Mud-to-Mozart Atheology (Or, Who are the real skeptics?)

_{GilDodgen
October 22, 2011

Intelligent Design

1}_{Categories
Intelligent Design}

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I find the “skeptic” claim on the part of Darwinian materialists very interesting and equally illuminating. Darwinists exhibit no skepticism whatsoever about the thesis that physical stuff turned into Mozart by chance. (Don’t try to deny this, Darwinists, that is the essence of your claim. You can try to obfuscate with legion “peer-reviewed scientific papers,” but you’re not going to fool me and many others about what you are actually promoting and advocating.)

I choose Mozart not just because I am a classical concert pianist, but because his existence epitomizes everything that Darwinian theory is totally powerless to explain.

Darwinists, claiming to be skeptics, actually exhibit the antithesis of skepticism — making transparently ludicrous claims and providing a never-ending stream of unsupported extrapolations, based only on wildly imaginative speculation with no empirical support.

How is it that Darwinian atheists are the only ones who get to declare themselves legitimate skeptics? Is mud-to-Mozart-by-chance philosophy the only worldview immune to skeptical inquiry?

Comments

DrBot: How would you consider sequences sharing less than 10% identity, and with different structures and functions?gpuccio_{October 26, 2011
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domains are well separated functional islands.
What methods did you use to determine this?DrBot_{October 26, 2011
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Why do they have to be functional? All that really matters is that they are not too detrimental.
And anyway, thank you for trying some answers. I appreciate that. I am not impressed, but at least you tried.
Thanks for your kind words - I'm not impressed by you either! ;)DrBot_{October 26, 2011
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DrBot: A precursor would be a domain intermediate between a previous existing domain and the new one, and functional. IOWs, some trace of a gradual transition. Instead, domains are well separated functional islands. And anyway, thank you for trying some answers. I appreciate that. I am not impressed, but at least you tried. Answers are always good, because thay can be discussed and tested.gpuccio_{October 26, 2011
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I still think it is amazing that 1800 protein domains originated in such a short evolutionary time.
Well one explanation would be that early replicators are likely to have had a much higher mutation rate - great for exploring protein space but bad because a high proportion of offspring would be non-viable. A selective advantage would exist for replicators that were better at reducing error rates, resulting in less exploration of protein space, and less discovery of new domains, but more offspring (and consequently less energy cost when reproducing). This could explain the high rated of domain discovery at first followed by reducing rates later.DrBot_{October 26, 2011
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The important point is that new domains appear throughout natural history, even if with constantly decreasing rate. The lack of known precursors is self-evident, but if you are aware of them, please let me know.
What would a precursor actually be? I would assume that it would be a gene sequence that was close to coding for a new stable domain, possibly being an existing domain itself.DrBot_{October 26, 2011
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Elizabeth: I quote that paper, indeed, for two different reasons. In the context of this last discussion, I was referring to it because: a) I had said: "The appearance of 4000 independent functional protein domains in the course of natural history, without any trace of precursors, certainly requires explanation." in response to some other person, and you asked: "Do you have a reference for this?" My answer: "For the appearance, I think there is much. I usually refer to the paper I have already linked. I do it again: http://www.plosone.org/article.....tation=PDF Please refer in particular to Table 1. For the lack of known precursors: I have been asking examples of precursors for years. Nobody has ever given one." So yes, for this discussion the paper is useful in the sense that it gives a cronological order of appearance of the domains, and allows us to determine where they appeared (in what beings). That was my reference for "The appearance of 4000 independent functional protein domains in the course of natural history". The important point is that new domains appear throughout natural history, even if with constantly decreasing rate. The lack of known precursors is self-evident, but if you are aware of them, please let me know. The second reason that I quote that paper (and I have done, with you) is that I find really amazing that more than half of those domains were already present in LUCA. Now, I understand all your discussion about LUCA, but you seem to underestimate a very simple concept: as far as we know, and according to what is currently believed, LUCA lived a lot of time ago, probably only a few hundred million years after the formation of earth, or at least the moment earth became compatible with life. IOWs, LUCA is not too distant from OOL, whenever it happened. I still think it is amazing that 1800 protein domains originated in such a short evolutionary time. And let's say there was a FUCA. It is still amazing that we have no trace of it. IOWs, it is really amazing that all the supposed evolution from a simple FUCA to a very complex LUCA, while generating such a trasure trove of protein information, apparantly happened without any fundamental separation of living beings, and that the first radical separation was that between archaea and bacteria. That's why I don't believe in FUCA. At the same time, I am all for a parsimonious theory of the emergence of protein domains. If some explanatory mechanism can be invoked for the span: OOL - LUCA, and the emergence of almost 2000 domains, there is no reason to think that another explanation should be invoked for the remaining domains that appeared after. IOWs, one explanation is the parsimonious choice. Either neodarwinian evolution, from OOL to LUCA and after. Or design. Guess my choice?gpuccio_{October 26, 2011
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I don't know what you mean by "Thew appearance of 4000 independent functional protein domains in the course of natural history, without any trace of precursors, certainly requires explanation." That paper derives a family tree in which the lineage in which each new protein domain first appears is given. Is your problem that there is no "precursor" to each new domain? Or is it that 1984 domains were already present in our Last Universal Common Ancestor? If the second, why is that especially a problem? It just means that being the Last Common Ancestor, we have no extant species with which we share an earlier ancestor! So by definition, with this technique, we can only go back as far as the last node. If, by amazing good fortune, we discovered some extant population of critters that with which all extant species had a lot in common, but which had protein domains not found in the current LUCA, and lacked protein domains found in the current LUCA, then the new postulated LUCA that included the new population would be an earlier organism than the current LUCA. In which case that 1984 would be revised downwards. Not that that is likely but there are still habitats unexplored on the earth's surface so it's possible. But my point is that the LUCA is only the LUCA of the sampling of lineages for which we have genetic evidence. That is a very small subset of all lineages, so we should certainly not expect the LUCA to be the LUCA of all the unknown lineages, and we should certainly expect there to be a rather large lump of accrued domains sitting at the LUCA, unless, indeed it was also the FUCA. In which case we might still expect to see that lump! But we certainly can't infer that it was!Elizabeth Liddle_{October 26, 2011
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uoflcard @ 24.1.1.1.4 "You’re right that you absolutely cannot falsify someone’s belief that something is designed." Therefore, ID is not science. It is a belief tacked onto science. "ID is defeated in this instance (even though it actually was designed!) because the inference to the best explanation results in a probabilistically viable natural explanation." Above, I reference a study showing a gene evolving by apparently natural processes, which are demonstrably random with respect to need. It creates a new functional protein. Is ID not defeated in this case because I've demonstrated a viable natural explanation for creation of new information? And secondly, where is the design inference? Is a long process, random with respect to need, comparable to human design? "You still cannot prove that I did not design the location of that sand granule, but you can refute an actual design inference based on available observations. If someone recorded me placing the granule there, then the design inference is satisfied." As I've said before, the design inference is without empirical support. Has anyone recorded the designer creating improbable amounts of information at once? I was chuckling at KF's "you weren't there" reply on the comment thread he closed. I was preparing a response, but I guess he wasn't wanting to hear it. "The problem with theistic evolution is that it is like trying to say the beach was designed even though it is 100% indistinguishable from a natural beach." And what did ID say about the gene above? Looks like 100% natural process that yielded new information, but nah, it must be designed? That is JoeG's approach it seems. Thats why it seems like in the details ID=TE. "It is a pointless assertion. I think many theistic evolutionists are unwitting ID advocates" Agreed, ID devolves to TE, and probably vice-versa. "I’ve heard many of them talk about “guided” evolution…that is ID". Yep. Same thing. Neither adds anything to the natural study of the history of life, just superfluous add-ons, like adding Pat Robertson's theory of Katrina to a meteorology class. Scientifically useless, divisive and silly.DrREC_{October 26, 2011
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Elizabeth: I fully agree with your 43.1.1.1.10 (I will never get accustomed to this kind of nested hyerarchy!). I would only rephrase the last sentence as follows: "That said, the evidence for Common Descent seems to me overwhelming enough, while the evidence for Darwinian evolution as an explanation of Common Descent is completely lacking!" By the way, my personla reason for believing in CD is, just to stay consistent, molecular. I don't love fossils and similar, but the pattern of homologies and differences between similar proteins in different species is very convincing, IMO, at least of some physical reutilization of the code in the development of design.gpuccio_{October 26, 2011
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No one disputes evolution is capable of adapting existing species. But evidence suggests it can’t do more than that. Evidence suggests that evolution is not powerful enough to produce new species.
What "evidence suggests that evolution is not powerful enough to produce new species"? And by "new species" do you the subdivision of a single population into two non-interbreeding populations, of which one may resemble the original population more closely than the other? In which case why not? The evidence from island populations seems very powerful in this regard. Or do you mean longitudinal functional change in a population that exceeds some threshold? In which case, what threshold?Elizabeth Liddle_{October 26, 2011
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Elizabeth: What is it that you don't understand? Table 1 lists the levels at which new domains emerge. 1984 out of 3464 are already present in LUCA (before separation of archaea and bacteria). 31 appear after in Archaea (13+14+4). 144 + 9 + 2 + 2... appear in bacteria And so on. For instance, the 492 listed as Eukaryota are domains specific to eukaryota, therefore more recent than the oroigin of Eukaryota, but not much more recent, because they are common to all of them. 58 new domains are common to all metazoa, and others originated later, in specific phyla (15, for example, common to chordata). There is no special interpretation. This is just a reasonable timeline of when new domains emerge in the proteome.gpuccio_{October 26, 2011
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I agree that natural selection has a stochastic component,
cool :)
but that does not change the dynamics: the selection is negative, elimination of some variants.
Selection is just heritable differential reproduction. Some new variants will result in phenotypes that reproduce better than the average of their peers, some worse. Those that reproduce better will tend to become more prevalent; those that reproduce worse will tend to become less prevalent. Most new variants will fare just the same as all the others, and may or may not be drift through the population. It isn't any truer to say "selection is negative" than to say "selection is positive". What there is is variance in reproductive success.
That leaves chance variation as what has to write the complex digital code we find in body plans.
Please let's leave "chance" out of it, for reasons you yourself gave! It leaves a probability distribution for what new variants will appear that is strongly biased in favour of variants that basically work. Within this narrow range of possible variants, the variants that actually occur, the probability of one that results in a successful body-plan variant (bilateral symmetry for example) may be quite high. If bilateral symmetry turns out to be advantageous, future variants will be highly constrained (i.e. not "random" in the common-or-garden sense) to variants on bilateral symmetry. Front and back ends, for instance. Now you have the beginning of hox genes. Rinse and repeat. But remember that what you are calling "Chance" is by no means an equiprobable draw. Genetic variants that are produced are highly constrained to produce phenotypic variants close to the already-successful parent variant. It's "Chance" as in drawing a three digit number from a barrel of tickets numbered 1 to 1000, not "Chance" as in drawing ticket number 327.Elizabeth Liddle_{October 26, 2011
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A specification is independent of the particular implementation, and defines a zone of interest T in the config space, where we find particular outcomes E; and, specifications can be deduced from reverse engineering and routinely are. Biofunction in particular ways is a valid specification, and demonstrably occurs in various ways since each organism within a species is an individual.kairosfocus_{October 26, 2011
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Chance circumstances and factors that follow stochastic patters do play a factor in many proceedings, so to say that chance variation and natural selection lead to descent with mods is a fair summary of the basic darwinian frame. I agree that natural selection has a stochastic component, but that does not change the dynamics: the selection is negative, elimination of some variants. That leaves chance variation as what has to write the complex digital code we find in body plans. Which simply does not add up. The dominant Darwinian Scheme may explain adaptations of varieties within body plans, but it does not properly explain the origin of basic body plans.kairosfocus_{October 26, 2011
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How would you know it is an ancient alien spacecraft, unless it resembles spacecraft constructed by humans? I ask this in all sincerity, because there are numerous stone formations cited as lost cities and such by some investigators. Many are controversial. When you encounter an ambiguous structure you have to ask if it has key features found on objects known to be made by humans or animals. At the same time you also ask if it resembles things formed by natural processes. Sometimes, as in the case of stone tools, there are disputes over interpretation. The problem with interpreting living populations as designed is that we have a candidate for a natural process that produces incremental change over time. We have no candidate for a designer capable of anticipating the results of sequence changes in DNA. The large numbers cited as as evidence of design also make anticipation of genetic change impossible. there simply isn't any way, even in principle, to anticipate changes in protein folding or regulatory sequences.Petrushka_{October 26, 2011
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"Chance" does not "drive" anything, kf. You made this point quite eloquently yourself recently. Chance is simply the word we use when something has a probability of less than one, given well-specified conditions (as most things do, in fact). Much better to talk of probability distributions. The probability distribution of mutations by selection coefficient is by no means flat. In other words mutations are not "random" in the common-or-garden sense at all. Near-neutral mutations are much more likely than extreme mutations, and extremely deleterious mutations, even if they happen, are very unlikely to propagate to many, if any, offspring. So "random mutation" is a misnomer. Mutations aren't "random" at all, but they are drawn from a non-flat probability distribution. Similarly, differential reproduction is neither "random" nor "non-random" in the common-or-garden sense either. An organism's probability of replicating may be slightly higher than average if, for example, it has better than average camouflage, but it could still be stamped on or drown. So both "rm" and "ns" are highly stochastic processes, and neither are "random" in the usual sense of the word. So even "blind" and "undirected" are poor words to describe "rm+ns". Variants that work are generated in preference to variants that don't (in other words the variance-generation mechanism isn't entirely blind, and favours variants that sort-of-work), and differential reproduction is biased in favour of phenotypes that manage to stay alive long enough to find a mate and breed successfully. Be careful the metaphors don't wag the dog.Elizabeth Liddle_{October 26, 2011
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What all these comparisons with found-objects (including Paley's watch) is that the found-objects don't reproduce themselves. Obviously if you find an object that looks designed to do something, then your first question is: what might it have been designed to do? And if it looks like an instrument of some sort, or an implement, you ask who might have used it to do that thing. But if it's a self-reproducing object, and it looks designed to enable itself to reproduce, you don't need to look for someone else who might have designed it for their own purposes, you can see straight away that it is of use to itself in the task of reproducing itself. Which means that it's capable of Darwinian evolution, because Darwinian evolution simply states the obvious that if a self-replicator replicates with heritable variation in reproductive success, variants that are best at reproducing themselves will become most prevalent. Now, it could still have been "intelligently designed", but that is no longer the only inference we can make. We now have an alternative mechanism - one tends to maximise reproductive success.Elizabeth Liddle_{October 26, 2011
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DrREC
You believe the gene presented above is designed. How would I falsify that? Be specific.
You're right that you absolutely cannot falsify someone's belief that something is designed. Say I'm on a beach and decide I want a specific grain of sand to rest in a certain location on the beach; I move it there, precisely as I wanted. Then you walk up. I say that the location of that grain of sand is designed. You do not believe me because you can show me that natural forces (wind, water, etc) are adequate explanations of such a phenomenon. ID is defeated in this instance (even though it actually was designed!) because the inference to the best explanation results in a probabilistically viable natural explanation. You still cannot prove that I did not design the location of that sand granule, but you can refute an actual design inference based on available observations. If someone recorded me placing the granule there, then the design inference is satisfied. The problem with theistic evolution is that it is like trying to say the beach was designed even though it is 100% indistinguishable from a natural beach. It is a pointless assertion. I think many theistic evolutionists are unwitting ID advocates. I've heard many of them talk about "guided" evolution...that is ID. Either it's guided or unguided; even if only 1% of its history was guided, it is still guided. They are saying it is at least somewhat guided, yet it is still 100% natural (i.e. unguided). It is simply self-contradictory.uoflcard_{October 26, 2011
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I have to say, I'm not understanding your interpretation of that paper.Elizabeth Liddle_{October 26, 2011
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Elizabeth: For the appearance, I think there is much. I usually refer to the paper I have already linked. I do it again: http://www.plosone.org/article/fetchObjectAttachment.action;jsessionid=254465B051A03F448EBEA7F8F4632837.ambra02?uri=info%3Adoi%2F10.1371%2Fjournal.pone.0008378&representation=PDF Please refer in particular to Table 1. For the lack of known precursors: I have been asking examples of precursors for years. Nobody has ever given one. About the number of basic protein domains, I want to make a clarification. I refer to numbers from the SCOP classification of the known proteome. You can give different numbers according to the level of definition, but essentially the concept is the same. So we have: Folds: 1195 Superfamilies: 1962 Families: 3902 Sequences with less than 10% identity: 6311 Sequences with evalue > 1: 6680 So, we have separated groups in a number of about 1195 - 6680, sequences completely separated in the sequence space, without any identity beyond random, and in most cases with no structural similarity.gpuccio_{October 26, 2011
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Elizabeth: We should not call “explanatory models” facts. Does that put us on the same page? Yes! Cool. :)gpuccio_{October 26, 2011
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Thew appearance of 4000 independent functional protein domains in the course of natural history, without any trace of precursors, certainly requires explanation.
Do you have a reference for this?Elizabeth Liddle_{October 26, 2011
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Elizabeth: I agree in general with much of what you say here. And still, I think that a separation between observables (facts) and inferences (theories) must be kept.
Yes indeed. My point is that they need to be rigorously ranked rather than separated, but in practice, at any given level, we can separate what is given (literally, "data") from what we infer (our model).
Let’s take a measure, for instance. It is true that it is an approximation, and it is true that it implies many concepts (such as the concept of number) that go well beyond the physical act of measuring. But still, the measuring is a fact, an observable. It is not an inference.
Sure, for all practical purposes, anyway. Though you ignore "measurement error" at your peril!
Inferences make statements about things that we are not certain of. Especially, they try to explain things. An explanation is never an observable. It is always an inference.
Well, no. Your measurement is still an inference, even though you have just called it a "fact". As it happened, I just measured the window embrasures in our spare bedroom in order to make extremely close-fitting acoustic baffles so that my son can practice his brand new souped-up drumkit in there! And I am very aware that "991mm" is an inference from the fact that my father and I measured it several times and got 990mm, 992mm, and 989mm. So I'm still being nickety pickety here. But I do agree that a "mean" or some other kind of summary value is only a "model" in a very specialist sense, and is not an "explanatory model". We should not call "explanatory models" facts. Does that put us on the same page?
So, with all the due attention to the problems you point to, I would definitely maintain a strict separation between facts and theories. One important point is: facts are not always certain. In a sense, facts are facts, and therefore real. But we must rememebr that we know facts thorugh observation. And our observation of facts is not always correct, or reliable. But explanatory theories are all another set of things.
We agree :) Cool.Elizabeth Liddle_{October 26, 2011
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GinoB: Common descent is a theory. A theory I agree with, but a theory just the same. Have you observed common descent of species? And universal common descent? Have you observed LUCA? Npo. Those are only inferences. Starting form many facts, an inference is made (a good inference, IMO), that living species we observe now are derived from a common ancestor. That is a theory.gpuccio_{October 26, 2011
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Yes, I think it is true that "neodarwinism" (still not sure what that means!) and "common descent" are conflated. Common descent is strongly indicated by the distribution of anatomical features in living things (if plants and bacteria can be said to have "anatomy). Evolutionary theory is model that explains the common descent model of that distribution. But evolutionary theory could also apply to, for example, a YEC model, in which Darwinian mechanisms apply to post-Ark radiation, but there is no universal common ancestor. Similarly, common design could explain nested hierarchies without invoking common descent. And ID could be a guiding factor in guiding evolution down the lineages from a universal common ancestor, without Darwin's theory having to be true. So falsifying Common Descent wouldn't falsify Darwinian evolution, nor would falsifying Darwinian evolution falsify Common Descent. That said, the evidence for Common Descent seems to me even more overwhelming than the pretty overwhelming evidence for Darwinian evolution as an explanation of Common Descent!Elizabeth Liddle_{October 26, 2011
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GinoB
The way archaeologists determine if a find is human produced (say a primitive stone ax) or just a natural rock is by comparing the object with other known human designed similar objects. Not superficial similarities, not analogies (like flagella and outboard motors) but actual known designed objects. They don’t just look at the rock itself but look for other signs of manufacture, things like specific chipping patterns, flint flakes, a work area where the tool was produced, and the source of the material. They also go to great lengths to identify the likely designer - who was living in the area at the time, what was their level of technology at the time, etc. The whole ID party line “it’s not about the designer, just the design” is one of the most intellectually vacuous bits of nonsense that’s ever come down the pike.
Archaeologists compare those items to known, like items and identify designers because they can. That information is readily available and there is plenty of evidence to make sound judgments on those types of things. To my knowledge, we have no physical evidence or observations for who the designer(s) could have been. I think ID skeptics say what you say (that it is "vacuous" to not address the identity of the designer) because you know it is currently impossible to do so without speculation or faith. But archaeologists DON'T need to know who the object came from or have other known designs of that specific type of object in order to declare an object designed. They can find any object, observe patterns that closely resemble those of a known human manufacturing method, and if no other sources of those patterns in the natural world are known (such as erosion, animal behavior, impacts, etc.) then they can infer design without any further knowledge. Inference to the best known explanation. The process does not stop there for archaeologists, of course, because they usually have other information they can work from, and identifying designers, uses, etc. is generally much more interesting to their field than simply identifying objects as natural or man made. It would be thrilling to be able to scientifically talk about the identity of the designer, but from our current observations that is not possible. That doesn't mean we can't infer design. Your assertion that that is intellectually vacuous is either willfully misrepresentative or carelessly ignorant. Unless you can explain why an archaeologist needs to know the identity of the people who created a tool in order say that the tool was designed, your assertions remain unsupported Imagine that we find an object deep in the Antarctic ice that is made from materials we've never seen, has seemingly specified contours and performs amazing activities like hovering, cold fusion, etc. We would have no idea how it was made, who made it or what it is for, but we would know that it was designed. So your asserted archaeological design-detection process would fail. (Note: I am not saying that this is ID, to just look at biology as see that it is obviously designed. I'm just pointing out the fallacy that is your made-up design-detection requirements of archaeologists.)uoflcard_{October 26, 2011
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Elizabeth: I agree in general with much of what you say here. And still, I think that a separation between observables (facts) and inferences (theories) must be kept. Let's take a measure, for instance. It is true that it is an approximation, and it is true that it implies many concepts (such as the concept of number) that go well beyond the physical act of measuring. But still, the measuring is a fact, an observable. It is not an inference. Inferences make statements about things that we are not certain of. Especially, they try to explain things. An explanation is never an observable. It is always an inference. So, with all the due attention to the problems you point to, I would definitely maintain a strict separation between facts and theories. One important point is: facts are not always certain. In a sense, facts are facts, and therefore real. But we must rememebr that we know facts thorugh observation. And our observation of facts is not always correct, or reliable. But explanatory theories are all another set of things.gpuccio_{October 26, 2011
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gpuccio
Luckily, that is irrelevant to this discussion about my integrity. Indeed, both neodarwinism and common descent (and, obviously, ID) are certainly theories, and not facts.
Wrong. "Neodarwinism" is a theory. Common descent is a fact. ID is an unsupported hypothesis. Don't play at science if you don't understand the terminology.GinoB_{October 26, 2011
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gpuccio
GinoB: From Wikipedia:
Exactly as I said, no one in the scientific community labels theories as facts. That only happens with ignorant laymen, or intellectually dishonest scoundrels with an agenda to push. Which one are you?GinoB_{October 26, 2011
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