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Proteins Fold As Darwin Crumbles

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A Review Of The Case Against A Darwinian Origin Of Protein Folds By Douglas Axe, Bio-Complexity, Issue 1, pp. 1-12

Proteins adopt a higher order structure (eg: alpha helices and beta sheets) that define their functional domains.  Years ago Michael Denton and Craig Marshall reviewed this higher structural order in proteins and proposed that protein folding patterns could be classified into a finite number of discrete families whose construction might be constrained by a set of underlying natural laws (1).  In his latest critique Biologic Institute molecular biologist Douglas Axe has raised the ever-pertinent question of whether Darwinian evolution can adequately explain the origins of protein structure folds given the vast search space of possible protein sequence combinations that exist for moderately large proteins, say 300 amino acids in length.  To begin Axe introduces his readers to the sampling problem.  That is, given the postulated maximum number of distinct physical events that could have occurred since the universe began (10150) we cannot surmise that evolution has had enough time to find the 10390 possible amino-acid combinations of a 300 amino acid long protein.

The battle cry often heard in response to this apparently insurmountable barricade is that even though probabilistic resources would not allow a blind search to stumble upon any given protein sequence, the chances of finding a particular protein function might be considerably better.  Countering such a facile dismissal of reality, we find that proteins must meet very stringent sequence requirements if a given function is to be attained.  And size is important.  We find that enzymes, for example, are large in comparison to their substrates.  Protein structuralists have demonstrably asserted that size is crucial for assuring the stability of protein architecture.

Axe has raised the bar of the discussion by pointing out that very often enzyme catalytic functions depend on more that just their core active sites.  In fact enzymes almost invariably contain regions that prep, channel and orient their substrates, as well as a multiplicity of co-factors, in readiness for catalysis.  Carbamoyl Phosphate Synthetase (CPS) and the Proton Translocating Synthase (PTS) stand out as favorites amongst molecular biologists for showing how enzyme complexes are capable of simultaneously coordinating such processes.  Overall each of these complexes contains 1400-2000 amino acid residues distributed amongst several proteins all of which are required for activity.

Axe employs a relatively straightforward mathematical rationale for assessing the plausibility of finding novel protein functions through a Darwinian search.  Using bacteria as his model system (chosen because of their relatively large population sizes) he shows how a culture of 1010 bacteria passing through 104 generations per year over five billion years would produce a maximum of 5×1023 novel genotypes.  This number represents the ‘upper bound’ on the number of new protein sequences since many of the differences in genotype would not generate “distinctly new proteins”.  Extending this further, novel protein functions requiring a 300 amino acid sequence (20300 possible sequences) could theoretically be achieved in 10366 different ways (20300/5×1023). 

Ultimately we find that proteins do not tolerate this extraordinary level of “sequence indifference”.  High profile mutagenesis experiments of beta lactamases and bacterial ribonucleases have shown that functionality is decisively eradicated when a mere 10% of amino-acids are substituted in conservative regions of these proteins.  A more in-depth breakdown of data from a beta lactamase domain and the enzyme chorismate mutase  has further reinforced the pronouncement that very few protein sequences can actually perform a desired function; so few in fact that they are “far too rare to be found by random sampling”.

But Axe’s landslide evaluation does not end here.  He further considers the possibility that disparate protein functions might share similar amino-acid identities and that therefore the jump between functions in sequence space might be realistically achievable through random searches.  Sequence alignment studies between different protein domains do not support such an exit to the sampling problem.  While the identification of a single amino acid conformational switch has been heralded in the peer-review literature as a convincing example of how changes in folding can occur with minimal adjustments to sequence, what we find is that the resulting conformational variants are unstable at physiological temperatures.  Moreover such a change has only been achieved in vitro and most probably does not meet the rigorous demands for functionality that play out in a true biological context.  What we also find is that there are 21 other amino-acid substitutions that must be in place before the conformational switch is observed. 

Axe closes his compendious dismantling of protein evolution by exposing the shortcomings of modular assembly models that purport to explain the origin of new protein folds.  The highly cooperative nature of structural folds in any given protein means that stable structures tend to form all at once at the domain (tertiary structure) level rather that at the fold (secondary structure) level of the protein.  Context is everything.  Indeed experiments have held up the assertion that binding interfaces between different forms of secondary structure are sequence dependent (ie: non-generic).  Consequently a much anticipated “modular transportability of folds” between proteins is highly unlikely. 

Metaphors are everything in scientific argumentation.  And Axe’s story of a random search for gem stones dispersed across a vast multi-level desert serves him well for illustrating the improbabilities of a Darwinian search for novel folds.  Axe’s own experience has shown that reticence towards accepting his probabilistic argument stems not from some non-scientific point of departure in what he has to say but from deeply held prejudices against the end point that naturally follows.  Rather than a house of cards crumbling on slippery foundations, the case against the neo-Darwinian explanation is an edifice built on a firm substratum of scientific authenticity.  So much so that critics of those who, like Axe, have stood firm in promulgating their case, better take note. 

Read Axe’s paper at: http://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2010.1

Further Reading

  1. Michael Denton, Craig Marshall (2001), Laws of form revisited, Nature Volume 410, p. 417
Comments
Cabal: Pardon, but you have presented a classic example (familiar to me from watching Marxism implode late 80's - early 90's) of how a failed paradigm distorts one's view. Observe just above how you speak of "ID hype" and "magic" etc. Do you not see how warped, prejudicial and loaded that choice of language is? Do you not see that it reflects an emotional intensity that is very likely to be blinding? Then, pause and -- bearing in mind the weak argument correctives above right on every UD page -- reflect: 1 --> We exist as intelligent creatures in a real world that we share. 2 --> We know that we often do things that are artificial, which is a credible opposite to "natural." So, we ne3ed not resort to the false dichotomy "natural/supernatural" or in its latest guises, extra-natural/magical. 3 --> Indeed, as has been repeatedly pointed out at UD, the analysis in terms of nature [phusis] vs art [techne] goes back to the very first design analysis on record, i.e. Plato's The Laws, Bk X. So, it would be reasonable to expect that a responsible analysis would reflect that fact of 2,300 years' standing. 4 --> Now, too, we know that we often analyse based on inference to best current explanation. Candidate explanations for a given phenomenon are tabled, analysed on factual adequacy, coherence and explanatory power, the best being selected on a provisional basis and put up for a programme of further testing. Explanations that turn out to be best and robust across time are generally seen as good ones. 5 --> Indeed, this is the basis of scientific methods, as we can see from say Newton's classic 1705 summary in Opticks, Query 31. (Our classic school level descriptions of science and its generic methods look to me to be pretty much a simplification of Newton's remarks on analysis and composition in the context of empirical investigation.) 6 --> Coming back, we personally are intelligent, and live in a technologically based world that is filled with artifacts of intelligence. One common pattern that marks out such artifacts and allows them to stand out from the phenomena of chance and mechanical necessity of nature is: complex, functional organisation and associated information. 7 --> Consistently, we directly observe and experience how such FSCI is a hallmark of design in action. Starting with posts in this thread, and going on to case after case after case. (NONE of the above posts were produced by monkeys banging away at keyboards at random, or by faulty keyboards forcing a keystroke sequence.) 8 --> Using insights from mathematics, information theory and statistical mechanics, we can see that once a functional entity depends on a sufficiently complex pattern [500 - 1,000 bits is a useful threshold], the functional configurations will as a rule be so deeply isolated in the space of possible configurations, that a random walk from an initially arbitrary config, even with selection for function, will be well beyond the search capacity of the observed cosmos. (Onlookers, cf here for my latest summary on such, in context.) 9 --> So, we see an analytical reason for why we routinely observe that intelligence produces FSCI, but blind chance + necessity will not credibly do so. 10 --> Actually, this is not controversial, even Dawkins admits it. What evolutionary materialists try to do is to suggest that very simple entities are sufficiently functional that some form of favourable natural selection will reward their accidental coming into existence. Then, further favourable, small-step accidents and selection based on success in environments gets us first to life then to body plan level biodiversity. 10 --> But to do that, predictably, they duck the issue of threshold of complex organisation to achieve function. As a major current example, they often invite us to shut our eyes tot he obvious designed, purposeful context and unwarrantedly simplistic threshold of function in genetic algorithms and other simulations, starting with Dawkins' notorious Weasel, and going up to Avida etc. 11 --> But in fact, to get to the first successful organism, we have to fulfill the von Neumann requisites for a self-replicating automaton [where the entity haws an independent function, i.e autocatalysis of molecules will not do]:
(i) an underlying storable code to record the required information to create not only (a) the primary functional machine [e.g. a metabolising entity that interacts with its environment] 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.
12 --> Such an entity is well past the 1,000 bit limit. And, we routinely observe examples, starting with unicellular life forms, including the so-called simplest cases. These we know start out with DNA in the 100 - 1,000 k bit class [where each 4-state base is 2 bits]. 13 --> As the video top right every UD page shows, such entities are in fact exactly the sort of entity von Neumann envisioned. 14 --> So, we have very good reason to view the living cell in its organism precisely as PaV described it:
We see self-replicating, self-constructing, nanoscale machines operating via sophisticated energy transfer schemes and using quantum level computing and communication which, working in tandem, give rise to incredible macro-level organisms capable of flight, navigation using magnetic orientation, sonar, and star formations, and running 4-minute miles.
15 --> Maybe Denton, circa 1985 will add details: _____________ >> To grasp the reality of life as it has been revealed by molecular biology, we must magnify a cell a thousand million times until it is twenty kilometers in diameter [[so each atom in it would be “the size of a tennis ball”] and resembles a giant airship large enough to cover a great city like London or New York. What we would then see would be an object of unparalleled complexity and adaptive design. On the surface of the cell we would see millions of openings, like the port holes of a vast space ship, opening and closing to allow a continual stream of materials to flow in and out. If we were to enter one of these openings we would find ourselves in a world of supreme technology and bewildering complexity. We would see endless highly organized corridors and conduits branching in every direction away from the perimeter of the cell, some leading to the central memory bank in the nucleus and others to assembly plants and processing units. The nucleus itself would be a vast spherical chamber more than a kilometer in diameter, resembling a geodesic dome inside of which we would see, all neatly stacked together in ordered arrays, the miles of coiled chains of the DNA molecules. A huge range of products and raw materials would shuttle along all the manifold conduits in a highly ordered fashion to and from all the various assembly plants in the outer regions of the cell. We would wonder at the level of control implicit in the movement of so many objects down so many seemingly endless conduits, all in perfect unison. We would see all around us, in every direction we looked, all sorts of robot-like machines . . . . We would see that nearly every feature of our own advanced machines had its analogue in the cell: artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of components, error fail-safe and proof-reading devices used for quality control, assembly processes involving the principle of prefabrication and modular construction . . . . However, it would be a factory which would have one capacity not equaled in any of our own most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours . . . . Unlike our own pseudo-automated assembly plants, where external controls are being continually applied, the cell's manufacturing capability is entirely self-regulated . . . . [[Denton, Michael, Evolution: A Theory in Crisis, Adler, 1986, pp. 327 – 331. ] >> _______________ Cabal, that is what evolutionary materialists need to credibly account for in a factually adequate, coherent, explanatorily powerful way. After many decades, on both the origin of life and the origin of body plan level biodiversity fronts, the failure is getting more and more obvious. (Don't even mention the origin of mind, morality and man!) But, we know how to produce code, machines to implement it, and even nanomachines. It is sixty years ago that von Neumann published his analysis on self replicating automata, though we have yet to build a 3-d implementation. (Computer simulations don't count.) More shockingly, in Ch II of his book, Paley looked at the hypothetical example of a self-replicating watch and made the case that its additional capacity to replicate itself -- additional to time-telling is key -- ADDS to the case for its intelligent design. In short, right from the beginning of the school of thought, Darwin willfully begged the key questions, as he was quite familiar with Paley. He simply assumed the can opener to open the can, and that there was a smooth tree of life path from amoeba to man. We know much more than that today, and in that light Paley sounds a lot closer to the truth than Darwin. (And, I am making no inferences to the supernatural on biological complex functional organisation and information, only to the intelligent. It is the complex functional organisation of the cosmos that points beyond it to an extracosmic, extremely powerful intelligence. Of course such an entity sounds a lot like what theists have discussed for thousands of years, and is a good candidate for the originator of biologically functional complexity. But, that is to say that the theistic worldview in the Judaeo-Christian frame is exposed to serious empirical tests and is plainly passing them, despite the pretensions of the evolutionary materialistic magisterium that dominates science in our day. Heavens declaring the glory of God, check. Our world without and inner life point to an Author, check. Our conscience and moral intuitions point to a moral law and lawgiver that transcends opinions and politics or rhetoric of the day, check. Time to take God seriously again. And, to get over the glorified teenager rebellion that rejects God as the supreme Father figure.) In short, evolutionary materialism is plainly falling apart before our eyes. G'day GEM of TKIkairosfocus
July 14, 2010
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Cabal: And as far as we know and are able to determine, nothing mysterious is going on, just chemistry. That's one of the most arrogant and foolish statements I have ever read. I suppose that when you use your computer, nothing more than electromagnetic events is taking place? And when Skakespeare wrote Hamlet, nothing more than mechanical neuronal activity? You know, the development of a multicellular being from the zygote is certainly mysterious, at least in the sense that we cannot explain it at all. Understanding the laws of physics and biochemistry does not imply explanation of the facts of biology, any more than understanding the physical laws implies explanation of how a software works. From what you write, may I suggest that what you are trying to say is that the explanation is that what we see is unnatural, there is magic or something like that at work here? I don't know if you consider unnatural functional information, consciousness, intelligence and design. It's just a question of qords. Your choice. Let's just say that the explanation of complex functional information implies conscious intelligent beings and design.gpuccio
July 14, 2010
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Petrushka: You seem willing to accept all known facts from mainstream biology I always accept facts. It's on interpretations that I often disagree with mainstream biology. And again, it's not a problem of gaps, but of good and bad theories.gpuccio
July 14, 2010
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All right. Let’s try again. We leave out references to “Darwinism” as well as ID hype, ok? We go straight to the explanatory power of ID.
I wrote that ID tries to explain what we see.
Sounds promising. But what do we get?
You seem to get tripped up on the question of what it is that we see. We see self-replicating, self-constructing, nanoscale machines operating via sophisticated energy transfer schemes and using quantum level computing and communication …
That is, according to you, what we see. But wait a minute, is that really what we see? Could it be, let’s for a minute consider the alternative, that that is just your, and maybe other design proponents artistic rendering of what we see? Isn’t it, basically, all just expressions of chemistry at work? We know that from the very beginning of, say, a human being as a single cell, it grows to a complete, fully functional body over just nine months. And as far as we know and are able to determine, nothing mysterious is going on, just chemistry. Now that, in a nutshell, is an explanation, and AFAIK, a correct interpretation of what we see in terms of chemistry. Is anything besides chemistry involved? It is of course also eligible for poets to expand upon, and the images Lennart Nilsson have ‘painted’ for us are of course awesome. But putting what we see into words is not by itself an explanation. Would you like to try again, explaining what it is that we see? What you have said so far is just that “yes, we see lots of things going on”, to which I may add “Yes indeed, but what is the explanation for what we see? (My personal thought on that is that what we see in biology as well as in all other aspects of the universe are expressions of nature, the so-called natural forces at work.) From what you write, may I suggest that what you are trying to say is that the explanation is that what we see is unnatural, there is magic or something like that at work here?Cabal
July 14, 2010
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This sounds like the mechanism I was referring to earlier on when speaking of ORF’s. Using RNA editing, a “start” codon could be placed at the beginning of the intron, thus leading to its translation as a protein. Quite some software, eh?!
Too bad such sophisticated software allows its carrier to go extinct on a frequent basis. You'd think such sophisticated software could anticipate need rather than relying on disease, competition and predation to weed out the bugs. Just a quick question: when a disease like AIDS employs sophisticated software to wear down a human immune system -- let's say in a child who acquired the disease in a blood transfusion -- is that a score for front loading, or a score for genetic entropy? How does the ID research program distinguish between the sophisticated products of front loading, and the degeneration implied by genetic entropy? Can you provide an example of each in operation, and the characteristics that identify which process in in effect?Petrushka
July 13, 2010
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Petrushka [266]:
You seem willing to accept all known facts from mainstream biology, but seem to add some invisible guy pushing the atoms around at just the right times and places.
You mean you've never heard of Maxwell's Demon?! ;) Phaedros quoting Petrushka's paper:
For example,in the Drosophilasperm-specific dynein intermediate chain gene Sdic,a previously intronic sequence has been converted into a coding exon.”
This sounds like the mechanism I was referring to earlier on when speaking of ORF's. Using RNA editing, a "start" codon could be placed at the beginning of the intron, thus leading to its translation as a protein. Quite some software, eh?!PaV
July 13, 2010
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The reason for ID being superior to Darwinism has to do with its greater explanatory powers.
1. When confronted with an historical mystery or a phenomenon not yet understood, attribute it to an unseen entity having unspecified powers, acting at unspecified times and places, using unspecified methods, for unspecified reasons. 2. See Number one. 3. See number two.Petrushka
July 13, 2010
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Cabal [230]:
So far, I have searched in vain for that explanation. What has ID contributed to our understanding beyond the level of Genesis?
You seem full of yourself. I wrote that ID tries to explain what we see. Can Darwinism really explain what we see? Using Darwinism to explain biological complexity is like trying to pull an 18-wheeler out of the mud using a 125cc Honda motorcycle. It will get you absolutely nowhere. You seem to get tripped up on the question of what it is that we see. We see self-replicating, self-constructing, nanoscale machines operating via sophisticated energy transfer schemes and using quantum level computing and communication which, working in tandem, give rise to incredible macro-level organisms capable of flight, navigation using magnetic orientation, sonar, and star formations, and running 4-minute miles. And you want to say that this all happened by chance. Oh yeah, and a tornado passing through a junkyard can fashion a Boeing 747! The rather sensible explanation is that all of this was designed. veils of maya [250]: You think Darwinism is real, and ID is nothing more than a convoluted elaboration of what is real. However, what is Darwinism is not real; then, maybe, Darwinism is nothing more than a convoluted elaboration of ID. But, of course, Darwinists love tautologies. I don't really know why you think Darwinism has much of anything to do with reality. Oh, yes, there is this built in ability of organisms to adapt to their environments and to one another, and this ability does employ stochastic methods (or, at least what at this point look like strictly stochastic methods). But maybe we should just tip our hat to the wonderful Designer who thought of such an ability. (As did Asa Gray, a defender of Darwin) But I think your great faith in Darwinism comes from the sense you seem to have that Darwinism can actually predict things. The fact is is that if Darwinism could explain anything halfway well, then it actually could make predictions. But it can't---oh, well, it can to the degree that it is right about the adaptational abilities that organisms have. But this is really only trivial. But almost all of the really important predictions that Darwinism has tried to make have turned out to be wrong. Doesn't this raise any doubts in your mind, then, about Darwinism? In the early 60's, neo-Darwinism predicted that gel electophoresis would demonstrate rather homogenous families of proteins, that is, they would be mostly homozygous at virtually all of their lengths. WRONG. Along comes Kimura and the Neutral Theory. Since Darwinism sees its putative genetic mechanisms as the source of all phenotypic change, Darwinism predicts (dismisses) all non-coding DNA as junk. WRONG! When genome-wide sequencing promised to open up the secrets of the human genome, Darwinism was sure that there would be little genetic variation intraspecies. WRONG! OTOH, whereas ID would be somewhat neutral as to polymorphisms, it CORRECTLY predicted the role---the very important role---of non-coding DNA, and, because of its emphasis on regulatory mechanisms, is fully consistent with the great level of intraspecific variation we find in humans. Switching to another of your themes, you again aren't being logical. You want to denigrate ID by supposing that the only answer it can give, or that it is interested in, is that God did it. So you fault it because you think it won't give us answers. And then you say that Darwinism, just like quantum mechanics fails to explain gravity, can't give us, AND MAY NEVER GIVE US, all the answers. But I thought you wanted answers???? So you like Darwinism even thought it might not ever give you the answers you're looking for, but you don't like ID because, in your mind, it isn't interested in the answers that you're looking for. The reason for ID being superior to Darwinism has to do with its greater explanatory powers. ID would say that the crashed space vessel was designed by the aliens that crashed in them. Darwinism would say, no, this heap of metal was formed by natural forces. You know, like fashioning a 747 by having a tornado pass through a junkyard!PaV
July 13, 2010
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From Petrushka's paper... "De novo origination.Although the true de novo origination ofnew genes from previously non-coding sequences is rare,there are genes with a portion of coding-region sequence that has originated de novo.For example,in the Drosophilasperm-specific dynein intermediate chain gene Sdic,a previously intronic sequence has been converted into a coding exon." Could this actually be evidence of more functionality within the genome rather than "de novo" gene creation? That would make much more sense to me.Phaedros
July 13, 2010
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I absolutely agree. I am a big fan of transposons as a design implementation tool.
You seem willing to accept all known facts from mainstream biology, but seem to add some invisible guy pushing the atoms around at just the right times and places. As an observation from history, Newton used just such a conjecture to explain the stability of the solar system, when his calculations suggested it was unstable. Gaps theories evaporate with knowledge.Petrushka
July 13, 2010
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Petrushka: I still can't understand what we should rebut of the paper you quote. Or what it really "explains". Let's take some random examples: "Todd et al.63 investigated 31 diverse structural enzyme superfamilies for which structural data were available, and found that almost all have functional diversity among their members that is generated by domain shuffling as well as sequence changes. Emphasis mine. And so? What is that telling us? That an enzyme has to change to change? Mobile elements.Makalowski et al.14 were the first to describe the integration of an ALU ELEMENT into the coding portion of the human decay-accelerating factor (DAF ) gene. They found that mobile element-derived diversity was not limited to the human genome or to the Alu family15 (TABLE 1). Further analyses of human genome sequences16 and vertebrate genes17 have shown that the integration of MOBILE ELEMENTS into nuclear genes to generate new functions is a general phenomenon. I absolutely agree. I am a big fan of transposons as a design implementation tool. A more straightforward conjecture is that adaptive evolution might have had a principal role throughout the creation and subsequent evolution of new genes — we call this the ‘immediate model’, because it requires no waiting time for the evolution of a new function. Several case studies and theoretical works (for example, see REFS 29,30) have shown that the evolution of recently created genes involves accelerated changes in both protein-coding sequences and gene structures from the onset, which supports the immediate model. An important role of positive Darwinian selection has been detected in these processes and these studies have uncovered some interesting results. For example, the initial functions of new genes are rudimentary and further improvement under selection might be crucial. So, new gene functions that are created by altering a sequence that encodes one or a few amino acids might be special cases rather than the general situation. Also, the rapid changes in well-defined new genes with new functions could help to explain a past conjecture in molecular evolution studies: that rapid sequence evolution in many old genes might reflect a diverged function under selection31. Very clear indeed! How shall we ever be able to rebut such a straightforward, immediate, enlightening explanation! Petrushka, perhaps if you condescended to specify what is to be rebutted, we poor IDists could spare some of our idle time.gpuccio
July 13, 2010
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Petrushka: Perhaps you mistake science for some other enterprise. Science doesn’t do “why.” It does “how.” No, I mean "why it happened that way" in the sense of "what was the cause of what happened". Don't equivocate on words. Biochemical laws only explain why existing biological structures work. They can't explain why (or, if you prefer, how) they originated. A cause must be appropriate to explain what we observe. Show me the violation of the laws of physics and chemistry. No violation is needed for this post to appear. And yet it can be traced to a designer. I don’t need to show a specific sequence arose for the simple reason that biology doesn’t anticipate or strive for specific outcomes. Your old mantra. But the truth is that biology needs functional structures. Functional proteins. Functional biochemical machines. And so on. You have no need to anticipate all those things because you see them already in place. But how did they come in place? The fact that most known species are extinct should make that clear. ????? Why? Evolution doesn’t solve problems, search for solutions or exhibit any intelligent anticipation. That is maybe true of darwinists... Species that do not have the right alleles available at a time of significant ecological or environmental change simply go extinct. Again, true. And so? What has that to do with all the rest? Are you implying that designed things never go extinct? Do you want a list?gpuccio
July 13, 2010
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And if a gene did not derive from another gene, how did it originate?
Did you read the pdf I linked? Can you explain why this paper remains unrebutted, five years after Dover? What are the technical errors? You could make a name for yourself if you are smarter than Behe and Meyers, who testified at Dover. As I mentioned before, ID has a journal that's practically begging for a great paper.Petrushka
July 13, 2010
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Petrushka:
In other words, Is it part of the ID research program to test theories of how design is implemented by teasing out the way information is front loaded, if it is? Or how the designer anticipates all the myriad interactions of the ecosystem to insure that every living thing occupies a survivable niche? Or how the designer sometimes seamlessly transitions objects like jawbones into middle ear bones?
Yes.gpuccio
July 13, 2010
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No, it isn’t. You have to show a credible model of why that would happen, and why RV and NS could generate that new gene in the assumed time, and so on.
Perhaps you mistake science for some other enterprise. Science doesn't do "why." It does "how." Show me the violation of the laws of physics and chemistry. I don't need to show a specific sequence arose for the simple reason that biology doesn't anticipate or strive for specific outcomes. The fact that most known species are extinct should make that clear. Evolution doesn't solve problems, search for solutions or exhibit any intelligent anticipation. Species that do not have the right alleles available at a time of significant ecological or environmental change simply go extinct.Petrushka
July 13, 2010
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It’s the consciousness and intelligence of the designer which interacts with matter, and confers to matter a special order which corresponds to his mental representations governed by intelligent information.
So is of part of the research program of ID to work out the entailments of this theory. For example, an archaeologist, studying sharp pieces of flint, might attempt to replicate them to see if the patterns on the found objects match the patterns on objects known to be made by humans. In other words, Is it part of the ID research program to test theories of how design is implemented by teasing out the way information is front loaded, if it is? Or how the designer anticipates all the myriad interactions of the ecosystem to insure that every living thing occupies a survivable niche? Or how the designer sometimes seamlessly transitions objects like jawbones into middle ear bones?Petrushka
July 13, 2010
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Petrushka: In the meantime, observation and experimentation provides us with rates of change which, when taken with the observation of nested hierarchies in genomes, tell us approximately when certain changes occurred and whether the changes were point mutations, replications, or any of a dozen other kinds of mutations. That's very fine for me. And when will they also tell us how all those changes were generated by the RV + NS model? Haven't you understood yet that the whole problem is about causation? If a gene derives form another gene, how did it change? Can RV and NS account for that? And if a gene did not derive from another gene, how did it originate? Let's pretend you answer: "OK, a completely different gene was duplicated, and after it underwent changes which modified 80% of its primary structure, and created a new sequence that happende to fold orderly and have a new function, which was then integrated into what already existed". Is that even the beginning of an answer? No, it isn't. You have to show a credible nodel of why that would happen, and why RV and NS could generate that new gene in the assumed time, and so on.gpuccio
July 13, 2010
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Petrushka- "If “information” interacts with matter. Does it form mutual potential energy wells with other information or with matter? Can it scatter off matter? Can particles of information form orbits around matter, or vice-versa? In other words, how does information influence or determine the spatial arrangements of matter?" From this and from other things you've recently posted it seems to me that your fundamental problem with ID is that you simply do not get it. You don't.Phaedros
July 13, 2010
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It's interesting to note, that on one hand, the information orally passed down to progeny is bound to contain copying mistakes, according to these telephone-game-philosophers, and on the other hand, the progeny itself is bound to be a copying mistake. So, according to the telephone-game-philosophers, there is an ever-morphing story and an every-morphing storyteller. Of course, they plead special-pleading with regard to the timeless truth of the telephone-game-philosophy and the changeless truth of the telephone-game-philosophers. One the one hand, the telephone-game-philosophy (with respect to an oral tradition), would have us believe that there is a loss of sophistication and complexity as the oral tradition is passed from one generation to the other. But the telephone-game-philosophy (with respect to evolution), would have us believe that all of the animal's future generation's copying mistakes create animals that are more sophisticated and more complex. To summarize, atheist evolutionists, who hold to the telephone-game-philosophy, believe that the telephone-game degrades its subject (oral tradition) and also improves its subject (evolving animals) through the exact same mechanism of "copying errors". Inconsistent? Yes. Very much so. Clive Hayden
July 13, 2010
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about which we can certainly build scientific theories
I'm sure a lot of people are eagerly waiting for such theories of agency. In the meantime, observation and experimentation provides us with rates of change which, when taken with the observation of nested hierarchies in genomes, tell us approximately when certain changes occurred and whether the changes were point mutations, replications, or any of a dozen other kinds of mutations. A rather good discussion of this was entered as evidence at the Dover trial and was not rebutted by the defence. http://medicine.tums.ac.ir/FA/Users/Javad_TavakoliBazzaz/Genetic%20Changes/Genetic%20Change/The%20origin%20of%20new%20genes.pdfPetrushka
July 13, 2010
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@PaV (#229) You wrote:
First, this isn’t a logical statement. If ID is trying to explain away neo-Darwinism, then it’s anti-neo-Darwinist, not a form of neo-Darwinism.
Pav, Take solipsism, which is clearly anti-external reality. The solipsist experiences everything you and I accept as external to ourselves, but claims it is somehow internal to themselves. Since solipsism predicts exactly the same empirical observations we observe, this means every every discovery in technology, medicine and particle physics also “supports” solipsism. They just happen to be internal to the solipsist, rather than external. Furthermore, it's designed to explain away reality, not actually explain what we observe. Solipsism suggests there are dream-like aspects of myself that act like autonomous conscious beings which surprise me, have different personalities and even disagree with me on Solipsism. And there object-like facets of myself that obey laws of physics like facets even though, as a non-physicist, I can’t do the math that describes their behavior. Not to mention that these supposed people-like facets of myself discover new things about myself (physics like facets) all the time, which I wasn’t aware of previously. However, Solipsism makes no attempt to explain *why* object-like facets of one's self would obey laws of physics-like facets of one's self, etc. No explanation is presented at all. Instead, the claim is based on a supposed limitation that we cannot know anything exists outside of ourselves. In other words, Solipsism consists of the theory of realty with the added exception of it all being elaborate facets of the internal self. It merely attempts to explain way the currently tenable theory of reality. As such, solipsism is a convoluted elaboration of reality, despite being anti-reality, which can be discarded. We can make a similar comparison with biological ID. It's essentially the same as neo-darwinsm except, at a point depending on which variant of ID you happen to support, a designer caused/selected a change rather than a natural process. The empirical observations are the same, except a mysterious designer causes all of the positive changes, or orchestrated a specific series of positive and negative changes that resulting in a specific desired outcome, etc. (i'm obviously simplifying here to keep things short) Now, you might suggest the implications of this detail represents a massive difference between ID and neo-Darwinism, so it's something completely different. However, as I've illustrated above, the implications between solipsism and realism are massive as well, despite solipsism being an obvious convoluted elaborate of reality. Nor does ID explain why the changes in biology we observe even remotely match predictions of neo-Darwinism, but is caused by a intelligent designer instead. The particular rate of change we observe is simply the rate the designer happened to have chosen, etc. it's a non-explanation. Since it asserts that we can't explain what we observe, ID claims a designer must have done it. This is similar to the solipsist's claim that we cannot know anything outside of ourselves, therefore everything must be internal to himself and external reality does not exist. Despite being incredibly useful, we simply cannot know the method designer used to determine which changes to make, when to make them and how to make only the desired changes in just the right organisms without changing others. Furthermore, the reason why ID claims such information cannot be known is obvious. You "know" exactly who the designer supposedly is and such knowledge is impossible by definition. As such, biological ID it appears to be a convoluted elaboration of neo-darwinism.
My earlier point about population genetics/neo-Darwinism being dead addresses the fact that we are now seeing genetic mechanisms at work that are so sophisticated, with such higher levels of interplay than ever suspected, that PG/ND just can’t begin to deal with them.
Again, the incompleteness of PG is non-controversial, just as the incompleteness of quantum-gravity is non-controversial. No biologist claims we know everything. This appears to be hand waiving.
We’re dealing with sophisticated machinery driven by a “software system” that is mind-boggling in its complexity.
Which is why it's no surprise that our current understanding is incomplete. Nor may we ever understand it completely. However, this would in no way necessitate that a designer must have done it. Nor does posing a designer actually provide an explanation. You're merely accounting for what we observe, not explaining it.
That ID, in the face of this elaborately complex cellular mechanisms and machines, says that this is the product of design, not of chance, seems to me to be rather sensible. Don’t you agree?
If you're asking my option, the answer is no. I do not think it's sensible. I'm not a sophist or a ID supporter because they both represent convoluted elaborations of reality and neo-Darwinism, respectively. As such, I think they are bad explanations we can discard. Should ID start providing explanations, this could change. However, it seems clear that explanations will not be forth coming for reasons that are obvious.
As an analogy, all of this is like watching ’scientists’ examining the remains of a crashed, alien space vessel and claiming the whole time that what they’re looking at and investigating can really be explained by natural processes alone. Well, please excuse me if I say: “No, it can’t.”
You "can't" because you presuppose who the designer is. And we all know it's NOT some alien civilization. By very definition, the designer's ways cannot be understood, studied, etc. As such, you presuppose no explanation is possible or will be forthcoming.veilsofmaya
July 13, 2010
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Petrushka: In other words, how does information influence or determine the spatial arrangements of matter? and: But in any case, what part of the machinery of the cell is not chemistry? If part is information, what are the rules of interaction between disembodied information and atoms? Wrong, wrong, wrong! It's not information which interacts with atoms. Where do you take those ideas form? It's the consciousness and intelligence of the designer which interacts with matter, and confers to matter a special order which corresponds to his mental representations governed by intelligent information. Information is just "written" in the higher level order (semantic order) imparted by the designer's consciousness. We can’t have a discussion if you try to change the topic. Look who's talking :)gpuccio
July 13, 2010
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Petrushka,
Have you ever actually played telephone? Does the message turn to random gibberish, or does it morph into something different, but still a coherent message?
It's a message, in the respect that it's usually still words, but it isn't coherent.Clive Hayden
July 13, 2010
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Petrushka: Have you ever actually played telephone? Does the message turn to random gibberish, or does it morph into something different, but still a coherent message? That's really easy! Who plays telephone? Answer: conscious intelligent beings. So I ask: who "morphs the message into something different, but still a coherent message"? Try to answer yourself...gpuccio
July 13, 2010
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The arrangement of adenine-cytosine-adenine only results in threonine in the context of DNA transcription ...
We can't have a discussion if you try to change the topic. I asked about replication and imperfect replication. You are trying to change the subject to transcription. But in any case, what part of the machinery of the cell is not chemistry? If part is information, what are the rules of interaction between disembodied information and atoms?Petrushka
July 13, 2010
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Petrushka: So the basic entailment of ID is that some unspecified agency did some unspecified thing or things at unspecified times and places using unspecified methods for unspecified purposes, and that has made all the difference? Let's say that: the basic entailment of ID is that some unspecified agency (about which we can certainly build scientific theories) did some very specified thing (input functional information in the genomes of living beings) at unspecified times and places (not more unspecified than they are for darwinists: only the empirical knowledge and correct evaluation of genomes and of their evolution can give us the right scenario about times and places), using unspecified methods ((about which we can certainly build scientific theories, and certainly not more unspecified of those through which our consciousness interacts with our brains) for unspecified purposes (not really completely unspecified: the immediate purpose of many designed functions is obvious, and for higher level purposes reasonable inferences can be made, and possibly tested), and that has certainly made all the difference.gpuccio
July 13, 2010
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The animal, through reproduction, is bound to make copying mistakes as it’s progeny is passed down to future generations (so they contend), and will eventually become something else, something different, from what the animal was originally, and thus, evolution should be believed.
Analogies and metaphors always have limited domains, but I'll play along for a moment. Have you ever actually played telephone? Does the message turn to random gibberish, or does it morph into something different, but still a coherent message?Petrushka
July 13, 2010
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"Replication is chemistry. Copy errors are chemistry. If not, point to the place in the process that is not chemistry. And if it’s not chemistry, what exactly is it?" The arrangement of adenine-cytosine-adenine only results in threonine in the context of DNA transcription (and only in that context). One thing means (stands for, is mapped to) another, but is not the physical product of it. There is nothing you can chemically do to adenine and cytocine to end in threonine (outside of the semiotic context instantiated within DNA transcription). In other words, chemistry alone cannot provide an explaination for it; it requires the semiotic context (rules) within transcription in order to operate. The semiotic context is not chemistry. That is the point. As far as relying on the idea that "its all chemistry" as a way to ignore the larger point, I would just remind you that a red plasic ball is all chemistry - but there is nothing in the plastic that tells it to form a sphere and dye itself red. That little part of the red plastic ball is not in the chemistry. You take too much for granted.Upright BiPed
July 13, 2010
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I could have sworn it is molecules being replicate and not disembodied abstractions. But I will borrow a question from another poster on an unrelated forum:
If “information” interacts with matter. Does it form mutual potential energy wells with other information or with matter? Can it scatter off matter? Can particles of information form orbits around matter, or vice-versa? In other words, how does information influence or determine the spatial arrangements of matter?
Petrushka
July 13, 2010
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It occurred to me that the entire worldview of atheist evolutionists can be summarized as the telephone game. The telephone game (of which I'm assuming everyone is familiar) is used by atheists as an argument against the oral tradition of religion; an oral tradition is bound to make copying mistakes as the tradition is passed down to future generations (so they contend), and will eventually become something else, something different, from what was originally believed and passed down, and thus, religion should not be believed. The atheist evolutionist also believes that the telephone game (minor changes over time) is the real story in biological evolution. The animal, through reproduction, is bound to make copying mistakes as it's progeny is passed down to future generations (so they contend), and will eventually become something else, something different, from what the animal was originally, and thus, evolution should be believed. The telephone game is the atheist evolutionist's mantra. The telephone game for goodness sakes. You would think that it would be based on something more substantial; but it's not. Belief in evolution is based on a belief in the telephone game. Skepticism of an oral tradition is based on a belief in the telephone game.Clive Hayden
July 13, 2010
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