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Coordinated Evolution

by MikeGene

Arabidopsis thaliana is a plant that underwent a duplication of its entire genome about 20-40 million years ago. Researchers from the University of Texas recently tested the rate of expression divergence between these duplicated genes.

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This entry was posted on Friday, May 18th, 2007 at 2:23 pm and is filed under Evolution, Intelligent Design. You can follow any responses to this entry through the RSS 2.0 feed. You can leave a response, or trackback from your own site. The trackback link is: http://telicthoughts.com/coordinated-evolution/trackback/

60 Responses to “Coordinated Evolution”

  1. Bradford Says:
    May 18th, 2007 at 2:48 pm

    Quoting from the link:

    What's teleological point of all this? For most people focused on evolution, gene duplication is considered as a brute give - something that happens and something that happens to affect evolution. Yet I am becoming increasingly convinced that gene duplication echoes the teleological essence of evolution. In this example, gene duplication functions in the overall context of the cell's architecture and physiology such that evolution proceeds quite smartly. The genes closest to interfacing with the environment behave almost like "feelers," helping organisms to find their way across evolutionary time. Yet because of the same cell architecture/physiology, the same process of gene duplication functions more as a buffer in the developmental context, allowing the cell to tweak a constrained process in conjunction to what the "feelers" find.

    Is it your view that the tweaking process occurs after the gene duplication and that subsequent mutations could be directed by cellular mechanisms or do you view the tweaking process as including the gene duplication itself? If mutations are random they could become less so, at least with respect to their number and genomic location, by an adjustment of genomic repair functions as a response to environmental stress. Would this be a "feeler" adjustment in your view?

  2. Comment by Bradford — May 18, 2007 @ 2:48 pm

  3. MikeGene Says:
    May 18th, 2007 at 6:26 pm

    Hi Bradford,

    Is it your view that the tweaking process occurs after the gene duplication and that subsequent mutations could be directed by cellular mechanisms or do you view the tweaking process as including the gene duplication itself?

    Good question. I would include gene/genome duplication, as it unlocks this search.

    If mutations are random they could become less so, at least with respect to their number and genomic location, by an adjustment of genomic repair functions as a response to environmental stress. Would this be a "feeler" adjustment in your view?

    Could be. I raise one possibility here.

  4. Comment by MikeGene — May 18, 2007 @ 6:26 pm

  5. magnan Says:
    May 18th, 2007 at 6:26 pm

    "What's teleological point of all this? ….. The genes closest to interfacing with the environment behave almost like "feelers," helping organisms to find their way across evolutionary time. Yet because of the same cell architecture/physiology, the same process of gene duplication functions more as a buffer in the developmental context, allowing the cell to tweak a constrained process in conjunction to what the "feelers" find."

    This seems to be along the line of epigenetics - reverse flow of information from the environment to the genome, re. Mae Wan Ho. Gene duplication is supposed to be a random event, much less likely than point mutations and other relatively simple mutations. The research cited seems to be saying that the organism can respond more "intelligently" to these random events than merely by natural selection processes.

    It seems to me that if these events truly are random there is still a big statistical problem. Evolution of many incredibly complex intertwined structures/mechanisms required very many "coordinated" evolutionary developments that in turn required too many fortuitously and simultaneously occurring special mutations, whether the organism had "feelers" responding to them or not. For the model to work at all, the gene duplications and subsequent mutations to the duplicated genes would have to be "directed" by the organism in response to environmental stresses. Of course orthodox MET claims that the sheer number of mutations occurring and being fixed in a large population easily overcomes the statistical argument.

    Anyway, such a mechanism would have to be able to sense specific environmental and physiological stresses, have a model of which genes and non-coding regulatory DNA code for particular biological characters and related physiological stresses including how the genes/regulatory DNA for different systems interact, do the correlation between them, and finally modify or duplicate the appropriate genes/regulatory DNA.

    This mechanism would itself also have to be encoded in DNA in addition to genes and developmental regulatory DNA. This "epigenetic" mechanism would have to be at least as complex as the design structural coding, and would have to also have a model of origin, which couldn't be through itself.

    Some recent research perhaps relates to this. Long sections of non-coding DNA was found to still be conserved in evolution despite not apparently being needed for any detectable function in the mice involved, i.e. the mice were perfectly normal and healthy after this DNA was knocked out. Could this be because it is part of such a system?

    Even if this is the case, there would still not be any real intelligence in the process. The "teleology" would just be a robotic mechanical tinkering with genes in response to physiological stresses. Would such an epigenetic mechanism have been able to originate the actual apparently designed complexity of organisms? The essence of ID theory and concepts seems to me to be the strong perception that some sort of "real", creative, and non-robotic/mechanical intelligence must have been involved in the evolutionary process.

  6. Comment by magnan — May 18, 2007 @ 6:26 pm

  7. Joy Says:
    May 18th, 2007 at 7:16 pm

    Mike:

    Good question. I would include gene/genome duplication, as it unlocks this search.

    Hi, Mike. Isn't Arabidopsis the plant that reverted to ancestral flower structure after a mutant development didn't work out, despite NOT having the original genes in their genome anymore? I presume that would include the entirety of the genome, i.e., the original doubled.

  8. Comment by Joy — May 18, 2007 @ 7:16 pm

  9. MikeGene Says:
    May 18th, 2007 at 7:24 pm

    Hi Joy,

    I have not heard this before. Do you have a link?

  10. Comment by MikeGene — May 18, 2007 @ 7:24 pm

  11. Joy Says:
    May 18th, 2007 at 7:58 pm

    Sure Mike, it's Plants defy Mendel's Inheritance Laws, May Prompt Textbook Changes. For interesting side-note, check out Flowers Shape Themselves to Guide Pollinators. Arabidopsis seems to be an evolutionary prodigy!

  12. Comment by Joy — May 18, 2007 @ 7:58 pm

  13. Thought Provoker Says:
    May 19th, 2007 at 10:33 pm

    Hi Mike and Joy,

    Yeah, let's do science. :mrgreen:

    Nice article Mike. And, once again, Joy comes through with a very interesting piece of information she just happen to have in one of the pockets of her "professional fool" uniform.

    Using the links Joy provided, I tracked down a PubMed link. here

    At the risk of embarrassing myself, I think some of what it being said appears to have RNA World finger prints on it.

    Regards,
    TP

  14. Comment by Thought Provoker — May 19, 2007 @ 10:33 pm

  15. MikeGene Says:
    May 19th, 2007 at 10:53 pm

    Hi TP,

    At the risk of embarrassing myself, I think some of what it being said appears to have RNA World finger prints on it.

    I bet yer right. I haven't looked into it, but RNA editing seems to be a candidate.

    BTW, thanks to a handy little protein known as reverse transcriptase, the RNA world also acts as a "feeler." There's a subversive thought.

  16. Comment by MikeGene — May 19, 2007 @ 10:53 pm

  17. magnan Says:
    May 20th, 2007 at 2:29 pm

    I won't bother you any more, but I was wondering why no feedback. I guess my thoughts are considered too amateurish and ignorant to bother with. I am indeed a rank amateur not a biologist, but I have still been trying to learn something of this subject using my background as an engineer. At least a little feedback would be appreciated so that I could correct my thinking on this.

  18. Comment by magnan — May 20, 2007 @ 2:29 pm

  19. Bradford Says:
    May 20th, 2007 at 6:54 pm

    Magnan wrote:

    Some recent research perhaps relates to this. Long sections of non-coding DNA was found to still be conserved in evolution despite not apparently being needed for any detectable function in the mice involved, i.e. the mice were perfectly normal and healthy after this DNA was knocked out. Could this be because it is part of such a system?

    I'm familiar with the relevant research. I suspect there is function related to the knocked out DNA but that it is either some sort of redundancy or a function that would become activated under unusual conditions. I could be wrong though and this is strictly my personal view.

    Even if this is the case, there would still not be any real intelligence in the process. The "teleology" would just be a robotic mechanical tinkering with genes in response to physiological stresses. Would such an epigenetic mechanism have been able to originate the actual apparently designed complexity of organisms? The essence of ID theory and concepts seems to me to be the strong perception that some sort of "real", creative, and non-robotic/mechanical intelligence must have been involved in the evolutionary process.

    The "real", creative, and non-robotic/mechanical intelligence" view is an apt description of my own position but there is another that attributes teleology to conditions present at origins that dictated the course of subsequent evolution. The two paradigms are not necessarily in conflict although the first one described has an additional causal component. The second would be more likely to be endorsed by David Berlinski for example.

  20. Comment by Bradford — May 20, 2007 @ 6:54 pm

  21. Joy Says:
    May 20th, 2007 at 9:01 pm

    magnan:

    Even if this is the case, there would still not be any real intelligence in the process. The "teleology" would just be a robotic mechanical tinkering with genes in response to physiological stresses.

    Why must it be "robotic?" Because it operates via physical mechanics? I ask because there's a version of ID I think has meat, called Endogenous Adaptive Mutation. It isn't particularly random, and incoming evidence supports this view on several levels. The "intelligence" in the design originates in the organism itself, obeying the prime directive (so to speak) - Survive, Propagate.

    Life forms do this aggressively. Whenever they can. Yet another driver of evolution, among several identified that are less-than random as well as less-than uniformitarian.

    Why can't science incorporate endogenous design, in a front-loaded framework? It's not automatically verboten, is it?

  22. Comment by Joy — May 20, 2007 @ 9:01 pm

  23. Thought Provoker Says:
    May 20th, 2007 at 9:03 pm

    Hi Magnan,

    You wrote…

    I won't bother you any more, but I was wondering why no feedback. I guess my thoughts are considered too amateurish and ignorant to bother with. I am indeed a rank amateur not a biologist, but I have still been trying to learn something of this subject using my background as an engineer. At least a little feedback would be appreciated so that I could correct my thinking on this.

    First of all, being ignored is probably one of the highest compliments you can get in a blog. It is the short, stupid comments that get the most feedback.

    For my part, I apologize for not acknowledging your thoughtful comment. But frankly, I didn't know you from Adam. I didn't even know if you would ever come back. Welcome to the Wild, Wild West of blogging where strangers are either ignored, rudely dismissed or tarred and feathered. Consider yourself lucky considering the alternatives.

    As an engineer, you may find this open letter to ID proponent Salvador T. Cordova amusing.

    Please accept my belated welcome. I hope you can find the patience to stick around. Trust me, you will need patience.

    As to your post, it looks like Joy and Bradford are responding. I will try to get my thoughts in after reading their POV.

    Regards,
    TP

  24. Comment by Thought Provoker — May 20, 2007 @ 9:03 pm

  25. Thought Provoker Says:
    May 20th, 2007 at 9:35 pm

    Hi Magnan,

    Let me try to help you come up to speed. Hopefully, I won't corrupt you too much to my way of thinking. I don't think TT needs two Thought Provokers.

    Here is a link to some ID background from my perspective. It includes links for Joy's EAM and other topics you will run into at TT.

    BTW, you wrote…

    Even if this is the case, there would still not be any real intelligence in the process.

    The groans you hear in the background is the dread that I will get out my soap box again. Engineer to engineer, let me clue you in on the use of the word "intelligence" around here. It doesn't mean having the ability to learn. Never mind what the dictionary says.

    I have already said too much. You need to find things out for yourself.

    Wishing you Luck,
    TP

  26. Comment by Thought Provoker — May 20, 2007 @ 9:35 pm

  27. Joy Says:
    May 21st, 2007 at 12:25 am

    TP:

    Engineer to engineer, let me clue you in on the use of the word "intelligence" around here. It doesn't mean having the ability to learn. Never mind what the dictionary says.

    Don't be misleading, TP. Trial and error is a big part of both EAM and front-loading, and any/all (that I've heard of) directed evolution - i.e., "design" on a teleological framework. Random on the origin end doesn't work for me. It also doesn't explain the evidence.

    I have said more than a few times that I don't have a religious horse in this race. You may disbelieve that as you wish, but that doesn't change what's real. Bottom line is that religious people don't need science to confirm or advocate their beliefs and never did. It's the EAs who claim the NDS antiquated pablum somehow "proves" their metaphysics (atheism). I think they're wrong, and a corruption of science so long as science allows them to serve as PR. Foolish if one counts on the public coffer to support one's lifestyle.

  28. Comment by Joy — May 21, 2007 @ 12:25 am

  29. magnan Says:
    May 21st, 2007 at 7:40 am

    Thanks for the responses. As you noticed I tried to outline one possible design of an EAM-like system in living organisms, and found that it seemed to imply a sort of "robotic/mechanical" information processing system modifying the genome in response to current physiological stresses. The minimum system would have no memory, no foresight and no engineering design capability as understood by humans. It would build complex designs step by step in direct response to environmental change and competition. Natural selection would have its normal role as assumed in MET, but the source of individual adaptive genetic variations would not be a tiny percentage of random mutations filtered by selection. Instead it would be generated by a basic "intentionality" or desire to survive and to reproduce existing in all living organisms.

    This seems to be along the lines of what is envisioned by some proponents of EAM. I like the EAM concept myself, but it seems to me that despite being much better than MET it still has problems explaining the actual evolution of organisms in their complexity in the time allowed by the fossil record. This is the problem of "irreducibly complex" structures and systems. I think this concept is not that a gradual stepwise building of the systems is impossible in principle, but that for some biological systems at least some of the necessary steps are so large and complicated in their own right to be extremely unlikely to the point of practical impossibility to be produced by random variation. The difficulty is increased by the fact that some of the steps are neutral in terms of selective advantage. This means the phenotypical change corresponding to the genetic change is not any advantage to the organism. It is just needed as one of the steps leading to the final optimized design.

    This is a big problem for EAM and other epigenetic theories because EAM hypothesizes an "unintelligent" or mechanical system, however complex, that does the environmental stress-to genome correlation and tinkering. The big steps sometimes required in evolutionary development seem instead to require the ability of the agent responsible for non-random variation to actually design, including the faculties of memory, visualization or model-building, prediction and other reasoning processes expected only with a quasi-sentient being.

    It seems to me that in order to retain the concept of an "unintelligent" (in the self-aware or sentient sense) agent having only the basic quality of "intentionality", it would have to be combined with a vastly enhanced capability outside itself to compute and apply needed genetic changes. One tentative approach to this involves the apparent existence of retrocausal effects of consciousness interacting with physical systems, especially quantum mechanical systems. I know that you will probably automatically reject this, but many experiments in parapsychology have demonstrated this phenomenon where simple "intentionality" or desire for something in human and animal consciousness apparently can influence the past state of a causally related system, in particular an electronic random event generator. The investigations of Helmut Schmidt are the most extensive. These experiments have demonstrated that retrocausation may be involved in natural biological systems and even unknowingly in conventional scientific experimentation. With biological systems this would be a form of "quantum computing" involving DNA base pairs.

    I know this is really "far out", but something extraordinary seems to be required to avoid hypothesizing a sentient at least humanly intelligent designer or agent continually intervening in evolution.

    Of course another approach would be to hypothesize an original genetic front-loading, only requiring a very high intelligence in the beginning. My thoughts on this are that there are problems on the same level as with EAM. One would be the difficulty of envisioning how huge sections of pre-designed DNA could have been conserved in evolution until they were needed. Another lesser problem would be having to assume that the original designing intelligence had the ability to accurately predict the vicissitudes of global tectonic, climatic and atmospheric changes over ages of geologic time. Also, major asteroid or cometary impacts have caused several major extinctions. These catastrophic events redirected evolution, and even though basically random also would have had to be predicted or predetermined by this intelligence. I suppose this would be no problem for an omniscient or near-omniscient Being, but it seems one of the other concepts might be more parsimonious.

  30. Comment by magnan — May 21, 2007 @ 7:40 am

  31. Thought Provoker Says:
    May 21st, 2007 at 8:00 am

    Hi Magnan,

    You wrote…

    One tentative approach to this involves the apparent existence of retrocausal effects of consciousness interacting with physical systems, especially quantum mechanical systems. I know that you will probably automatically reject this, but many experiments in parapsychology have demonstrated this phenomenon where simple "intentionality" or desire for something in human and animal consciousness apparently can influence the past state of a causally related system, in particular an electronic random event generator. The investigations of Helmut Schmidt are the most extensive. These experiments have demonstrated that retrocausation may be involved in natural biological systems and even unknowingly in conventional scientific experimentation. With biological systems this would be a form of "quantum computing" involving DNA base pairs.

    Oh oh, TT may end up with two Thought Provokers after all. Links man, we need links! :grin:

    I assume this is the Helmut Schmidt you are talking about, yes?

    Is this the experiment you were talking about with the "electronic random event generator"

    I agree this is "far out" but it may provoke some open mindedness to other ideas that may find traction for both ID proponents and standard MET proponents.

    Yea, Let's do Science :mrgreen:

    Regards,
    TP

  32. Comment by Thought Provoker — May 21, 2007 @ 8:00 am

  33. Thought Provoker Says:
    May 21st, 2007 at 8:11 am

    Hi Joy,

    You wrote…

    Don't be misleading, TP. Trial and error is a big part of both EAM and front-loading, and any/all (that I've heard of) directed evolution - i.e., "design" on a teleological framework. Random on the origin end doesn't work for me. It also doesn't explain the evidence.

    You and I have had many fruitful discussions about intelligence. However, have you noticed some of the responses to this issue I have received from others? That being said, I agree I was misleading in my sweeping characterization. I apologize.

    I was just so excited at the possibility of someone else creating an ID-like proposal that I got carried away in trying to be helpful.

    Regards,
    TP

  34. Comment by Thought Provoker — May 21, 2007 @ 8:11 am

  35. Joy Says:
    May 21st, 2007 at 10:18 am

    magnan:

    It seems to me that in order to retain the concept of an "unintelligent" (in the self-aware or sentient sense) agent having only the basic quality of "intentionality", it would have to be combined with a vastly enhanced capability outside itself to compute and apply needed genetic changes. One tentative approach to this involves the apparent existence of retrocausal effects of consciousness interacting with physical systems, especially quantum mechanical systems.

    The physical mechanics of life and evolution are not necessarily "unintelligent" just because they primarily operate on sub-conscious levels. I mean, do people (and other plants/animals) really have to sit and think about the molecular forms of some invasive pathogen before the immune system can respond? Should such things have to be directed by focused awareness rather than normally and automatically at the level of cells and systems in order to qualify as 'intelligently designed'?

    It just seems to me that the physical 'stuff' of life forms display organization and coordinated activity on a number of levels - only one of which is fully self conscious. IOW, levels of causation from cells to organs to systems to sensory input to processing to awareness, then a whole other level of downward causation from awareness to sensory attentional focusing to systems and organs and even cells. Holistically speaking, the entire organism operates itself in form and function like one conglomerate dually-causal intelligent designer.

    These experiments have demonstrated that retrocausation may be involved in natural biological systems and even unknowingly in conventional scientific experimentation. With biological systems this would be a form of "quantum computing" involving DNA base pairs.

    There is evidence of complex quantum electrodynamic operations in chromatin - the form of DNA operative when the cell isn't replicating (thus dividing its DNA into chromosomes). This, with help from the recently discovered 'histone code' sets up multi-complex 'suites' of genes expressing at any given time in the cell, based on the cell's sensory and communications (interior and exterior) and state-sampling prowess. Gene expression, even in designed 'suites' of genes from all over the genome, is fast, fast, fast in real time! This seems to necessitate a sort of 'brain' in the cells to coordinate all that complexity.

    That may well operate via quantum weirdness as well, at least per the Penrose-Hameroff Orch-OR model of consciousness - where tubulin dimers in the microtubules of centrioles and cytoskeleton perform quantum computational information processing by configurational state-switching.

    The fact that physical life forms must operate by physical mechanics in no way makes them immune from intelligent design. A piano is an intelligently designed artifact that does nothing but sit there. It takes a pianist to make it sing. Bad analogy… sorry! Hope you can follow anyhoo… §;o)

  36. Comment by Joy — May 21, 2007 @ 10:18 am

  37. Thought Provoker Says:
    May 21st, 2007 at 10:50 am

    Hi Magnan,

    BTW, I forgot to warn you about Joy. She is very intelligent. While others may be capable of sounding like they know what they are talking about. Joy actually does. In every case I have checked her facts, she comes out on target.

    So, don't get intimidated. Work through it, it is worth it. She is full of gems like these.

    Go, Joy, Go.

    More science stuff. This is great! :mrgreen:

    Regards,
    TP

    P.S. I found this link to be helpful in understanding the impact of Penrose's opinions concerning Consciousness. I am rereading the Hawking/Penrose debate as my "light" evening reading.

  38. Comment by Thought Provoker — May 21, 2007 @ 10:50 am

  39. onething Says:
    May 21st, 2007 at 12:28 pm

    Hi Magnum

    Thanks for the responses. As you noticed I tried to outline one possible design of an EAM-like system in living organisms, and found that it seemed to imply a sort of "robotic/mechanical" information processing system modifying the genome in response to current physiological stresses. The minimum system would have no memory, no foresight and no engineering design capability as understood by humans. It would build complex designs step by step in direct response to environmental change and competition. Natural selection would have its normal role as assumed in MET, but the source of individual adaptive genetic variations would not be a tiny percentage of random mutations filtered by selection. Instead it would be generated by a basic "intentionality" or desire to survive and to reproduce existing in all living organisms.

    Still there is something unaccounted for, in part that this system is even more amazing than the neoDarwinian one and one wonders at its origin, and also how does this intentionality translate into the nuts and bolts decisions that would seem necessary for the organism's advancement

    This seems to be along the lines of what is envisioned by some proponents of EAM. I like the EAM concept myself, but it seems to me that despite being much better than MET it still has problems explaining the actual evolution of organisms in their complexity in the time allowed by the fossil record.

    But EAM seems much better at it than your first paragraph, quoted above, which names only the intention that organisms have to survive as the intelligence.

    What I am considering, and EAM hints at, is that intelligence itself, likewise consciousness of which it is derivative, may be more deeply integral to reality than we had thought, especially in living things. It looks like Joy is saying that as well.

    One tentative approach to this involves the apparent existence of retrocausal effects of consciousness interacting with physical systems, especially quantum mechanical systems. I know this is really "far out", but something extraordinary seems to be required to avoid hypothesizing a sentient at least humanly intelligent designer or agent continually intervening in evolution.

    Oh, OK, so it looks like your first paragraph does not stand alone but is entirely dependent upon this retrocausality.

    The question naturally arises why would we want to resort to extraordinary explanations in order to avoid hypothesizing a sentient being? Just asking. But in my case it isn't so much a desire to avoid said being but rather just that creationism doesn't jive with how I suppose things really work and how the sentient being would accomplish things, or even jive with the nature of that being vis a vis the universe.

    I just can't accept the retrocausality as a source of the design in things. I'm not against it in a psi kind of way, but somehow, and this is just my intuition, I don't think it's the same thing, i.e., people may be able to influence the past, but I don't think that can account for the creation of biological organisms from the start. There is something deeply illogical about that.

    As to frontloading, I can't accept it as a one-time event, there would have to have been at minimum two, nonetheless, the various climate changes and so forth are not really all that unpredictable for a being/s of galactic knowledge.

  40. Comment by onething — May 21, 2007 @ 12:28 pm

  41. Thought Provoker Says:
    May 21st, 2007 at 12:55 pm

    Hi Joy,

    That may well operate via quantum weirdness as well, at least per the Penrose-Hameroff Orch-OR model of consciousness…

    "quantum weirdness" I like it! :grin:

    Here is the link I am referencing so I can pretend to understand what is going on about "histone code". I hope you agree with what it says because I'm in no position to argue for or against it.

    Gene expression, even in designed 'suites' of genes from all over the genome, is fast, fast, fast in real time!

    This reminded me of a "dissertation" written by the well-known chemist, Dr. Isaac Asimov.

    The Endochronic Properties of Resublimated Thiotimoline
    "Dedicated researcher Isaac Asimov describes his discoveries regarding an interesting organic compound, thiotimoline, which has the ability to dissolve in water before the water is added."link

    Joy, is the gene expression fast enough to suspect that is might be predictive?

    Provoking Thought

    P.S. to the listening audience, if you don't know who Isaac Asimov is, please don't say anything, I might cry.

  42. Comment by Thought Provoker — May 21, 2007 @ 12:55 pm

  43. Joy Says:
    May 21st, 2007 at 2:33 pm

    TP:

    More science stuff. This is great!

    Well, now that you've familiarized yourself with Orch-OR in neurons (they are more stable in these specialized cells), check out Hameroff's
    Did Consciousness Cause the Cambrian Evolutionary Explosion?

    It gives some impressively precise calculations of at what level of complexity 'higher' coordinated consciousness emerges from complexity itself in the most significant evolutionary development known - eukaryotes-to-multicellular, differentiated life forms. The explanations and graphics in the Cytoskeleton, Intelligent Behavior and Differentiation are particularly good, and not difficult to follow.

    As AI (quantum computing) researchers report that they are able to maintain superpositions of increasingly large conglomerations of atoms, it should soon be demonstrated that this quantum behavior can apply to molecules and even macromolecules (like protein and DNA) in certain vital environments (like cells). Whatever field-like (and time-like, and space-like) influences there are operating consciousness, it seems quite clear to me that it has to function via physical mechanism at the crossover phase-space. I think, based on research Hameroff did way back in the '70s and '80s on the mechanisms of anesthesia that microtubules are intimately involved.

    And these are the same structures known to explore the exterior growth-space of plants as they grow and flower and seed, (quantify the space as the form develops), and provide cillia and flagella for cell motility. Worse than mitichlorians, they are! Margulis thinks they were once independent spirochetes (like a virus of tubulin/actin instead of DNA), which provided useful sensory, molecular transport, signal transduction (the dimers are dipolar state-switchers) and information processing advantages to primitive single-celled life forms. They proved SO useful that life was enabled to evolve.

  44. Comment by Joy — May 21, 2007 @ 2:33 pm

  45. Thought Provoker Says:
    May 21st, 2007 at 5:43 pm

    Hi Joy,

    Thanks for the link. I am probably going to have to read it two or three more times to "get it". But it is definitely persuasive.

    I think I am getting a better understanding on why you feel biologists need to incorporate more physics into there explorations. If Hameroff is correct…

    In Penrose's OR the size of an isolated superposed system (gravitational self-energy E of a separated mass) is inversely related to the coherence time T according to the uncertainty principle E=h /T, where h (actually "hbar") is Planck's constant over 2 pi. T is the duration of time for which the mass must be superposed to reach quantum gravity threshold for self-collapse. Large systems (e.g. Schrodinger's 1 kg cat) would self-collapse (OR) very quickly, in only 10-37 seconds. An isolated superposed single atom would not OR for 106 years. Somewhere between those extremes are brain events in the range of tens to hundreds of milliseconds. A 25 millisecond brain event (i.e. occurring in coherent 40 Hz oscillations) would require nanogram (10-9 gram) amounts of superposed neural mass.

    link

    …If Hameroff is correct… :shock:

    …Do you understand the implications?!?!?

    …Of course you do….

    I'm going to need some time to digest this. :neutral:

    I think I am going to go play with Stunney and Bradford for a while.

    Boy, my head is hurts.

    Regards,
    TP

  46. Comment by Thought Provoker — May 21, 2007 @ 5:43 pm

  47. Joy Says:
    May 21st, 2007 at 8:57 pm

    TP:

    "¦Do you understand the implications?!?!?

    Indeed I do. Or, as Firesign Theatre once put it…

    How can you be in two places at once if you're not anywhere at all?

    It's all about not-time, since everything computed (sampled or data extracted) during the superposition can be anytime it wants. It just has to be in the same light-cone. Everything here belongs to the same light-cone.

    P.S. to the listening audience, if you don't know who Isaac Asimov is, please don't say anything, I might cry.

    LOL!!! My, I so loved that man's deadly mind! [...Nick Danger, Third Eye, with a vial of deadly influence taped to his leg...]. You know Asimov was the lecturer for my (only) college level genetics course, don't you? I took it not because I was big into genetics, but because I so loved his sci-fi. Don't recall if I learned anything, but I sure did enjoy it! §;o)

  48. Comment by Joy — May 21, 2007 @ 8:57 pm

  49. magnan Says:
    May 23rd, 2007 at 4:43 pm

    Joy:

    "The physical mechanics of life and evolution are not necessarily "unintelligent" just because they primarily operate on sub-conscious levels. I mean, do people (and other plants/animals) really have to sit and think about the molecular forms of some invasive pathogen before the immune system can respond? Should such things have to be directed by focused awareness rather than normally and automatically at the level of cells and systems in order to qualify as 'intelligently designed'?"

    The immune system is one of the extremely complicated systems that "seem" to have required the influence of a focused and aware intelligence to design as opposed to some automatic process at the level of cells. I look at it from the standpoint of engineering or programming. I know from experience that only a sentient intelligent programmer can design a complicated new program, given at the start all the output requirements, input and output definitions and formats, continuity and computation rate constraints, and the like. The initial raw material and initializing information may include a symbolic language, set of basic subroutines carrying out relatively simple functions, and a large database. These could be analogous to the living cells making up the programmer's body, but these cells are inherently incapable of thinking through a complicated design with multiple interlinked inputs, outputs, levels of processing, time recursive processes, interfaces, etc. Changes to each prototype have to be very carefully thought through to avoid making the system degrade or just stop. This seems to me requires a sentient, aware, focused and intelligent agent that can see patterns and correlations taking into account diverse pieces of apparently unrelated data, and creatively make correlations and deductive and inductive insights to come up with a new design. For human levels of intelligence it usually also requires an iterative conceptual design process.

    Joy:

    "Holistically speaking, the entire organism operates itself in form and function like one conglomerate dually-causal intelligent designer."

    I just can't wrap my mind around this concept. It seems to be kind of fuzzy. As I stated above, it is very hard to see how anything but a focused aware intelligence can do things like creatively see patterns and correlations, make insights, try out new deductively and inductively derived structures, etc. I think Dembski's famous phrase "no free lunch" may apply here.

    If the only "intelligence" is at the level of the cell, then some non-deterministic quantum weirdness effect seems to be necessary, in which complex specified information somehow originates from quantum mechanical collapse of wave function on observation phenomena as in "quantum computing". This could either involve retrocausal phenomena or in the "now" phenomena, but I agree with Onething that it deeply offends common sense, to suggest that something (in the sense of complex specified information) emerged from nothing through quantum mechanical processes.

    I conclude that there are many reasons that the source of "intelligence" in evolution is most likely a real, sentient, aware intelligence existing apart from nature but capable of intervening in nature. It seems to me the EAM and front-loading hypotheses are somewhat less likely, though certainly not impossible on principle given present knowledge.

  50. Comment by magnan — May 23, 2007 @ 4:43 pm

  51. keiths Says:
    May 23rd, 2007 at 5:13 pm

    Readers should be aware that the Penrose/Hameroff hypothesis is rejected almost universally by neuroscientists, and rightfully so.

    Grush and Churchland explain some of the reasons why in their paper, Gaps in Penrose's Toilings. Here is the abstract:

    Using the Gödel Incompleteness Result for leverage, Roger Penrose has argued that the mechanism for consciousness involves quantum gravitational phenomena, acting through microtubules in neurons. We show that this hypothesis is implausible. First, the Gödel Result does not imply that human thought is in fact non algorithmic. Second, whether or not non algorithmic quantum gravitational phenomena actually exist, and if they did how that could conceivably implicate microtubules, and if microtubules were involved, how that could conceivably implicate consciousness, is entirely speculative. Third, cytoplasmic ions such as calcium and sodium are almost certainly present in the microtubule pore, barring the quantum mechanical effects Penrose envisages. Finally, physiological evidence indicates that consciousness does not directly depend on microtubule properties in any case, rendering doubtful any theory according to which consciousness is generated in the microtubules.

    Here is a quote from Susan Blackmore's book Consciousness:

    Grush and Churchland (1995) ask why such a flimsy theory has proved so popular. Perhaps, they suggest, because some people find the idea of explaining consciousness by neuronal activity somehow degrading or scary, whereas "explaining" it by quantum effects retains some of the mystery. They conclude that "the argument consists of merest possibility piled upon merest possibility teetering upon a tippy foundation of 'might-be-for-all-we-knows'…we judge it to be completely unconvincing and probably false."

  52. Comment by keiths — May 23, 2007 @ 5:13 pm

  53. Thought Provoker Says:
    May 23rd, 2007 at 5:26 pm

    Hi Keiths,

    They conclude that "the argument consists of merest possibility piled upon merest possibility teetering upon a tippy foundation of 'might-be-for-all-we-knows'"¦we judge it to be completely unconvincing and probably false."

    Hmmm, that's sounds like the kind of argument Dembski would make on another topic.

    I am still looking into it, including the counter-arguments. And while I think Hameroff may have gone to an extreme, his Cambrian Explosion suggestion is intreguing. However, dismissing it with an argument of incredulity would be… ironic. :wink:

    Provoking Thought

  54. Comment by Thought Provoker — May 23, 2007 @ 5:26 pm

  55. keiths Says:
    May 23rd, 2007 at 5:39 pm

    TP,

    Don't mistake the conclusion for the argument. The paper is 32 pages long.

  56. Comment by keiths — May 23, 2007 @ 5:39 pm

  57. Joy Says:
    May 23rd, 2007 at 8:27 pm

    magnan:

    The immune system is one of the extremely complicated systems that "seem" to have required the influence of a focused and aware intelligence to design as opposed to some automatic process at the level of cells. I look at it from the standpoint of engineering or programming. I know from experience that only a sentient intelligent programmer can design a complicated new program, given at the start all the output requirements, input and output definitions and formats, continuity and computation rate constraints, and the like.

    I don't know if a focused and aware intelligence designed the immune system. I just know that I don't have to redesign it myself every time a germ happens along, and that it can be darned clever in its responses to novel pathogens even without me having to direct it. As a system, it works very well *as* a system, and I do not have to consciously direct it.

    I just can't wrap my mind around this concept. It seems to be kind of fuzzy. As I stated above, it is very hard to see how anything but a focused aware intelligence can do things like creatively see patterns and correlations, make insights, try out new deductively and inductively derived structures, etc. I think Dembski's famous phrase "no free lunch" may apply here.

    If you cannot see that cells and organs and systems can operate themselves without your focused attention and awareness, there's not much I can say about it. You must be pretty busy focusing your attention and awareness on basic bodily functions, so it's a wonder you've time to surf the internet!

    And if you can't believe that focused awareness and attention can order the functioning of lesser physiological systems (the "placebo" effect and such, as well as simply driving a car or taking a walk), it would be impossible for me to convince you that you're not a meat puppet. ["you" is figurative in my usage].

    I conclude that there are many reasons that the source of "intelligence" in evolution is most likely a real, sentient, aware intelligence existing apart from nature but capable of intervening in nature. It seems to me the EAM and front-loading hypotheses are somewhat less likely, though certainly not impossible on principle given present knowledge.

    That's a fine conclusion, magnan. But it holds exactly zip in scientific potential, since science isn't designed to deal with anything supernatural ["apart from nature"]. For the practical collective purposes of science - which is quantification and control - the possible existence of anything greater-than we are is the cut-off point. Such a thing would not be material, materially detectible by us, materially controllable by us.

    Science's mileau is the material world. That is all it's chartered to investigate and quantify. It can say nothing about qualitative phenomena, nothing about moral "oughts," nothing about non-material beings or realities we cannot pin down, stick on a slide and view under a microscope. People are free to believe as they choose about such things.

    Where science oversteps its bounds is in the pretense that nothing exists which is beyond its circumscribed turf to quantify and control. They do not know this, will never know this, and couldn't do anything with it if they did know it. Not science's job.

  58. Comment by Joy — May 23, 2007 @ 8:27 pm

  59. magnan Says:
    May 23rd, 2007 at 8:37 pm

    Onething:

    "Still there is something unaccounted for, in part that this system is even more amazing than the neoDarwinian one and one wonders at its origin, and also how does this intentionality translate into the nuts and bolts decisions that would seem necessary for the organism's advancement"

    A good point and I agree, but it seems to me something of this order seems to be required to make EAM reasonable, as it is usually proposed following a "bottom up" scheme based on cell "intelligence".

    Onething:

    "What I am considering, and EAM hints at, is that intelligence itself, likewise consciousness of which it is derivative, may be more deeply integral to reality than we had thought, especially in living things. It looks like Joy is saying that as well."

    Maybe so, but it seems impossible to pin down what this really is in any humanly understandable terms. That is, how does a group of individual cells or a combination of rocks "think" The only way we know of that living cells "think" is in the incredibly complex neural structures of the brain, where the best explanation is that thought is the expression through physical brain structures of an immaterial spiritual consciousness. The only "intelligence" we are aware of that can design things has the humanlike characteristics of awareness, sentience (sensory or sensing ability), memory and reasoning capacity.

    It seems to me the EAM concept is a sort of philosophy of materialistic emergence, that carefully avoids the necessity to presuppose dualism, the separate existence of matter and spirit. "Spirit" is supposed to be inherent in the organization and nature of matter, an emergent property of matter. This is closely related to the epiphenominalism theory of mind that it is an evolutionary accident emerging from the increasing complexity of brains as an "epiphenomenon" or side effect of neural complexity. Maybe I am making too wide ranging inferences, but EAM-like concepts seem to be attempts to admit the existence of a form of "spirit" while salvaging the common wisdom of our intellectual elite, that dualism is dead, that there is no separate existence of spirit and matter/energy.

    Onething:

    "The question naturally arises why would we want to resort to extraordinary explanations in order to avoid hypothesizing a sentient being? Just asking."

    The reason I did was to attempt to demonstrate the even greater problems of other types of explanatory models, i.e. EAM, frontloading, direct one-time creation.

    Onething:

    "I just can't accept the retrocausality as a source of the design in things. I'm not against it in a psi kind of way, but somehow, and this is just my intuition, I don't think it's the same thing, i.e., people may be able to influence the past, but I don't think that can account for the creation of biological organisms from the start. There is something deeply illogical about that."

    I agree. I posed this in a last-ditch attempt to try to make a bottom-up information flow EAM concept plausible, at least to me. Retrocausal effects may still contribute to the process even if not being the primary source of innovation. The important point is that for these effects to occur only a simple organismal "intention" or desire seems to be necessary, which is what simple cellular and lower animal intelligence seems able to muster.

  60. Comment by magnan — May 23, 2007 @ 8:37 pm

  61. magnan Says:
    May 23rd, 2007 at 9:32 pm

    Joy:

    "I don't know if a focused and aware intelligence designed the immune system. I just know that I don't have to redesign it myself every time a germ happens along, and that it can be darned clever in its responses to novel pathogens even without me having to direct it. As a system, it works very well *as* a system, and I do not have to consciously direct it."

    Of course; I would never claim otherwise. Its design itself incorporates very clever techniques to detect and counter novel pathogens. The fact that I don't have to consciously direct it has nothing to do with how or if it was consciously designed in the first place.

    Joy:

    "If you cannot see that cells and organs and systems can operate themselves without your focused attention and awareness, there's not much I can say about it. You must be pretty busy focusing your attention and awareness on basic bodily functions, so it's a wonder you've time to surf the internet!"

    I was not arguing that. Of course and it is obvious that my bodily systems of organs, tissues, etc. operate independently of my conscious mind, to a large extent through the so-called autonomic nervous system and chemical communications. The whole issue here is whether this incredibly complex interconnected system of systems of subsystems including the autonomic nervous system could have originated from some sort of built-in "intelligence" inherent in the cells themselves, or matter in general.

    Joy:

    "And if you can't believe that focused awareness and attention can order the functioning of lesser physiological systems (the "placebo" effect and such, as well as simply driving a car or taking a walk), it would be impossible for me to convince you that you're not a meat puppet. ["you" is figurative in my usage]."

    You seem to be putting words in my mouth. Of course I am aware that "focused awareness and attention" can affect the functioning of the body through the effect of suggestion, the placebo effect and so on, where the mind certainly does not know the actual mechanism by which conscious desire is transformed into physiological response. What I was saying was that it seems unlikely that the lower order biological systems can somehow create the design inherent in the higher order systems, including the brain which makes human consciousness possible. You seem to be saying that the lower order biological systems or entities like cells collectively possess an aware focussed intelligence that can reason and deduce, so that they can produce the higher order organization and complexity. This is what I was doubting.

    Joy:

    "That's a fine conclusion, magnan. But it holds exactly zip in scientific potential, since science isn't designed to deal with anything supernatural ["apart from nature"]."

    I agree, but I believe we should follow where the data leads. If it leads to the conclusion that something exists that is for the most part uninvestigatable by science, so be it, it's just too bad it is "zip in scientific potential". If we really are dedicated to trying to find truth, whatever it is, then we should not shy away from such a conclusion and keep trying to force reality to conform to our philosophy. Instead we should keep our philosophy flexible and insist that our philosophy conform to reality.

  62. Comment by magnan — May 23, 2007 @ 9:32 pm

  63. Thought Provoker Says:
    May 23rd, 2007 at 10:03 pm

    Hi keiths,

    You wrote…

    Don't mistake the conclusion for the argument. The paper is 32 pages long.

    And Dembski has written multiple books each with hundreds of pages.

    Like I said, I am looking at both sides of Penrose/Hameroff. I will post my understanding after I am done.

    Regards,
    TP

  64. Comment by Thought Provoker — May 23, 2007 @ 10:03 pm

  65. keiths Says:
    May 23rd, 2007 at 11:01 pm

    TP,

    The point was to correct your misconception that Grush and Churchland were putting forth, as you put it, an "argument of incredulity."

  66. Comment by keiths — May 23, 2007 @ 11:01 pm

  67. Thought Provoker Says:
    May 23rd, 2007 at 11:26 pm

    Hi Keiths,

    Did you notice that Grush and Churchland are from the Philosophy Department at UCSD? It would be very surprising indeed to find philosophers and/or neuroscientists NOT rejecting physicists' hypotheses for consciousness. It would have to be ironclad proof for them to admit they had it all wrong. That being said, thank you for the link. I will read it more carefully based on your suggestion there is more to it. But I don't hold out that much hope considering their closing statement was"¦

    "Nothing we have said in this paper demonstrates the falsity of the quantum consciousness connection. Our view is just that it is no better supported than any one of a gazillion caterpillar-with-hookah hypotheses." link

    This is exactly the type of reaction I would expect from scientists/philosophers unable to poke a hole in a theory that, if true, would be embarrassing and detrimental to their field of study.

    Regards,
    TP

  68. Comment by Thought Provoker — May 23, 2007 @ 11:26 pm

  69. keiths Says:
    May 23rd, 2007 at 11:44 pm

    TP,

    After you read and understand the paper, you won't be under the impression that they were unable to poke holes in Penrose's theory.

  70. Comment by keiths — May 23, 2007 @ 11:44 pm

  71. magnan Says:
    May 24th, 2007 at 4:31 am

    Thought Provoker:

    "I assume this is the Helmut Schmidt you are talking about, yes?"

    Yes, but the paper you linked to isn't on retrocausal effects and one of the ones I was thinking of. Two of these are: Helmut Schmidt, PK Effect on Pre-Recorded Targets, at http://www.fourmilab.ch/rpkp/r..., and
    Helmut Schmidt, PK Tests with Prerecorded and Pre-inspected Seed Numbers, at http://www.fourmilab.ch/rpkp/p....
    A good overview of this area is:
    Dean Radin, Time-reversed human experience: Experimental evidence and implications, at http://www.boundary.org/articl...

    Some of the experiments discussed demonstrated that human agents are able to influence previously recorded (on hard drives and magnetic tapes) random bits. Other experiments described in this paper demonstrated retroactive psychokinesis influencing the behavior of living systems. In this case the pre-recorded data were of things like the spontaneous fluctuations of human skin conductance and heart rate and gerbil's use of an exercise wheel. Radin concludes (quoting William Braud): "Once an event has occurred, it remains so; it does not "un-occur" or change from its initial form. It appears, instead, that the intentions, wishes, or PK "efforts" influence what happens (or happened) in the first place."

    Another reference, on non-retrocausal psychokinesis by animals (chicks), at http://www.parapsych.org/pa_co...: title: Psychokinesis experiments with human and animal subjects upon a robot moving at random, by Rene Peoc'h, M.D.

  72. Comment by magnan — May 24, 2007 @ 4:31 am

  73. Joy Says:
    May 24th, 2007 at 10:17 am

    TP, the Churchlands are hard core metaphysical materialists whose only firm belief about consciousness (far as I can tell) is that we're all Zombies. A good many neuros are in the Zombie camp as well, but I've never found that denial of one's own consciousness - and all its attributes, including intelligence - makes a strong case against anything but one's own consciousness and intelligence.

    Zombies have nothing meaningful to say about anything.

    magnan, I think you misunderstand my position and EAM (which is quite strongly dualistic/vitalistic). Metaphysical extrapolations on whatever the evidence "means" are always going to be not-science. That's okay, since mass mind control was never science's job in the first place. It's as unreasonable to expect science to 'prove' the existence of a supernatural intelligence as it is to expect religion to 'prove' people don't have bodies made of regular old everyday matter.

    Also, I do NOT believe in anything resembling "living matter." That's the most ridiculous thing I ever heard of! Matter is just stuff, it's cheap too - all around us all the time. Our amazingly well-designed bodies are material artifacts, which we use for as long as they last to interact here in 3+1 space-time. When we're done with them (or they're done doing our bidding), they get left behind. The arrangement of atoms is just the same a moment after death as it was a moment before, but now it's merely matter to be recycled as matter always is recycled. "We" are gone elsewhere.

  74. Comment by Joy — May 24, 2007 @ 10:17 am

  75. bj Says:
    May 24th, 2007 at 11:42 am

    magnan wrote:

    I conclude that there are many reasons that the source of "intelligence" in evolution is most likely a real, sentient, aware intelligence existing apart from nature but capable of intervening in nature.

    In my opinion, these kinds of threads are the best of TT. It's an example of how those who are not a part of the cultural movement do ID.

    Regarding this real, sentient, aware "intelligence", perhaps I am misunderstanding and I would admit that a great deal of this discussion is above my head, but I would ask, "Why does this intelligence have to be apart from nature?" Why can't it be a part of nature or in depths of nature that we can't now or perhaps ever understand? I guess this gets at pantheism or panentheism.

  76. Comment by bj — May 24, 2007 @ 11:42 am

  77. Joy Says:
    May 24th, 2007 at 11:02 pm

    An excellent overview from Fortune City:
    Zombies, Dolphins and Blindsight

    …and Hameroff's response to Churchland:
    More Neural Than Thou (Psych-B)

  78. Comment by Joy — May 24, 2007 @ 11:02 pm

  79. keiths Says:
    May 25th, 2007 at 3:04 am

    Joy,

    I'm beginning to wonder… do you ever bother to understand your opponents' views before attacking?

    You wrote:

    …the Churchlands are hard core metaphysical materialists whose only firm belief about consciousness (far as I can tell) is that we're all Zombies.

    Read what Patricia Churchland actually has to say about zombies:

    What drives the left-out hypothesis? Essentially, a thought-experiment, which roughly goes as follows: we can conceive of a person, like us in all the aforementioned easy-to-explain capacities (attention, short term memory, etc.), but lacking qualia. This person would be exactly like us, save that he would be a Zombie — an anaqualiac, one might say. Since the scenario is conceivable, it is possible, and since it is possible, then whatever consciousness is, it is explanatorily independent of those activities.

    I take this argument to be a demonstration of the feebleness of thought-experiments. Saying something is possible does not thereby guarantee it is a possibility, so how do we know the anaqualiac idea is really possible? To insist that it must be is simply to beg the question at issue. As Francis Crick has observed, it might be like saying that one can imagine a possible world where gases do not get hot, even though their constituent molecules are moving at high velocity. As an argument against the empirical identification of temperature with mean molecular KE, the thermodynamic thought-experiment is feebleness itself.

    Joy:

    A good many neuros are in the Zombie camp as well…

    How about naming some of them for us? You're wrong about the Churchlands. You used to make that claim about Dennett, until I showed that his actual beliefs were the exact opposite (good grief, he even wrote a paper called The Unimagined Preposterousness of Zombies!). Do you know of any "neuros" who believe we are zombies?

    Zombies have nothing meaningful to say about anything.

    You even managed to get that wrong. Philosophical zombies do have meaningful things to say. After all, they're defined to be externally indistinguishable from ordinary humans, but with "nobody home" inside. If humans are capable of saying meaningful things, then so are zombies.

    To help you understand what eliminative materialists really believe, here's an excerpt from the Stanford Encyclopedia of Philosophy:

    By contrast, our notion of demons did not come to find a new home in contemporary theories of mental disorder. There is nothing in the theories of schizophrenia, Tourette's Syndrome, neuropathology or any of the other modern explanations for bizarre behavior, that we can sensibly identify with malevolent spirits with supernatural powers. The notion of a demon is just too far removed from anything we now posit to explain behavior that once was explained by demonology. Consequently, the transition from demonology to modern accounts of this behavior was ontologically radical. We dropped demons from our current ontology, and came to realize that the notion is empty — it refers to nothing real.

    Eliminative materialists claim that an ontologically radical theory change of this sort awaits the theoretical posits of folk psychology. Just as we came to understand that there are no such things as demons (because nothing at all like demons appear in modern accounts of strange behavior), so too, eliminative materialists argue that various folk psychological concepts — like our concept of belief — will eventually be recognized as empty posits that fail to correspond with anything that actually exists.

    Only in your strawman world do eliminative materialists brush off consciousness and its attributes altogether. In reality, they recognize that these phenomena require explanation, but they argue that the concepts of folk psychology are not up to the job, just as demons are inadequate to account for mental illness.

  80. Comment by keiths — May 25, 2007 @ 3:04 am

  81. Joy Says:
    May 25th, 2007 at 9:44 am

    keiths:

    I'm beginning to wonder"¦ do you ever bother to understand your opponents' views before attacking?

    Why yes I do. The Great Zombie debates have been ongoing for years, and have generated lots and lots of ink, particularly on the side that claims humans *are* zombies, thus zombies aren't an issue (haha!). I find them quite amusing. Churchland doesn't like the Chinese Room or the floating iron bars either. Some folks just can't stand the implications of their own self-denial. "Eliminative materialists" eliminate themselves from consideration by anyone who has a consciousness and freedom of will. What YOU think about other people's consciousness and freedom of will is entirely irrelevant.

    How about naming some of them for us? You're wrong about the Churchlands.

    No, thanks. If people are interested they can do their own homework. Simply stomping your feet and shouting not so with fingers in your ears doesn't change a thing. You've proven yourself to be less than honest and less than civil. So go fight with your eliminated self in a mirror.

  82. Comment by Joy — May 25, 2007 @ 9:44 am

  83. magnan Says:
    May 25th, 2007 at 2:46 pm

    BJ:

    "Why does this intelligence have to be apart from nature? Why can't it be a part of nature or in depths of nature that we can't now or perhaps ever understand? I guess this gets at pantheism or panentheism."

    I explained in my response to Joy why as an engineer I find living organisms to be designed in a very real way, very much as if by a focused aware intelligence: I know from experience that only a sentient intelligent programmer can design a complicated new program, given at the start all the output requirements, input and output definitions and formats, continuity and computation rate constraints, and the like. The initial raw material and initializing information may include a symbolic language, set of basic subroutines carrying out relatively simple functions, and a large database. These could be analogous to the living cells making up the programmer's body, but these cells are inherently incapable of thinking through a complicated design with multiple interlinked inputs, outputs, levels of processing, time recursive processes, interfaces, etc. Changes to each prototype have to be very carefully thought through to avoid making the system degrade or just stop. This seems to me requires a sentient, aware, focused and intelligent agent that can see patterns and correlations taking into account diverse pieces of apparently unrelated data, and creatively make correlations and deductive and inductive insights to come up with a new design.

    This is how the unknown creative intelligence in evolution seems to operate. Indeed somehow, in the absence of any knowledge about it, this intelligence could be inherent in Nature. We can't exclude this as a possibility. But the only form of focused aware intelligence we know of is our own, a very localized manifestation of conscious intelligence in a specific structure - the brain. It just seems to me more plausible that the creative intelligence behind evolution is also somehow discrete and localized in some sense, for it to have the characteristics I enumerated. If it is discrete and localized in even some (unknowable) sense, it seems more reasonable to me that its basic nature and its home is, rather than our physical world, a realm of existence apart from or above nature though still of course capable of interacting or intervening in it.

  84. Comment by magnan — May 25, 2007 @ 2:46 pm

  85. keiths Says:
    May 25th, 2007 at 2:59 pm

    Joy wrote:

    The Great Zombie debates have been ongoing for years, and have generated lots and lots of ink, particularly on the side that claims humans *are* zombies, thus zombies aren't an issue (haha!).

    Joy,

    Even that attenuated claim doesn't fly. As I explained in my previous comment, the definition of a philosophical zombie requires that there be "nobody home" to experience qualia. Philosophers don't believe that about humans, which is why you can't name any who do (much less prominent ones like Dennett and the Churchlands). Yet you continue to pretend that they do, because that gives you a convenient strawman to beat up.

    I wrote:

    How about naming some of them for us?

    You responded:

    No, thanks. If people are interested they can do their own homework.

    Right. You're willing to type in line after line of comments, but when it comes to typing a few names, you're suddenly too tired.

    What was that you were saying about honesty?

  86. Comment by keiths — May 25, 2007 @ 2:59 pm

  87. magnan Says:
    May 25th, 2007 at 3:16 pm

    Joy:

    "magnan, I think you misunderstand my position and EAM (which is quite strongly dualistic/vitalistic)."

    Perhaps so. I'll paraphrase what I said earlier: You seem to be saying that the lower order biological systems or entities like cells (or Nature in general) collectively possess an aware focussed intelligence that can reason and deduce, so that they can produce the higher order organization and complexity.

    If this isn't your view or version of EAM, could you describe or give a link to what it really is?

    Joy:

    "The arrangement of atoms is just the same a moment after death as it was a moment before, but now it's merely matter to be recycled as matter always is recycled. "We" are gone elsewhere."

    I certainly agree.

  88. Comment by magnan — May 25, 2007 @ 3:16 pm

  89. bj Says:
    May 25th, 2007 at 3:23 pm

    magnan,

    This is how the unknown creative intelligence in evolution seems to operate. Indeed somehow, in the absence of any knowledge about it, this intelligence could be inherent in Nature. We can't exclude this as a possibility. But the only form of focused aware intelligence we know of is our own, a very localized manifestation of conscious intelligence in a specific structure - the brain. It just seems to me more plausible that the creative intelligence behind evolution is also somehow discrete and localized in some sense, for it to have the characteristics I enumerated. If it is discrete and localized in even some (unknowable) sense, it seems more reasonable to me that its basic nature and its home is, rather than our physical world, a realm of existence apart from or above nature though still of course capable of interacting or intervening in it.

    Of course, your right as to the reasonableness of thinking of the intelligence as discrete, localized and having a home apart from or above nature, to use your well chosen words. I think that this intelligence would be consistent with traditional religion, but not limited to that. I wonder if we don't have to first address the question as to whether it is correct to use our experience and nature as the ground state of this intelligence. It seems to me that we could say maybe yes, maybe no. How do we know? I like to stick with what I can see. I can see the universe. I haven't seen the other realm. So, for me for now I just prefer to try and investigate this intelligence as existing within or in greater depths of our only seen reality. I don't know if this is wise and was just asking for other thoughts regarding that possibility. But, I am certainly not in a position to try and prove your belief as being incorrect. How would I do that? We do have common ground in believing in "something more". I suppose "intelligence" is a good starting point. I am quite intrigued by EAM and would love to see it discussed more.

  90. Comment by bj — May 25, 2007 @ 3:23 pm

  91. Raevmo Says:
    May 25th, 2007 at 3:28 pm

    The arrangement of atoms is just the same a moment after death as it was a moment before, but now it's merely matter to be recycled as matter always is recycled. "We" are gone elsewhere.

    The arrangement is of course not exactly the same, it's slightly different. All the above statement proves is that it usually doesn't make sense to say that someone is alive at one moment, and dead a tiny fraction of a second later. Dying is usually a bit more continuous than that (being blown up is a different story).

  92. Comment by Raevmo — May 25, 2007 @ 3:28 pm

  93. Rock Says:
    May 25th, 2007 at 4:16 pm

    I admit I'm not following the conversation, and only got this far:

    magnan Says: These could be analogous to the living cells making up the programmer's body, but these cells are inherently incapable of thinking through a complicated design with multiple interlinked inputs, outputs, levels of processing, time recursive processes, interfaces, etc. Changes to each prototype have to be very carefully thought through to avoid making the system degrade or just stop. This seems to me requires a sentient, aware, focused and intelligent agent that can see patterns and correlations taking into account diverse pieces of apparently unrelated data, and creatively make correlations and deductive and inductive insights to come up with a new design. For human levels of intelligence it usually also requires an iterative conceptual design process.

    I'm sure I misunderstood, but it seems to me that cells do exactly what you said they don't do. I don't find it in the least bit implausible that a single cell is quite capable of "human levels of intelligence." Single cells do all the things you suggest about "human levels of intelligence." The only difference I see is quantitative and not qualitative.

    Single cells selectively gather information (by "selectively" I mean on the basis of prior experiential knowledge, information, ~4-billion yrs experience) about what is/not relevant"”and so make an implicit categorization, an example of abstract thinking"”logically process that information, and on the basis of that processing select from any number of alternative possible behavioral responses available to them, choose the response that adapts to the conditions that they have detected, perceived.

    I call that intelligence and my model is, of course, the only model we have (exclusive of religion and science fiction) is human intelligence.

    You wouldn't be alive if cells were not capable of human-like intelligence.

    I believe they are far more intelligent than that! Because with humans "intelligence" tends to deteriorate quite rapidly in cooperativity. We have the saying that two heads are better than one, which is generally true. But its also true that >4 heads is worse than none. Yet the godzillion single cells (>1000 different cell-types) of your body all act coordinately to keep you alive. Manifesting a form of collective intelligence that far exceeds that of mere human-level intelligence!

    Human society continuously teeters on the brink of bloody chaos and collapse because our much vaunted "intelligence" cannot do what all the cells in your body can do"”Live and work together in peace and harmony to achieve a collective goal.

    I'm not so vain as to think that even a single cell is as smart, even smarter, than me.

    Remember the old TV commercial: "Plastics." That's the way to go. Nonsense! Living cells are the philosopher's stone of design science: Smart materials.

  94. Comment by Rock — May 25, 2007 @ 4:16 pm

  95. Rock Says:
    May 25th, 2007 at 4:35 pm

    You repeated essentially the same argument: "This is how the unknown creative intelligence in evolution seems to operate. Indeed somehow, in the absence of any knowledge about it, this intelligence could be inherent in Nature. We can't exclude this as a possibility. But the only form of focused aware intelligence we know of is our own, a very localized manifestation of conscious intelligence in a specific structure - the brain."

    And what is a "brain"? A collection of billions of single cells, all acting in coordinated way to produce what you call "intelligence." I think you're seeing the forest but not the trees.

    That "creative intelligence in evolution" is not "unknown." Its those cells. We are not the "only form of focused aware intelligence we know of." All life forms we know of are intelligent by your own definitive criteria. We are not alone! We may be so vainly self-obsessed we've failed to notice that the world is crawling with intelligent life forms!

    What in G's Name are we doing searching the skies for extraterrestrial intelligence when scientists can't even recognize more than one form of intelligence at all!"”They're own, rather dubious, form of intelligence. Intelligent life forms are all around us, and inside us, and we don't even know it!

  96. Comment by Rock — May 25, 2007 @ 4:35 pm

  97. Thought Provoker Says:
    May 26th, 2007 at 8:51 pm

    Hi Joy,

    I have begun researching Penrose/Hameroff in earnest. This stuff is hard! I think it might take me longer than the three day weekend to solve the riddle of consciousness. It's a good thing I took the whole week off from work. :roll:

    Seriously. I am finding this stuff fascinating. Is there any chance I could talk you or MikeGene into bringing this topic forward as a new post? Give it a tantalizing title like "ID and Consciousness". There is something for everyone in here. I think it might generate some interesting discussions.

    I have to thank Keiths for providing the link to Grush & Churchland's paper While this paper is arguing against Penrose's attempt to hoist his hypothesis' "… status from 'campfire possibility' to 'scientific possibility'" it provided a useful summary. Here is a summary of Penrose's logic…

    Part A: Nonalgorithmicity of human conscious thought.
    A1) Human thought, at least in some instances, is sound, yet nonalgorithmic (i.e. noncomputational). (Hypothesis based on the Gödel result.)
    A2) In these instances, the human thinker is aware of or conscious of the contents of these thoughts.
    A3) The only recognized instances of nonalgorithmic processes in the universe are perhaps certain kinds of randomness; e.g. the reduction of the quantum mechanical state vector. (Based on accepted physical theories.)
    A4) Randomness is not promising as the source of the nonalgorithmicity needed to account for. (Otherwise mathematical understanding would be magical.)
    Therefore:
    A5) Conscious human thought, at least in some cases, perhaps in all cases, relies on principles which are beyond current physical understanding, though not in principle beyond any (e.g. some future) scientific physical understanding. (Via A1 - A4)

    Part B: Inadequacy of Current Physical Theory, and How to Fix It.
    B1) There is no current adequate theory concerning the 'collapse' of the quantum mechanical wave function, but an additional theory of quantum gravity might be useful to this end.
    B2) A more adequate theory of wave function collapse (a part, perhaps, of a quantum gravity theory) could incorporate nonalgorithmic, yet nonrandom, processes. (Penrose hypothesis.)
    B3) The existence of quasicrystals is evidence for some such currently unrecognized, nonalgorithmic physical process.
    Therefore:
    B4) Future theories of physics, in particular quantum gravity, can be expected to incorporate nonalgorithmic processes. (via B1 - B3)

    Part C: Microtubules as the means of harnessing quantum gravity.
    C1) Microtubules have properties which make certain quantum mechanical phenomena (e.g. super-radiance) possible. (Hameroff/Penrose hypothesis.)
    C2) These nonalgorithmic nonrandom processes will be sufficient, in some sense, to account for A5. (Penrose hypothesis.)
    C3) Microtubules play a key role in neuron function.
    C4) Neurons play a key role in cognition and consciousness.
    C5) Microtubules play a key role in consciousness/cognition (by C3, C4 and transitivity).
    Therefore:
    C6) Microtubules, because they have one foot in quantum mechanics and the other in conscious thought, provide a window for nonalgorithmicity in human cognition.

    THEREFORE:
    D) Quantum gravity, or something similar, via microtubules, must play a key role in consciousness and cognition.

    Even if it is a "campfire possibility" at this stage, I am interested in listening to such stories when told by someone who is knowledgeable enough in mathematics and quantum level physics to predict Black Holes and their implications before they were discovered.

    The weakest link in the logic chain appears to be the first (A1) assumption that consciousness is nonalgorithmic. In other words, nondeterministic. In more religious terms, having free will. Even as an Atheist I have trouble fully accepting that I am just a glorified Turing Machine. Or as Joy says a "zombie". However, technically, Penrose is coming close to assuming his conclusion here and that makes it a weak link Grush and Churchland point to.

    However, I think Penrose more than makes up for this "weak" assumption by offering evidence and working mechanisms that do not rely on this assumption.

    First the supporting evidence…
    Penrose is arguing that the nonalgorithmic nature of quantum mechanics can manifest itself at the macro level. Penrose points to an unrelated example of a nonalgorithmic object in nature, Quasicrystals.

    From the Wikipedia link…
    "In 1961 Hao Wang proved that the tiling of the plane is an algorithmically unsolvable problem, which implied that there should be aperiodic tilings"¦. in 1976 Roger Penrose proposed a set of two tiles which produced an aperiodic tiling with fivefold symmetry when some rules were observed."

    In 1984, Quasicrystals were found that matched Penrose's nonalgorithmic, aperiodic tiling. Of course people like Grush and Churchland want to dismiss Quasicrystals as, somehow, algorithmic based. But sometimes "it's just a coincidence" doesn't hold up. Was the discovery of real Black Holes just a coincidence? For being just a "campfire possibility" it makes a compelling case that nonalgorithmic things can and do exist in nature.

    Now for the Microtubules mechanism…
    Hopefully I haven't been too boring up to now, because this is the best part. ID science generally hypothesizes that there is too much apparent intelligence in biological organisms. Joy pointed me to a VERY thought provoking paper, Did Consciousness Cause the Cambrian Evolutionary Explosion?

    Here is an excerpt"¦

    How did intelligent behavior come to be? Dennett (1995) describes the "birth of agency": the ability to perform purposeful actions in complex macromolecules, and thus very early in the course of evolution. He emphasizes that agency and behavior at the macromolecular level are non-conscious and clearly preceded Cambrian multicellular organisms. For example purposeful behavior surely occurred in unicellular eukaryotic ancestors of modern organisms like paramecia and euglena who perform rather complex adaptive movements. Paramecia swim in a graceful, gliding fashion via coordinated actions of hundreds of microtubule-based cilia on their outer surface.

    As MikeGene's film clips have shown, there seems to be a lot of interesting things going on in organisms that don't have brains.

    The presence of microtubules is also a common trait of all these "intelligent" organisms. And guess what, the tubulin dimers that make up the microtubules are small enough to be influenced by quantum level effects. If you have never clicked a link before, click this one. It is a very interesting and thought provoking.

  98. Comment by Thought Provoker — May 26, 2007 @ 8:51 pm

  99. magnan Says:
    May 26th, 2007 at 10:12 pm

    Rock:

    "I'm sure I misunderstood, but it seems to me that cells do exactly what you said they don't do. I don't find it in the least bit implausible that a single cell is quite capable of "human levels of intelligence." Single cells do all the things you suggest about "human levels of intelligence." The only difference I see is quantitative and not qualitative.

    Single cells selectively gather information (by "selectively" I mean on the basis of prior experiential knowledge, information, ~4-billion yrs experience) about what is/not relevant"”and so make an implicit categorization, an example of abstract thinking"”logically process that information, and on the basis of that processing select from any number of alternative possible behavioral responses available to them, choose the response that adapts to the conditions that they have detected, perceived."

    I think you are describing the kind of "robotic" or machine intelligence being developed by human engineers for complicated devices like space probes, weapon systems, etc. ID thinkers like Denton and Behe have aptly described the cell as now known by molecular biology as having many aspects of a vast automatic factory complex. Organisms are coming to be understood in engineering terms as incorporating complicated data processing with multiple possible responses based on different configurations of inputs, with these responses adjusted by feedback. This is analogous in many ways to human engineered digital software controlled automation.

    What nonhuman living organisms and human designed machine systems lack is conscious awareness and the concomitant ability to create solutions to new engineering problems. Automatic systems no matter how complex cannot surmount or transcend themselves with a higher level of abstraction and insight. I disagree that these machinelike systems have anything like the capability of abstract thought, reasoning, and all the other mental faculties I enumerated that are needed by a human engineer designer. This is a difference of kind, of basic nature, not of quantity. These capacities are unique in our experience to humans.

    If such capacities are achievable just by increasing the complexity and sophistication of the biological machinery or the digital logic networks, then the dreams of the AI (artificial intelligence) researchers can be expected to be met, and advanced data processing techniques and faster processors will result in something similar to human intelligent conscious self-awareness. If this happens it will be hard to maintain any non-materialist position on consciousness, or on anything else. Consciousness will be seen by the example of AI to be ultimately the data processing carried out by neural structures in the brain.

    Your statement about the brain seems to reflect this materialist view: "And what is a "brain"? A collection of billions of single cells, all acting in coordinated way to produce what you call "intelligence." I think you're seeing the forest but not the trees." If you really believe that the brain produces intelligent conscious self-awareness like the liver produces bile, then we have little common ground in discussion of ID, and maybe the discussion should transfer to a new thread on theories of consciousness.

  100. Comment by magnan — May 26, 2007 @ 10:12 pm

  101. keiths Says:
    May 27th, 2007 at 1:06 am

    TP,

    You quoted Grush and Churchland's summary of the Penrose/Hameroff argument, but you left off the best part, at the end, where they explain exactly why it is so flimsy:

    Briefly, our analysis of this argument indicates that A1 is most likely false, and Section III below provides some reasons for denying it. This undercuts the case for A5, and hence Part A. B3 is almost certainly false (this is the subject of Section IV), and given its falsity, B2 is entirely speculative as well. This undercuts the case for B4, and hence the conclusions of Part B are exposed as entirely speculative. C1 is quite speculative, C2 is no more than a guess, and C5 is simply a bad inference (these are discussed in Section V), and hence Part C looks tenuous. In short, it appears to us that even if D did happen to be true, the argument embodied in parts A, B and C provides no reason to believe that it is. In Section VI, we provide independent reasons for thinking that D is probably false.

    They weren't exaggerating when they said that

    …the argument consists of merest possibility piled upon merest possibility teetering upon a tippy foundation of 'might-be-for-all-we-knows'"¦we judge it to be completely unconvincing and probably false.

  102. Comment by keiths — May 27, 2007 @ 1:06 am

  103. Raevmo Says:
    May 27th, 2007 at 5:28 am

    Magnan:

    What nonhuman living organisms and human designed machine systems lack is conscious awareness and the concomitant ability to create solutions to new engineering problems.

    New Caladonian Crows refute your claim:

    Kenward B, Weir AAS, Rutz C, Kacelnik A (2005) Tool manufacture by naive juvenile crows. Nature 433:121.

  104. Comment by Raevmo — May 27, 2007 @ 5:28 am

  105. Thought Provoker Says:
    May 27th, 2007 at 10:55 am

    Hi Keiths,

    You wrote…

    You quoted Grush and Churchland's summary of the Penrose/Hameroff argument, but you left off the best part…

    First of all, I read and reread the Grush and Churchland's paper to the point where I understand it well enough I could make their arguments in my own words. I am wondering if you understand things well enough to make the counter-argument without simply quoting verbatim.

    I echo Joy's sentiment that it appears you haven't done your homework. This stuff is HARD. Rocket science is simple compared to this. I know, I test missile parts for a living.

    However, I am interested in fermenting discussion on this so I will do some of your work for you in hopes others will join in.

    As I indicated in my previous comment. Grush and Churchland point to the weakest link, A1. Of course this "undercuts the case for A5" and turns the whole exercise into a might-be-for-all-we-know "campfire possibility". Trying to prove the existence of "Free Will" isn't easy. It is down right hard, and this is just the "A1" assumption. Being philosophers, Grush and Churchland had no trouble using up seven pages rehashing and restating old arguments. Frankly, I am impressed they exercised restraint in limiting it to ONLY seven pages.

    As good as Penrose is, he hasn't solved a riddle that has eluded solution for thousands of years. I'm willing to cut Penrose a little slack here.

    Now to the "B3 is almost certainly false". While Grush and Churchland spent seven pages saying "Free Will is an illusion" they spend only a page and a half saying "The discovery of quasicrystals wasn't significant."

    Think about this. Penrose is one of the world's top mathematicians. He uses his math skills to model things based on the nonalgorithmic properties of quantum mechanics. IOW, he builds mathematical models based on things that are impossible to model mathematically. What Penrose does is HARD. It borders on being impossible.

    Modeling the existence of Black Holes is an example of what Penrose does. I suggest that if Black Holes were accidentally discovered shortly after being predicted by Hawking/Penrose there would have been "it's just a coincidence" attitude. I suggest this is what is Grush and Churchland is trying to do with "B3 is almost certainly false".

    After Hao Wang/Berger proved aperiodic tilings exist in 1966, people tried to find them. "The first such set…consisted of 20,426 Wang tiles". Other people reduced the minimum set to fewer and fewer tiles. In 1974 Roger Penrose demonstrated it could be done with only two. For his efforts (he called it a "hobby") the set was thereafter referred to as "Penrose Tilings".

    Meanwhile in the world of crystals. It was firmly understood that all natural crystal formations must conform to certain rules, one of which was periodicity. Any other crystal formation was thought impossible, until such a crystal was found in 1982. It took two years for those in the established field to recognize the impossible was possible but even then they balked at just calling them "crystals", thus the name "quasicrystals". So how do we model something that appears to be impossible to mathematically model? Sounds like a job for PENROSE! Oh, he already did it? Hmmm, thanks but it's just a coincidence. Penrose really doesn't know what he is talking about. "B3 is almost certainly false".

    In this case, I wouldn't even call it cutting Penrose slack. If anyone can know, Penrose most certainly knows about nonalgorithmic things in nature.

    Finally to the third part ("Part C looks tenuous"). This is where Grush and Churchland attempt to fight the battle on ground that clearly includes fundamental properties of quantum mechanics (or as Hameroff says "funda - mental").

    For this, I will take a page out of Joy's book. Do your own homework. Here is Hameroff's response to this…