From The First Gene, Chapter 9: “Inanimate nature … cannot scheme to locally and temporarily circumvent the 2nd Law.”

_{Denyse O'Leary

February 22, 2012

News, Origin Of Life}

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In The First Gene, David Abel’s Chapter 9 covers “Examining specific life-origin models for plausibility”:

Abstract: All models of life-origin, whether Protometabolism-First or pre-RNA / RNA World early informational self-replicative models, encounter the same dead-end: no naturalistic mechanism exists to steer objects and events toward eventual functionality. No insight, motive, foresight or impetus exists to integrate physicochemical reactions into a cooperative, organized, pragmatic effort.

Inanimate nature cannot pursue the goal of homeostasis; it cannot scheme to locally and temporarily circumvent the 2nd Law. This deadlock affects all naturalistic models involving hypercycles, composomes and chemotons. It precludes all spontaneous geochemical, hydrothermal, eutectic, and photochemical scenarios. It affects the Lipid, Peptide and Zinc World models. It pertains to Co-evolution and all other code-origin models.

No plausible hypothetical scenario exists that can convert chance and/or necessity into an organized protometabolic scheme. In this paper the general principles of previous chapters are applied to the best specific models of life origin in the literature. Tibor Ganti’s chemoton model and the pre-RNA and RNA World models receive more attention, as they are the most well-developed and preferred scenarios.

Here are the chapter topic heads:

Introduction: Every naturalistic life-origin model encounters the same great impasse 232
1. Cairns-Smith clay life 233
2. Silicon and Boron based life 234
3. Geochemical self-organization models 236
4. Protometabolism First Models 238
4.1 Composomes 239
4.2 Compartmentalization 240
4.3 The problem of sequencing 241
4.4 Hypercycles 241
4.5 Tibor Ganti’s well-developed chemoton model 242
5. Self-replicative, auto-catalytic, informational models 256
5.1 RNA World models 256
5.2 PreRNA World and RNA analogs 260
6. Early photosynthetic models 262
7. Code-origin models 264
8. Composome, Chemoton, and RNA evolution models would have been extremely 265
limited
9. Panspermia 269
10. Conclusions

Comments

Natural Selection Is Ubiquitous Higgs Particle? Dark Energy/Matter? Epigenetics? These Are YOK! Update Concepts-Comprehension… http://universe-life.com/2011/12/13/21st-century-science-whence-and-whither/ Evolution Is The Quantum Mechanics Of Natural Selection. The quantum mechanics of every process is its evolution. Quantum mechanics are mechanisms, possible or probable or actual mechanisms of natural selection. ================= Universe-Energy-Mass-Life Compilation http://universe-life.com/2012/02/03/universe-energy-mass-life-compilation/ A. The Universe From the Big-Bang it is a rationally commonsensical conjecture that the gravitons, the smallest base primal particles of the universe, must be both mass and energy, i.e. inert mass yet in motion even at the briefest fraction of a second of the pre Big Bang singularity. This is rationally commonsensical since otherwise the Big would not have Banged, the superposition of mass and energy would not have been resolved. The universe originates, derives and evolves from this energy-mass dualism which is possible and probable due to the small size of the gravitons. Since gravitation Is the propensity of energy reconversion to mass and energy is mass in motion, gravity is the force exerted between mass formats. All the matter of the universe is a progeny of the gravitons evolutions, of the natural selection of mass, of some of the mass formats attaining temporary augmented energy constraint in their successive generations, with energy drained from other mass formats, to temporarily postpone, survive, the reversion of their own constitutional mass to the pool of cosmic energy fueling the galactic clusters expansion set in motion by the Big Bang. B. Earth Life Earth Life is just another mass format. A self-replicating mass format. Self-replication is its mode of evolution, natural selection. Its smallest base primal units are the RNAs genes. The genesis of RNAs genes, life’s primal organisms, is rationally commonsensical thus highly probable, the “naturally-selected” RNA nucleotides. Life began/evolved on Earth with the natural selection of inanimate RNA, then of some RNA nucleotides, then arriving at the ultimate mode of natural selection, self-replication. C. Know Thyself. Life Is Simpler Than We Are Told The origin-reason and the purpose-fate of life are mechanistic, ethically and practically valueless. Life is the cheapest commodity on Earth. As Life is just another mass format, due to the oneness of the universe it is commonsensical that natural selection is ubiquitous for ALL mass formats and that life, self-replication, is its extension. And it is commonsensical, too, that evolutions, broken symmetry scenarios, are ubiquitous in all processes in all disciplines and that these evolutions are the “quantum mechanics” of the processes. Human life is just one of many nature’s routes for the natural survival of RNAs, the base primal Earth organisms. Life’s evolution, self-replication: Genes (organisms) to genomes (organisms) to mono-cellular to multicellular organisms: Individual mono-cells to cooperative mono-cells communities, “cultures”. Mono-cells cultures to neural systems, then to nerved multicellular organisms. Human life is just one of many nature’s routes for the natural survival of RNAs, the base Earth organism. It is up to humans themselves to elect the purpose and format of their life as individuals and as group-members. Dov Henis (comments from 22nd century) An Embarrassingly Obvious Theory Of Everything http://universe-life.com/2011/12/10/eotoe-embarrassingly-obvious-theory-of-everything/Dov Henis_{April 27, 2012
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I’ve now gone through most of Pross’ paper (2005) Stability in chemistry and biology: Life as a kinetic state of matter. In an attempt to keep this at least mercifully brief, I will just summarize what I’ve found. (If it is too big for a comment and needs a thread, I’ll leave that to the moderators.) 1. Pross recognizes the validity of the thermodynamic issue that has been raised against spontaneous generation of living systems from non-living matter. It is unclear to me whether his use of the word “thermodynamic” is completely consistent or accurate throughout the paper, but he understands and accepts that it is a live issue. It is assumed throughout his paper as the underlying problem he is trying to address, and one passage in particular makes the point:
. . . living systems are far-from-equilibrium systems that must constantly tap into some external source of energy in order to maintain that far-from-equilibrium state. Failure to obtain a continuing supply of energy necessarily leads the animate system toward equilibrium—to death. Inanimate systems on the other hand, though not necessarily in an equilibrium state, do at all times tend toward that lower Gibbs energy state. Clearly, the thermodynamic pattern of behavior expressed by animate as opposed to inanimate systems is quite different and raises the question as to how, from a thermodynamic point of view, the emergence of energy-consuming, far-from-equilibrium systems would arise in the first place.
I would add that it is not just that living systems tap into external sources of energy, but that they are capable of using that energy in just the right way. But in any event, Pross acknowledges it is a real issue and that it raises a real question, in contrast to many evolutionists’ quick dismissal of the thermodynamic issue as a non-issue, as a creationist talking point, or as being solved by the silly “open-system” argument. I don’t happen to think the thermodynamic issue is as important as information, for example, but it is a real issue and needs to be acknowledged as such. 2. Pross does not claim that he has found a way to overcome the thermodynamic issue per se. Rather, what he claims is that thermodynamics becomes a minor player to the “kinetic” considerations he is proposing, as discussed below. Thermodynamics is thus held at bay or overcome by kinetics, in other words. 3. Pross builds his ideas on a “replication first” model. In short, the model is that at some point a molecule of inanimate matter gained the ability to self-replicate. It self-replicated with variation. That variation led to greater complexity. That complexity turned to systems and eventually to the point where it could be considered “alive.” Pross contrasts this view with that of the “emergent property” school of thought, a la Kauffman, and states that emergence is not a viable answer. He also dismisses panspermia because it simply relocates the problem to another location. My estimation is that Pross’ view – the replication-first view – is probably the most common view among proponents of abiogenesis. For example, Szostak's lab at Harvard is specifically operating under this assumption. 4. Pross should be commended for laying out his assumptions up front, which he does in some detail. The most telling, for purposes of this thread and Abel’s work, is the following:
Our second base assumption is to presume that the existing laws of physics and chemistry can explain the process of complexification that inanimate matter must have undergone in order to have generated chemical systems with the unusual characteristics mentioned above. After all, living beings are nothing more than physicochemical systems, so it seems reasonable to believe that the existing laws of physics and chemistry, which account satisfactorily for all other known physicochemical processes, should be able to account for the emergence of living systems as well.
Well, that is the $64,000 question, isn’t it!? Pross’ work, by definition, does not address ID proponents’ challenge to the ability of natural laws to create life without intelligent input, because Pross doesn’t address the issue – indeed, he assumes it away. I’m not necessarily faulting Pross on this point. His paper is intended to address a separate issue: thermodynamics. But it is important to keep our eye on the ball here so that we understand what is demonstrated and what is assumed. There are additional interesting quotes on this theme, but the above will suffice. 5. Pross develops his concept of “kinetic stability” as a term that he can apply to populations of replicators (either single molecules or organisms). His basic idea is that, yes, thermodynamics tends to drive inanimate systems to a stable state, but that something else drives replicating systems to a different stable state. And what stable state would that be? Well, Pross adopts Dawkins’ argument that “stable” means “persistent, unchanging with time.”
Dawkins goes on to point out that the Darwinian principle, survival of the fittest, then just becomes a special case of that broader law since fit individuals and fit species are more likely to survive, and therefore to persist.
In other words, Pross argues, “stability” in the living realm is equated with “survival of the fittest.” If at this point, it seems to you that Pross has gone off the rails, you are not alone. This is simply a rhetorical exercise of re-labeling “survival of the fittest” with the term “stability.” Then the magic begins. 6. Pross argues that because survival of the fittest of replicating organisms (or early molecules) represents a kind of “stability,” populations can continue to thrive and replicate at such stability, indeed, will even tend toward that stability. In other words, although inanimate systems tend toward thermodynamic stability, living replicating systems tend to continue living and replicating (i.e., tend toward Pross’ and Dawkins’ concept of stability). This is, unfortunately, a non-substantive labeling exercise. What causes the organism to replicate? What controls the replication reactions? What determines the timing and frequency of the replication? All we’ve done really is redefine successful “replication” to mean “stability.” 7. Pross’ idea seems to have credence only insofar as the biological details remain sufficiently vague. Indeed, there are some statements that appear simply incorrect from a biological standpoint. Pross may be forgiven for referring to the hypothetical first self-replicating molecule (can anyone point me to a self-replicating molecule?), but it seems even less appropriate for him to discuss a phage or virus as a two-part “replicating system.” He later acknowledges that “the cell’s replication machinery is then taken over” for the virus to propagate, but it doesn’t seem to sink in how important it is that embedded in this cellular machinery is a whole suite of systems, controls, translation machinery, software protocol hierarchies, and so on. 8. Pross further acknowledges that his phage example “is only applicable in a biotic environment where the phage can exploit the metabolic and replicative machineries of its host cell.” What relevance would this have to a pre-biotic world? Well, let’s just assume it is relevant!
We have provided an example from a biotic environment because that is the environment we are familiar with! Clear examples from prebiotic times would be somewhat harder to produce! We would argue however that the symbiotic principle that forms the basis of the example would apply in any environment—biotic or abiotic. For replicating systems, any process of self-assembly that leads to the formation of kinetically stable aggregates would be kinetically selected.
There is much here to critique, but let’s just parse that last reference. What does it mean to be “kinetically selected?” As near as can be ascertained, this simply refers back to the idea that organisms that effectively replicate (i.e., are “stable” populations under Dawkins or Pross) will be selected. Selected, of course, in the sense of “survival of the fittest,” which a la Dawkins, means the population is “stable.” If this seems to you an exercise in circularity, you are not far off. 9. One of the most astounding statements in the paper, however, is the following:
The pioneering work of Orgel and von Kiedrowski demonstrated that single-molecule replication is not a facile process and attempts to carry out such reactions without enzymatic catalysis have met with only limited success—molecular replicators tend to be kinetically unstable. By comparison, complex replicators (e.g., bacteria) display remarkably high kinetic stability and replicate prodigiously under highly variable conditions, including those considered extremely hostile, with no need for a sophisticated laboratory or human direction. Thus, the fact that complex replicators are generally kinetically more stable than simple ones, would mean that successful transitions in replicator space would tend to be those that lead to an increase in complexity, that is, the (effective) kinetic driving force tends to transform less stable replicators that are simpler, into more stable ones that are complex.
Did you catch the logic? If you need to re-read that quote, please do. The assertion is that because we don’t have good examples of simple replicators (especially that elusive self-replicating molecule), but we do have lots of examples of complicated replicators, then obviously complicated replicators are more successful at replicating. This in turn means, if you allow us to throw in our new definitions, complicated replicators are more "stable," in which case, replicating systems do tend toward complication and, therefore, stability. Thus there is no violation of thermodynamic concerns. I’m trying to think of a charitable way to characterize all this . . . The paper continues in a similar vein and we could labor the point, but this is already too long and covers the essentials. In Sum Deapite the title of the paper, Pross has not identified any new property of matter. He has not identified any new form of organizational structure. He has not identified any law of physics or chemistry that would cause the first replicator to form. He has not identified any engine to drive the wheels of change and development. He has not addressed the fundamental issues of information content and control. Once we strip away the new terminology and focus on the real substance there isn’t much to go on. In essence, what Pross has done is (i) take the general concept of “survival of the fittest,” (ii) re-label it to mean “stability,” (iii) apply this concept of “stability” to molecular systems and label it “kinetic stability,” and (iv) argue that because these systems are “stable” the law of thermodynamics is overcome and not violated in the case of replicating living systems. This is interesting. Not interesting in a scientific sense, mind you, but interesting in the sense of a couple of friends throwing out ideas over drinks at the pub after work. We’ll perhaps hear some more about this “kinetic” idea of life in the future and I wish Pross well in his efforts. Just don’t hold your breath waiting for anything meaningful to come of it. ----- For the Onlookers: This has been an interesting experience the past day or two, and one that has been replicated numerous times in the past on this site and others. Specifically, some very cogent and serious issues have been raised with respect to many aspects of evolutionary theory, perhaps particularly in the origin of life area. One of the most time-worn (and annoying) tactics of evolutionary proponents in responding to these cogent criticisms is to (i) accuse critics of being “out of touch with the literature” and then (ii) throw out a literature bluff – a citation or several citations of papers that allegedly address the issue. This literature bluff tactic is a particular favorite of Nick Matzke, who has regularly employed it on this site. He generally sees a post, does a quick PubMed or similar search, finds a couple of articles that include the relevant terms in the abstract (in this case “evolution” “thermodynamics”, etc.), and then throws the articles over the transom to see what will stick, with the obligatory sniff-and-stick-the-nose-in-the-air accusation that people aren’t up on the latest literature. In the present case, the abstract Nick quoted from Pross and the more up-to-date article I reviewed above, turned out to be yet another literature bluff. Pross’ idea is interesting in some minor facets, but doesn’t even come close to addressing the issues Abel raises. Nick would have known that if he had read Pross’ work. Or perhaps he does know, but just likes to pull our chain, as has been done so many times in the past. The reality is that the issues raised by ID proponents (and many critics of evolutionary theory who don't hold to ID) relating to information content, digital coding, translation mechanisms, cybernetic controls and the like are so critical and so fundamental that if there were good materialistic answers to them you can be sure the answers would be shouted from the rooftops with Nobel prizes showering down far and wide, not contained in an old paper in some obscure journal archive.Eric Anderson_{February 28, 2012
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Folks: The basic problem being dodged on this one is that with cell based life, we are dealing with a von Neumann self replicator, involving:
(i) an underlying storable code to record the required information to create not only (a) the primary functional machine [[here, for a "clanking replicator" as illustrated, a Turing-type “universal computer”; in a cell this would be the metabolic entity that transforms environmental materials into required components etc.] but also (b) the self-replicating facility; and, that (c) can express step by step finite procedures for using the facility; (ii) a coded blueprint/tape record of such specifications and (explicit or implicit) instructions, together with (iii) a tape reader [[called “the constructor” by von Neumann] that reads and interprets the coded specifications and associated instructions; thus controlling: (iv) position-arm implementing machines with “tool tips” controlled by the tape reader and used to carry out the action-steps for the specified replication (including replication of the constructor itself); backed up by (v) either: (1) a pre-existing reservoir of required parts and energy sources, or (2) associated “metabolic” machines carrying out activities that as a part of their function, can provide required specific materials/parts and forms of energy for the replication facility, by using the generic resources in the surrounding environment. Also, parts (ii), (iii) and (iv) are each necessary for and together are jointly sufficient to implement a self-replicating machine with an integral von Neumann universal constructor.
The existence of carefully set up autocatalytic reaction sets does not answer to the origin of such an irreducibly complex entity. In short, this is a case of the two drunks. A: what are you looking for? B: My contact lenses. A: Let me help. { . . . 1/2 hr passes) A: Are you sure you lost them here? B: No, I lost them over there in the dark, but this is where the light is. KFkairosfocus_{February 28, 2012
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Thanks, kuartus. I've downloaded the paper and it looks to be somewhat interesting. Will take a while to go through, but hopefully in the next few days. However, as far as origin of life goes (the subject of this thread), I'm not too optimistic. The abstract doesn't give me much confidence (again, I'll see what the rest of the paper says).Eric Anderson_{February 27, 2012
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Sorry, wrong link. Here it is: www.bgu.ac.il/~pross/PDF-6%20PAC.pdfkuartus_{February 27, 2012
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Eric Anderson @36 I found a paper which expains more clearly the authors view of how he thinks kinetic stability relates to lifes origins. Here is the link: www.bgu.ac.il/~pross/PDF6%20PAC.pdfkuartus_{February 27, 2012
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Nick Matzke @19: Thanks for the link. I didn’t look into this carefully enough and thought the abstract was referring to classical physics kinetics, which I see was my bad. I therefore withdraw my comment #10, which was obviously too hasty. However, I don’t see how Pross’ paper is at all helpful. The head post to this thread quoted Abel as saying, in sum:
. . . no naturalistic mechanism exists to steer objects and events toward eventual functionality . . .

No plausible hypothetical scenario exists that can convert chance and/or necessity into an organized protometabolic scheme.
Part, though by no means all, of Abel’s argument appears to rest on his assessment of the inability of inanimate nature to, as he says, “pursue the goal of homeostasis; it cannot scheme to locally and temporarily circumvent the 2nd Law.” Now, with that thermodynamic issue in mind, you have offered the Pross article, which builds on “Eigen’s ‘replication first’ model for life’s emergence.” Pross suggests that he is providing a new framework for “understanding life’s evolutionary driving force.” This driving force, according to Pross, can be summarized as “the kinetic consequences of autocatalysis operating on specific biopolymeric systems.” So the basic approach is this: (i) we have a biopolymer (let’s set aside for a moment how it came to exist), (ii) the biopolymer is involved in a chemical reaction, with the help of a catalyst, (iii) the reaction produces, in part, the catalyst (thus, autocatalysis), (iv) the reaction occurs at a particular rate (the “kinetic” part of the chemistry), and (v) because the reaction produces the catalyst that catalyzed the reaction in the first place the reaction can continue apace with a new biopolymer and/or even increase its rate if the original catalyst is not altered in the particular process and can be re-used. Can anyone please explain how any of this could conceivably solve the thermodynamic/entropy issue that Pross acknowledges exists? What is it about autocatalysis and reaction rates that can possibly solve the problem? If what Pross is arguing is that because autocatalysis produces the very catalyst needed to perform the reaction in the first place, then fine, I’m on board with that. And in that sense, we could hypothesize that, given enough raw material, a particular reaction could continue to take place at a certain rate or even an increasing rate (the kinetic part of the theory). But there are two fundamental problems with this idea. First, the catalyst simply facilitates (typically by speeding up) the reaction. The reaction could occur without it, it would just take longer, so all we’ve done is buy time, I haven’t changed anything fundamental about the replication process or the evolving or any of that. Second, the reaction continues, either linearly or exponentially, until it runs out of raw material. But I can get the same result from a forest fire. Again, whether the reaction rates are maintained or increased doesn’t tell us anything about what controls the rate or maintains a stable state. No-one is arguing that catalysts aren’t involved in life’s reactions. They obviously are. No-one is arguing that life has the ability to temporarily beat back the incessant march of entropy. It of course does; that is one of its most interesting features. But to suggest that reaction rates and autocatalysis have, of themselves, resolved the issue is absurd. For the record, I don’t think Pross is suggesting this much. He seems to be simply saying that some autocatalytic reactions can temporarily overcome classical thermodynamic considerations. If that is all he is saying, fine. I don’t disagree. But I also don’t think it is relevant to the question of life’s origin or subsequent diversification. Pross’ abstract summarizes by saying “the replication reaction is an extreme expression of kinetic control.” It's not real clear what this means, but yeah, OK. But wait a minute, what provides the control? There must be some kind of mechanism (apart from the pure chemical reactions and reaction rates) that provides this “extreme” control. What provides this control? Pross doesn't say. And that is part of Abel's point about mechanistic origins theories. Finally, Pross ends with a cute word play on natural selection:
Darwin’s principle of natural selection: that living things replicate, and therefore evolve, may be phrased more generally: that certain replicating things can evolve, and may therefore become living.
In essence, this is just a restatement of the ‘replication-first’ idea: we have some polymers that start to replicate, and they slowly evolve to add new features, and then one bright day they have added so many features that they are considered living. It is not at all clear how taking note of chemical reaction rates – important as they are – has any relevance to inanimate matter’s ability to come together in the right way, replicate, evolve, and become living. Incidentally, I would also note that in proposing his new “replicative chemistry” Pross acknowledges that the thermodynamic issue and increasing entropy is a live problem for the evolutionary process and an active area of debate. So it is strange to hear people still deriding the entire issue as some “creationist” nonsense. I applaud Pross for trying to come up with a solution, but his “replicative chemistry” does not appear to provide any meaningful answer to the thermodynamic issue Pross acknowledges exists. It is even further from addressing the other critical issues of information content and control, which I consider to be more central than thermodynamics. ----- Nick: “Life is a kinetically-dominated process, not a thermodynamically-dominated one.” Life is dominated by chemical reaction rates? Yeah, sure, whatever. What does this even mean? There is nothing in chemistry -- kinetic or otherwise -- that even begins to explain the origin of living systems. Nick, I may be wrong, but it appears that you saw this thread, did a quick PubMed search, and then threw out a paper that included some of the key terms in the abstract (evolution, thermodynamics), but which doesn’t actually address the well-known problems with origin of life scenarios, including those issues raised by Abel. I am sure that Pross is doing great science and that his work can add to our understanding of biochemistry. But, based on his abstract, I don’t think his paper demonstrates what you claim it demonstrates (or rather, what you implied, but purposely did not explicitly state, it claims). It sure feels like another one of your all-too-common literature bombs (although, mercifully, a small one).Eric Anderson_{February 27, 2012
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Michael Behe on Falsifying Intelligent Design - video http://www.youtube.com/watch?v=N8jXXJN4o_Abornagain77_{February 26, 2012
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The following may have been updated: Irreducible Complexity:
IC- A system performing a given basic function is irreducibly complex if it includes a set of well-matched, mutually interacting, non-arbitrarily individuated parts such that each part in the set is indispensable to maintaining the system’s basic, and therefore original, function. The set of these indispensable parts is known as the irreducible core of the system. Page 285 NFL

Numerous and Diverse Parts If the irreducible core of an IC system consists of one or only a few parts, there may be no insuperable obstacle to the Darwinian mechanism explaining how that system arose in one fell swoop. But as the number of indispensable well-fitted, mutually interacting,, non-arbitrarily individuated parts increases in number & diversity, there is no possibility of the Darwinian mechanism achieving that system in one fell swoop. Page 287

Minimal Complexity and Function Given an IC system with numerous & diverse parts in its core, the Darwinian mechanism must produce it gradually. But if the system needs to operate at a certain minimal level of function before it can be of any use to the organism & if to achieve that level of function it requires a certain minimal level of complexity already possessed by the irreducible core, the Darwinian mechanism has no functional intermediates to exploit. Page 287
Dr Behe responds to IC criticisms:
One last charge must be met: Orr maintains that the theory of intelligent design is not falsifiable. He's wrong. To falsify design theory a scientist need only experimentally demonstrate that a bacterial flagellum, or any other comparably complex system, could arise by natural selection. If that happened I would conclude that neither flagella nor any system of similar or lesser complexity had to have been designed. In short, biochemical design would be neatly disproved.- Dr Behe in 1997
Joe_{February 26, 2012
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NickMatzke:
IDists assert that SC cannot evolve.
No, Nick. IDists say that blind and undirected processes cannot produce IC- and that does not refer to all IC because it is clear that a two-part configuration would be IC.
IDists also assert that IC is a form of SC. Therefore, if IC can evolve, then SC can evolve. It could still be that some SC cannot evolve for other reasons, but being SC isn’t the reason, since that generalization has been falsified.
See above. As for your "evidence" similarities does not = evolution. And again it does not say that blind and undirected processes didit. Your whole problem is that you just refuse to understand what Intelligent Design is and you have some straw man version that you keep refuting. That nonsensical act does not fly on a Pro-ID blog- it may fly amongst your evobuds, but here it is a joke.Joe_{February 26, 2012
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Nice line about Chewbacca, Nick.Aleta_{February 26, 2012
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Moreover, for whatever 'transposon' processes you listed, it seems readily apparent to me that the processes are NOT neo-Darwinian processes, in that they are not 'random variations:
Revisiting the Central Dogma in the 21st Century - James A. Shapiro - 2009 Excerpt (Page 12): Underlying the central dogma and conventional views of genome evolution was the idea that the genome is a stable structure that changes rarely and accidentally by chemical fluctuations (106) or replication errors. This view has had to change with the realization that maintenance of genome stability is an active cellular function and the discovery of numerous dedicated biochemical systems for restructuring DNA molecules.(107–110) Genetic change is almost always the result of cellular action on the genome. These natural processes are analogous to human genetic engineering,,, (Page 14) Genome change arises as a consequence of natural genetic engineering, not from accidents. Replication errors and DNA damage are subject to cell surveillance and correction. When DNA damage correction does produce novel genetic structures, natural genetic engineering functions, such as mutator polymerases and nonhomologous end-joining complexes, are involved. Realizing that DNA change is a biochemical process means that it is subject to regulation like other cellular activities. Thus, we expect to see genome change occurring in response to different stimuli (Table 1) and operating nonrandomly throughout the genome, guided by various types of intermolecular contacts (Table 1 of Ref. 112). http://shapiro.bsd.uchicago.edu/Shapiro2009.AnnNYAcadSciMS.RevisitingCentral%20Dogma.pdf
bornagain77_{February 26, 2012
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Nick you state that IC (Irreducible Complexity) CAN evolve, yet I know of not one example of a molecular machine being evolved from scratch. For you to claim that these machines can evolve without actually demonstrating the origination of such a IC molecular machine from scratch, by purely neo-Darwinian processes, is certainly begging the question. Exactly why should I, or anyone else, take your thousands upon thousands of words that any IC system can evolve without you, or anyone else, actually physically evolving one by neo-Darwinian processes??? It is simply ludicrous beyond belief for you to be so dogmatic, not to mention 'unscientific': Notes: In spite of the fact of finding molecular motors permeating the simplest of bacterial life, there are no detailed Darwinian accounts for the evolution of even one such motor or system.
"There are no detailed Darwinian accounts for the evolution of any fundamental biochemical or cellular system only a variety of wishful speculations. It is remarkable that Darwinism is accepted as a satisfactory explanation of such a vast subject." James Shapiro - Molecular Biologist
The following expert doesn't even hide his very unscientific preconceived philosophical bias against intelligent design,,,
‘We should reject, as a matter of principle, the substitution of intelligent design for the dialogue of chance and necessity,,,
Yet at the same time the same expert readily admits that neo-Darwinism has ZERO evidence for the chance and necessity of material processes producing any cellular system whatsoever,,,
,,,we must concede that there are presently no detailed Darwinian accounts of the evolution of any biochemical or cellular system, only a variety of wishful speculations.’ Franklin M. Harold,* 2001. The way of the cell: molecules, organisms and the order of life, Oxford University Press, New York, p. 205. *Professor Emeritus of Biochemistry, Colorado State University, USA Michael Behe - No Scientific Literature For Evolution of Any Irreducibly Complex Molecular Machines http://www.metacafe.com/watch/5302950/ “The response I have received from repeating Behe's claim about the evolutionary literature, which simply brings out the point being made implicitly by many others, such as Chris Dutton and so on, is that I obviously have not read the right books. There are, I am sure, evolutionists who have described how the transitions in question could have occurred.” And he continues, “When I ask in which books I can find these discussions, however, I either get no answer or else some titles that, upon examination, do not, in fact, contain the promised accounts. That such accounts exist seems to be something that is widely known, but I have yet to encounter anyone who knows where they exist.” David Ray Griffin - retired professor of philosophy of religion and theology
further notes: List and videos of specific molecular machines
Bacterial Flagellum - A Sheer Wonder Of Intelligent Design - video http://www.metacafe.com/watch/3994630 The ATP Synthase Enzyme - exquisite motor necessary for first life - video http://www.youtube.com/watch?v=W3KxU63gcF4 Powering the Cell: Mitochondria - video http://www.youtube.com/watch?v=RrS2uROUjK4 Molecular Machine - Nuclear Pore Complex - Stephen C. Meyer - video http://www.metacafe.com/watch/4261990 Kinesin Linear Motor - Video http://www.youtube.com/watch?v=kOeJwQ0OXc4 Ribosome Translation High Quality - video http://pubs.acs.org/cen/multimedia/85/ribosome/translation_bacterial.html Myosin - video http://www.youtube.com/watch?v=j8F5GGPACkQ
The following article has a list of 40 (yes, 40) irreducibly complex molecular machines in the cell:
Molecular Machines in the Cell - http://www.discovery.org/a/14791
bornagain77_{February 26, 2012
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Joe says:
YOU said that IC is a SPECIAL CASE of SC. So that does not mean if you refute IC that you have refuted SC, just that special case.
Um, no. IDists assert that SC cannot evolve. IDists also assert that IC is a form of SC. Therefore, if IC can evolve, then SC can evolve. It could still be that some SC cannot evolve for other reasons, but being SC isn't the reason, since that generalization has been falsified. Joe says:
No one knows how any immune system evolved. There isn’t any way to test any of the speculations pertaining to that subject.
...completely ignoring the evidence of just such testing that was presented:
The timing for the criticism could not have been worse, as soon after publication of Darwin’s Black Box, solid evidence for the transposon hypothesis began accumulating with the demonstration of similarities between the variable-diversity-joining recombination and transposition mechanisms16 and also between shark RAG1 and certain bacterial integrases17. Since then, a steady stream of findings has continued to add more substance to the model, as RAG proteins have been shown to be capable of catalyzing transposition reactions, first in vitro18, 19 and then in vivo20, 21, 22, and to have even closer structural and mechanistic similarities with specific transposases23. Finally, in 2005, the original key prediction of the transposon hypothesis was fulfilled with the identification of a large invertebrate transposon family bearing both recombination signal sequence–like integration sequences and a RAG1 homolog24.
See original for links to the cited papers. In places like Nature. *This* behavior of determined ignorance -- of totally uninformed, yet brazenly confidence opposition to mainstream science -- is why you ID guys are never going to be taken seriously in science. You might as well go to a Star Wars convention and start yelling to people that Chewbacca doesn't have any hair.NickMatzke_UD_{February 26, 2012
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Hi NickMatzke:
2. You apparently don’t know the difference between a claim about an evolution-like-process working in the current operation of today’s adaptive immune system, and a claim about how the adaptive immune system evolved. I was talking about the latter, your rebuttals are mostly about the former. How can we even discuss something if you just toss random unrelated links around? Why should any scientist take you seriously?
No one knows how any immune system evolved. There isn't any way to test any of the speculations pertaining to that subject.
Dembski and other IDists have stated that irreducible complexity is a special case of specified complexity. If Behe is wrong about IC, then Dembski et al. are wrong about specified complexity.
That does not follow. What level is your education that you would say such a thing? YOU said that IC is a SPECIAL CASE of SC. So that does not mean if you refute IC that you have refuted SC, just that special case. However you are far from refuting IC, and you don't have any idea of how to even go about doing such a thing.Joe_{February 26, 2012
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The following describes how quantum entanglement is related to functional information:
Quantum Entanglement and Information Excerpt: A pair of quantum systems in an entangled state can be used as a quantum information channel to perform computational and cryptographic tasks that are impossible for classical systems. http://plato.stanford.edu/entries/qt-entangle/
Anton Zeilinger, a leading researcher in Quantum mechanics, relates how quantum entanglement is related to quantum teleportation in this following video;
Quantum Entanglement and Teleportation – Anton Zeilinger – video http://www.metacafe.com/watch/5705317/
A bit more detail on how teleportation is actually achieved, by extension of quantum entanglement principles, is here:
Quantum Teleportation Excerpt: To perform the teleportation, Alice and Bob must have a classical communication channel and must also share quantum entanglement — in the protocol we employ*, each possesses one half of a two-particle entangled state. http://www.cco.caltech.edu/~qoptics/teleport.html
And quantum teleporation has now shown that atoms, which are suppose to be the basis from which ALL functional information ‘emerges’ in the atheistic neo-Darwinian view of life, are now shown to be, in fact, reducible to the transcendent functional quantum information that the atoms were suppose to be the basis of in the first place!
Ions have been teleported successfully for the first time by two independent research groups Excerpt: In fact, copying isn’t quite the right word for it. In order to reproduce the quantum state of one atom in a second atom, the original has to be destroyed. This is unavoidable – it is enforced by the laws of quantum mechanics, which stipulate that you can’t ‘clone’ a quantum state. In principle, however, the ‘copy’ can be indistinguishable from the original (that was destroyed),,, http://www.rsc.org/chemistryworld/Issues/2004/October/beammeup.asp Atom takes a quantum leap – 2009 Excerpt: Ytterbium ions have been ‘teleported’ over a distance of a metre.,,, “What you’re moving is information, not the actual atoms,” says Chris Monroe, from the Joint Quantum Institute at the University of Maryland in College Park and an author of the paper. But as two particles of the same type differ only in their quantum states, the transfer of quantum information is equivalent to moving the first particle to the location of the second. http://www.freerepublic.com/focus/news/2171769/posts
Thus the burning question, that is usually completely ignored by the neo-Darwinists that I’ve asked in the past, is, “How can quantum information/entanglement possibly ‘emerge’ from any material basis of atoms in DNA, or any other atoms, when entire atoms are now shown to reduce to transcendent quantum information in the first place in these teleportation experiments??? i.e. It is simply COMPLETELY IMPOSSIBLE for the ’cause’ of transcendent functional quantum information, such as we find on a massive scale in DNA and proteins, to reside within, or ever ‘emerge’ from, any material basis of particles!!! Despite the virtual wall of silence I’ve seen from neo-Darwinists thus far, this is not a trivial matter in the least as far as developments in science have gone!!
Does Quantum Biology Support A Quantum Soul? – Stuart Hameroff - video (notes in description) http://vimeo.com/29895068
It is very interesting to point out that even though 'transcendent' quantum entanglement/computation/information is found in molecular biology, on a massive scale, scientists are having a extremely difficult time achieving even the first tiny steps of quantum entanglement in machines, even though the payoff, and investment, is huge!;
Quantum life: The weirdness inside us - 03 October 2011 by Michael Brooks Excerpt: "It sounds harsh but we haven't learned a thing apart from the obvious." A better understanding of what is going on might also help us on the way to building a quantum computer that exploits coherent states to do myriad calculations at once. Efforts to do so have so far been stymied by our inability to maintain the required coherence for long - even at temperatures close to absolute zero and in isolated experimental set-ups where disturbances from the outside world are minimised. http://www.newscientist.com/article/mg21128321.500-quantum-life-the-weirdness-inside-us.html?full=true Physicists Entangle 8 Photons in 'Spooky' Experiment - February 2012 Excerpt: Entanglement is a fragile state, and entangling photons with any efficiency is a major challenge; physicists generally produce a huge number of photons for every pair of successfully entangled particles. The difficulty of creating multiple pairs of entangled photons grows exponentially as more are added. Xing-Can Yao and his colleagues at USTC calculated that if they simply extended previous six-photon experiments to include another pair of entangled photons, it would take roughly 10 hours of experimental time to generate one entangled eight-photon set. (Physicists verify the presence of entanglement by running statistical tests that require large samples of photons, so an experiment that takes hours to produce a single entangled state is impractically slow.) To overcome that limitation, the researchers used an optical scheme that filters out fewer photons and hence boosts the output of entangled photons. http://www.livescience.com/18504-quantum-entanglement-photons.html
And despite all this Nick and his Darwinbot cohorts will continue pretend with all their strength that neo-Darwinism is fact as well established as gravity! Go Figure?!? Verse and music:
1 Corinthians 2:14 The natural person does not accept the things of the Spirit of God, for they are folly to him, and he is not able to understand them because they are spiritually discerned. Brooke Fraser – Lord of Lords(Legendado Português) - http://www.youtube.com/watch?v=rkF3iVjOZ1I
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Quantum Entanglement/Information is confirmed in DNA by direct observation here;
DNA Can Discern Between Two Quantum States, Research Shows – June 2011 Excerpt: — DNA — can discern between quantum states known as spin. – The researchers fabricated self-assembling, single layers of DNA attached to a gold substrate. They then exposed the DNA to mixed groups of electrons with both directions of spin. Indeed, the team’s results surpassed expectations: The biological molecules reacted strongly with the electrons carrying one of those spins, and hardly at all with the others. The longer the molecule, the more efficient it was at choosing electrons with the desired spin, while single strands and damaged bits of DNA did not exhibit this property. http://www.sciencedaily.com/releases/2011/03/110331104014.htm Coherent Intrachain energy migration at room temperature - Elisabetta Collini & Gregory Scholes - University of Toronto - Science, 323, (2009), pp. 369-73 Excerpt: The authors conducted an experiment to observe quantum coherence dynamics in relation to energy transfer. The experiment, conducted at room temperature, examined chain conformations, such as those found in the proteins of living cells. Neighbouring molecules along the backbone of a protein chain were seen to have coherent energy transfer. Where this happens quantum decoherence (the underlying tendency to loss of coherence due to interaction with the environment) is able to be resisted, and the evolution of the system remains entangled as a single quantum state. http://www.scimednet.org/quantum-coherence-living-cells-and-protein/ Quantum states in proteins and protein assemblies: The essence of life? - STUART HAMEROFF, JACK TUSZYNSKI Excerpt: It is, in fact, the hydrophobic effect and attractions among non-polar hydrophobic groups by van der Waals forces which drive protein folding. Although the confluence of hydrophobic side groups are small, roughly 1/30 to 1/250 of protein volumes, they exert enormous influence in the regulation of protein dynamics and function. Several hydrophobic pockets may work cooperatively in a single protein (Figure 2, Left). Hydrophobic pockets may be considered the “brain” or nervous system of each protein.,,, Proteins, lipids and nucleic acids are composed of constituent molecules which have both non-polar and polar regions on opposite ends. In an aqueous medium the non-polar regions of any of these components will join together to form hydrophobic regions where quantum forces reign. http://www.tony5m17h.net/SHJTQprotein.pdf Myosin Coherence Excerpt: Quantum physics and molecular biology are two disciplines that have evolved relatively independently. However, recently a wealth of evidence has demonstrated the importance of quantum mechanics for biological systems and thus a new field of quantum biology is emerging. Living systems have mastered the making and breaking of chemical bonds, which are quantum mechanical phenomena. Absorbance of frequency specific radiation (e.g. photosynthesis and vision), conversion of chemical energy into mechanical motion (e.g. ATP cleavage) and single electron transfers through biological polymers (e.g. DNA or proteins) are all quantum mechanical effects. http://www.energetic-medicine.net/bioenergetic-articles/articles/63/1/Myosin-Coherence/Page1.html
The necessity of 'transcendent' information, to ‘constrain’ a cell, against effects towards thermodynamic equilibrium is noted here:
Information and entropy – top-down or bottom-up development in living systems? A.C. McINTOSH Excerpt: This paper highlights the distinctive and non-material nature of information and its relationship with matter, energy and natural forces. It is proposed in conclusion that it is the non-material information (transcendent to the matter and energy) that is actually itself constraining the local thermodynamics to be in ordered disequilibrium and with specified raised free energy levels necessary for the molecular and cellular machinery to operate. http://journals.witpress.com/paperinfo.asp?pid=420
i.e. It is very interesting to note, to put it mildly, that quantum entanglement, which conclusively demonstrates that ‘information’ in its pure ‘quantum form’ is completely transcendent of any time and space constraints, should be found in molecular biology on such a massive scale, for how can the quantum entanglement ‘effect’ in biology possibly be explained by a material (matter/energy space/time) ’cause’ when the quantum entanglement ‘effect’ falsified material particles as its own ‘causation’ in the first place? (A. Aspect) Appealing to the probability of various configurations of material particles, as neo-Darwinism does, simply will not help since a timeless/spaceless cause must be supplied which is beyond the capacity of the energy/matter particles themselves to supply! To give a coherent explanation for an effect that is shown to be completely independent of any time and space constraints one is forced to appeal to a cause that is itself not limited to time and space! i.e. Put more simply, you cannot explain a effect by a cause that has been falsified by the very same effect you are seeking to explain! Improbability arguments of various ‘specified’ configurations of material particles, which have been a staple of the arguments against neo-Darwinism, simply do not apply since the cause is not within the material particles in the first place! ,,,To refute this falsification of neo-Darwinism, one must overturn Alain Aspect, and company’s, falsification of local realism (reductive materialism) ! And to dovetail into Dembski and Marks’s previous work on Conservation of Information;,,,
LIFE’S CONSERVATION LAW: Why Darwinian Evolution Cannot Create Biological Information William A. Dembski and Robert J. Marks II http://evoinfo.org/publications/lifes-conservation-law/
,,,Encoded ‘classical’ information such as what Dembski and Marks demonstrated the conservation of, and such as what we find encoded in computer programs, and yes, as we find encoded in DNA, is found to be a subset of ‘transcendent’ (beyond space and time) quantum entanglement/information by the following method:,,,
,,,This following research provides solid falsification for the late Rolf Landauer’s decades old contention that the information encoded in a computer is merely physical (merely ‘emergent’ from a material basis) since he believed it always required energy to erase it; Quantum knowledge cools computers: New understanding of entropy – June 2011 Excerpt: No heat, even a cooling effect; In the case of perfect classical knowledge of a computer memory (zero entropy), deletion of the data requires in theory no energy at all. The researchers prove that “more than complete knowledge” from quantum entanglement with the memory (negative entropy) leads to deletion of the data being accompanied by removal of heat from the computer and its release as usable energy. This is the physical meaning of negative entropy. Renner emphasizes, however, “This doesn’t mean that we can develop a perpetual motion machine.” The data can only be deleted once, so there is no possibility to continue to generate energy. The process also destroys the entanglement, and it would take an input of energy to reset the system to its starting state. The equations are consistent with what’s known as the second law of thermodynamics: the idea that the entropy of the universe can never decrease. Vedral says “We’re working on the edge of the second law. If you go any further, you will break it.” http://www.sciencedaily.com/releases/2011/06/110601134300.htm
,,,And to dot the i’s, and cross the t’s, here is the empirical confirmation that quantum information is in fact ‘conserved’;,,,
Quantum no-hiding theorem experimentally confirmed for first time Excerpt: In the classical world, information can be copied and deleted at will. In the quantum world, however, the conservation of quantum information means that information cannot be created nor destroyed. This concept stems from two fundamental theorems of quantum mechanics: the no-cloning theorem and the no-deleting theorem. A third and related theorem, called the no-hiding theorem, addresses information loss in the quantum world. According to the no-hiding theorem, if information is missing from one system (which may happen when the system interacts with the environment), then the information is simply residing somewhere else in the Universe; in other words, the missing information cannot be hidden in the correlations between a system and its environment. http://www.physorg.com/news/2011-03-quantum-no-hiding-theorem-experimentally.html
Further notes:
Three subsets of sequence complexity and their relevance to biopolymeric information – Abel, Trevors Excerpt: Shannon information theory measures the relative degrees of RSC and OSC. Shannon information theory cannot measure FSC (Functional Sequence Complexity). FSC is invariably associated with all forms of complex biofunction, including biochemical pathways, cycles, positive and negative feedback regulation, and homeostatic metabolism. The algorithmic programming of FSC, not merely its aperiodicity, accounts for biological organization. No empirical evidence exists of either RSC of OSC ever having produced a single instance of sophisticated biological organization. Organization invariably manifests FSC rather than successive random events (RSC) or low-informational self-ordering phenomena (OSC).,,, Testable hypotheses about FSC What testable empirical hypotheses can we make about FSC that might allow us to identify when FSC exists? In any of the following null hypotheses [137], demonstrating a single exception would allow falsification. We invite assistance in the falsification of any of the following null hypotheses: Null hypothesis #1 Stochastic ensembles of physical units cannot program algorithmic/cybernetic function. Null hypothesis #2 Dynamically-ordered sequences of individual physical units (physicality patterned by natural law causation) cannot program algorithmic/cybernetic function. Null hypothesis #3 Statistically weighted means (e.g., increased availability of certain units in the polymerization environment) giving rise to patterned (compressible) sequences of units cannot program algorithmic/cybernetic function. Null hypothesis #4 Computationally successful configurable switches cannot be set by chance, necessity, or any combination of the two, even over large periods of time. We repeat that a single incident of nontrivial algorithmic programming success achieved without selection for fitness at the decision-node programming level would falsify any of these null hypotheses. This renders each of these hypotheses scientifically testable. We offer the prediction that none of these four hypotheses will be falsified. http://www.tbiomed.com/content/2/1/29
bornagain77_{February 25, 2012
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Nick you ask:
Show me where I was advocating atheism in this thread. In fact, show me anywhere, anyplace, where I have ever advocated atheism. Good luck.
So Nick, if you are not advocating atheism, do you now admit that the Bacterial Flagellum is Intelligently Designed? Or have all your thousands upon thousands of words you've authored saying the Bacterial Flagellum was not Intelligently Designed just been a sham to hide your Theistic belief? Speaking of which Nick, let's see how far we can establish Theism as true for molecular biology shall we? Falsification Of Neo-Darwinism by Quantum Entanglement/Information Neo-Darwinian evolution purports to explain all the wondrously amazing complexity of life on earth by reference solely to chance and necessity processes acting on energy and matter (i.e. purely material processes). In fact neo-Darwinian evolution makes the grand materialistic claim that the staggering levels of unmatched complex functional information we find in life, and even the ‘essence of life’ itself, simply ‘emerged’ from purely material processes. And even though this basic scientific point, of the ability of purely material processes to generate even trivial levels of complex functional information, has spectacularly failed to be established, we now have a much greater proof, than this stunning failure for validation, that ‘put the lie’ to the grand claims of neo-Darwinian evolution. This proof comes from the fact that it is now shown from quantum mechanics that ‘information’ is its own unique ‘physical’ entity. A physical entity that is shown to be completely independent of any energy-matter space-time constraints, i.e. it does not ‘emerge’ from a material basis. Moreover this ‘transcendent information’ is shown to be dominant of energy-matter in that this ‘information’ is shown to be the entity that is in fact constraining the energy-matter processes of the cell to be so far out of thermodynamic equilibrium. notes: Falsification of neo-Darwinism; First, Here is the falsification of local realism (reductive materialism). Here is a clip of a talk in which Alain Aspect talks about the failure of ‘local realism’, or the failure of reductive materialism, to explain reality:
The Failure Of Local Realism – Reductive Materialism – Alain Aspect – video http://www.metacafe.com/w/4744145
The falsification for local realism (reductive materialism) was recently greatly strengthened:
'Quantum Magic' Without Any 'Spooky Action at a Distance' - June 2011 Excerpt: A team of researchers led by Anton Zeilinger at the University of Vienna and the Institute for Quantum Optics and Quantum Information of the Austrian Academy of Sciences used a system which does not allow for entanglement, and still found results which cannot be interpreted classically. http://www.sciencedaily.com/releases/2011/06/110624111942.htm Falsification of Local Realism without using Quantum Entanglement - Anton Zeilinger - video http://vimeo.com/34168474 Physicists close two loopholes while violating local realism – November 2010 Excerpt: The latest test in quantum mechanics provides even stronger support than before for the view that nature violates local realism and is thus in contradiction with a classical worldview. http://www.physorg.com/news/2010-11-physicists-loopholes-violating-local-realism.html Quantum Measurements: Common Sense Is Not Enough, Physicists Show – July 2009 Excerpt: scientists have now proven comprehensively in an experiment for the first time that the experimentally observed phenomena cannot be described by non-contextual models with hidden variables. http://www.sciencedaily.com/releases/2009/07/090722142824.htm
of note: hidden variables were postulated to remove the need for ‘spooky’ forces, as Einstein termed them — forces that act instantaneously at great distances, thereby breaking the most cherished rule of relativity theory, that nothing can travel faster than the speed of light. This following video illustrates just how 'spooky', to use Einstein’s infamous word, this quantum action truly is:
Light and Quantum Entanglement Reflect Some Characteristics Of God – video http://www.metacafe.com/watch/4102182/
And yet, this ‘spooky’ quantum entanglement, which rigorously falsified local realism (reductive materialism) as the ‘true’ description of reality, and blatantly defies our concepts of time and space, is now found in molecular biology on a massive scale!
Quantum Information/Entanglement In DNA & Protein Folding – short video http://www.metacafe.com/watch/5936605/ Quantum entanglement holds together life’s blueprint – 2010 Excerpt: When the researchers analysed the DNA without its helical structure, they found that the electron clouds were not entangled. But when they incorporated DNA’s helical structure into the model, they saw that the electron clouds of each base pair became entangled with those of its neighbours (arxiv.org/abs/1006.4053v1). “If you didn’t have entanglement, then DNA would have a simple flat structure, and you would never get the twist that seems to be important to the functioning of DNA,” says team member Vlatko Vedral of the University of Oxford. http://neshealthblog.wordpress.com/2010/09/15/quantum-entanglement-holds-together-lifes-blueprint/ The relevance of continuous variable entanglement in DNA – July 2010 Excerpt: We consider a chain of harmonic oscillators with dipole-dipole interaction between nearest neighbours resulting in a van der Waals type bonding. The binding energies between entangled and classically correlated states are compared. We apply our model to DNA. By comparing our model with numerical simulations we conclude that entanglement may play a crucial role in explaining the stability of the DNA double helix. http://arxiv.org/abs/1006.4053v1
bornagain77_{February 25, 2012
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Nick, how come this song reminds me of you robotic Darwinbots?:
Red - Feed The Machine http://www.youtube.com/watch?v=zj2uZO7xnus
bornagain77_{February 25, 2012
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Hi ba77. 1. Show me where I was advocating atheism in this thread. In fact, show me anywhere, anyplace, where I have ever advocated atheism. Good luck. 2. You apparently don't know the difference between a claim about an evolution-like-process working in the current operation of today's adaptive immune system, and a claim about how the adaptive immune system evolved. I was talking about the latter, your rebuttals are mostly about the former. How can we even discuss something if you just toss random unrelated links around? Why should any scientist take you seriously? As for Ewert, I'll see your one guy with dubious expertise in evolutionary immunology, making unpublished, and rather vague, claims about evolutionary immunology, under the careful guidance of Casey Luskin, who is desperate to get something, anything, with which to rebut the crashing defeat of Behe in the Kitzmiller case, versus the published, peer-reviewed work of hundreds of scientists in top journals. Any judge would pick our side faced with that evidence, it wasn't some fluke unique to Judge Jones. Dembski and other IDists have stated that irreducible complexity is a special case of specified complexity. If Behe is wrong about IC, then Dembski et al. are wrong about specified complexity. If Dembski et al. are wrong about specified complexity, then even the emergency-backup attempt to save the bogus, much-scorned "evolution violated the 2nd Law of Thermodynamics, just like the YEC fundamentalists said 50 years ago, yay!" fails as well. That's an argument. Try making one instead of posting random links.NickMatzke_UD_{February 25, 2012
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Although just about everything Nick wrote is severely misleading, as usual, lets just focus on his claim, in the last part of his 'atheistic' diatribe, that claimed the immune system evolved to show just how severely misleading Nick is with the actual evidence: Nick claims 'tons of answers':
Yes, yes, I’m aware that Behe did not use the words “not good enough”. But it’s true that he didn’t think they were good enough to rebut his claim that the scientific literature had “no answers” on the evolution of the immune system — when in fact it has a ton of answers, in a ton of peer-reviewed articles published in top journals.
Yet in the real world the fact is this: It is interesting to note that many times evolutionists will try to use the highly choreographed mutation/selection process of the immune system itself, claiming that the brilliantly designed immune system is actually proof of evolution. Yet the immune system is almost exactly what we have with the evolutionists claims for 'evolutionary algorithms' in that the immune system is carefully designed from the outset to converge on a solution. It would be surprising, and deadly, if the immune system did not do exactly what it was 'designed' to do:
Falk’s fallacy - Feb. 2010 Excerpt: This (the immune system) is one of the most amazing processes ever described.,,, Whatever may be said about it, it is a highly regulated, specified, directed and choreographed process. It is obviously the product of overwhelmingly brilliant design,,, https://uncommondescent.com/intelligent-design/falks-falacy/ Response to Kathryn Applegate - Caroline Crocker PhD.- cell biologist and immunologist - October 2010 Excerpt: Diversity of antibodies generated by B cells is due to deliberate, cell-engineered changes in the DNA sequence, not random mutations. In fact, I have never before heard the process whereby functional antibodies are formed (before they encounter antigen) described as mutation. And it is well-known that the appearance of functionality as a result of a mistake-mutation is extremely rare. Of course, after encountering antigen the hypervariable regions of the antibody DNA do undergo somatic hypermutation, but again this is in particular places and is controlled by enzymes.,,, https://uncommondescent.com/intelligent-design/comments-on-kathryn-applegate%E2%80%99s-may-posts-on-biologos/#more-15176 Generation of Antibody Diversity is Unlike Darwinian Evolution - microbiologist Don Ewert - November 2010 Excerpt: The evidence from decades of research reveals a complex network of highly regulated processes of gene expression that leave very little to chance, but permit the generation of receptor diversity without damaging the function of the immunoglobulin protein or doing damage to other sites in the genome. http://www.evolutionnews.org/2010/11/response_to_edward_max_on_talk040661.html "A Masterful Feat of Courtroom Deception": Immunologist Donald Ewert on Dover Trial - audio http://intelligentdesign.podomatic.com/player/web/2010-12-20T15_01_03-08_00
In this following podcast, Casey Luskin interviews microbiologist and immunologist Donald Ewert about his previous work as associate editor for the journal Development and Comparitive Immunology, where he realized that the papers published were comparative studies that had nothing to do with evolution at all.
What Does Evolution Have to Do With Immunology? Not Much - April 2011 http://intelligentdesign.podomatic.com/entry/2011-04-06T11_39_03-07_00
The blatant deception (literature bluff), from neo-Darwinists at Dover, did not stop with immunology;
The NCSE, Judge Jones, and Bluffs About the Origin of New Functional Genetic Information – Casey Luskin – March 2010 http://www.discovery.org/a/14251
Cue Christian Rock song for you Nick;
Red - Breathe Into Me http://www.youtube.com/watch?v=yH-k_6tU9Wc
bornagain77_{February 25, 2012
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Hump that strawman Nick!
The ID movement’s common claim that evolution cannot produce “new genetic information”
That is not the claim and you have been told that on several occasions. So either you have a learning disability or you are dishonest. Also, Nick, ID is not anti-evolution so your continued equivocations are a fool's folly. See also Dr Behe Responds to JonesJoe_{February 25, 2012
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Oops, quotes and subquotes somewhat screwed up in last quote of previous, see links for original.NickMatzke_UD_{February 25, 2012
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So, life is characterized by movement (kinetic), rather than thermodynamic processes? What the heck does that even mean? What is driving and controlling this movement?
Hi guys, Please go read the wikipedia page on "kinetics" as it is used in the field of chemistry. You obviously do not know what it means or how it applies here, as no one has even addressed Pross's point. Re: Thaxton & co (1984) -- I am very familiar with it. E.g.: http://www.pnas.org/content/104/suppl.1/8669.full
Like the irreducible complexity argument, the other prominent claims made by the ID movement, and often the specific terminology, trace back to creation science. “Specified complexity” entered the antievolution literature in Thaxton et al. (63), in the midst of a chapter that attempted to repair the infamous creation science shibboleth, much ridiculed by scientists, that a decrease in entropy in biological systems contradicts the Second Law of Thermodynamics. The authors grudgingly conceded that local decreases in entropy were not prohibited in open systems like the earth, which experience a continuous energy flow, but claimed that genetic information exhibits specified complexity, and that thermodynamic limitations block any nonintelligent increase in information. More generic “no new information” arguments had been made by the European creation scientist A. E. Wilder-Smith, who has been repeatedly cited as an inspiration by many ID proponents (64).
As for the "no new information" argument:
Dembski's argument inferring design from specified complexity, besides relying entirely on Behe's argument for its application to biology, has been shown to rely on misconstruals of probability and information theory (28–31). The ID movement's common claim that evolution cannot produce “new genetic information” is contradicted by numerous papers documenting the origin of new genes (e.g., ref. 32) or even entire multiprotein catabolic pathways for artificial compounds that humans have released into the environment in recent decades (33, 34). Behe's claim has been rebutted in general (35–37) and for specific complex systems such as bird wings (38), the vertebrate blood clotting cascade (39), the vertebrate immune system (40), and the ID movement's favorite system, the bacterial flagellum (23, 41, 42). Faced with such rebuttals, Behe and Dembski typically make the unsupported assertion that indirect pathways are highly improbable or, ironically, given the absence of any detail in their own explanation, complain that the proffered explanations lack sufficient detail to be empirically tested.
And for the not-enough-detail argument: http://www.nature.com/ni/journal/v7/n5/full/ni0506-433.html
In particular, Behe criticizes a 1994 Proceedings of the National Academy of Science paper advancing the hypothesis that the RAG system evolved by lateral transfer of a prokaryotic transposon13, an idea initially suggested in a 1979 paper14 and expanded in 1992 (ref. 15). Behe ridicules the idea as a "jump in the box of Calvin and Hobbes,"2 with reference to the comic strip in which a child and his stuffed tiger imaginary friend use a large cardboard box for fantasy trips and amazing physical transformations. The timing for the criticism could not have been worse, as soon after publication of Darwin's Black Box, solid evidence for the transposon hypothesis began accumulating with the demonstration of similarities between the variable-diversity-joining recombination and transposition mechanisms16 and also between shark RAG1 and certain bacterial integrases17. Since then, a steady stream of findings has continued to add more substance to the model, as RAG proteins have been shown to be capable of catalyzing transposition reactions, first in vitro18, 19 and then in vivo20, 21, 22, and to have even closer structural and mechanistic similarities with specific transposases23. Finally, in 2005, the original key prediction of the transposon hypothesis was fulfilled with the identification of a large invertebrate transposon family bearing both recombination signal sequence–like integration sequences and a RAG1 homolog24. When faced with that evidence during an exchange on the internet, Behe simply 'shrugged' and said that evidence was not sufficient, asking instead for an infinitely detailed, step-by-step mutation account (including population sizes, relevant selective pressures and so on) for the events leading to the appearance of the adaptive immune system (http://www.pandasthumb.org/archives/2005/06/behes_meaningle.html). That background set the stage for the crucial face-off at the trial. Kenneth Miller of Brown University, a cell biologist and textbook author who has written extensively on evolution and creationism, was the lead witness for the plaintiffs. Over the course of his testimony, Miller did his best to explain to the nonscientist audience the mechanisms of antibody gene rearrangement and the evidence corroborating the transposon hypothesis. Then, 10 days later, Behe took the stand. During cross-examination by the plaintiffs' lead counsel Eric Rothschild, Behe reiterated his claim about the scientific literature on the evolution of the immune system, testifying that "the scientific literature has no detailed testable answers on how the immune system could have arisen by random mutation and natural selection." Rothschild then presented Behe with a thick file of publications on immune system evolution, dating from 1971 to 2006, plus several books and textbook chapters. Asked for his response, Behe admitted he had not read many of the publications presented (a small fraction of all the literature on evolutionary immunology of the past 35 years), but summarily rejected them as unsatisfactory and dismissed the idea of doing research on the topic as "unfruitful." This exchange clearly made an impression on Judge Jones, who specifically described it in his opinion:
In particular, Behe criticizes a 1994 Proceedings of the National Academy of Science paper advancing the hypothesis that the RAG system evolved by lateral transfer of a prokaryotic transposon13, an idea initially suggested in a 1979 paper14 and expanded in 1992 (ref. 15). Behe ridicules the idea as a "jump in the box of Calvin and Hobbes,"2 with reference to the comic strip in which a child and his stuffed tiger imaginary friend use a large cardboard box for fantasy trips and amazing physical transformations. The timing for the criticism could not have been worse, as soon after publication of Darwin's Black Box, solid evidence for the transposon hypothesis began accumulating with the demonstration of similarities between the variable-diversity-joining recombination and transposition mechanisms16 and also between shark RAG1 and certain bacterial integrases17. Since then, a steady stream of findings has continued to add more substance to the model, as RAG proteins have been shown to be capable of catalyzing transposition reactions, first in vitro18, 19 and then in vivo20, 21, 22, and to have even closer structural and mechanistic similarities with specific transposases23. Finally, in 2005, the original key prediction of the transposon hypothesis was fulfilled with the identification of a large invertebrate transposon family bearing both recombination signal sequence–like integration sequences and a RAG1 homolog24. When faced with that evidence during an exchange on the internet, Behe simply 'shrugged' and said that evidence was not sufficient, asking instead for an infinitely detailed, step-by-step mutation account (including population sizes, relevant selective pressures and so on) for the events leading to the appearance of the adaptive immune system (http://www.pandasthumb.org/archives/2005/06/behes_meaningle.html). That background set the stage for the crucial face-off at the trial. Kenneth Miller of Brown University, a cell biologist and textbook author who has written extensively on evolution and creationism, was the lead witness for the plaintiffs. Over the course of his testimony, Miller did his best to explain to the nonscientist audience the mechanisms of antibody gene rearrangement and the evidence corroborating the transposon hypothesis. Then, 10 days later, Behe took the stand. During cross-examination by the plaintiffs' lead counsel Eric Rothschild, Behe reiterated his claim about the scientific literature on the evolution of the immune system, testifying that "the scientific literature has no detailed testable answers on how the immune system could have arisen by random mutation and natural selection." Rothschild then presented Behe with a thick file of publications on immune system evolution, dating from 1971 to 2006, plus several books and textbook chapters. Asked for his response, Behe admitted he had not read many of the publications presented (a small fraction of all the literature on evolutionary immunology of the past 35 years), but summarily rejected them as unsatisfactory and dismissed the idea of doing research on the topic as "unfruitful." This exchange clearly made an impression on Judge Jones, who specifically described it in his opinion: In fact, on cross-examination, Professor Behe was questioned concerning his 1996 claim that science would never find an evolutionary explanation for the immune system. He was presented with fifty-eight peer-reviewed publications, nine books, and several immunology textbook chapters about the evolution of the immune system; however, he simply insisted that this was still not sufficient evidence of evolution, and that it was not 'good enough.' We find that such evidence demonstrates that the ID argument is dependent upon setting a scientifically unreasonable burden of proof for the theory of evolution.

Yes, yes, I'm aware that Behe did not use the words "not good enough". But it's true that he didn't think they were good enough to rebut his claim that the scientific literature had "no answers" on the evolution of the immune system -- when in fact it has a ton of answers, in a ton of peer-reviewed articles published in top journals. Any response to this that does not acknowledge the existence of the transposon hypothesis, exhibit a decent understanding of that hypothesis and the evidence scientists cite in favor it, and give a more detailed alternative explanation, isn't serious and isn't worth responding to. The IDists haven't provided one yet, I'm sure you guys won't be able to either.NickMatzke_UD_{February 25, 2012
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Dr Selensky: UD has reverted to timelined comments. And I too have found Abel refreshing reading. KFkairosfocus_{February 23, 2012
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KF, For some reason, it is not possible to leave a comment under another comment. So here it goes. Spot on. Control defined by Abel as a formal procedure to steer a system to a goal state needs intelligent interference because upon massive observation it is clear that nature is inert to teleology. Inanimate nature can only provide constraints, not controls. I believe that in 50-100 years time they will count the likes of David Abel among the greatest thinkers of our time. Another profound thought I found in his book is that mathematics and the scientific method themselves due to (a) their formality and (b) their ability to grasp the essence of material reality point to an intelligent cause behind it. Formalism and control are reliable markers of intelligent agency. It's that sort of books which you read and keep asking yourself, why haven't I thought about this before?Eugene S_{February 23, 2012
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LOL Axel, :) sort of reminds me of this humorous article a while back lamenting the lack of any coherent creation account for atheists:
When Nothing Created Everything - JOE CARTER http://www.catholiceducation.org/articles/science/sc0120.htm
Likewise, Steve Martin laments the fact that Atheists really don't have any traditional songs since they really have nothing to sing about:
Steve Martin - Atheists Don't Have No Songs http://www.youtube.com/watch?v=lFWA1A9XFi8
But alas, what can you do for a philosophy that has everything backwards?
From Atheism to Theism In Reverse - video http://www.godtube.com/watch/?v=9C2E1MNU
bornagain77_{February 23, 2012
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Yeah, Nick is right- we exist and we know there wasn't any dang-darn designer involved, so we know the second law was not violated. Unfortunately for Nick and Andy Pross we are still waiting for a testable hypothesis, predictions and positive evidence for the premise living organisms are reducible to chemicals (matter & energy) and undirected endo + exothermic reactions.Joe_{February 23, 2012
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Dr Selensky: You are quite right. The issue is that we are here dealing with organisation, in very special zones of the space of possible configs of the atoms and molecules in say our warm little pond. The organisation includes: smart polymers sequenced to fold and fulfill specific functions, grouped in ways that are integrated to form a metabolising, self replicating automaton, where the self-replication facility involves digital codes, instructions, data storage elements, algorithms and the like, what Abel so carefully discusses as prescriptive information. Indeed we have a metabolic entity with a von Neumann self-replicator. The "fluctuation" to get to such a co-ordinated functional state defies the statistical imperatives of stat mech. H'mm maybe this will help us see what is going on. Take a can of soup, open and pour into a pot. Keep on pouring in cans and turn on low heat. If you want you can pass electric currents through it and shine lights on it. Will you be likely to somehow end up with organisation of a new form of life, using the rich soup of life components in the pot? Why or why not? Similarly, set up a sterile flask, and do a prick and decant exercise with the contents of a living cell. Keep on pricking and pouring in. Will you at all be likely to form a new cell from the actual cell components? Why or why not? Remember, you are adding both relevant matter and energy in both cases. (NB for onlookers: Statistical mechanics refines classical thermodynamics to not say things are outright forbidden on induction from experiment and related analysis, just that things that are sufficiently unusual will be so swamped by the bulk of ultramicroscopic possibilities for distributing energy and mass relative to the available macro-level constraints that they will not be observed with all but certainty. Classical thermodynamics worked from the macro observables to the famous laws, stat thermodynamics gives the molecular underpinnings in effect. Here's the tickler, dumping in energy in an un-co-ordinated way will as a rule simply go into boosting available energy for random effects, i.e an energy importing subsystem tends strongly to get more disordered. Which is exactly what Clausius' analysis to ground the 2nd law in classical form is saying. Remember, form the informational perspective, as Gilbert N Lewis and Jaynes et al put it, the entropy is in effect the measure of the freedom to form new configs that a system has under certain macro constraints. Of course, once we have life in hand the functionality of life is a constraint that can then be associated with a new dynamic, or metabolism and self replication, but the issue here is to get to that. And the challenge is to find a fluctuation which delivers the sort of organisation we are looking at. the numbers are simply out of reach for the available resources on our solar system or observed cosmos. That is what we are not seeing being fully and frankly faced.) So, let us hear a good explanation for the origin of the relevant organisation, backed up by empirical evidence. Otherwise it is all blue smoke and mirrors. Here are Orgel and Shapiro on that, to what looks like mutual ruin for metabolism first and genes first models:
[[Shapiro:] RNA's building blocks, nucleotides contain a sugar, a phosphate and one of four nitrogen-containing bases as sub-subunits. Thus, each RNA nucleotide contains 9 or 10 carbon atoms, numerous nitrogen and oxygen atoms and the phosphate group, all connected in a precise three-dimensional pattern . . . . [[S]ome writers have presumed that all of life's building could be formed with ease in Miller-type experiments and were present in meteorites and other extraterrestrial bodies. This is not the case. A careful examination of the results of the analysis of several meteorites led the scientists who conducted the work to a different conclusion: inanimate nature has a bias toward the formation of molecules made of fewer rather than greater numbers of carbon atoms, and thus shows no partiality in favor of creating the building blocks of our kind of life . . . . To rescue the RNA-first concept from this otherwise lethal defect, its advocates have created a discipline called prebiotic synthesis. They have attempted to show that RNA and its components can be prepared in their laboratories in a sequence of carefully controlled reactions, normally carried out in water at temperatures observed on Earth . . . . Unfortunately, neither chemists nor laboratories were present on the early Earth to produce RNA . . . [[Orgel:] If complex cycles analogous to metabolic cycles could have operated on the primitive Earth, before the appearance of enzymes or other informational polymers, many of the obstacles to the construction of a plausible scenario for the origin of life would disappear . . . . It must be recognized that assessment of the feasibility of any particular proposed prebiotic cycle must depend on arguments about chemical plausibility, rather than on a decision about logical possibility . . . few would believe that any assembly of minerals on the primitive Earth is likely to have promoted these syntheses in significant yield . . . . Why should one believe that an ensemble of minerals that are capable of catalyzing each of the many steps of [[for instance] the reverse citric acid cycle was present anywhere on the primitive Earth [[8], or that the cycle mysteriously organized itself topographically on a metal sulfide surface [[6]? . . . Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own . . . . The prebiotic syntheses that have been investigated experimentally almost always lead to the formation of complex mixtures. Proposed polymer replication schemes are unlikely to succeed except with reasonably pure input monomers. No solution of the origin-of-life problem will be possible until the gap between the two kinds of chemistry is closed. Simplification of product mixtures through the self-organization of organic reaction sequences, whether cyclic or not, would help enormously, as would the discovery of very simple replicating polymers. However, solutions offered by supporters of geneticist or metabolist scenarios that are dependent on “if pigs could fly” hypothetical chemistry are unlikely to help.
KFkairosfocus_{February 23, 2012
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If Nick could answer your question, bornagain77, let me see if I can guess what it would be... "Pass..." Now, he'll respond, but it'll be a cockameenie evasion. IDers' adducing empirical evidence is dealing from the bottom of the deck to the evolutionists' eyes. 'There are more things in Randomness and Chaos than were ever dreamt of in your philosophy, IDers.' A whole universe and.. and... a multiverse.. with G-String theories and everthang.'Axel_{February 23, 2012
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