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Emphatic non-buttressation of ID

The language in the following paper is hilarious. Basically the researchers are saying “We know this looks like an engineered feedback control loop. We analyzed it and found it statistically impossible to have come about through a stochastic processs. But we will strenuously object to anyone calling it evidence of design.” ROFLMAO

“Chakrabarti and Rabitz analyzed these observations of the proteins’ behavior from a mathematical standpoint, concluding that it would be statistically impossible for this self-correcting behavior to be random, and demonstrating that the observed result is precisely that predicted by the equations of control theory. By operating only at extremes, referred to in control theory as “bang-bang extremization,” the proteins were exhibiting behavior consistent with a system managing itself optimally under evolution.

“In this paper, we present what is ostensibly the first quantitative experimental evidence, since Wallace’s original proposal, that nature employs evolutionary control strategies to maximize the fitness of biological networks,” Chakrabarti said. “Control theory offers a direct explanation for an otherwise perplexing observation and indicates that evolution is operating according to principles that every engineer knows.”

The scientists do not know how the cellular machinery guiding this process may have originated, but they emphatically said it does not buttress the case for intelligent design, a controversial notion that posits the existence of a creator responsible for complexity in nature.

Evolution’s new wrinkle: Proteins with cruise control provide new perspective
by Kitta MacPherson · Posted November 10, 2008; 10:00 a.m.

The rest of the paper is below the fold or at the link above.

A team of Princeton University scientists has discovered that chains of proteins found in most living organisms act like adaptive machines, possessing the ability to control their own evolution.

The research, which appears to offer evidence of a hidden mechanism guiding the way biological organisms respond to the forces of natural selection, provides a new perspective on evolution, the scientists said.

The researchers — Raj Chakrabarti, Herschel Rabitz, Stacey Springs and George McLendon — made the discovery while carrying out experiments on proteins constituting the electron transport chain (ETC), a biochemical network essential for metabolism. A mathematical analysis of the experiments showed that the proteins themselves acted to correct any imbalance imposed on them through artificial mutations and restored the chain to working order.

“The discovery answers an age-old question that has puzzled biologists since the time of Darwin: How can organisms be so exquisitely complex, if evolution is completely random, operating like a ‘blind watchmaker’?” said Chakrabarti, an associate research scholar in the Department of Chemistry at Princeton. “Our new theory extends Darwin’s model, demonstrating how organisms can subtly direct aspects of their own evolution to create order out of randomness.”

The work also confirms an idea first floated in an 1858 essay by Alfred Wallace, who along with Charles Darwin co-discovered the theory of evolution. Wallace had suspected that certain systems undergoing natural selection can adjust their evolutionary course in a manner “exactly like that of the centrifugal governor of the steam engine, which checks and corrects any irregularities almost before they become evident.” In Wallace’s time, the steam engine operating with a centrifugal governor was one of the only examples of what is now referred to as feedback control. Examples abound, however, in modern technology, including cruise control in autos and thermostats in homes and offices.

The research, published in a recent edition of Physical Review Letters, provides corroborating data, Rabitz said, for Wallace’s idea. “What we have found is that certain kinds of biological structures exist that are able to steer the process of evolution toward improved fitness,” said Rabitz, the Charles Phelps Smyth ’16 Professor of Chemistry. “The data just jumps off the page and implies we all have this wonderful piece of machinery inside that’s responding optimally to evolutionary pressure.”

The authors sought to identify the underlying cause for this self-correcting behavior in the observed protein chains. Standard evolutionary theory offered no clues. Applying the concepts of control theory, a body of knowledge that deals with the behavior of dynamical systems, the researchers concluded that this self-correcting behavior could only be possible if, during the early stages of evolution, the proteins had developed a self-regulating mechanism, analogous to a car’s cruise control or a home’s thermostat, allowing them to fine-tune and control their subsequent evolution. The scientists are working on formulating a new general theory based on this finding they are calling “evolutionary control.”

The work is likely to provoke a considerable amount of thinking, according to Charles Smith, a historian of science at Western Kentucky University. “Systems thinking in evolutionary studies perhaps began with Alfred Wallace’s likening of the action of natural selection to the governor on a steam engine — that is, as a mechanism for removing the unfit and thereby keeping populations ‘up to snuff’ as environmental actors,” Smith said. “Wallace never really came to grips with the positive feedback part of the cycle, however, and it is instructive that through optimal control theory Chakrabarti et al. can now suggest a coupling of causalities at the molecular level that extends Wallace’s systems-oriented approach to this arena.”

Evolution, the central theory of modern biology, is regarded as a gradual change in the genetic makeup of a population over time. It is a continuing process of change, forced by what Wallace and Darwin, his more famous colleague, called “natural selection.” In this process, species evolve because of random mutations and selection by environmental stresses. Unlike Darwin, Wallace conjectured that species themselves may develop the capacity to respond optimally to evolutionary stresses. Until this work, evidence for the conjecture was lacking.

The experiments, conducted in Princeton’s Frick Laboratory, focused on a complex of proteins located in the mitochondria, the powerhouses of the cell. A chain of proteins, forming a type of bucket brigade, ferries high-energy electrons across the mitrochondrial membrane. This metabolic process creates ATP, the energy currency of life.

Various researchers working over the past decade, including some at Princeton like George McClendon, now at Duke University, and Stacey Springs, now at the Massachusetts Institute of Technology, fleshed out the workings of these proteins, finding that they were often turned on to the “maximum” position, operating at full tilt, or at the lowest possible energy level.

Chakrabarti and Rabitz analyzed these observations of the proteins’ behavior from a mathematical standpoint, concluding that it would be statistically impossible for this self-correcting behavior to be random, and demonstrating that the observed result is precisely that predicted by the equations of control theory. By operating only at extremes, referred to in control theory as “bang-bang extremization,” the proteins were exhibiting behavior consistent with a system managing itself optimally under evolution.

“In this paper, we present what is ostensibly the first quantitative experimental evidence, since Wallace’s original proposal, that nature employs evolutionary control strategies to maximize the fitness of biological networks,” Chakrabarti said. “Control theory offers a direct explanation for an otherwise perplexing observation and indicates that evolution is operating according to principles that every engineer knows.”

The scientists do not know how the cellular machinery guiding this process may have originated, but they emphatically said it does not buttress the case for intelligent design, a controversial notion that posits the existence of a creator responsible for complexity in nature.

Chakrabarti said that one of the aims of modern evolutionary theory is to identify principles of self-organization that can accelerate the generation of complex biological structures. “Such principles are fully consistent with the principles of natural selection. Biological change is always driven by random mutation and selection, but at certain pivotal junctures in evolutionary history, such random processes can create structures capable of steering subsequent evolution toward greater sophistication and complexity.”

The researchers are continuing their analysis, looking for parallel situations in other biological systems.

The research was funded by the National Science Foundation.

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41 Responses to Emphatic non-buttressation of ID

  1. “The research, which appears to offer evidence of a hidden mechanism guiding the way biological organisms respond to the forces of natural selection, provides a new perspective on evolution, the scientists said.”

    Gee, a hidden mechanism. I wonder if that’s like dark matter or dark energy? lol.

  2. Chakrabarti said that one of the aims of modern evolutionary theory is to identify principles of self-organization that can accelerate the generation of complex biological structures.

    Self-organization? We’re not talking about the inherent properties of some chemicals that produce complexity or structures under certain circumstances. We’re looking at an information-based system which has a function, with the programmed goal of tweaking information via guided self-modification to correct the damage done by mutations. They seem to want to extend self-organization theory beyond its normal scope.

    The scientists do not know how the cellular machinery guiding this process may have originated, but they emphatically said it does not buttress the case for intelligent design

    Of course it does not…even though ID proponents had predicted we would find such things.

    More on that topic:

    ID-Compatible Predictions: Foresighted Mechanisms Identified?

  3. “Control theory offers a direct explanation for an otherwise perplexing observation and indicates that evolution is operating according to principles that every engineer knows.”

    And yet, “Control Theory” is Engineering discipline, a manifestation of intelligent design by engineers. “Control Theory” isn’t random chance, it is the engineering practice of using deliberate pre-planned designed-in mechanisms to effect desired pre-determined outcomes.

    No doubt every engineer will henceforth be sent to re-education camps to receive true enlightenment on how randomly evolved is their methodology, all the better to more consistently explain perplexing observation with perplexing theory.

  4. If it looks like a duck, walks like a duck, talks like a duck, it’s random chance. :-/

    I’m reminded of the neo-darwinian experiment wherein a frog’s legs are successively amputated and the frog successively jumps shorter and shorter distances in response to repeated verbal commands, culminating in the final data point of a frog with zero legs jumps zero distance, and the obvious explanation that a frog with no legs can’t hear because neo-darwinian evolution dictates hearing redundancy is too expensive a trait to evolve and confers no surivability. QED.

  5. Patrick,

    I think you might be onto what I was thinking. Doesn’t this experiment just simply show that when proteins are damaged they have a mechanism that allows them to rebuild so as to be better functioning?

    For instance, “Darwin’s Finches” changed over a drought, but once the drought was over the finches went back to normal. Is not this similar to what they’re finding in these proteins?

    If so it seems more like an anti-evolution mechanism, rather than some strange self-organization working to evolve organisms.

  6. Don’t rely on the press release. Two articles are available here.

    The opening paragraph of “Mutagenic Evidence for the Optimal Control of Evolutionary Dynamics” is a striking example of the philosophical cretinism of scientific geniuses. The authors seem to be utterly oblivious to the distinction between the model and the modeled entity.

    Take just the opening sentence:

    Evolution is guided by the optimization of ?tness meaures that balance functionally bene?cial properties.

    Wow! Axiomatic teleology, model reification, and circular definition, all in 14 words.

    The authors are surely competent to conduct isolated scientific studies, but are clearly incompetent to state the ramifications of their work for modern evolutionary theory.

  7. Evolution is guided by the optimization of fitness meaures that balance functionally beneficial properties.

    Ligature of “fi” got me.

  8. Here’s the sentence that stands out to me:

    “The authors sought to identify the underlying cause for this self-correcting behavior in the observed protein chains. Standard evolutionary theory offered no clues”

    Standard evolutionary theory offers NO CLUE! And, of course, the answer is immediately obvious from an ID perspective—hence their disclaimer—and yet ID is “not scientific”. Somehow ID can explain, and predict, phenomena; yet it’s “not scientific”. Darwinism “doesn’t [offer] a clue”, but it’s “science”. In fact, NOTHING IN BIOLOGY MAKES SENSE WITHOUT IT.

  9. Hey this is great! These findings confirm what I have been thinking for a long time! It is not only an intelligently designed universe but and intelligently *piloted* universe… oops…there goes my career in science.

  10. Having a AA degree in instrumentation; I know that This control is no small thing: the feedback (proportional; integral; derivative) pid equation for each controller is set to many independent “finely tuned” parameters for each individual process to be controlled. Not to mention the precise setting/engineering for each sensing mechanism and the precise setting/engineering for each actuator mechanism that has to implemented into each control loop that is utilized. Seeing as many proteins have different “folding” rates I can easily see where each and every protein would have to be carefully accounted for in the design of the loops.

    This site has the pid equations:

    http://bestune.50megs.com/PID.htm

  11. How in the world can they possibly claim this:

    “the proteins were exhibiting behavior consistent with a system managing itself optimally under evolution.”

    The system is managing itself optimally period. Control loops are set to precise UNCHANGING setpoints for a desired output that will will fall within a precise 0 to 100% range, again with no change built in. The fact that the control loops exist in fact adds countless layers of poly-functional complexity to the life system that makes it extremely more resistant to any “random evolutionary changes” of the proteins themselves. i.e. the proteins are being precisely controlled to within a specific tolerance…This Control Loop is a extremely anti-Darwinian finding to say the least.

  12. William Brookfield:

    “It is not only an intelligently designed universe but and intelligently *piloted* universe…”

    Indeed it is! Pehaps we should chenge our ID from ID (Intelligent Design) to IM (Intelligent Management). How does that sound?

    Obviously, our “friends” in the other field would immediately rename us as IMbeciles…

  13. From what I’m gathering from all these posts, it seems like this is looking really, really bad for neo-Darwinism. If there is a mechanism set into proteins that keep proteins in check from too much change… the theory is screwed.

    I just hope I’m understanding this process correctly…

  14. I suppose a diehard Darwinian would say that this is just another example of a system optimised by natural selection, albeit at a fundamental level.

    I can forsee them arguing that this observed mechanism is so fundamental that it has to form part of the platform of basic processes that support all cellular life, and hence a platform for evolvable organisms.

    Just playing devil’s advocate here.

  15. *closesearsandyellsCHANCEDIDIT!*

    …ahem.

    This is a significant finding. Now what would be even more interesting, is when this mechanism “evolved” (pardon the faulty lingo).

    If it is statistically impossible, and it was present in the earliest bacteria (~500million years after earth was formed last I read – correct me if I’m wrong)…

    Darwin’s theory is seriously running out of time for the (chance + time) algorithm to work.

  16. LOL!

    Ignore the man behind the curtain, folks. We’ve already used our super duper powers of scientistic genius to determine there is absolutely nothing telic about this!

    Classic.

    Thanks for sharing, Dave.

  17. It sounds like these people are into their own ID research.

    Sequence optimization and designability of enzyme active sites
    Raj Chakrabarti et al 2005

    “Many residues in enzyme active sites can be computationally predicted by the optimization of scoring functions based on substrate binding affinity. We explore the generality of this surprising observation. We introduce the notion of the designability of an enzyme active site, a metric that may be used to guide the search for protein scaffolds suitable for the introduction of de novo activity for a desired chemical reaction.

    All known natural proteins adopt one of only ?1,000 distinct protein folds. Researchers apply this knowledge to the construction of unnatural proteins.

    We endeavor to extend the conceptual foundation for theoretical active-site design by asking: what is the macroscopic state associated with the active site that corresponds to the structure of the protein fold in core designability?

    We explore the effects of moving the ligand from its native conformation on predicted sequence distributions. Implications of these results for de novo active-site design and the notion of active-site designability are analyzed.”

  18. In #14 avonwatches wrote:

    “If it is statistically impossible, and it was present in the earliest bacteria (~500million years after earth was formed last I read – correct me if I’m wrong)…”

    You are indeed wrong. The electron transport chain that was studied in the research reported on this thread is located in the inner membranes of mitochondria, not all bacteria (a similar chain is located in the thylakoid membranes of chloroplasts). Mitochondria are cellular organelles of eukaryotes, which evolved approximately a billion years ago. Given the currently accepted date for the origin of life on Earth – 3.8 billion years ago – this means that there were at least 2.8 billion years for the cytochrome electron transport chain to evolve a homeostatic regulatory system in the bacterial ancestors of mitochondria. That’s almost five times as long as the length of time that complex multicellular organisms have existed on the planet (i.e. about 600 million years).

    As to the assertion by the authors of the paper in Physical Review Letters that the homeostatic regulatory mechanism they discovered is not predicted by evolutionary theory, that would only apply to the “modern evolutionary synthesis”, which is based on the idea that all phenotypic change is preceded (and caused by) genotypic change. This assumption, while warranted in the 1920s, is now known to be so inadequate a description of reality as to be essentially wrong.

    For more on what evolutionary biologists currently think about the relationship between phenotypic and genotypic change, I recommend reading Jablonka & Lamb/Evolution in Four Dimentions.

  19. Viva la’ “Secret Handshake”

  20. Allen,

    Yesterday I wanted to make a remark, and suppressed it because I’m not equipped to follow through. You say:

    As to the assertion by the authors of the paper in Physical Review Letters that the homeostatic regulatory mechanism they discovered is not predicted by evolutionary theory, that would only apply to the “modern evolutionary synthesis”, which is based on the idea that all phenotypic change is preceded (and caused by) genotypic change.

    I was going to comment that a parent transmits an entire cell, and not just a genotype, to the offspring. From this perspective, it is not surprising that some critical cellular processes would evolve to be robust under genetic mutation. But processes of the mitochondria are quite special, in light of endo- symbiotic theory. That is, mitochondria appear to have descended from Proteobacteria living within other cells. It seems to me that we should expect particular, rather than general, explanations of the evolution of mitochondria.

    Care to elaborate? set me straight?

  21. 21

    Obviously, our “friends” in the other field would immediately rename us as IMbeciles…

    ^ LOL

  22. Does anyone know how many billions of years of selecting “dust-bunnies” it takes to get a real (non-dust) bunny? And does anyone know how many billions of years of selecting Darwinian randomness-bunnies it takes to get a real (ordered/structured) bunny? Hint: “randomness” and “order” are opposites and the word “impossible” is a possible answer.
    “Mutations” are random wrt the structural needs of organisms. The same goes for random variation, random gene duplication, random genetic drift, random gene transfer, random frame shifting etc, etc… All of these are random wrt the structural needs of new species and new biological structures (such as feedback loop control guidance systems). Targeting (order) is real and it cannot be produced by randomness (the absence of targeting).

  23. For more on what evolutionary biologists currently think about the relationship between phenotypic and genotypic change, I recommend reading Jablonka & Lamb/Evolution in Four Dimentions.

    While I’ve agreed with you in the past that attacking an old should-be-dead-but-is-not idea is a waste of time, how does recommending reading those books (which many of us have) even begin to tackle the problem of evolving such a system via non-foresighted mechanisms? I’ve yet to see any good examples of how current ideas fare better to the point where they overcome all known obstacles.

  24. Only a sit-down meeting with the designer will convince these guys. But anyway-

    Sounds to me like more evidence for Biological Information in 3 Dimensions.

  25. Only a sit-down meeting with the designer will convince these guys.

    Hundreds of millions of Buddhists sit to open themselves to Mind.

    A telling anomaly of the ID movement is that it does not embrace the Buddhists as non-materialists who have no problem seeing design in all experience. Might it be that there is no way to personify Mind?

    If you know God, then you know the Creator, and you have no problem doing science with methodological naturalism (which has the value of forcing you to explain as many observations in terms of other observations as you can, rather than fall back lazily on supernatural intervention).

    I am sympathetic to observations by Johnson and Dembski in the 1990′s that methodological naturalism tends to get turned into philosophical naturalism. My response to this is to educate people, not to “renew” science.

  26. Patrick:

    “how does recommending reading those books (which many of us have) even begin to tackle the problem of evolving such a system via non-foresighted mechanisms?”

    I obviously agree with you. Allen McNeill is rather optimistic about how much the present academic establishment could agree that the “modern evolutionary synthesis” is essentially wrong. And, to be frank, his “post-modern evolutionary synthesis” does not look much better in terms of scientific credibility.

    Let’s take, for instance, the essential problem of the generation of functional information, which is the core of the ID theory. Essentially, the new “synthesis” seem satisfied with multiplying the sources of random variation, without understanding that random variation has always the same limits, be it in the genome or epigenetic, or what else. Random is random, that is, undirected.

    But maybe that the “very new synthesis” is betting on non random principles. Such as? Design? I don’t think so. And then? Maybe adaptation.

    Well adaptation is an interesting principle, and I will not deny its importance. I am among those who see with favour the new wave of neo Lamarckism, because I do believe that something may be there.

    But adaptation, too, has its limits. First of all, there are two kind of adaptations: automatic (which is designed), and conscious. In other words, living beings could be able to adapt because they have been designed to do so (and that is probably the main kind of adaptation), or because they “learn” to adapt.

    The first form of adaptation is essentially a further argument for design, and I will not spend more on that. After all, I do believe in design.

    The second form of adaptation, by “learning”, is more interesting, and I would be very happy to give it some space, even in “primordial” cells like bacteria, if the evidence supports it.

    But, in the end, even that kind of adaptation cannor solve the fundamental problem: how is complex functional information generated?

    It cannot solve it because, as should be obvious, we are, in the living realm, in front of levels of design so deep and complex that they cannot certainly come from learning adaptation. Just to make an example, guessing the correct primary structure of a protein which can ensure the correct folding and active site for a necessary function is a problem which is still far beyond our complete control, even with all we know of physical laws, and with all our computing and experimental power. How can we think that the same functional information be in the range of adaptive learning (unguided, undesigned?). It cannot be.

    Obviously, another source of complex functional information must be active. That other source is some kind of designer(s), and nothing else. And the designer(s) can be anyone or anything, but it is certainly a better designer then we presently are.

  27. Sal Gal:

    the theory of design is, in my opininon, perfect methodological naturalism. As I have often debated here, the problem with the words “nature” and “natural” is that they can be defined in a lot of different ways.

    Naturalism is materialism for materialists, because they think that there is only matter in nature. Maybe naturalism is materialism even for extreme dualists, who believe that there is only matter in nature, and that spirit is completely something else. But naturalism is not materialsm for me, because I don’t believe that reality is only material.

    ID ia perfectly naturalistic. It starts with observations about the nature of biological information, and goes on with observations about the nature of human design. Isn’t that natural? Isn’t biological information part of nature? Isn’t human design part of nature?

    The problem is: are biological information abd human design only the product of the known laws of matter? For ID, and for me, the answer is a very strong “No”. You cannot explain biological information without a designer, and you cannot explain the process of design only on the basis of the laws of matter. You need the concept of consciousness, and you need to address the laws of consciousness.

    Isn’t consciousness a part of nature? I would definitely say it is. Isn’t intelligence a part of nature? It certainly is.

    So, let’s be naturalistic in the only possible and correct way. Let’s admit that nature is not the sum of what we know or think we know, but much more. Present day darwinists are not methodological naturalists, and not even philosophical naturalists. They are, indeed, philosophical materialists, and of the reductionist kind, because even their conception of matter is unrealistic, and essentially based on the assumed absolute validity of what they presently believe to be true. They are, in essence, dogmatic scientists, and no naturalists at all.

  28. Sal Gal:

    “A telling anomaly of the ID movement is that it does not embrace the Buddhists as non-materialists who have no problem seeing design in all experience.”

    Why do you say that? Have you read “The spiritual brain”?

  29. Some diehard evolutionists will presume that natural selection most have been operating in a pre-biotic environment in some as yet unknown way.

    I think there’s a general push into theroretical investigation of pre-biotic times, spurred largely by the acceptance of the findings of Carl Woese with respect to the Archaeans.

    These are a form of “bacteria” which are not bacteria, as evidenced by differences in the RNA encoding of fundamental cellular processes. New technology has opened up a whole new realm of comparitive biology between “domains” of life, “domain” being a classification more fundamental and more primitive than “Kingdom”, and completely unknown before the 1970’s.

  30. This is the precious statement:

    “Biological change is always driven by random mutation and selection, but at certain pivotal junctures in evolutionary history, such random processes can create structures capable of steering subsequent evolution toward greater sophistication and complexity.”

    That is, everything is random mutation and selection, until, well, it isn’t!

  31. Sal Gal,

    I think you’re misinformed. On this very site I’ve seen buddhist conflicts with materialism highlighted in posts – even shinto, muslim, and other conflicts.

    The ID movement at large may have a distinctly judaeo-christian aspect to it, but I’ve never seen any incident of ID obfuscating on the question of whether buddhism is a materialist worldview.

    (With the exception of strange and explicitly Western-materialist ‘interpretations’ of buddhism, an extreme minority that traditional/eastern buddhists seem to regard with some horror.)

  32. Also regardless of what they say it does buttress the case for intelligent design.

    And ID does NOT posit the existence of a creator responsible for complexity in nature.

    IDists understand that complexity can arise without the aid of a designing agency.

  33. 33

    Joseph said:

    And ID does NOT posit the existence of a creator responsible for complexity in nature./blockquote]

    Amen, brother!

  34. “…the researchers concluded that this self-correcting behavior could only be possible if, during the early stages of evolution, the proteins had developed a self-regulating mechanism…”

    That’s a mighty big “if”. Or it could be that, like my car’s cruise control, it was intelligently designed.

  35. In other words, you find it hard to believe that chance and chance alone could do it, but you stick with evolutionary theory because an Intelligent Designer (God), who is superior in intelligence, could not possibly have designed it or anything else.

    Contrast that to Hebrews 3:4: ‘For every house is constructed by someone, but He that constructed all things is God.’

  36. Digdug:
    It seems to me that Intelligent Design can be summed up as such: “I can’t possibly believe that the complexity of life could have come about on its own, so therefore I’ll believe that it was designed by an even MORE complex being who came about on its own!”

    It isn’t just complexity. We know complexity can arise without an inteligent designer.

    And all someone has to do is to demonstrate that a living organism (specified complexity) can arise without any agency involvement and ID falls.

    And no one says that the designer came into being all on its own.

    We don’t know anything about the designer except what we can learn by studying the design.

    The bottom-line is we exist and there is only ONE reality behind that existence.

    And just what do you think are the alternatives to ID?

    I know of two- Special Creation and sheer-dumb-luck.

  37. Digdug:
    I believe that evolutionary science is correct because, quite simply, everything else I’ve heard makes far less sense.

    So you believe that we owe our existence to an accumulation of genetic mistakes?

    Did you know that there isn’t any data which would demonstrate that the transformations required are even genetically obtainable?

    IOW no one knows whether genetics can account for the diversity observed. The premise cannot even be objectively tested.

    Did you also know we don’t even know what suite/ combination of genes are responsible for our vision system?

  38. I personally know someone who won the grand prize in a contest – a trip for four to France! The odds were astronomical against her.

    I don’t know what contest this was but let’s presume the odds were close to 1 in 10^8 (around the odds of Powerball). That’s a far cry from the Universal Probability Bound of 10^150 (or 500 informational bits).

    But that’s only the Complexity, not the Specification, of CSI. Your friend would have to win a number of such contests in a row to qualify.

    Keep in mind these are not the numbers for the entire evolutionary history of Earth. This is just for one information-based system!

    We could start with just the Origin of Life:

    “The first enzyme very possibly contained the sequence Asp-Ser-Gly, which is part of the active centers of phosphoglucomutase, trypsin, and chymotrypsin. Ribonuclease contains 124 amino acid residues. If all were equally common, this would mean 540 bits. The number is actually a little less than that. This number could be somewhat reduced if some amino acids were rare both in the medium and in the enzyme. I suggest that the primitive enzyme was a much shorter peptide of low activity and specificity, incorporating only 100 bits or so. But even this would mean one out of 1.3 x 10^30 possibilities. This is an unacceptable, large number. If a new organism were tried out every minute for 108 years, we should need 10^17 simultaneous trials to get the right result by chance. The earth’s surface is 5 x 10^18 cm2. There just isn’t, in my opinion, room. Sixty bits, or about 15 amino acids, would be more acceptable probabilistically, but less so biochemically. I suggest that the first synthetic organisms may have been something like a tobacco mosaic virus, but including the enzyme or enzymes needed for its own replication. More verifiably, I suggest that the first synthetic organisms may be so constituted. For natural, but not for laboratory life, a semipermeable membrane is needed. This could be constituted from an inactivated enzyme and lipids. I think, however, that the first synthetic organism may be much larger than the first which occurred. It may contain several different enzymes, with a specification of 5000 bits or so-about the information on a page of Chamber’s 7-figure logarithm tables. This should be quite within human possibilities. The question will then arise: How much smaller may the first natural organism have been? If this minimum involves 500 bits, one could conclude either that terrestrial life had had an extraterrestrial origin (with Nagy and Braun) or a supernatural one (with many religions, but by no means all).” (Haldane, Ibid., p.14).

    Although Haldane’s comment is old, I find that interesting considering Koonin’s recent comments regard the unguided Origin Of Life (OOL) scenarios and as a conservative estimate he calculated 1 in 10^-1018 for the possibility that such a system could have arisen.

    Also, keep in mind that the relatively “simple” minimal system created by JCVI is a 582970 base pair genome. (On a site note I was able to do some design detection in regards to this genome.) And even simpler viruses, which rely on hosts for survival, are composed of thousands of informational bits.

    BTW, keep in mind that many ID proponents support Intelligent Evolution. That is, evolution did occur but intelligence was involved as well as none-foresighted mechanisms. There are multiple popular hypotheses as such. Some even believe that only intelligence was involved with the origin of LUCA and the system was “designed to evolve via non-foresighted mechanisms”.

  39. Also, keep in mind that the relatively “simple” minimal system created by JCVI is a 582970 base pair genome. (On a site note I was able to do some design detection in regards to this genome.)

    Do you refer to your comments at http://www.uncommondescent.com.....challenge/

  40. This is being discussed here:
    http://dilbert.com/blog/entry/.....ttle_deal/

    Thought this comment was interesting. Can anyone respond to this?

    “The authors are trying to explain this puzzle: They looked at cytochrome oxidiase c’ in 4 different species. In two of them, the active heme site had a very low redox potential, compared to the possible range found in 4-residue mutants. In the other two, it had a very high redox potential.

    They then had 2 possible explanations:

    1. For some reason we don’t yet know, a low redox potential for this protein is good in two of these species, but bad in the other two.

    2. There is a magical force animating evolution, and this one study of one protein in 4 species overturns everything everybody thought they had learned about evolution over the past 150 years.

    They chose the second.

    The authors found that “redox potential” (just black-box that term and pretend we know what it means) of one protein was maximized in 2 organisms, and minimized in 2 other organisms.

    They then reasoned:
    We don’t know how redox potential affects the efficiency of ATP generation.
    Therefore, we know that redox potential doesn’t affect ATP generation. (That’s the crucial leap-of-illogic.)
    Therefore, the fact that this is minimized in 2 organisms, and maximized in 2 other organisms, may be because there is a general mechanism that has evolved that tries to set all properties of a protein at either a maximum or at a minimum, regardless of whether those properties are important.”

  41. sparc,

    Yes, and here is the quick use for the EF: did Musgrave purposely pull these sequences from the Venter sequences, an instance of design?

    1. No law is known to be capable.

    2. A minimum of 1920 informational bits seems to say so.

    3. The specification is the marked overlap with the watermark along with Musgrave’s designation that the source of some of the information would be human. So using the EF we can be perfectly clear that Musgrave did intentionally pull from Venter.

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