligence unnatural but we often use the term natural to indicate what happens using the laws of nature only. So there is a gap here between the normal usage of the terms "natural" and "unnatural." Generally most of us use the term "naturalistic" to mean processes flowing under the forces of physics which would include all of chemistry which is probably a subset of physics. Then there is other uses of the term where it would include processes operating under the forces of physics once some initial and boundary conditions have been set up by an intelligence. A good example is building a river bed to divert a river in a different direction but then leaving it alone. Maybe another example would be to build a system with extremely complicated built in constraints and parts and then let it operate according to the laws of physics and chemistry which I have said is a subset of physics. Such a system could be biological matter. It could be something else designed by an intelligence such as a garden or a farm that proceeds according to the built in initial conditions and boundary conditions. Sometimes gardens need intelligent intervention but other times not so. For the later case look at various places people have planted wild flowers to enhance a landscape and then just left them alone or seeded a lake with trout which is not a garden but a similar concept. So are there any processes that are neither natural and not unnatural. I would say to make things easier to communicate that processes that involve the intervention of an intelligence would be such a case. So assume that is how I use the terms. If you want to quibble, be my guest but you have to accommodate the distinctions which I think you already understand. Your feigned non understanding is always suspect as you always quibble with the non relevant. You are too consistent to be honestly seeking understanding. Maybe this should start a discussion on how we should use the terms natural, unnatural and intelligent processes. Certainly we do not want to call intelligent process unnatural but while they are perfectly natural are they what biologist mean when they say that evolution proceeds under naturalistic causes only. I am sure you understand this and I do not think I have made any contradictions. But maybe there should be more precise use of the terms in the future but again as I said I doubt anyone misunderstood what was meant including yourself. jerry

---faded glory: "Jerry, you introduced the term ‘natural(istic)’ in this thread yourself, in post no. 2, and elaborated on it in post no. 9. Others merely took you up on this. If you say that these concepts of natural, non-natural or supernatural have no place in science I totally agree with you. Why not present some possible ID mechanisms for the origin of novel genes so we can discuss those instead?" When ID advocates use the term “natural,” in a scientific sense, they are talking about “natural causes” as opposed to “non-natural” causes, such as law or chance. Under those circumstances, the term’s meaning is precise enough to use as part of the rational discourse. On the other hand, when anti-ID partisans enter the arena, they look for ways to muddy the debate waters by ignoring ID’s scientific definition of “natural” and use their own formulation, which has never been defined. At best, they play on the dichotomy between “natural” and “supernatural,” even though they have never explained the meaning of one in the context of the other. That is why they don’t know what to do with words such as, “mind” or “brain.” For them, both faculties would have to be “in nature,” whatever that means, so there cannot be any substantial difference between the two. Further, and more importantly, they cannot conceive of the universal nature of the origins of various patterns in nature. If a human “mind” designs something and leaves evidence of complex-specified information, that is, for Darwinists, a natural event. Yet, if a “supernatural” mind, or for that matter, a Divine mind, designs a universe, leaving that same texture of complex-specified information, it is, for them, a supernatural event, which means, we are told, that we cannot compare the similarity between the patterns coming from the two kinds of intelligent agents because one is supernatural and the other is natural. That is the kind of illogical nonsense they give us. Calling it “methodological naturalism,” doesn’t make it any less illogical. That is why I, for one, ask them to use the word “natural,” only with reference to undirected evolution or with respect to that which was not caused by an intelligent agent. Of course, they continually refuse to do that because such a discipline would lend itself to the very kind of clarity they seek to avoid. . . When ID advocates use the term “natural,” in a scientific sense, they are talking about “natural causes” as opposed to “non-natural” causes, such as law or chance. Under those circumstances, the term’s meaning is precise enough to use as part of the rational discourse. On the other hand, when anti-ID partisans enter the arena, they look for ways to muddy the debate waters by ignoring ID’s scientific definition of “natural” and use their own formulation, which has never been defined. At best, they play on the dichotomy between “natural” and “supernatural,” even though they have never explained the meaning of one in the context of the other. That is why they don’t know what to do with words such as, “mind” or “brain.” For them, both faculties would have to be “in nature,” whatever that means, so there cannot be any substantial difference between the two. Further, and more importantly, they cannot conceive of the universal nature of the origins of various patterns in nature. If a human “mind” designs something and leaves evidence of complex-specified information, that is, for Darwinists, a natural event. Yet, if a “supernatural” mind, or for that matter, a Divine mind, designs a universe, leaving that same texture of complex-specified information, it is, for them, a supernatural event, which means, we are told, that we cannot compare the similarity between the patterns coming from the two kinds of intelligent agents because one is supernatural and the other is natural. That is the kind of illogical nonsense they give us. Calling it “methodological naturalism,” doesn’t make it any less illogical. That is why I, for one, ask them to use the word “natural,” only with reference to undirected evolution or with respect to that which was not caused by an intelligent agent. Of course, they continually refuse to do that because such a discipline would lend itself to the very kind of clarity they seek to avoid. StephenB

"The appropriate question is, “what would an ID scientist do that a non ID scientist would not do.” The answer is 1) occasionally make different conclusions from some of the data and 2) occasionally design some different studies. But there is no study that a non ID scientist would do that an ID scientist wouldn't do. Can I be any clearer. "Absent from your scenario of ID scientists gathering data identically, but analyzing that data in light of a broader set of conceptual categories, is theory guiding observation." Nonsense. Is it a theory that an intelligence could be an explanation of an effect. Such a theory is incorporated all the time in typical science. ID just expands it to all phenomena and rejects its relevance in 99.99999% of the cases. Aren't you embarrassed at how inane your two questions were? I would be. So I have to wonder what was the motive for asking such drivel. jerry

Jerry:

I have often said tell me what one thing an ID scientist would not do that a an non ID scientist would do.

The appropriate question is, "what would an ID scientist do that a non ID scientist would not do." The answer is: make empirical predictions that arise as necessary entailments of ID theory, then test those predictions by means of observations, such that failure to observe what is predicted places a tenet of ID theory at risk of disconfirmation. Absent from your scenario of ID scientists gathering data identically, but analyzing that data in light of a broader set of conceptual categories, is theory guiding observation. Voice Coil

jerry: ID is not a theory. It is an approach to science.

Then you are explicitly saying that ID is not science, but metaphysics. Only specific claims can be evaluated scientifically, and only those claims that have clear empirical implications entailed in the claim. Many (if not most) people use the term "ID" to mean intelligent intervention in biology, either the direct creation of kinds, guided evolution, or front-loading, or any of a number of inconsistent or ill-defined claims.

jerry: So when the conclusion points to intelligence as a possible cause of an observable fact, it does not mean some new theory is being employed.

Of course it does. You would be claiming or hypothesizing the interaction of an intelligent agent with observable consequences entailed in that interaction. Zachriel

Jerry, you introduced the term 'natural(istic)' in this thread yourself, in post no. 2, and elaborated on it in post no. 9. Others merely took you up on this. If you say that these concepts of natural, non-natural or supernatural have no place in science I totally agree with you. Why not present some possible ID mechanisms for the origin of novel genes so we can discuss those instead? fG faded_Glory

ID is not a theory. It is an approach to science. It is a more logical and comprehensive approach to science than that practiced by most current scientists. I have often said tell me what one thing an ID scientist would not do that a an non ID scientist would do. The answer is nothing. What an ID scientist would do differently is consider a wider range of possible conclusions as causes of observable physical facts. So when the conclusion points to intelligence as a possible cause of an observable fact, it does not mean some new theory is being employed. It only means an more intense analysis has been employed. It is possible to speculate further on the nature of the intelligence if there is enough data to do so but often there is not. People who support ID often let themselves get put in a box by anti ID people and start considering things that have no place in ID. The fall for the trap that these extraneous discussions have something to do with ID when to do not. They rightly belong in some other category of discussion and are legitimate topics but they are not ID. As I just said in my previous comment, discussions of the unnatural or super natural are not ID but represent some philosophical area and ID is not philosophy but a broader approach to science that is not restricted ideologically as are most modern scientists by an extraneous philosophy called methodological naturalism. It is ironic that it is the anti ID people who are in a philosophical straight jacket while the pro ID supporter are more intellectually free. jerry

"Science limits itself to empirically observable mechanisms – something that ID by its own admission does not concern itself with at all." Nonsense. Science limits itself to observable events. So does ID. Science also considers the intervention of intelligence in many natural processes which has the effect of intervening in the normal processes that natural laws would produce. It happens all the time. So does ID. What so called modern science does and it is completely arbitrary is to say that certain phenomena can not be the result of intelligent intervention. This is a non sequitur since they consider intelligent intervention all the time in other phenomens. ID being the more logical and comprehensive "scientific" approach says that is pure ideological bulls__t. There is no reason to arbitrarily limit certain phenomena from such an analysis. Modern science is ideologically based while ID is not and willing to accept a wider range of possible conclusions to physical phenomena. Anyone who brings up the topic of unnatural or super natural is this discussion is playing an intellectually bankrupt game that is a non sequitur. It is done solely to shore up an equally bankrupt philosophy. Everyone here understands this so those who bring up the unnatural as a consideration are playing a game. jerry

Mung, The quick answer is that I don't understand if there is any difference at all between 'unknown' and 'non-naturalistic'. Saying that the novel gene has an unknown origin and saying that it has a non-naturalistic origin seems to me to have exactly the same explanatory value - namely zero. Neither tells us anything about how the gene originated. Exactly because of the unclear definition of 'non-natural' isn't 'unknown' the more honest answer? Your counterexample of gravity misses the point - we indeed can't see gravity but we can most definitely empirically observe it, and formulate theories around it that lead us to further predictions subject to empirical investigation. This doesn't work for ID. And yes, I agree with you that naturalism is just as metaphysical an interpretation as non-naturalism. Both are concepts that should be kept out of science. Science limits itself to empirically observable mechanisms - something that ID by its own admission does not concern itself with at all. fG faded_Glory

Mr Mung, I don’t speak for Dr. Hunter, but I would not be at all surprised to see a similar response from him. The most reasonable explanation for your failure to find his argument convincing is simply that you don’t understand it. Note how I am not accusing you of any motives whatsoever. Just a lack of understanding. If you think so, I would appreciate your pointers for where I have missed the key part of Dr Hunter's message. The probabilistic resources necessary to generate s de-novo gene by naturalistic mechanism? Indeed. If Dr Hunter thinks the odds against this gene arising are 1 in 10 million, then planting ten million stalks of corn makes it likely we sill see this gene in one year. Nakashima

I’ve tried to follow your argument across several of the posts on your blog. I can’t say that I find either part of your position convincing.

I don't speak for Dr. Hunter, but I would not be at all surprised to see a similar response from him. The most reasonable explanation for your failure to find his argument convincing is simply that you don't understand it. Note how I am not accusing you of any motives whatsoever. Just a lack of understanding.

Accepting your one in ten million probability at face value, yes there are more than ten million corn plants alive each year, many more. So there are the probabilistic resources necessary.

The probabilistic resources necessary for what? The probabilistic resources necessary to generate s de-novo gene by naturalistic mechanism? Mung

"ID is indeed the perfect theory for determining whether the virus was designed or not. But that seems to be as far as it goes. How does that help us to know if a virus was designed? We would need to be able to distinguish between designers.If we can’t tell the difference between the Intelligent Designer and a human designer, we haven’t advanced any, have we?" Oh, but it would advance us very much if we could determine that life itself, or aspects of it, were definitely designed. Buying into notions of a non-natural God is also a source of confusion. I would say that the Intelligent Creator Source is perfectly natural. avocationist

Dr Hunter, I've tried to follow your argument across several of the posts on your blog. I can't say that I find either part of your position convincing. Accepting your one in ten million probability at face value, yes there are more than ten million corn plants alive each year, many more. So there are the probabilistic resources necessary. The other part is also weak. Yes, you can do massive substitution of amino acids and still have some level of function. Even Axe 2004 has examples. If you were trying to show how easy it would be for this protein to develop, you did a great job. Nakashima

Mung: We should find the same pattern in the genome as the theory predicts for the evolution of species. Which genes evolved from which within the same genome?

Look here for one such example: http://www.nature.com/nature/journal/v387/n6634/full/387708a0.html And here is more info on the evolution of genes within closely related species: http://wolfe.gen.tcd.ie/ygob/

jerry: But it appears there exist a large number of proteins that species specific and their origin should be an interesting area of study to clarify just how and where do proteins originate,

Indeed, it is an interesting area of study. There is an enormous wealth of publications out there on this topic. hrun0815

Collin-

Also, how do we know if a virus has been genetically engineered by terrorists? Must we know how it was designed before we can know that it was designed? Isn’t ID the perfect theory to help biologists in that type of endeavor?

ID is indeed the perfect theory for determining whether the virus was designed or not. But that seems to be as far as it goes. How does that help us to know if a virus was designed? We would need to be able to distinguish between designers.If we can't tell the difference between the Intelligent Designer and a human designer, we haven't advanced any, have we? Walter Kloover

But it appears there exist a large number of proteins that species specific and their origin should be an interesting area of study to clarify just how and where do proteins originate,

Yes, species-specific genes is an interesting area, but why get sidetracked on that? Evolutionary theory predicts that most or all of the genes in any given genome are historically related to each other through a process of "descent with modification." Who cares about genes across taxa if even this basic claim of evolutionary theory is false? Where's the evidence of the relatedness of all genes in the genome to each other and their ancestors? Is anyone taking the genome of even the simplest organism and submitting it to a taxonomic analysis? We should find the same pattern in the genome as the theory predicts for the evolution of species. Which genes evolved from which within the same genome? Mung

fg @13

What kind of observations would lead one to decide if novel gene development took place via naturalistic means or not? This is a serious question, I think this is the most crucial point in the debate if ID is science or not.

ok, that is a serious question. So why not treat it as such?

My view: there are actually no possible observations that would decide this, because the ‘non-naturalistic’ (what is that exactly anyway?) is not empirically observable in the first place. Ergo, ID is a metaphysical interpretation of our empirically observable reality.

But is it not also true, that there are no possible observations that would decide this in favor of the alternative either. So where does that leave you?

the ‘non-naturalistic’ (what is that exactly anyway?) is not empirically observable in the first place.

Indeed, what is that? It's rather vacuous to assert that "natural" means "observable" that "non-natural" means "not observable" and then arrive at the conclusion that non-natural means non-observable. How do you know that the non-natural is not observable unless you define it to be such? When is the last time you saw gravity? Is it therefore non-natural? When is the last time you saw one of your own thoughts? Does that mean they are non-natural?

Ergo, ID is a metaphysical interpretation of our empirically observable reality.

Oops! That doesn't follow. One might as well claim: Ergo, naturalism is a metaphysical interpretation of our empirically observable reality. So where does that get you? Mung

Colin, Your are expecting intelligent responses from the anti ID people who come here. Ocassionaly we get one or two but most have nothing to offer but rhetoric saying how dumb we are. jerry

ID does not have to be non-naturalistic anyway. When a programmer designs a computer program, is that a non-naturalistic event? If we did not know how he designed it (say he used an unknown kind of computer) could we never say that it was designed? How would we know? Also, how do we know if a virus has been genetically engineered by terrorists? Must we know how it was designed before we can know that it was designed? Isn't ID the perfect theory to help biologists in that type of endeavor? Collin

I do not pretend to understand this article and invite anyone who can explain it in general or in detail to do so. But it appears there exist a large number of proteins that species specific and their origin should be an interesting area of study to clarify just how and where do proteins originate, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1779552/ Here is the conclusion from the study The advent of genome sequences has reinvigorated an effort to understand the origins of species specificity. This is a daunting challenge, emphasized by the fact that in the 10 proteomes analyzed here we identified 44,236 phylogenetically specific proteins with undefined or obscure features (POFs). In contrast to PDFs, which have established domains or motifs that can be used to formulate working hypotheses about a protein's function, advancing our understanding of POFs must proceed without such clues. Our analysis here provides an expectation that, on average, 60% of a eukaryote's set of POFs will be highly divergent, and that functional studies will ultimately need to be conducted on a species-specific basis. For example, the human genome encodes 27 proteins that currently cannot be found in genome sequences of any model organism, including the chimpanzee sequence (Table 5S in Additional data file 1). Consistent with expectations from this study, these human-specific proteins are all POFs. Eventually, the function of these unique proteins will need to be studied in humans. Our results support a general expectation that to understand the unique biology of a given organism will ultimately involve understanding the functions of an unexpectedly large number of proteins that have: no defined motifs or domains; are likely to have significant regions of disordered structure; and are restricted to a single species or a closely related phylogenetic branch. jerry

When there is a trail, the designer "guides" it. When there isn't a trail, the designer also guides it (or more likely, we do not have a complete accounting of evidence). That's interesting. It is easy to measure sequencing data from one generation to the next. Why not look for evidence of a severe mutational discontinuity between generations? Do you have an example of one that's been observed? olin

"My view: there are actually no possible observations that would decide this, because the ‘non-naturalistic’ (what is that exactly anyway?) is not empirically observable in the first place. Ergo, ID is a metaphysical interpretation of our empirically observable reality." Nonsense. You interestingly assume that there would not be any naturalistic evidence for protein formation which is revealing. But as an ID supporter I would expect to find some and perhaps several. Naturalistic process leave a trail and that is how much of science is practiced, searching for these trails. Much of astronomy and cosmology is based on these trails such as red shifts, luminosity, super novas, parallax angles, movements of light and solar bodies. Geology leaves trails such as mid ocean ridges, changes in magnetic orientation, age of rocks etc. Biology should leave similar trails. When they don't is when people should step up and take notice. Species devolved/evolved from a common ancestor should leave a trail of all the changes that happened over time, including gene formation. If such a trail is not present then what could be the explanation since naturalistic process don't allow for poofing. Dare I say the non metaphysical, scientific answer would be the possibility of intelligent meddling in the process. The metaphysical answer would be to a priori deny the existence of an intelligence. So ID is the non metaphysical approach to science while the current academy is deeply entrenched in limiting metaphysical paradigm to the practice of science. jerry

"i see you are an advocate of good science. So am I. I see a good deal of very good science being done all the time, they even get Nobel prices. Just tell me, who are doing the good science these days, ID proponents or the despised mainstream scientists?" Why does there have to be a difference. Why can't a particle physicist be an ID advocate? Why can't a evolutionary biologist be an ID advocate? Name the field and tell me why the person working in that field cannot be an ID advocate? There is no reason so the distinction is meaningless. jerry

What kind of observations would lead one to decide if novel gene development took place via naturalistic means or not? This is a serious question, I think this is the most crucial point in the debate if ID is science or not. My view: there are actually no possible observations that would decide this, because the 'non-naturalistic' (what is that exactly anyway?) is not empirically observable in the first place. Ergo, ID is a metaphysical interpretation of our empirically observable reality. fG faded_Glory

olin, I still await the positive evidence that T-urf13 evolved. ellijacket

If you wish to cherry pick my posts, that is fine, but it is not convincing. Newtonian gravity is a red herring: the discussion is about intelligent design and evolution, how organisms develop. I still await the positive evidence that T-urf13 was designed. olin

jerry:

There are a lot of hurdles naturalistic evolution has to leap before they really can make their case and this is one of them. I am sure we will find more of them and that is good science, not what is practiced today which is making definitive conclusions without any supporting data.

i see you are an advocate of good science. So am I. I see a good deal of very good science being done all the time, they even get Nobel prices. Just tell me, who are doing the good science these days, ID proponents or the despised mainstream scientists? Cabal

"You may want to have a look at this one:" I am certainly not qualified to evaluate this type of research but have advocating for quite awhile that it is exactly this type of research that will determine one way or the other whether de nove gene development by naturalistic means is a common occurrence or not. This type of analysis has to show positive results a couple thousand times before the naturalistic evolutionists will have a solid case. There are a lot of hurdles naturalistic evolution has to leap before they really can make their case and this is one of them. I am sure we will find more of them and that is good science, not what is practiced today which is making definitive conclusions without any supporting data. jerry

Jerry

One way to test the de novo theory is to track genes across classes and orders.

You may want to have a look at this one: Heinen TJ, Staubach F, Häming D, Tautz D.(2009): Emergence of a new gene from an intergenic region.Curr Biol 19(18):1527-31

It is generally assumed that new genes would arise by gene duplication mechanisms, because the signals for regulation and ranscript processing would be unlikely to evolve in parallel with a new gene function. We have identified here a transcript in the house mouse (Mus musculus) that has arisen within the past 2.5-3.5 million years in a large intergenic region. The region is present in many mammals, including humans, allowing us to exclude the involvement of gene duplication, transposable elements, or other genome rearrangements, which are typically found for other cases of newly evolved genes. The gene has three exons, shows alternative splicing, and is specifically expressed in postmeiotic cells of the testis. The transcript is restricted to species within the genus Mus and its emergence correlates with indel mutations in the 5' regulatory region of the transcript. A recent selective sweep is associated with the transcript region in M. m. musculus populations. A knockout in the laboratory strain BL6 results in reduced sperm motility and reduced testis weight. Our results show that cryptic signals for transcript regulation and processing exist in intergenic regions and can become the basis for the evolution of a new functional gene.

osteonectin

Olin-6:

If ID has no idea as to biological mechanism by your own advocates’ admission, how can it be science?

So Newtonian physics was not science because it had no mechanism for gravity? Cornelius Hunter

I have the same question: Where does ID say genes come from? What story, explanation or mechanism does ID have at all? Did genes just appear? When, and how did you know? How is that not a just-so story? If ID has no idea as to biological mechanism by your own advocates' admission, how can it be science? (There must be a means to come into existence, after all, as life didn't always exist.) olin

olin, I'm curious exactly where genes came from. Please no just-so stories. ellijacket

I’m curious if Cornelius Hunter could provide us with the mechanism that he as an intelligent design proponent proposes for this gene...

I don't know that Cornelius is claiming this gene was intelligently designed. What evidence do you have that he is? I certainly don't find any such claim in his article. Also, last time I checked, ID isn't "a mechanistic theory of desiqn." Why do you think it is? Lastly, so what if he has no mechanistic theory of design to offer. Does that make your theory correct? As Elliott Sober writes:

The lazy way to test a hypothesis H is to focus on one of its possible competitors H0, claim that the data refute H0, and then declare that H is the only hypothesis left standing.

An even lazier way to test a hypothesis is to claim that there is no "scientific" alternative to H, and then declare that H is the only hypothesis left standing. Sober:

This is an attractive strategy if you are fond of the hypothesis H but are unable to say what testable predictions H makes.

Mung

I'm curious if Cornelius Hunter could provide us with the mechanism that he as an intelligent design proponent proposes for this gene, or for that matter, any gene, and how it differs from the perspective of evolutionary biology. When did the designer generate T-urf13 (suddenly, over time, how many years ago, etc.), and what mechanism did the designer do? How do you distinguish this mechanism from the regular mutations and natural selection? Did the gene spontaneously appear in the whole population? After the proposal, I'd be interested in the evidence that the proposal is valid as well. olin

One way to test the de novo theory is to track genes across classes and orders. Their rise should be visible in like organisms with stubs in some and functioning ones in others if they arose naturally. There should be thousands of genes that different from genera to genera across wide spectrums of organisms. Genomic mapping of these in the near future will enable biologist to see where they could have possibly originated and if there is any naturalistic trace for the genes and the regulatory mechanisms in the various genomes. So in about 20-30 years we will have a good grip on the possible origin or non origin of genes. jerry

Evolutionists usually say that these resulted from the reuse of existing protein coding genes. For instance, we are able to see in color because the photocells in our retina contain different proteins that are sensitive to different colors of light.

Does this mean that evolutionary theory predicts a "nested hierarchy" of the genes within the genome of each species? Mung