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    The Popular View Of DNA
    By Gerhard Adam | January 29th 2013 05:13 PM | 128 comments | Print | E-mail | Track Comments
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    To many, DNA represents the definitive code which governs all life.  It has been compared to a sophisticated computer program from which every aspect of an individual organism is built.

    Equally it has been stated that DNA is not destiny, so there is some basic recognition that DNA is not the absolute arbiter of everything biological.

    However, we find that there is still a general reluctance to reduce the prominence of DNA from our understanding of biological systems.  There's no question that it is an important central figure in development, but it is only part of the process.  From this perceived role of central control, came ideas of the "selfish gene" and even the idea that random mutations are the driving mechanism of evolution (1).  In most cases, these views are misleading and often just wrong.  

    When genomes were mapped, especially the human genome, there was the anticipation that this would unlock the secrets of biology and that all manner of understanding would suddenly be available for exploitation.  To our surprise, it was discovered that the overwhelming majority of DNA didn't code for any proteins, and was relegated to the status of "junk" in the popular view.  Of course, biologists knew that it wasn't "junk", but rather that it was simply non-coding, but there were no good ideas or explanations, initially, as to the role it might play. 

    In short, it was discovered that not all DNA was necessarily utilized, and that there could be considerable variability in what a coded sequence might represent, versus what was actually expressed in the organism.  It couldn't even be fully stated that anything not encoded in DNA wasn't possible.  In fact, even foreign DNA could play a role.

    Enter epigenetics.  

    With epigenetics, it was discovered that possessing a particular DNA sequence didn't mean that the same results would be produced, or that any results would be produced.  The biological functions were a lot more specific than that, and so identical DNA did not produce identical results.  DNA regulation was a major factor in establishing the phenotype of an organism.

    In recent years, it has also become apparent that the microbiota associated with each organism, not only influenced, but sometimes played a major role in the survival, and ultimate fitness of an organism.  In many cases, the microbiota interacted with the organism's systems [such as the immune system] and "trained" or calibrated the responses.  In some instances, the bacteria were actually capable of utilizing the system to their own purposes.

    We still use terms like infection and disease to create an image that life is an "us vs them" situation, instead of recognizing that these terms really reflect a variety of interactions between organisms that are not so neatly described.  Infection may not relate to the organism, but rather where the organism is located.  Disease responses may not be the result of anything an organism is doing, but rather our immune response to it [i.e. meningitis].

    To an individual that is sick, such distinctions may not be particularly relevant, but if we intend to understand the dynamics of what constitutes life, then such considerations are fundamental.  Microbiota changes, may be as fundamental to natural selection, as the previously held notions of mutations.  To further complicate matters, the microbiota are also responsive to xenobiotic influences [i.e. chemicals that are foreign to an organism, such as antibiotics, toxins, etc.], which can further modify them, their behaviors, and their impact on the host organism.

    As one of the final considerations to ponder in all this, is a recent article that clearly shows that the most fundamental elements of what we consider to be "identical" are anything but. 
    Over the past decade, research groups from all over the world have reported similar trends: they have for instance found that cloned pigs have as much variation in the expression of certain genes as naturally bred pigs.
    http://sciencenordic.com/does-perfect-clone-exist
    There is no question that DNA is a "vital" element in encoding the necessary information required by future generations, but it should be equally apparent, that DNA is only one part of the process.  However, one of the difficulties in biology is reducing any element to the status of "vital" will be both correct and incorrect at the same time.  Is the heart more vital than the brain?  

    What is becoming increasingly apparent is that life's success depends on a continuous interaction of processes that keep everything viable.  Reductionism is necessary to understand specific elements of those processes, but invariably it is also a holistic approach that will help us make sense of things.  However, no matter what is discovered or understood today, there is no guarantee that these processes will look the same in the future (2).

    ------------------------------------------
    (1) There is often a sense that random mutations are a major force in evolution, rather than recognizing it as a relatively minor force for everything except possible novel traits.  The biggest factors are genetic drift and selection.

    (2) This isn't to suggest that many biological processes are not conserved in the long-term and applicable to understanding life.  The biggest issue is in the continuous evolution and selection that is experienced by the organisms themselves and how that affects the overall nature of the biosphere.  Some effects may manifest in decades while others may take millions of years.  The only thing that is assured, is that it will continuously change.

    Comments

    vongehr
    From this perceived role of central control, came ideas of the "selfish gene" and even the idea that random mutations are the driving mechanism of evolution ... There is often a sense that random mutations are a major force in evolution, rather than recognizing it as a relatively minor force for everything except possible novel traits.
    I think this is the most important point, except, why add "for everything except novel traits"?  The randomness is important in early evolution, but becomes more and more steered via evolved mechanisms of adaptation, especially for "novel traits".  Sexual mixing is not a simple random DNA "mutation" but a quite steered randomness "mutating" the code instead.  The question is, how far do we want to stress DNA as being the most important memory in this game (rather than the environment say).  It is almost a matter of taste.
    Gerhard Adam
    I used that qualifier, because it is possible for random mutations to potentially produce such modifications, but specifically I was thinking that it would be a much more significant force in single-celled organisms.  So, my thinking about "novel traits" was geared towards the microbial world more than multi-celled organisms.
    Mundus vult decipi
    UvaE
    Even "clones" are not carbon copies of each other due to epigenetics.  
    Gerhard Adam
    Yes, which is precisely the point.  Since even clones are not identical, then it places the traditional view of DNA and genes being the sole influence on heredity in a different light.  In fact, it changes the entire perspective of how fitness may be achieved.  When we consider that genes provide basic information, that is epigenetically regulated to produce a particular result, but that we also have commensal microbes, or even parasites/symbionts that all have their input into the process as well.  From this collection, we may suddenly find an organism whose fitness is not so simplistically evaluated simply by genetic distribution.
    Mundus vult decipi
    John Hasenkam
    The question is, how far do we want to stress DNA as being the most important memory in this game (rather than the environment say).  It is almost a matter of taste.
    Good point. I would add that there is no single answer to this, that in some instances one or the other may predominate. Still to be worked out. Only today an old friend pointed out how even in identical twins various cell strutures can be quite quite different, the key variable being they were raised in different neighborhoods. That is one reason why I don't like to think of genes are stores of information but rather as response sets to environmental contingencies.



    BTW Sascha, you might be interested in the idea of Susan Lindquist: hsp90 as an evolutionary capacitor. The concept is straightforward: organisms possess an intrinsic capacity for morphological change independent of new mutations, there is a "reservoir" of adaptive potential that is mediated by heat shock protein 90. 
    Even "clones" are not carbon copies of each other due to epigenetics.  
    Not just epigenetics, the environment will impact on gene expression and modify the impact of gene expression. That is why twins can display different characteristics even when they are raised in broadly similiar environments. 


    There are a  host of problems with the concept of cloning. For eg. In Dolly the sheep it was silly to use one sheep for the DNA and other sheep for the ovum and another for the implantation.  

    The central tenet of DNA genetics is that all heritable traits are encoded in DNA. That a particular gene may be expressed differently in different individuals or in different circumstances is not a big issue.  The popular view may be simplistic and overlook the very occasional exception - see below - but it  is hardly wrong in the wholesale manner you imply.

    What would be interesting would be to discuss cases where the central tenet is violated - that a heritable trait is carried by something other than DNA. However, even methylation, which can render a gene switch persistent through many cell generations, is reversible. Our own cells differentiate during embryonic development partly through the use of methylation but it is removed when we produce germ cells so it is not inherited at the level of the reproductive unit, the whole organism. 

    Likewise heritable methylation in plants comes and goes:
    Jörg Hagmann therefore cautions not to overestimate the importance of DNA methylation during evolution: "Our experiments show that methylation changes are often reversible". In other words: New epimutations are often not maintained over the long term. "Only when selection wins out over reversion can these epimutations affect evolution," says Hagmann.
    To say that DNA's role is not the whole story requires cases where the epimutation is not reversible. If such cases exist at all they are a tiny and insignificant fraction of all the mechanisms broadly classed as epigenetics and do not create a significant dent in the central tenet of inheritance-by-DNA.
    Gerhard Adam
    Good points, but mine is an even simpler one.  DNA is insufficient to producing a viable living organism, regardless of epigenetics.

    However, I didn't say it was wrong.  I said that too much focus has been placed on DNA and genetics being the only source of information necessary to understand biological outcomes.  This has clearly been demonstrated to be incorrect.
    The central tenet of DNA genetics is that all heritable traits are encoded in DNA.
    I'm assuming that by "heritable" you mean inherited, such that DNA is the source of all information that will be passed onto a future generation, regardless of its actual heritability.  If one wants to confine the discussion solely to that level, then that's not a problem, but it doesn't address evolution.

    Evolution is also subject to behavioral and symbolic variations that are every bit as heritable and influential in fitness as anything encoded in DNA. 
    Our own cells differentiate during embryonic development partly through the use of methylation but it is removed when we produce germ cells so it is not inherited at the level of the reproductive unit, the whole organism.
    Yes, and persistence of methylation would be a relatively rare occurrence.  However, that misses the larger point that during development methylation can and does occur in the developing embryo.  So, would you consider that to be a heritable trait based on the conditions of the mother's pregnancy? 

    The notion that epigenetics must demonstrate instances of where it is not reversible misses the point.  The fact that we are all under the influence of epigenetic factors indicates that they are very much a part of the developmental process.  Reversibility has nothing to do with it.  If even one trait is produced as a result of methylation that improves fitness, then it is a factor in natural selection and it can't be credited back to DNA. 

    As I said, there's no question that DNA represents the fundamental store house of information that will be used in all future generations.  If it isn't present in the DNA, then it can't be operated against [although external agencies can still exert a selection influence].  However, for the most part, we can consider DNA as the basic set of information against which most other actions are taken.

    This doesn't diminish the importance of DNA, unless we exclude all other considerations in our desire to explain evolutionary processes.  In that case, it is flatly wrong.
    Mundus vult decipi
     "If it isn't present in the DNA, then it can't be operated against [although external agencies can still exert a selection influence]."What does that mean, actually?  Give an example?  Because if an organism learns some new and effective defensive or offensive behaviors from experience, what could be absent from DNA that would prevent it from adapting any of it's defensive or offensive behaviors accordingly?
    Gerhard Adam
    Here's a straightforward example; the bobtail squid [Sepiola atlantica] and the bioluminescent bacteria [Aliivibrio fischeri].

    Here we have an example of a symbiotic relationship that provides a specific service to both.  For the squid, we have a "trait" that is beyond the capabilities of the DNA present in the squid, and yet provides an important feature that impinges directly on the squid's fitness.

    In the same way that our own immune system is "tweaked" by our microbiota.  As a result, we find that without the influence of that external agency [i.e. our gut bacteria] our immune system is deficient.  There are clearly numerous other instances, whether it be the protozoans responsible for termite digestion, etc.  What is often lost in our explanation of symbiosis or parasitism, is that these "relationships" are not just convenient, but absolutely essential for survival.  In these instances, the host DNA offers no explanation whatsoever.

    I should also clarify that my point about DNA has little or nothing to do with behavior.  Since much of this may well be the result of behavioral inheritance, then DNA would not carry the necessary information into future generations, but rather that "trait" would be developed by the surrounding parents or community.  An individual that merely acquires a behavioral trait through experience isn't particularly relevant unless than information can be conveyed beyond its personal use.

    Apologies if my response sounds confused, but I started off thinking you were talking about phenotypic influences, and then realized you were probably talking about behaviors.  Sorry, if I confused things.
    Mundus vult decipi
    Well, this is where I respectfully disagree, since in the end all evolution involves behaviors, even if those behaviors will require the evolution of their structures, and structures that we gain genetically, symbiotically or by genetic drift, will inevitably affect an organism's relevant behaviors.
    Gerhard Adam
    Yes, but the problem is how that information gets conveyed to future generations.  In some cases that information will be coded by genes, in others it will be "taught". 

    More specifically the issues of "behaviors" is a tough one, because it invariably involves teleonomy where all actions/behaviors displayed by organisms convey a kind of purpose.  The difficulty occurs because this is present even in those organisms that lack the necessary structures to have cognition or even a nervous system.  As a result, defining what is meant by "behavior" can be a bit tricky.

    There's no question that the way an organism acts will be constrained by its phenotype, so one could argue that genetics determines the behavior, or more specifically the boundaries of that behavior.  Bear in mind that my primary point was that DNA is not the final word on evolution.  So, I'm quite prepared to acknowledge that there are a complex arrangement of traits, behaviors, learning, etc. etc. etc. that will all result in producing an organism that can satisfy it's primary "purpose" in surviving and reproducing.

    However without a more explicit definition of what is meant by "behavior", it is hard to examine the origins of this.  In the case of DNA, we have a specific mechanism that is used to convey information to the next generation.  In the case of behavioral inheritance, we have an additional system that is not covered by DNA to produce these changes.  In humans one could include a symbolic inheritance where there is an additional avenue for learning/development.  Each is dependent on a specific mechanism by which it will be realized in future generations, and each will have a fitness impact.

    Consider that if we examine microbes, and viruses one can't help but be struck by their "purposeful" pursuit of their objectives, and yet one would be hard-pressed to articulate what exactly is meant in addressing their "behavior" [beyond simply invoking teleonomy].

    As I mentioned previously, whatever an organism learns or gains from experience, is irrelevant from a fitness perspective unless that can be conveyed into future generations.  Hence the need for describing whatever system that is.  A single organism's behavior isn't a significant enough evolutionary force, although it may contribute to genetic drift, in the same way that predation or some other accident can exert an influence.
    Mundus vult decipi
    "because it invariably involves teleonomy where all actions/behaviors displayed by organisms convey a kind of purpose."  Correct, because all behaviors obviously are intended to serve the organism's purpose, even when the don't succeed.

    "even in those organisms that lack the necessary structures to have cognition or even a nervous system." 
    Well; since according to a number of prominent scientists (Mae-Wan Ho, James A. Shapiro, Eva Jablonka, Lynn Margulis, Dennis Bray, and on and on), there are no organisms that can't cognitively compute, and in addition, you must recognize that all organisms are making choices every time they choose to move, which again, since these choices seem to be goal seeking, would also seem to serve the purposes for such seeking.



    "In the case of DNA, we have a specific mechanism that is used to convey information to the next generation."
    But your argument seems to be that DNA doesn't contain information that we or earlier organisms have learned, or that changed our behaviors as a result.  And that even though DNA contains intelligent instructions, they were somehow conferred by an unintelligent and random process.  Obviously this defies common sense and logic, but that's the prevailing dogma most of us are taught.


    "A single organism's behavior isn't a significant enough evolutionary force, although it may contribute to genetic drift, in the same way that predation or some other accident can exert an influence."

    A random mutation by accident on a single organism would be an even less significant evolutionary force. But luckily, all organisms live at some point in groups, and all communicate (again see the above scientists to confirm this).  And the reason or purpose for communication is to share experiences that all will learn from.  And these "cultures" as we've come to call them have been necessary to all species evolution from the start.



    And think about this: If behaviors are explained as instinctive and not necessarily learned, how did these instincts become fixed genetically to begin with, if not originally fixed from prior experience?  Again by the unintelligent stochastic process many of us have been taught to believe?
    Gerhard Adam
    But your argument seems to be that DNA doesn't contain information that we or earlier organisms have learned, or that changed our behaviors as a result.
    Yes.  This is clearly where we part ways.  The process you're describing sounds almost Lamarckian, but there is no feedback mechanism to incorporate something learned back into the DNA and into the germ line.
    And that even though DNA contains intelligent instructions, they were somehow conferred by an unintelligent and random process.  Obviously this defies common sense and logic, but that's the prevailing dogma most of us are taught.
    It is an unintelligent process.  It doesn't defy common sense nor logic, because it has been demonstrated to work [I believe this is the link www.pnas.org/content/69/10/3038.full.pdf]. 
    A random mutation by accident on a single organism would be an even less significant evolutionary force.
    This was explicitly stated in the article.  Although the effect would likely be more significant in microbes, it isn't a major evolutionary force.
    If behaviors are explained as instinctive and not necessarily learned, how did these instincts become fixed genetically to begin with, if not originally fixed from prior experience?  Again by the unintelligent stochastic process many of us have been taught to believe?
    Fixation is due to natural selection.  Obviously certain behaviors improved fitness.  Nothing more is necessary.  Unfortunately it seems that you're assigning behaviors to bacteria as comparable to the behaviors of dogs, or even humans.  Without differentiating, you're assigning the trait of "cognition" beyond the level suggested by the scientists you mention.  There are clearly boundaries and limitations dependent on specific phenotypes, so to associate "cognition" to bacteria is a stretch and unless you're prepared to provide a more explicit definition of what you mean [again, beyond simply teleonomy which doesn't actually explain anything], then I have to disagree.
    Mundus vult decipi
    "but there is no feedback mechanism to incorporate something learned back into the DNA and into the germ line."Well, the scientists that L've named will tell you that there is.  And they're not Lamarckian although Lamarck and later Baldwin were on the right track.  This approach by these and other evolutionists is sometimes called adaptive mutation and sometimes self engineering.  It is not creationism, if that's to be your next response.


    Cognition betond the level of the scientists I mentioned?  If you'd read their papers, you wouldn't have to suggest that these ideas are Lamarkian.  Read this for example: 
    James A. Shapiro, Department of Biochemistry and Molecular Biology,
    University of Chicago: 
    Bacteria are small but not stupid:  Cognition, natural genetic engineering, and sociobacteriology.   
    http://shapiro.bsd.uchicago.edu/2006.ExeterMeeting.pdf
    Excerpt: 
    "The realization that most DNA changes in bacteria (and eukaryotes, too) occur by the action of natural genetic engineering systems removes the source of variation in the genome from the category of stochastic events or unpredictable accidents and places it in the context of cellular biochemistry. This reclassification has major conceptual consequences because cellular biochemistry is subject to regulation and operates in predictable ways.”



    Here's excerpts from Mae-Wan Ho, Geneticist and Biophysicist, excerpted from The End of Bad Science and Beginning Again with Life: 
    “Finally, the ultimate neo-Darwinian taboo has been broken. Wiesmann’s barrier has been breached, and in many different forms, some of which I mentioned already (see box 2).   
    Box 2
    The inheritance of acquired characters
    Epigenetic inheritance - inheritance of cellular or gene-expression states such as patterns of DNA methylation, cortical inheritance in ciliates, dauermodifications.
    Inheritance of induced changes in genomic DNA - fertilizer treatment of flax and other plants; drug-resistance in mammalian cells insecticide- resistance in insect pests and herbicide-resistance in plants.
    Feedback from somatic cells to germ cells - reverse transcription and insertion of cDNA into germ cells, eg. immunoglobulin V genes
    'Adaptive' mutations in bacteria, yeast and other cells.”


    “ -- others including myself have written on how those newly discovered processes seriously undermine neo-Darwinian evolutionary theory over 15 years ago. The evidence against the natural selection of random mutations has grown overwhelming since. Simply stated, organisms can mutate their genes as they are selected; and there is a large degree of non-randomness to mutations.
    Recently, molecular geneticist James Shapiro has joined the debate. He is critical of neo-Darwinians like Richard Dawkins and John Maynard Smith who are still clinging to the discredited paradigm. "Localized random mutation, selection operating "one gene at a time" (John Maynard Smith’s formulation), and gradual modification of individual functions are unable to provide satisfactory explanation for the molecular data, no matter how much time for change is assumed. There are simply too many potential degrees of freedom for random variability and too many interconnections to account for."
    And yet, the variations are far from random. The processes responsible for the fluidity of the genome form a highly sophisticated regulatory system, which can provide hyper-variability or stability for genes or genomes as required. All organisms, from bacteria to human beings, possess a wide range of repair and proof-reading functions to remove accidental changes to DNA sequences and correct errors resulting from physiological and physical insults. The same cells also possess numerous biochemical mechanisms for changing and reorganizing DNA through ‘natural genetic engineering’ – processes that include cutting and splicing of DNA molecules into new sequence arrangements (like the immunoglobulin genes). Most frequently, natural genetic engineering involves mobile genetic elements, found in all genomes, which can move from one position to another, enabling organisms to respond to environmental challenges.”

    I have more, but that's how we're ramblin' these days.
    Gerhard Adam
    I'll read the paper and review some of your references again, so I'll respond more fully later.

    However, I wanted to re-iterate that I do not advocate nor suggest that random mutation [especially the one gene at a time approach] makes any sense.  It sounds like we're in agreement on many aspects of this, but I'm a bit disturbed by your use of the term "intelligence".

    My apprehension comes from the fact that it doesn't seem to be clearly defined, at least to me.  So, if you could indicate what your working definition is, I'd appreciate it.  That's also why I want to read the paper you linked, because terms like "cognition" are problematic if we don't have a specific definition regarding how it is to be applied.

    These terms are heavily loaded and denote certain assumptions, so if those are not to be used, or if there are different assumptions/conditions being considered then I want to be clear on what they are.
    Mundus vult decipi
    So let me define intelligence more specifically as the ability to use the trial and error process to solve predictive problems.   Simply put, organisms make use of a complicated algorithmic process to examine the environmental patterns from their sensory input and compare these moving “mental” holographs to the patterns they’ve either memorized from previous experiences or been instinctively provided. (Instincts that were also derived from experiences of some organisms back down the line of heritability).  Intelligently looking for what’s there and happening that shouldn’t be, or not there and happening that should.  

    From this information, they select from their particular set of pretested optional behaviors that the patterns found can be expected to fit, and send signals to their motor apparatus that will trigger the appropriate actions in response.  Not a process that’s been conferred upon these organisms by accident.
    Gerhard Adam
    Sorry, but that definition would apply equally to many machines/computers.  Are you prepared to consider them intelligent?
    Mundus vult decipi
    Gerhard Adam
    Sorry, this link might be more appropriate to illustrate the unintelligent processes involved.
    http://www.pnas.org/content/106/19/7780.full
    Mundus vult decipi
    Nowhere does that paper say there are unintelligent processes involved.  Further, they've done a modeling experiment which doesn't attempt to tell us why things happen, but how,  And even then this experiment shows an intelligently constructed process at work.
    Gerhard Adam
    Then please explain your definition of intelligence in this context.
    Mundus vult decipi
    John Hasenkam
    Up, up and away! That discussion could go on forever! 

    How brainless slime molds redefine intelligence


    Great article!
    Gerhard Adam
    The problem is that many simple rule-based systems can behave "intelligently" without possessing the trait we consider to be "intelligence".  We can see this clearly with something like computer programs, so it becomes even more important that we define what is meant by the term.

    We already know that organisms behave with a "purpose" and we can describe that using terms like teleonomy.  However this doesn't explain anything.  Similarly, people have even described the behavior of something like a forest fire as if it were alive or behaving intelligently [or at least with a purpose].

    So, one of the central tenets that I'm operating from is that all life originated from non-life processes.  There is nothing extra that goes into life beyond that which can be demonstrated using the laws/rules of chemistry.  There is no doubt this behavior is sophisticated and complex, but is it intelligent?  Can it choose to do one thing versus another, or is it constrained by specific rules?

    Certainly one can argue that even our brains are constrained by specific rules and therefore how can we lay claim to intelligence with such definitions, but that's exactly the problem.  Perhaps the whole concept of intelligence is little more than increasingly complicated rule-based systems.  OK, but then we need to define the various thresholds we expect to encounter.  One can't simply pronounce bacteria as intelligent without some attempt to quantify the varying degrees in which we find it manifest.

    We all know, colloquially, what we mean by "intelligence", so if we're going to apply it in more unique or novel situations, then we need to be more specific in its definition.  If we can't define it, then let's not use it, lest we carry more assumptions than warranted into the discussion.

    I'm quite content to consider the human brain and bacteria to be separated by a more complex rule-based system.  One of the primary difficulties is that attributing intelligence to organisms that don't even possess a nervous system effectively re-introduces a type of mind-body duality by suggesting that intellect [or mind] exists separately from the brain. 

    I happen to disagree that this is really the case, because I don't believe that complexity necessarily requires intelligence.
    Mundus vult decipi
    "There is no doubt this behavior is sophisticated and complex, but is it intelligent?  Can it choose to do one thing versus another, or is it constrained by specific rules?"As I pointed out earlier, it can choose to do one of several things versus the others.  But of course all biological strategies are constrained by their organisms limitations, which include limits in the ranges of all our intelligences.


    John Hasenkam
    We all know, colloquially, what we mean by "intelligence", so if we're going to apply it in more unique or novel situations, then we need to be more specific in its definition.  If we can't define it, then let's not use it, lest we carry more assumptions than warranted into the discussion.
    Yeah to that. Skinner was at pains to demonstrate the dangers of utilising "folk psychology" concepts. One example is the attempts to define emotions. One reason the medical profession relied on using latin terms was because it was a dead language, hence the meaning could remain fixed. Using everyday words and concepts often leads to much confusion. 



    Intelligence is perhaps best perceived as an operational concept. There isn't a single intelligence but rather specific individual behaviors we label as intelligent. This is why don't like Spearman's G concept or Gardiners multiple intelligences model. Instead I believe it is more useful to think that behavior A results in A1. That is at least hopefully quantifiable and avoids any attempt to look "behind" that behavior, to look at some mysterious element at play. 




    So shall we let the slime mold redefine intelligence or not?
    John Hasenkam
    Forget about intelligence. Bad concept. Throw it down. I have no interest in defining intelligence. Red herring. In relation to the slime mould, I want to know the causal relations that give rise to the specific behaviors. For example it has been suggested that the slime mould behavior is arising via memristors. Don't know, not a convincing explanation in the provided link but that is a much more fruitful avenue of investigation than trying to define intelligence.  
     Intelligence is the ability to acquire and apply knowledge and skills.  There's no need to redefine it, just a need to recognize it where we had thought there was none. "Therefore, the above memristive circuit model, which has learning properties, is useful to better understand the origins of primitive intelligence."   

     Intelligence is mysterious, but not a concept we can get away with ignoring.  I can't in any case.
    Up, up and away! That discussion could go on forever! 
    Pass the popcorn, John. Don't you love it when a full-blown argument turns out to be just a matter of definitions - and the proponents *still* don't give up? :) 
    John Hasenkam
    Why assume the information goes from the bottom up? The environment is also a source of information. There is plenty of information "encoded" in the environment. For example, a single gene can encode for many proteins, not just one. A central tenet of the Dogma has been overthrown. 
    Obviously the environment is a source of information, and obviously if you don't experience it, it isn't.  And the biggest or most important source of information in that environment is the culture or cultures you were born into, or later moved into, worked in, etc.  Books are part of it, and so are the ways your house is built, your schools operate, etc., etc.
    Gerhard Adam
    Obviously the environment is a source of information, and obviously if you don't experience it, it isn't.
    Not true.  Even as germ cells, the cells are exposed to the "environment", so it simply isn't possible to be alive and not experience the environment.
    And the biggest or most important source of information in that environment is the culture or cultures you were born into, or later moved into, worked in, etc.
    That's only true for an infinitesimally small portion of the biosphere.
    Mundus vult decipi
    Of course t's true that everything experiences their environment, because to point out the obvious, if you didn't, you wouldn't.And as to the truth about the effects of one's culture, you would need to understand that all creatures have and had a communicative culture, which to point out the obvious, you don't.
    Gerhard Adam
    I'm sorry, but you're introducing way too many concepts and ideas without background.  The ability to communicate doesn't automatically give rise to culture.  It seems that your applying terms that have specific connotations and diluting their meaning beyond any recognition.
    Mundus vult decipi
    Good god, I'd assumed you had some prior knowledge of these matters.  What do you think communication does if not furnish and support the lessons of each family or group.  All organisms need to learn to survive, and who or what do you think they learn from, their alleged instincts straight from mother nature?  I'm not going to quote chapter and verse from someone's biology books in any case.  In the end you'll have to educate or re-educate yourself.
    John Hasenkam
    Bad reality, I had assumed the biologists would not make reference to ill-defined concepts. Ha! Instincts are tricky! Organisms from viruses to us "learn" to survive so intelligence must be pervasive. Throw it down. 
    If you don't think viruses learn, then as far as you're concerned I guess they don't.
    Gerhard Adam
    Simple question.  Where and how is the "learned" information stored?
    Mundus vult decipi
    Actually the same places that your "instincts" are stored.
    Gerhard Adam
    Wrong.
    Mundus vult decipi
    Gerhard Adam
    It seems like you have an axe to grind, so unless and until you actually have some linked papers that support your views, I would suggest you stop being a smart ass.

    I get that you have your own opinions in these matters, but if you want to get condescending or insulting without evidence, then I'm quite prepared to write you off as a crackpot.

    Your earlier Shapiro paper wasn't impressive, and it appears that he doesn't exactly have the respect of the scientific community for much of his writings.  In fact, much of what he claims simply isn't true, or is his own misunderstandings.

    So, again.  If you wish to contradict the views being expressed, then it will require more than your opinion, when it goes against commonly accepted knowledge.
    Mundus vult decipi
    I gave you a slew of references, and you read Shapiro, and then all you can say is that he doesn't have the respect of the scientific community and thus I'm a crackpot.  The fact is that he has enormous respect worldwide, as do most of the others that I mentioned.  Your reaction here is typical of the old guard who can't handle the possibility that they're wrong, because if they are, they'll have to start all that painful thinking process over.  Look, you wrote an article here and invited comments, and the comments have put you completely on the defensive.  You have no responses left that are reasonable and so resort to insulting the commentators and others abilities and characters.  And guess what, you've learned nothing.
    Gerhard Adam
    You gave no references in defense of your assertions.  I'm quite familiar with the authors you've mentioned and none have stretched the boundaries in the manner you have.

    There's nothing wrong with establishing new possibilities and new explanations, but they need to be done in a manner that offers explanation, and not simply some declaration without substance.  I'm hardly on the defensive here. 

    It appears that you didn't actually read the article.  You keep making comments about random mutations, despite the clear quote from the article:
    There is often a sense that random mutations are a major force in evolution, rather than recognizing it as a relatively minor force for everything except possible novel traits.  The biggest factors are genetic drift and selection.
    You're making a claim that everyone is wrong.  So prove it.  Assertions are not proof.  In short, provide some evidence for your claims. 

    As for insulting commentators ... ???  
    Mundus vult decipi
    Random mutations are, as you quoted, a minor force, but you seem to think that justifies your theories as being the major force.  Or that without that selection process, there'd be no genetic drift and selection (which means selection BY the organism and not BY mother nature).What you need to understand (but likely won't) is that randomness makes evolution necessary, as all organisms take advantage of it.  Randomness is probable, and organisms learn to defend themselves from the probable.  Evolution has both offense and defense as its purposes.
    But in your theory, it's randomness that takes advantage of the organism.  How, when randomness has no intelligence (unless the intelligence comes from some secret god that mother nature is a stand-in for).
    But then I digress as usual.
    As to providing evidence for my claims, the more I provide, the more you say the evidence is not by your reckoning evidence.  Pleasing the unpleasable is apparently beyond my abilities.
    In any case I like to think I'm writing for other readers and am under no obligation to "prove" anything to those that do nothing but demand it.
    Gerhard Adam
    You haven't provided any evidence, and now you appear to be heading down the rabbit hole.
    In any case I like to think I'm writing for other readers and am under no obligation to "prove" anything to those that do nothing but demand it.
    Yep, that's about as unscientific as it gets.  In any case, as a former investigator [from you profile] I would've thought that you understood what it takes to make a case.  Apparently not.
    Mundus vult decipi
    John Hasenkam
    Roy,
    I didn't have to read Shapiro or anyone to question the sufficiency of random mutations as the principle evolutionary driver, this issue has long bothered me. I have frequently been abused for raising this matter. One reason I made the slime mould reference is for me that raises some serious philosophical issues about the intrinsic qualities of the universe. We think intelligence requires a nervous system, or at least most think that. Yet we see intelligent behaviors in very simple organisms. I have never accepted the neoDarwinian view, that all this amazing complexity and behavior can be understood from the bottom up. 

    In one sense at least the issues you are raising remind of the themes being explored by Ian Stewart and Kaufmann, mathematical biologists who are exploring emergent properties in biological processes. For Stewart it is about how geometry is very important and I think he is onto something there. Nearly all of biology ignores the importance of geometric structures as causal factors in biological processes, they think with chemistry and physics. Stewart, IIRC, is claiming this is a massive oversight. When one thinks of receptor-ligand interactions, pathogen associated molecular patterns, antibodies, all of which involve the shape of the molecules, not necessarily their amino acid sequence, one sees evidence.

    There was a fascinating experiment which explored this issue. I can't reference it at present but it involved creating "plastic antibodies" that were moulded into the same shape as biological antibodies. These worked, these plastic antibodies did bind to the relevant structures in the same way as biological antibodies but obviously the host immune response could not replicate these antibodies. A big tick for Mr. Stewart. Plastic antibodies. The shape not the sequence. 

    You are trying to articulate a novel and nascent perspective on biological processes. If I have understood you correctly you are arguing that emergent properties overwhelm any random effects and give rise to processes that are the big drivers in evolution. I think that is far more plausible than a lucky strike. However even single gene mutations, a single base change, one set of repeats, can have profound consequences for the organism. So while it is dangerous to think of the single gene as a unit of selection, sometimes a single gene change makes all the difference. 

    At present though the research is so new, so novel, that in order for you to adequately express these views to a wider audience requires something much more substantive than commenting on blogs. It is probably better to articulate a new perspective independently of criticizing the old perspective, the latter can dissolve in the light of the new. New perspectives and ideas need to be very carefully articulated and commenting on blogs is a very difficult way to do that.

    Be warned Rye, the way you have expressed yourself makes it easy to misinterpret you as an enemy of evolution. You are not that, you are an opponent of neoDarwinism.  

    Have I understood you correctly?





    Yes.
    Gerhard Adam
    Regarding Shapiro

    http://sandwalk.blogspot.com/2012/09/james-shapiro-claims-credit-for.html

    http://whyevolutionistrue.wordpress.com/2012/12/02/james-shapiro-gets-evolution-wrong-again/

    While he may have some significant points, he seems to straddle the fringe by indulging in much speculation.
    Mundus vult decipi
    Hank
    Generally speaking, if Larry Moran and Jerry Coyne say someone is wrong, that someone is wrong. They are not circling the wagons around any pet position or anyone.
    They are both died in the wool neoDarwinists, and they don't deny it.
    Hank
    Why would they deny accepting evolution?  You can call me a Darwinist or neo-Darwinist or anything you want, it makes no difference. That is why philosophy is not science and never has been.
    They don't deny accepting evolution, they deny that the newer theories are viable.  And t's a red herring to point out that "philosophy is not science and never has been."  Philosophy developed science, and science relies on philosophy for its hypotheses.  In any case you seem to be saying that a philosopher should not even quote scientists to support some scientific views that the philosopher finds reasonable.  And yet you have contributors here such as Massimo P who do that all the time.  And further I am a trained psychologist, which should allow me to at least comment on that part of science that I'm qualified to understand, which is the science of our animal behaviors, if not the mineral.
    Hank
    Massimo has a PhD in biology too - what has no value is postmodernists with no science training who get PhDs in philosophy who think they somehow 'ground' science by talking gibberish about epistemology. I am not sure what you are getting at with the rest of your comment; you have a degree in psychology and decades of applied psychology experience so you get to debunk evolution? No, not really.   It would be like someone saying they watched every episode of "Law&Order" claiming they have the same credibility as you in understanding behavior.

    Also, you use the word 'theory' incorrectly, which is a red flag for a whole bunch of people in science.
    Debunking evolution?  I'm arguing with a layman about the evolution of  behaviors.  You don't seem to mind if that layman defends your favorite theories, but you mind if I present established scientists who support my theories as to how our behaviors evolved.  Your argument seems to be that I've made this stuff up, which of course I haven't.  I have of course made other stuff up that I'm not about to present here for excactly that reason.  You set the rules and I'm following them.  But now it seems that the rules are to always think as you do, and if that's the way it is, I'll stop commenting.
    And how do I use the word "theory" incorrectly?  Evolution is a theory.  The ideas presented by Shapiro, etal, are auxiliary theories, as are those of the neoDarwinists.

    But this is your blog.  If you don't want me here just say so.  You don't have to make up excuses to get rid of me.
    Hank
    It's Gerhard's blog, not mine. He hasn't deleted your comments so I assume he won't.
     You don't seem to mind if that layman defends your favorite theories, but you mind if I present established scientists who support my theories as to how our behaviors evolved.
    You have no theory. You use the word 'theory' incorrectly because you think speculation is equivalent to evolution and you use emotional verbage to claim that accepting evolution is simply me defending my "favorite theories". Gravity is theory too but I hope you don't jump off the roof of your house because you have an alternate belief.

    If Prof. Shapiro wants to write here and endorse your ideas, he is welcome to do so, but expecting  the world of science to stop and listen to you doe-eyed while you engage in amateur speculation is silly. Gerhard has earned his stripes and has been wrong plenty of times, and he gets smarter and moves on, as do we all.  At the first objection, you invoke a Big Science conspiracy against you, which is not a good sign.
    A big science conspiracy against me?  Hardly. Where's the plot and the planning required?  The only thing against me that I'm against is the ignorance that doesn't know it's ignorant.  I learn things every time I comment - that's why I do it.  I learn where the theories that I support can be objected to, except that so far I haven't found a good objection here.And  claiming that I support speculation as opposed to evolution is the same as saying that Shapiro and the others I've cited are speculators and not theorists.  And we all accept evolution as a theory, but the scientists that I'm learning from don't accept the illogical twisting of that theory that neoDarwinists have put on it.  Logic is perhaps not seen by you as important, since philosophers invented it, but you could be wrong.
    And when I said this was your blog, it's because you're the founder here that allowed me to become a member.  And it seems that you're looking for a reason, good or otherwise, to dismember me.  Otherwise, you haven't made an argument against the adaptive mutation theories that I'm espousing at all.  You're just upset at my unqualified temerity in supporting heresy.

    I do recall that I was asked to sign up and help.  Requiring that I have opinions that will fit with yours doesn't help.  

    You say, "You have no theory."  If you didn't see a theory in my comments somewhere, I suppose there was no point in citing all those fringe scientists who support it.  And no point in my commenting further here at all.
    Shapiro actually does the experimental work to back up his hypotheses.  These bloggers don't, and in many ways are typical of those in the blogosphere.  Which in your view makes them right because of course they're typical of the prevailing believers in natural selection, who call cutting edge science "fringe" science.And if you don't accept that science as evidence accordingly, it's your loss, not mine.
    Gerhard Adam
    "Toto, I've a feeling we're not in Kansas anymore."
    Mundus vult decipi
    No and neither are those other scientists whose writings you have so studiously ignored.
    Gerhard Adam
    Oh, but I haven't ignored them.  I've cited the criticisms where appropriate, and I've indicated to you, more than once, that neither I nor anyone else has made a claim that random mutations are the driving force in evolution.

    You keep insisting that this is the central tenet of your argument.  So, unless you can cite some relevant papers [something besides a single presentation by Shapiro], I'm going to assume that you have nothing except your opinion.

    Moreover, I'm willing to bet that NONE of the scientists you've cited support your point of view.

    I'm not interested in your tossing around the phrase "neo-Darwinism" as if it's some sort of epithet.  
    Mundus vult decipi
    Do you want me to repeat the long excerpt I posted from Mae Wan Ho's work?  Are you unable to do some research into the writings of the numerous other scientists I named?  So go ahead and pretend to assume I've nothing to offer except my opinion.  It's dishonest, but t seems to work for you.NeoDarwinism isn't an epithet, it's simply a wrong and outdated theory (or auxiliary theory to be pedantically  correct).
    You haven't claimed that random mutations are a driving force in evolution?  Interesting.  What have you claimed instead, since you clearly don't believe it's related to the organism's intelligence or experience.
    And you don't believe that instincts are intelligently acquired, so what selected them and on what basis?
    But these are of course rhetorical questions as you couldn't answer them before (and neither would your advocate here, Hank).
    Gerhard Adam
    As I said before.  You keep harping on about random mutations, which isn't being advocated.  Instead you presume that without random mutations, the only option left is your "theory" of intelligence and experience.  Sorry, but that just isn't so.

    The idea that you consider random mutations or "intelligence and experience" as the only two explanations illustrates just how poorly you understand the process.  As I said, unless you're prepared to offer evidence in support of your ideas and not merely more rants against random mutation, I'm not particularly interested, since you clearly have nothing to contribute.

    Whenever I've asked a question, you've dodged it.  When I asked where this "learned" information was stored, you simply responded as a smart-ass.  Of course, if you actually understood the process, then you'd have recognized that for learned information to be passed on, it would have to be integrated into the DNA.  For this to occur, it would represent something that can be definitively tracked and measured.  However, it also creates a new and potentially bigger problem, in that basic heritable traits may be lost because of parental epigenetic modifications.  This is precisely why germ line cells are effectively "erased", precisely so that they don't converge to potentially irrelevant or even harmful traits.

    However, you have elected to ignore the question and its ramifications, choosing instead to be a wise guy as if anyone questioning your assertions is somehow fundamentally wrong and that we should simply accept your pronouncements on faith.

    In any case, unless you actually have something useful to say, I'm done with your speculations.  If you can't offer an alternative explanation, beyond your perpetual rants against a straw man, then you clearly aren't relevant.
    Mundus vult decipi
    "When I asked where this "learned" information was stored, you simply responded as a smart-ass."  No, I told you the truth and you didn't believe it.  As to the rest of the above, to put it kindly, you're untruthful.  I just gave you some references that you pretended that you didn't have before and you're still pretending that all you ever got from me was Shapiro's stuff.
    Remember this?  If so, stop lying that you don't.
    Here's excerpts from Mae-Wan Ho, Geneticist and Biophysicist, excerpted from The End of Bad Science and Beginning Again with Life: 
    “Finally, the ultimate neo-Darwinian taboo has been broken. Wiesmann’s barrier has been breached, and in many different forms, some of which I mentioned already (see box 2).   
    Box 2
    The inheritance of acquired characters
    Epigenetic inheritance - inheritance of cellular or gene-expression states such as patterns of DNA methylation, cortical inheritance in ciliates, dauermodifications.
    Inheritance of induced changes in genomic DNA - fertilizer treatment of flax and other plants; drug-resistance in mammalian cells insecticide- resistance in insect pests and herbicide-resistance in plants.
    Feedback from somatic cells to germ cells - reverse transcription and insertion of cDNA into germ cells, eg. immunoglobulin V genes
    'Adaptive' mutations in bacteria, yeast and other cells.”


    “ -- others including myself have written on how those newly discovered processes seriously undermine neo-Darwinian evolutionary theory over 15 years ago. The evidence against the natural selection of random mutations has grown overwhelming since. Simply stated, organisms can mutate their genes as they are selected; and there is a large degree of non-randomness to mutations.
    Recently, molecular geneticist James Shapiro has joined the debate. He is critical of neo-Darwinians like Richard Dawkins and John Maynard Smith who are still clinging to the discredited paradigm. "Localized random mutation, selection operating "one gene at a time" (John Maynard Smith’s formulation), and gradual modification of individual functions are unable to provide satisfactory explanation for the molecular data, no matter how much time for change is assumed. There are simply too many potential degrees of freedom for random variability and too many interconnections to account for."
    And yet, the variations are far from random. The processes responsible for the fluidity of the genome form a highly sophisticated regulatory system, which can provide hyper-variability or stability for genes or genomes as required. All organisms, from bacteria to human beings, possess a wide range of repair and proof-reading functions to remove accidental changes to DNA sequences and correct errors resulting from physiological and physical insults. The same cells also possess numerous biochemical mechanisms for changing and reorganizing DNA through ‘natural genetic engineering’ – processes that include cutting and splicing of DNA molecules into new sequence arrangements (like the immunoglobulin genes). Most frequently, natural genetic engineering involves mobile genetic elements, found in all genomes, which can move from one position to another, enabling organisms to respond to environmental challenges.”

    Gerhard Adam
    OK, let me spell it out for you.

    I read that.  It says NOTHING in support of your thesis, regarding intelligence, communication, culture, etc. 
    Simply stated, organisms can mutate their genes as they are selected; and there is a large degree of non-randomness to mutations.
    What organisms?  What genes?  Give a context here.  The statement is true as far as it goes, but it explains nothing.
    Feedback from somatic cells to germ cells - reverse transcription and insertion of cDNA into germ cells, eg. immunoglobulin V genes

    Great!  Provide a citation that demonstrates when and where this occurs and has been documented.  Here's a problem for you to consider.  The human female produces all of her eggs formed before birth.  What is the mechanism by which somatic cells can "re-write" the DNA already present?  Similarly in human male sperm cells, given the billions upon billions that are produced, there's little basis for presuming that much somatic cell "feedback" is occurring in any meaningful way.
    Epigenetic inheritance - inheritance of cellular or gene-expression states such as patterns of DNA methylation, cortical inheritance in ciliates, dauermodifications.
    Inheritance of induced changes in genomic DNA - fertilizer treatment of flax and other plants; drug-resistance in mammalian cells insecticide- resistance in insect pests and herbicide-resistance in plants.
    Again, not in dispute, however it is also not quite as widespread as you might believe and there's quite a dependence on the particular organism in which it can play out.
    He is critical of neo-Darwinians like Richard Dawkins and John Maynard Smith who are still clinging to the discredited paradigm. "Localized random mutation, selection operating "one gene at a time" (John Maynard Smith’s formulation)
    Again, the comment about random mutations, one gene at a time, is NOT in dispute and you're simply using a straw man argument.

    The problem is that you have nothing.  You've got this quote that you keep peddling around, that doesn't support what you claim it does and then you think you're going to overthrow evolutionary theory?

    Natural genetic engineering doesn't explain anything.  Again, I refer you to the links I provided earlier for a critique.
    http://sandwalk.blogspot.com/2012/09/james-shapiro-claims-credit-for.html
    http://whyevolutionistrue.wordpress.com/2012/12/02/james-shapiro-gets-evolution-wrong-again/

    Let me be excruciatingly clear.  Almost everything you've mentioned was also mentioned in the article.  What was NOT mentioned and is NOT accepted, is your notion that this automatically relates to intelligence, experience, and culture, etc. etc. etc.  You're abusing all manner of words to try and make a radical point and arguing against straw-men.

    You're the one making the quantum leap from epigenetics to "learned experiences" and "intelligence" being translated back into the DNA for inheritance.  You're the one that made the comment about communication in bacteria being "culture".  You're the one that thinks that even RNA replication involves "intelligence".  There isn't a single quote or link you've provided that supports that view.
    Mundus vult decipi
    Both Shapiro and Mae Wan Ho support the findings that bacteria have intelligence, and you knew that when you read his paper, and if you read the easily accessed full paper from Mae Wan Ho, you'd know that as well.  And then I mentioned several other scientists to read, that you've pretended didn't happen, and they say the same thing, in addition to every other thing you just admitted I claimed, failing however to admit you didn't follow up on it.  And everything you keep parroting about the inability of sperm to transfer new genetically transcribed information has been overturned, just as Mae Wan Ho and Shapiro have told you.But you prattle on about epigenetics as if that accounts for the heritability of learned behaviors, when you know it really doesn't.  And to top it off you insist again that genes, regardless of information that has been learned and genetically transcribed during the organisms lifetime, will not allow that information to be transferred to the next generation.  Yet the papers and books of the scientists I referenced will tell you that it can.  It's common knowledge that this so called Weissman barrier has been broken, yet as a non scientist, it seems you've never heard of that.  And never heard that the RNA, DNA functional systems are intelligently constructed and operated by their organisms.
    So you continue to protest, "There isn't a single quote or link you've provided that supports that view."
    Completely ignoring all the links presented which, of course, support all that you've claimed they don't.
    You're in ether complete denial or bereft of any information and explanation that will counter these newer findings.  And I say it's both. And you don't even have the confidence in your beliefs (since they're not really yours but some data that you've studiously copied) to agree to disagree.  And I'm presuming that lack of understanding is the reason you don't read the material I've cited.  A fear that you won't understand it enough to even make a counter argument.
    Gerhard Adam
    Enough! ... I'm tired of your incoherent ramblings.  What you call common knowledge has been refuted on every blog post you've commented on, and you can't gain any consensus from anyone.  I am reassured by the fact that on every blog post you're as big a jerk as you are here, so at least I know it isn't just me.
    Completely ignoring all the links presented which, of course, support all that you've claimed they don't.
    What links?  You've provided ONE link to a Shapiro presentation.

    Even your point about bacterial intelligence is an abuse of language.  You dismiss the fundamental problems of information transfer back to the germ line because you clearly don't understand it and you don't know what you're talking about.
    It's common knowledge that this so called Weissman barrier has been broken, yet as a non scientist, it seems you've never heard of that.
    Oh, I know about it, but I also know that it isn't the nonsense you purport it to be.

    Here's an idea.  Write your own article and see if anyone is convinced.  I'm done with you.  I've seen some of your posts on other blogs and how you insist on this irrational drivel. 
    Mundus vult decipi
    Of course you're done with me. you don't even know what breaking of the Weissman Barrier has entailed, or otherwise you wouldn't pass it off as nonsense.  You really think I'm obliged to give you links to the books and papers written by the number of people I referenced, when if you really had some scientific curiosity, you'd look them up yourself.  So far I haven't called you a jerk, but I suppose I should if that's the style of argument you prefer.  I'd have preferred some other way of pointing out that you just aren't smart enough to write  on a science blog.  And I see that according to you and that other non-scientist, I'm not supposed to be either.  So I guess we'll see.  Bye bye for now. 
    John Hasenkam
    It's common knowledge that this so called Weissman barrier has been broken,
    It is not common knowledge. I learnt about it over a decade ago. It was an Australian immunologist who fought tooth and nail to illustrate this point and was condemned left, right and centre for his efforts. See Lamark's Signature.   Ted Steele's career has been ruined, some claims of academic misconduct. The tearing down of this barrier is an important issue because it overthrows another tenet of the Central Dogma. I've never followed this up because Steele's claims were repudiated on the grounds of dodgy statistical analysis but I am too ignorant to question these issues. 


    Other research has pointed to second generation effects in genetic transmission, and possibly even latter generation effects. A recent study claimed this with respect to BPA and related chemicals, and epidemiological studies have even raised the claim that the diet of grandparents affects the susceptibility to type 2 diabetes in the grandchildren. If that aint lamarkian mate I'll eat my thymus and eradicate my dendritic cells. :) 


    This signature may be epigenetic, I don't know. Methlyation is stripped during development but then another round of methylation ensues during development, that second round of methylation may well represent this immunological in vitro adaptation. To wildly speculate it could even be a case of plasmid like transfer of heavy\light chain genetic elements. What would be fascinating to know if this transfer of immunologic capacity is via the ovum or sperm. 





    I say it's common knowledge and you don't.  As philosophers might say, if it isn't and it could be then as knowledge goes, it should be.
    John Hasenkam
    The most important source of information in the environment is often the cell next to the other cell. It is quite amazing how sensitive cells can be to environmental cues. I once read that in relation to MHC class 1 protein fragment presentation to immune cells, all that is required to identify self from non-self is a 5-10 amino acid sequence. I can't believe that but it is very remarkable that protein fragments via either MHC 1 or 2 presentation is such a powerful means to detect cellular damage or pathogen presence in that cell. Typically there also needs to be at least a second danger signal like extra-cellular hsp60, grp78, hsp70, ATP ... . 
    Gerhard Adam
    It seems that it has become a kind of trend to introduce commonly used terms into uncommon situations, whether it be for the shock value, or simply to try and appear different.  This results in all manner of abuse regarding definitions and conflating ideas without proper justification.

    So, while there may be disagreement in my definitions, I will place them here so that we have some kind of demarcation to determine where I'm coming from. 

    Regarding intelligence.  In my view there is something I will call "instinctive behavior", that is more than merely an autonomous response [such as breathing, digestion, etc.] but nevertheless is innate in the organism.  For example, one does not need to teach an animal how to walk.  In short, even if there was no other example around, such a creature would learn to walk without instruction.  In one sense, this is a kind of instinctive behavior.  Similarly we can look to behaviors such as "fight, flight, or freeze" and consider that these also are not generally taught.  Certainly these behaviors can be refined over time with experience and teaching, but the innate behavior is instinctive.

    In the second case, I would define "rule-based behaviors", where there is the appearance of intelligence because the behavior is capable of being more selective in responses and application.  This could be considered in the same light as ants following pheromone trails, or bacterial quorum sensing.   They are behaviors that extend beyond simply instinctive, but again, they are not specifically "taught". 

    One common thread, regardless of how one chooses to classify them, is that they all relate specifically to the creature's survival and fitness.  In some cases, there can be a fair amount of teaching/learning involved [such as birds learning their songs].

    What distinguishes this from, what I would consider, intelligence, is that these are all specific biological traits that assist the organism in survival/fitness.  The hallmark of intelligence [again, in my view] is when a creature is capable of applying this trait in an area outside of it's immediate biological needs and utilize it in novel ways.

    Certainly we are all constrained by our phenotype, however we are also all aware of what makes us note that behavior may be intelligent.  Observing a particular act, observing the result, and then either copying or avoiding it, suggests some degree of intelligence.  The ability to solve novel problems well outside the scope of what would be expected to be biologically encountered would suggest intelligence [i.e. a bird figuring out how to open its cage]. 

    Now these definitions may not be as rigorous as some would like, but it approximately indicates where I draw these lines.

    Similarly the point was raised about communication and culture.  I'm sorry, but there's no way that bacterial quorum sensing rises to the level of culture. 

    The notion that everything possesses intelligence, culture, etc. simply renders these concepts meaningless.  It's like taking a mathematical equation and multiplying by one.  It changes nothing, it explains nothing, and it renders the few definitions we do have [regardless of how poorly we differentiate them] into a meaningless jumble.

    To suggest that every organism from viruses to humans has exactly the same traits is simply gibberish.
    Mundus vult decipi
    No-one suggested that organisms from viruses to humans have exactly the same traits, so this type of response is gibberish responding to your own inventions.  Bacteria communicate in ways much more complicated than in quorum sensing, and if you read Shapiro, you wold at least have been informed of that, although "knowing" it is another matter in your case."these are all specific biological traits that assist the organism in survival/fitness" you say.  Where did these traits come from?  And are these traits exercised without necessity of making any choices as to how, when, where, or why?
    And solving problems within the scope of what the biological entity expects to encounter is exactly what intelligence is required to do.  

    Worst argument on your part: "They are behaviors that extend beyond simply instinctive, but again, they are not specifically "taught".  
     I suppose that if an animal learns a new behavior by its own intelligence, it wasn't taught, except that apparently it was taught to learn things by itself.  Or is self learning by your understanding instinctive.  And then you've never addressed the question put to you earlier as to where these instincts that operate in lieu of intelligence were supposed to come from.  Did natural selection give intelligence to organisms initially as instincts, and if so, how did that happen, stochastically or otherwise? because your theory says it had nothing to do with the organisms prior experience.

    I could go on, but as you've said, to you it's all a meaningless jumble.  And perhaps your problem is that to you, it is a meaningless jumble.
    Gerhard Adam
    No response necessary.
    Mundus vult decipi
    Bonny Bonobo alias Brat
    Great article Gerhard, very informative and thought provoking. I haven't had time to read all the comments yet but I did get a bit confused by the following link in your article :-
    In some instances, the bacteria were actually capable of utilizing the system to their own purposes.

    When I followed that link it was an article saying 'Here we explore whether competitive interactions between microbes promote the acquisition of virulence characteristics.' and I don't see why that article is particuarly relevant to what you are saying here?

    I was expecting to find a nice interesting article about some kind of bacterial equivalent to say the protozoan parasite toxoplasmosis' behavioral changes that may cause infected rats or mice not be afraid of cats for example and even be attracted to cats, so that the cat then eats them and the toxoplasmosis then infects the cat too. There is also some evidence implying that people infected with the toxoplasmosis parasite are much more likely to exhibit risky behaviour, have car accidents and even commit suicide. 

    'Recent research has also linked toxoplasmosis with brain cancer, Attention Deficit Hyperactivity Disorder, Obsessive Compulsive Disorder, and Schizophrenia.'

    My latest forum article 'Australian Researchers Discover Potential Blue Green Algae Cause & Treatment of Motor Neuron Disease (MND)&(ALS)' Parkinsons's and Alzheimer's can be found at http://www.science20.com/forums/medicine
    Gerhard Adam
    Perhaps this will help.
    http://www.biologynews.net/archives/2005/07/23/bacteria_use_hosts_immune_response_to_their_competitive_advantage.html

    The other articles are more specifics.  I probably should've linked the one indicated above.

    From the original link:
    During model murine nasal colonization, Haemophilus influenzae outcompetes another member of the local flora, Streptococcus pneumoniae, by recruiting neutrophils and stimulating the killing of complement-opsonized pneumococci
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2913241/#bib4
    This links to a foot note:
    Thus, the recruitment and activation of neutrophils through selective microbial pattern recognition may underlie the H. influenzae–induced clearance of S. pneumoniae. This study demonstrates how innate immune responses may mediate competitive interactions between species and dictate the composition of the colonizing flora.
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1238736/
    Mundus vult decipi
    Bonny Bonobo alias Brat
    Thanks  Gerhard. Your first link is very interesting especially the bit about vaccines and antibiotics inadvertently altering the competitive interactions of other bacteria present in our bodies :-

    In a mouse model, Haemophilus influenzae--a common bacterium that infects children--stimulates the immune system to send out specialized white blood cells that attack its competitor, Streptococcus pneumoniae--a leading cause of pneumonia. "It is striking that the host's response can so completely eliminate the competitor," says Weiser.

    The findings also demonstrate how antibiotics and vaccines that target one microbe might inadvertently alter the competitive interactions among other species present.

    This makes me wonder if giving vaccines and antibiotics to very young childrena and even babies could be adversely affecting their intestinal, nasal and other internal bacteria and creating toxicities and immune problems at crucial or vulnerable stages in their development?

    I developed double bronchal pneumonia and very nearly died, shortly after being given the triple MMR vaccine when I was 6 month old baby for example. So many people claim to have seen changes in their children's health and behaviour shortly after vaccines and courses of antibiotics, could this be why?  Beneficial gut flora oral doses could possibly always be given to kids immediately afterwards, to try to counteract these negative effects maybe? Do you have the link to the study they are referencing?
    My latest forum article 'Australian Researchers Discover Potential Blue Green Algae Cause & Treatment of Motor Neuron Disease (MND)&(ALS)' Parkinsons's and Alzheimer's can be found at http://www.science20.com/forums/medicine
    Gerhard Adam
    Vaccines typically immunize against viruses, so it's hard to imagine that it would necessarily have much impact on the bacterial colonies.  Of course, I suppose it's possible, but it seems less likely.

    Antibiotics would be another matter entirely and would certainly warrant caution, especially with an immature immune system and gut bacteria.

    Yes, here's the link to the study.
    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1238736/
    Mundus vult decipi
    Bonny Bonobo alias Brat
    Well your first link clearly says 'The findings also demonstrate how antibiotics and vaccines that target one microbe might inadvertently alter the competitive interactions among other species present.' So why would they say that if it isn't true? That's why I asked you if you have a link to the paper so that i could look at their evidence. I will try to find it later, i don't have time now.
    My latest forum article 'Australian Researchers Discover Potential Blue Green Algae Cause & Treatment of Motor Neuron Disease (MND)&(ALS)' Parkinsons's and Alzheimer's can be found at http://www.science20.com/forums/medicine
    Gerhard Adam
    I didn't say it wasn't true.  I said that your example of the MMR vaccine was less likely to be relevant since it is an anti-viral vaccine.

    I also provided the link you asked for.
    Mundus vult decipi
    Bonny Bonobo alias Brat
    OK thanks.
    My latest forum article 'Australian Researchers Discover Potential Blue Green Algae Cause & Treatment of Motor Neuron Disease (MND)&(ALS)' Parkinsons's and Alzheimer's can be found at http://www.science20.com/forums/medicine
    Bonny Bonobo alias Brat

    Is it possible to simplify the basic argument between Gerhard and Roy in this comment section by giving some hypothetical examples of how their different viewpoints about DNA mechanisms would or would not be exhibited in some either hypothetical or real organisms? I've read the comments section three times and I'm still not sure exactly what you're arguing about in real terms? Simple is good sometimes :)

    My latest forum article 'Australian Researchers Discover Potential Blue Green Algae Cause & Treatment of Motor Neuron Disease (MND)&(ALS)' Parkinsons's and Alzheimer's can be found at http://www.science20.com/forums/medicine
    Gerhard Adam
    Yes, it's quite simple.  Roy is presenting many mechanisms that are true and have been mentioned in the article.  However, I do not accept the notion that:

    (1) There is a fundamental intelligence that drives evolution.
    (2) That all organisms, including single cells organisms, exercise their "choice" in how they evolve.
    (3) Phrases like "self-engineered" sound interesting, but explain nothing, so to invoke them offers no insight, but rather creates a kind of "magical" arena in which "intelligence", "life", etc. are already primed and capable of making choices to advance their own evolution.

    That's my quarrel.

    Also, let's note that to invoke "choice" in evolving [especially in invoking experience and learning] we have a fundamental problem since clearly any organism that survives by its own experiences, already possesses what it needs via natural selection.  Hence one can always argue that the successful organism "chose" wisely.  However, a major problem is that no organism can "choose" to invoke a trait that isn't already present.   But if the trait is already present, then there is no need to redefine it back into the germ line.  It's a circular argument.

    The exceptions would involve actually have to acquire and/or create novel modifications to the DNA, which is [I suspect] where the "self-engineering" comes into play.  However, this would suggest that not only is the organism manufacturing DNA, but that it possesses sufficient understanding and insight to recognize what trait needs to be applied to "solve" a particular problem [especially for the long-term in future generations].

    I understand the argument being put forth, and I reject it.
    Mundus vult decipi
    "However, a major problem is that no organism can "choose" to invoke a trait that isn't already present."The thing that's being studiously ignored here is that traits are never "already present" that the organism had not been motivated to develop.  The old theories have never even tried to account for the magical presence of instincts in all of life's creatures, including the earliest.


    Everything else there was boilerplate as usual.
    It was possible, but no longer probable.  But you can ask me some questions and I'll try to answer them.You realize of course that neither of us are biologists.  You could call me an evolutionary psychologist but then I disagree, philosophically, with most of them as well.  Disagreement is necessary for science, or sciences, to intelligently evolve.  Unless you disagree that intelligence evolves at all, of course.
      
    Bonny Bonobo alias Brat
    Roy, I asked if it 's it possible to simplify the basic argument between Gerhard and Roy in this comment section by giving some hypothetical examples of how their different viewpoints about DNA mechanisms would or would not be exhibited in some either hypothetical or real organisms?'

    And you have replied, 'it was possible, but no longer probable.....Disagreement is necessary for science, or sciences, to intelligently evolve. Unless you disagree that intelligence evolves at all, of course.'

    Can you just explain why it was possible but no longer probable? Can you also explain why disagreement is necessary for science to intelligently evolve if you can't even give simple examples of what the disagreement is about? Surely complicated disagreements that can't be simplified into the basics are not very intelligent, they are just intellectual brawls? Gerhard has simplified the discussion from his viewpoint, why can't you do the same? He also didn't give any examples yet, BTW I also have a psychology degree for what that's worth, which is not a lot around here.
    My latest forum article 'Australian Researchers Discover Potential Blue Green Algae Cause & Treatment of Motor Neuron Disease (MND)&(ALS)' Parkinsons's and Alzheimer's can be found at http://www.science20.com/forums/medicine
    Gerhard Adam
    Helen, it isn't a matter of specific examples as much as it is in defining the framework in which these things occur.  I am not a fan of invoking terms that have questionable meanings under the best of circumstances and then attempting to use them to explain things [i.e. "intelligence"].

    In my view, biology must ultimately be explainable in terms of chemistry/physics.  We cannot invoke mystical properties or invoke suppositions simply because of how things might appear.  In fact, the notion of life forms having a "purpose" is described by the term teleonomy.  This doesn't mean that they actually have a purpose, but rather that they behave in an orderly fashion as if they do.

    Some interesting papers on this point are:
    http://www.bgu.ac.il/~pross/PDF-5%20%28Teleonomy%29.pdf

    http://www.jsystchem.com/content/2/1/1

    http://www.sciencemag.org/content/323/5918/1229.abstract

    http://www.pnas.org/content/early/2009/04/29/0903397106.abstract

    If you have any problem getting the articles from the abstracted version, let me know and I can e-mail you the articles themselves.

    It's like the ridiculous assertions that life originated by panspermia [i.e. from space].  What makes the idea ridiculous in "origin of life" discussions is that it uniformly fails to answer any questions.  To argue about how it may have been introduced to Earth is trivial compared to the basic question of how it originated anywhere.  So I find such explanations pointless and a waste of time.

    Anyway ... you have my perspective.  I don't know that these papers signify a correct theory, or if there may be major problems discovered later.  What I do know, is that they represent a legitimate attempt to explain biology within the context of known science and don't require any "miracles".
    Mundus vult decipi
    I tried hard to simplify my discussion and was called a jerk.  A sentiment which was echoed by the site's moderator. It's not probable that I can simplify anything without being called a jerk for doing so.  And partly, as you say, a psychology degree is not worth a lot here, even to those who have no degrees in the soft or hard sciences at all.  And in addition I tend to philosophize, which really seems to bug them. (I have a degree there too.)

     OK, lets look at this from Wikipedia to deal with  the accusation of some false claim of “teleonomy,” in that I’m projecting evolution as an intentionally goal seeking process when it supposedly isn’t.

    Teleonomy is the quality of apparent purposefulness and of goal-directedness of structures and functions in living organisms that derive from their evolutionary history, adaptation for reproductive success, or generally, due to the operation of a program. Teleonomy is related to programmatic or computational aspects of purpose.

    The term was coined to stand in contrast with teleology, which applies to ends that are planned by an agent which can internally model/imagine various alternative futures and, enables intention, purpose and foresight. A teleonomic process, such as evolution, produces complex products without the benefit of a guiding foresight.”

    And at this point it’s I that must object to this definition.  In my conception of the process, it’s either teleonomic with at least a short term purpose, or we will now need either a newer definition or a newer word.  Because while there is no guiding agent outside of our biological selves to model our futures, it has become clear to me (and to those I have previously cited) that we do and have done our own trial and error self engineering process modeling quite satisfactorily, thank you.

    And I see that there was a bit of a concession in that article where the current status was that “Teleonomy is closely related to concepts of emergence, complexity theory and self-organizing systems.”  Well, OK I guess.

     

    Also I found this in my notes: “And then, for one more thing, there's a fluidity of purpose and subpurposes involved that are continuously revising the goals dependent on constant feedback from the effects of prior purposive efforts.  Hardly an "ultimate goal" directed process.”

    And for those who don’t believe evolution is concerned with purpose at all.  Talk Origins Archive, unfortunately, has a good example under “Bombardier Beetles and the Argument of Design.”

    It may seem obvious that the purpose of a bombardier beetle's defense mechanism is to protect it against predators--and indeed it is effective at such defense [Eisner, 1958]--but that is only our view; without reading the beetle's mind, we can't know what its purpose is. In fact, the bombardier mechanism is probably just a reflex, since it doesn't fire at some predators (such as some human collectors) and it does fire at some non-predators (such as a pair of forceps wielded by an experimenter). Ultimately, statements of purpose are statements of our own beliefs and nothing more.”

    Now this is the common view of those who can’t accept that organisms react strategically to their experience.  The article above goes on to say that:  “The bombardier beetle's defense doesn't work because that's its purpose; we attribute that purpose because the beetle's defense works.”

    I think they meant to say it doesn’t work for that ‘reason’ since clearly they don’t equate reasons to purposes when it comes to natural selection’s singularly stochastic features.  They’re arguing that the defense works simply because it turned out to work.  A mechanism that the beetle was surprised to find it had, perhaps, and apparently can’t always get to work right.  Was that blind watchmaker a rascal or what!

    Bonny Bonobo alias Brat

    “Teleonomy is the quality of apparent purposefulness and of goal-directedness of structures and functions in living organisms that derive from their evolutionary history, adaptation for reproductive success, or generally, due to the operation of a program. Teleonomy is related to programmatic or computational aspects of purpose.

    The term was coined to stand in contrast with teleology, which applies to ends that are planned by an agent which can internally model/imagine various alternative futures and, enables intention, purpose and foresight. A teleonomic process, such as evolution, produces complex products without the benefit of a guiding foresight.

    And at this point it’s I that must object to this definition. In my conception of the process, it’s either teleonomic with at least a short term purpose, or we will now need either a newer definition or a newer word. Because while there is no guiding agent outside of our biological selves to model our futures, it has become clear to me (and to those I have previously cited) that we do and have done our own trial and error self engineering process modeling quite satisfactorily, thank you.
    OK, I think I get your point, you're advocating something halfway between teleology and teleonomy, a sort of short term purpose, right? But where is your evidence 'that we do and have done our own trial and error self engineering process modeling quite satisfactorily'?

    David Hull also commented on the uses and abuses of the words and meaning of teleology and teleonomy by biologists saying the following here :-
    Haldane can be found remarking, "Teleology is like a mistress to a biologist: he cannot live without her but he’s unwilling to be seen with her in public". Today the mistress has become a lawfully wedded wife. Biologists no longer feel obligated to apologize for their use of teleological language; they flaunt it. The only concession which they make to its disreputable past is to rename it ‘teleonomy’
    Haldane, like you, also seemed to be quite interested by beetles and their evolutionary success as it says here.
    He is famous for the (possibly apocryphal) response that he gave when some theologians asked him what could be inferred about the mind of the Creator from the works of His Creation: "An inordinate fondness for beetles."[14] This is in reference to there being over 400,000 known species of beetles in the world, and that this represents 40% of all known insect species (at the time of the statement, it was over half of all known insect species)
    (BTW) The formatting in this comment has gone berserk.

    My latest forum article 'Australian Researchers Discover Potential Blue Green Algae Cause & Treatment of Motor Neuron Disease (MND)&(ALS)' Parkinsons's and Alzheimer's can be found at http://www.science20.com/forums/medicine
    "But where is your evidence 'that we do and have done our own trial and error self engineering process modeling quite satisfactorily'?"Well, I could argue that it's the only alternative to otherwise immaculate selection, but more seriously the evidence is cumulative that it's the adaptive mutation process, and the evidence produced by the Shapiros, the Jablonkas, et al, that shows our early organisms engineered themselves, with further evidence that the results reflected an intelligence that was later confirmed to be, and have been, in bacteria  from their start.
    If there's any speculation on  my part, it's that biological intelligence must have been, and is, of a predictive nature, and logically had therefor begun as, and continues to be, a trial and error process.
    Bonny Bonobo alias Brat
    OK, so let's imagine that the earliest life form was say a very simple bacteria like organism and that no matter how many times this simple life somehow spontaneously came into existence, maybe trillions upon trillions of times over billions of years throughout  the universe, it was only the life forms that could reproduce in that environment that then continued living, trillions of other non-reproducing life forms may have eventually died of old age and their spontaneous life and existence was no more.

    Maybe there were many different reproduction mechanisms over time but regardless the one and only thing they all had in common was that somehow they had to divide in order to reproduce. So every time they reproduced they always copied themselves and the only ones that survived that we know about, all did this by somehow using DNA to store the information that was needed to effectively code the new life, any other life forms that didn't use DNA, at least on this planet, died out.

    I used to be a computer programmer and very few programmers write programs from scratch, they usually just copy an existing program or template program and amend it to follow the instructions they want the program to perform. A program hypothetically can be massive with thousands of redundent data definitions and uncalled sub routines but if they are not used or performed from the procedure division then it really doesn't matter, it just looks a bit messy for anyone amending the program later.

    Maybe if life itself is the teleological and/or teleonomical life programmer of itself then it just is forced to always hang on to every bit of code, procedural or data, that has ever been useful, in case it is ever needed again and that is what we now call junk DNA.

    The junk DNA in its original form must have always been useful at one time for some past ancestral life form. Maybe life as a programmer doesn't even have its own delete function other than meiosis and mitosis and XX XY sexual reproduction, so it has to rely only upon external forces to spontaneously delete, alter or mutate the code or DNA to evolve and grow and adapt? These external DNA regulating forces most probably includde all the ones you guys have mentioned above, gene transfer from other bacteria and life forms and many more xenobiotic influences that e know and dont know about.

    If you think about it, that is how it almost must have been. Life uses DNA as a self replicating, eventually massive, messy computer program with many more xenobiotic influences in many varying environments over millions of years .

    Maybe its a bit like when I was a young IBM mainframe programmer and I or more likely a big, bad tempered, porn magazine reading, IBM computer operator, would accidentally drop my program job cards and feed them into the computer to compile anyway? Even if the cards were randomly reordered and some dropped down the air vent, there was always still a chance that the program would still run and work and then all of the code that remained was just altered original code. If the program didn't run then it was the equivalent of a non viable soon to be extinct life form. So is my rather childish description of life evolution teleological, teleonomical or just plain teletubbillogical?

    Feel free to delete this comment Gerhard if its too long, off topic or just a waste of comment space!
    My latest forum article 'Australian Researchers Discover Potential Blue Green Algae Cause & Treatment of Motor Neuron Disease (MND)&(ALS)' Parkinsons's and Alzheimer's can be found at http://www.science20.com/forums/medicine
    Gerhard Adam
    Wouldn't dream of it, not when you're using my most despised analogy [ugh ... computer program].  BTW, I won't rip you for the "junk DNA" reference, but I would suggest that you read the link provided in the article.
    Mundus vult decipi
    Bonny Bonobo alias Brat
    OK, you're right, I haven't read all the links yet, i'll do it now, anything rather than do the cleaning ;)
    My latest forum article 'Australian Researchers Discover Potential Blue Green Algae Cause & Treatment of Motor Neuron Disease (MND)&(ALS)' Parkinsons's and Alzheimer's can be found at http://www.science20.com/forums/medicine
    There's some evidence mixed with some speculation that junk DNA consists in part of information repositories for pre-learned (and likely pre-experienced) alternative behavior strategies made ready for a range of anticipated changes in the environment.  Showing me at least that, if so, life forms have developed intelligent strategies over the eons that we couldn't consciously prepare with our human cognitive functions even if we knew enough to try.
    Bonny Bonobo alias Brat
    There's some evidence mixed with some speculation that junk DNA consists in part of information repositories for pre-learned (and likely pre-experienced) alternative behavior strategies made ready for a range of anticipated changes in the environment
    That makes some teletubbillogical (I'm afraid that's my level!) sense to me, computer code can store information that the programmer has learnt but how could life the programmer write and store the pre-learnt and pre-experienced information in the new DNA code? The knowledge would have to initially reside in the brain or neurological or information processing location equivalent wouldn't it? Then that information processing location would have to somehow reprogram its own reproductive DNA to contain the new pre-learnt information using what? The missing links are whatever writes the new DNA code to contain the pre-learnt information, produces the job cards and then compiles them into the DNA reproduction program? Sorry Gerhard, for more computer program analogies!

    Maybe reproductive organs have DNA reprogramming mechanisms that we don't yet understand, other than the usual meiosis and mitosis, and these are somehow connected to or controlled by the organism's memory banks or pre-learnt information stores, wherever they reside? After all, we still don't understand how memories are stored and recalled even in our own brains yet do we? 

    So if you are right that maybe life forms have developed intelligent strategies over the eons, I don't see why we couldn't also consciously prepare such intelligent strategies with our human cognitive functions and genetic modification technology down the track, when we know enough to try. We are always learning and there is so much more that we don't know but if you compare what we humans and teletubbies know now, compared with what we knew only one century ago, the knowledge leap has been enormous and there is no reason why we shouldn't continue to keep bounding forwards gaining new knowledge like jumping kangaroos! 
    My latest forum article 'Australian Researchers Discover Potential Blue Green Algae Cause & Treatment of Motor Neuron Disease (MND)&(ALS)' Parkinsons's and Alzheimer's can be found at http://www.science20.com/forums/medicine
    Gerhard Adam
    One major problem with the whole analogy [including the computer bit].  In order to solve a problem, you must know the solution and how it applies to the problem.  How do these problems get solved?  Trial and error?  It can't, because that simply brings you back to the random processes which are claimed not to exist.

    So, unless one wants to promote the idea that cells "understand" the future problems they will encounter and "plan" accordingly, there's no vehicle for solving problems that allows anticipating the necessary DNA code.  More importantly, it would also require that the cells know what the DNA code is supposed to represent, both in terms of the proteins it codes for, as well as the regulatory mechanisms necessary to express the trait.
    Mundus vult decipi
    Trial and error is the opposite of randomness.  It's a purposive choice making process that all life forms use.  Computers don't make purposive choices in the sense that we do, and don't use trial and error because they can't.Yes, cells do, by necessity, develop an understanding of future probabilities, based on learning from past experiences.  Of course they "know" what the DNA code is supposed to represent because it's information that came from and was developed by them, not from the miracle of intelligently stochastic accidents.
    Gerhard Adam
    Trial and error is the opposite of randomness.
    Not in this context, since there is no reasoning that is occurring.  In effect, this is precisely what is already suggested by natural selection, since "errors" fail to propagate into future generations.  That's the whole point.  If an "error" doesn't kill the organism or impact its fitness, then it is not subject to selection.  If an "error" does, then it cannot serve as a "learning" device.  As a result, successes only occur in those organisms that already possess the requisite "traits".  There are no second-chances for failures.
    Computers don't make purposive choices in the sense that we do, and don't use trial and error because they can't.
    Sorry, but that simply isn't true.  Computers are specifically ideal for this kind of process.
    Yes, cells do, by necessity, develop an understanding of future probabilities, based on learning from past experiences.
    Not possible.  Since failures result in death, there is no learning process.  Only successes can propagate, so therefore they can never "learn" from their mistakes.
    Of course they "know" what the DNA code is supposed to represent because it's information that came from and was developed by them, not from the miracle of intelligently stochastic accidents.
    Again, not possible.  A bacteria cannot develop antibiotic resistance by constructing the necessary DNA code, since it would be dead by not possessing that trait.  Moreover, to argue otherwise, would require that bacteria "understand" what antibiotics are and to anticipate and prepare countermeasures. 
    Mundus vult decipi
    You've done nothing here but continue to deny that life forms need intelligence to be alive.Show me a computer that, without an operator, can provide it's own options for its trial and error assessments and i'll show you the artificial intelligence that everyone else in the business is still looking for.

    What you've never even tried to explain, because you obviously can't, is where this "information" you refer to in DNA and RNA ,and elsewhere in cellular systems, came from - or how and why it operates intelligently without any use of an intelligent system.

    All you continue to do is assert that the things you believe in are "true facts" and those who use both evidence and logic to show otherwise have, for some unexplained reason, no business doing so.  Because in the end you say it serves no purpose in a purposeless system.  Good luck with that.
    Gerhard Adam
    You've done nothing here but continue to deny that life forms need intelligence to be alive.
    Not at all.  You'll find that I'm quite a proponent of intelligence and even awareness in all organisms.  However, that isn't the extent of what you're claiming.  This isn't about intelligence, it's about self-engineering, which you have uniformly failed to demonstrate.
    Show me a computer that, without an operator, can provide it's own options for its trial and error assessments...
    Again, you're missing the point.  Show me an organism that can provide its own options without a stimulus?  In the case of a computer, the operator is simply the stimulus while the program defines the parameters being operated against.  This is precisely why I don't accept the notions of artificial intelligence any more than I accept them for bacteria [i.e. cognitive problem solving]. 
    ...where this "information" you refer to in DNA and RNA ,and elsewhere in cellular systems, came from - or how and why it operates intelligently without any use of an intelligent system.
    Oh please.  You're inventing wholesale "intelligent systems" without the slightest inclination to explain where they originated from, but then you want to hold me to the standard of explaining where information came from?  You can't have intelligence without the information and simply arguing that these organisms created it from "thin air" isn't an argument.

    You claim you have evidence.  Good, then provide it.  As I said before, not some diatribe against random mutations, but something that specifically supports your assertions [NOT Shapiro].  It's not really that hard.  If you can only quote from two scientists, then you already know it isn't an accepted idea.  If you have more far-reaching evidence, then by all means, provide it.

    There is no neo-Darwinist conspiracy.  You mention Jablonka, but it seems like you actually aren't familiar with her work. 
    In summary, we can say that epigenetics requires a broadening of the concept of heredity and the recognition that natural selection acts on several different types of heritable variation. Although the current gene-centered version of Darwinism—neo-Darwinism—is incompatible with Lamarckism, Darwinism is not. In the past, Lamarckism and Darwinism were not always seen as alternatives: they were recognized as being perfectly compatible and complementary. In the light of epigenetics, they still are. Recognizing the role of epigenetic systems in evolution will allow a more comprehensive and powerful Darwinian theory to be constructed, one that integrates development and evolution more closely.
    http://mechanism.ucsd.edu/teaching/philbio/readings/jablonka.changingconceptofepigenetics.2002.pdf
    Again, I've stated it before, so I'll state it again.  I am certainly no fan of the gene-centric approach and agree that there are numerous issues with that explanation. 
    Mundus vult decipi
    In spite of my continuously providing evidence for adaptive mutation, you continuously deny that I've done so.  Boring, to say the least.You keep saying that I've evoked some conspiracy by neoDarwinists?  You must know that's a lie, but one among others that you keep repeating.  That seems to be your only option, other than the occasional insults, since you can't win the argument knowledgeably.  I'm not here to win arguments but to inform.  You don't have to buy the information, but obviously you can't stand it if others don't wish to buy your version.
    You give us a quote from Jablonka to indicate I haven't understood her.
    "Darwinism is not. In the past, Lamarckism and Darwinism were not always seen as alternatives: they were recognized as being perfectly compatible and complementary. In the light of epigenetics, they still are. Recognizing the role of epigenetic systems in evolution will allow a more comprehensive and powerful Darwinian theory to be constructed, one that integrates development and evolution more closely."



    In your ignorance of the history of evolutionary theories, you don't seem to have known that Darwin originally took Lamarck's ideas seriously.  Which is right there in that quote that you seem to have missed, or more likely misunderstood to fit your purposes.  Darwin's natural selection, in short, was not the neoDarwinian version that found its modification necessary - Wiessmann barrier and all that, as you claimed to know.

    Jablonka then points out that epigenetics helps to make a more powerful Darwiniian (not neoDarwinian) theory to be constructed.  Doesn't that tell you anything when she says one that integrates development and evolution more closely?  Apparently not what you wanted it to mean.
    Boring.
    Gerhard Adam
    Argue however you like.  You keep pointing to these biologists and ranting about neo-Darwinism and random mutations.

    None of these papers, articles, etc. support your notion of "intelligence" and "self-engineering".  Obviously you can't make the case, so there's no point in continuing to ask.
    You keep saying that I've evoked some conspiracy by neoDarwinists?

    ...in short, was not the neoDarwinian version that found its modification necessary...

    Jablonka then points out that epigenetics helps to make a more powerful Darwinian (not neoDarwinian) theory to be constructed.
    You couldn't even stop ranting against neo-Darwinism in your own comment.  Let's remember that you were the one that dismissed Larry Moran and Jerry Coyne, because they were "die-hard" neo-Darwinists. 
    They are both died in the wool neoDarwinists, and they don't deny it.
    Mundus vult decipi
    Since failures result in death, there is no learning process. Only successes can propagate, so therefore they can never "learn" from their mistakes.
    You are assuming that the cell has no way to measure success other than the all-or-nothing criterion of death or survival. If I understand Roy's argument, the cell would be able to evaluate a strategy independently of testing it on itself. Neo-Darwinism has *only* survival to evaluate a strategy and if your phenotype is prone to dying out, that's the end of the subject. However I am not clear where Roy believes this testing to take place. There seem to be two possible places. Either as an emulation where it can do no harm or else by dangerous trial in the real world. Both of these scenarious require careful examination rather than dismissing them out of hand.
     
    Emulation means creating a model and running it to see how it fares with the proposed variation. However there is absolutely no requirement that the model bear any resemblance to the real and very complex world. For example, there is no need for the cell to have a model of how a proposed toxin would bind to a receptor on a competing species and how the organism would respond. It would be quite sufficient for the cell to have internal receptors which happen to mimic those of the competitor. But it would also need a mechanism that responds by retaining the information (e.g. that a binding occurred). Goodness knows how that is supposed to work but as neither you nor Roy seem to have any problem with information being stored outside the DNA, I'll leave that side of it to you. The point is, emulation can be a hugely simplified thing and yet still allow a cell line to accumulate experience without killing itself off every time it makes a "mistake". 
     
    Testing in the real world is also possible. Your all-or-nothing concept certainly means that the cell line that made a mistake would die out eventually. However the point here is that a cell may have a means of detecting that it's not doing very well and negate some of the features currently being tested long before death and extinction occur. It can negate the trial - both in its own phenotype (in order to ensure its own survival) and also in what it passes to the next generation (by whatever dubious means). In fact monitoring one's own "health" would be a rather simple mechanism for quite powerful information capture. Only the very worst mistakes need be terminal, anything less than instant death and the cell can abort the experiment and say "Brrrr! I won't do that again!"

     
    Gerhard Adam
    The problem with your scenario is that if it doesn't kill the cell, then arguably it doesn't impact fitness.  At that point you have to ask what all the energy expenditure for "testing" is for, if it doesn't impact the outcome.  Mistakes are just that.  If a "mistake" isn't lethal [i.e. impacts fitness], then it clearly isn't selectable either.

    Let's also keep in mind that most of these bacteria/microorganisms already have mechanisms to deal with stress.  So what does it mean to say that an organism "isn't doing very well"?

    There's no question that microbes are capable of turning genes on and off, which clearly indicates that they are adaptable to varying environmental circumstances.  However, that's a far cry from "designing" your own solution and "testing" it.

    An additional problem is why this has never been demonstrated?  Why have horizontal gene transfer if each organism "invents" its own solution?  Why is it that antibiotic resistance appears to only be conveyed by organisms that already possesses it?  What's the basis for cancers and all the myriad number of other genetic things that can go wrong, despite error-correction? 

    On the one hand, the idea being proposed is that these organisms are "intelligent" enough to recognize hazards and "engineer" solutions, and yet problems that have been around for centuries are somehow not solvable by them?  Are we to assume that a cancer cell is simply mounting a rebellion against the multi-celled organism? 

    Where is there one shred of evidence that organisms are capable of creating their own novel solutions to problems without already possessing the necessary traits?  In short, there may be many aspects of this that appear to imply "understanding", but my point is that bacteria no more understand how DNA operates than Hydrogen "knows" how to bond with Oxygen to produce water.
    The point is, emulation can be a hugely simplified thing and yet still allow a cell line to accumulate experience without killing itself off every time it makes a "mistake".
    That's fine, but then we should see such DNA differentiation that correlates to the relative degree of "learning" present in these organisms.  Of course, even suggesting such raises the question of how an organism should be able to determine "emulation" versus "real-world".  It also begs the question of how much cognition is required to assess such a situation. 

    After all, if there is any "learning" that modifies DNA, then it should be apparent in the DNA structure between those organisms that have "learned" something versus those that haven't.  In addition, we should be able to see such variations differentiated by levels of "experience". 
    However the idea of testing variations is not silly a priori.
    Good, then I would have no problem hearing an actual hypothesis and/or papers that support such an assertion.  Simply arguing that it is so, doesn't do it for me.

    There are many important questions involved.  While we can explain cell differentiation with epigenetics, we don't really know anything about the regulatory mechanisms that ensures compliance [other than possible communication with surrounding cells].  Clearly the biological system recognizes the need to erase most of these epigenetic markers.  However, I don't see that anything is explained or solved by invoking a homonculus.
    Mundus vult decipi
    The problem with your scenario is that if it doesn't kill the cell, then arguably it doesn't impact fitness...  If a "mistake" isn't lethal [i.e. impacts fitness], then it clearly isn't selectable either.
    There  were two scenarios.  Lethality does not even come into the "emulation" scenario. As for the "field-trial" scenario, lethality is always probabalistic so the cell does not have to die every time.
    Let's also keep in mind that most of these bacteria/microorganisms already have mechanisms to deal with stress. So what does it mean to say that an organism "isn't doing very well"?
    I don't understand your difficulty. The organism can use those very mechanisms as the measure of how well it is doing.
    It also begs the question of how much cognition is required to assess such a situation.
    Well as I proposed a couple of totally dumb mechanisms I would have to say "none". I suspect Roy thinks "quite a lot" but I can't speak for him. I have very little time for arguments that stretch the meaning of common words beyond recognition.
    Simply arguing that it is so, doesn't do it for me.
    I am highly skeptical of Roy's thesis. However  I would prefer to see it demolished by valid arguments! 


    Gerhard Adam
    As for the "field-trial" scenario, lethality is always probabalistic so the cell does not have to die every time.
    Agreed, so how is this different from random versus directed?  The emulation scenario could make sense, if one can demonstrate that the organism in question "understands" what it is emulating.  In other words, it suggests that there is some process that is being "emulated" so that things can be tried out, yet how is the organism to know that this is something that needs to be known or tested?
    Well as I proposed a couple of totally dumb mechanisms I would have to say "none".
    Yes, but that's the point.  I'm not disagreeing with "dumb mechanisms".  I'm disagreeing that there is an intelligence present that is directing affairs.
    I have very little time for arguments that stretch the meaning of common words beyond recognition.
    Which is also why I've objected to the use of "intelligence", "learning", "culture", etc. in this discussion.  These terms are too heavily loaded to mean much in this context.  This is precisely why I've tried to draw out what the actual arguments are so that a concept like "self-engineering" can be examined for what it actually claims.
    However  I would prefer to see it demolished by valid arguments!
    One of the primary claims is "self-engineering" or another phrase; adaptive mutations.  I just posted three articles that argue against such a proposition.  However, even adaptive mutations doesn't suggest that there is an intelligent process directing events.
    Mundus vult decipi
    " However, even adaptive mutations doesn't suggest that there is an intelligent process directing events."

    And you say you read that Shapiro paper, which says exactly the opposite?
    Gerhard Adam
    I expect that that's the difference in our views.  I require more than one author.
    Mundus vult decipi
    You mean if you only read one author that claimed one thing, you can lie and say no author made that claim?  And of course you read the quote from the other author who also said the same about intelligence and adaptive mutation.  And then you quoted Jablonka, who also says the same things about intelligence and adaptation.  And then there were at least four others that I asked you to read that have said the same thing.And now you're implying that even though I cited all those people, none of them except one had informed me that intelligence was a requisite for life and its adaptive mutation.  You tell the same lie over and over in different ways and assume that nobody will notice or care.  And apparently you're right, with me, the newcomer, being the negligible exception.
    Hank
    You are just a weird old crackpot. You know nothing yet think your bachelor's degree in psychology makes you an expert and biologists are stupid.  I can't figure out why he hasn't booted you from the site yet. But you call one more of us a liar in your fringe paranoid delusion and you're gone.

    Act like an adult, show some manners, or leave. 
    OK, You're a liar.
    Biologists aren't stupid, but on the other hand your pretense at running a science site is a con.  I wouldn't stay here if you let me.
    I'm only objecting to your arguemnt based on the idea that selection means that a disadvantageous variation means instant extinction and therefore no opportunity to learn. I suggested ways that the cell or cell line can learn from its mistakes without dying out.

    As for the intelligence stuff, you know my views: intelligent is as intelligent does. I do, however, appreciate that certain parties who appear to prefer word games to science and logic, are prone to apply the term to every successful strategy. Like slime molds solving a maze or plants having deep intellectual discussions through their use of chamical signals.
    As for the "field-trial" scenario, lethality is always probabalistic so the cell does not have to die every time.
    Agreed, so how is this different from random versus directed? 
    You omitted the vital part: cells with disadvantageous variations detecting that they are more prone to death without actually dying. That mechanism, coupled with the epigenetic one, creates a smart system that can accumulate knowledge without going extinct. 
    Gerhard Adam
    ...the idea that selection means that a disadvantageous variation means instant extinction and therefore no opportunity to learn. I suggested ways that the cell or cell line can learn from its mistakes without dying out.
    That's the problem, and admittedly I struggle with trying to imagine all the outcomes.  In my view the problem that I'm envisioning is primarily microbial [i.e. bacteria].  Since reproduction is through division, then all daughter cells are effectively clones. 

    So, if a lethal variation exists, then let's presume it exists in all the cells, so that exposure to the "threat" is uniform across all the cells.  The problem is that there is no pathway to introduce a new trait.  Without the parent actually "resolving" the threat and acquiring the trait, there is no opportunity to pass the "solution" on to offspring.  Certainly we can consider copy errors, etc., but then we're simply introducing mutations again, and not addressing the issue of "self-engineering".

    Again, one of the conditions is that the trait isn't already present [i.e. an unexpressed gene].  So, here we have a cell that is exposed to a lethal condition, that must put together a solution in order to pass this trait on to offspring.  I don't see it happening.

    Now, if we consider your point about a non-lethal trait which is simply disadvantageous, then we haven't actually changed any conditions beyond those that are already explained by epigenetic variation due to environmental influences.  Again, we already know that there are means of dealing with stress, just as there exists a means where a bacteria can turn genes on or off based on these types of pressures.

    This isn't a problem, but it also isn't manufacturing a new trait.  To the best of my knowledge, some of the previous links present information about how increased levels of mutations may result under stress, which can give rise to gene duplication, as well as modification of duplicates to introduce a new trait. 
    The Cairns system demonstrates, within the period of a single week, an evolutionary succession of stochastically determined events that provide progressive growth improvement.
    http://www.pnas.org/content/99/4/2164.full
    As you can see, the problem is that stochastic processes were what was being rejected.

    My problem ultimately revolves around the central concepts of "intelligence" and "self-engineering", because what it requires is that a cell [without the benefit of any cognitive process] would have to anticipate that a particular situation is a threat.  From this, it would then have to determine what kind of solution would be appropriate to neutralizing that threat.  So we have an issue of assessment, presumably some comparison to memory to establish what's taking place, and then the "knowledge" of how to resolve the problem.  After all, even trial and error requires requisite knowledge, otherwise it is simply another random process.

    Without emulation, as you pointed out, then it is simply a probabilistic situation which, again, is no different than a random process. 

    With emulation, there's the whole question of "knowledge", because one can't emulate what isn't known.  For example, if it's a binding site, or a particular neutralizing molecule, or a way to segregate a toxin, etc.  These all require some sense of what the problem being solved is all about. 

    So, if we're talking about a "dumb" process where many things are simply tried then there's no real issue, but it's not intelligent and it would be a stretch to claim that it is "self-engineered" any more than all variation is "self-engineered". 

    I fully understand how one can consider that these processes are "intelligent" because it is a legitimate question to ask [I know, because I ask it all the time], how something like a virus can "understand" how to enter a cell, hijack the nucleus, and perform the necessary asks to replicate itself.

    In my view though, the answer is not going to be found, by anthropomorphizing the virus, nor by adding more ill-defined terminology.  Personally, I expect that the answer lies in the historical evolution of life, such that the processes being exploited, are the same processes that gave rise to life in the first place.  So, what appears mysterious to us, is only in that state, because we don't fully understand it. 

    Personally I expect that the more origin of life issues are explored, we'll discover that there's a great deal of Darwinian selection that occurs amongst organic molecules, and that it is this force which is ultimately one of the prime factors that determines the kind of adaptations that are possible to address problems/threats.  So, in effect, I would agree with you that a cell could "test" its' less than optimal conditions against a better future.

    I don't consider emulation to be a viable explanation, and I also expect that the majority of variations are simply shared amongst the various organisms through horizontal gene transfer.  It seems that that particular process is probably much more fundamental, so that any particular trait that is obtained [probably through mutations, or epigenetics] becomes a part of the organisms "tool kit" which can be "exploited" in dealing with the unknowns.  No self-engineering intelligence required.

    Anyway, I'm sure you'll recognize that the last few paragraphs are purely speculative on my part.
    Mundus vult decipi
    All I said was that a cell line does not have to die out if it experiments with lethal variations, which is what you asserted. I am sorry if you cannot imagine how gradations of lethality allow the organism to experiment safely but I have outlined how it could happen - I don't say anything actually does this, I just don't know.  

    I think Roy has taken himself away or been booted... 
     

    Gerhard Adam
    That's the frustrating part about these discussions and the definitions.  Obviously mutations can arise, especially under stress, so I guess it depends on how one defines "experiment" in your example.

    BTW, for a more definitive rebuttal of "adaptive mutations" consider:
    http://whyevolutionistrue.wordpress.com/2012/04/07/jim-shapiro-continues-his-misguided-attack-on-neo-darwinism/

    http://en.wikipedia.org/wiki/Luria%E2%80%93Delbr%C3%BCck_experiment
    Mundus vult decipi
    Gerhard Adam
    One of the ideas proposed along the lines your suggesting was by John Cairns and his work on E coli.  The problem is that there is little to support the notion of adaptive mutation, although conventional explanations suggest that such stresses as originally identified increase the number of mutations.  However, this does not argue for an "engineered" approach, nor does it suggest any problem solving abilities.

    http://www.ncbi.nlm.nih.gov/pubmed/11084622

    http://www.genetics.org/content/148/4/1453.full

    http://www.pnas.org/content/99/4/2164.full

    As I said before, my argument is not with the concept of intelligence in organisms, nor is it with the idea of teleonomy.  I don't  have an argument with the role of epigenetics, etc. all having influences in the cell line and even into the germ line. 

    The point being that mutations [not random, but rather increased rates of] are certainly sufficient to satisfy the "trial and error" aspects of "solving a problem" and it doesn't need to be any more specifically directed than that.  If it's one thing that biology teaches, is that life is expendable as long as some organisms survive.  Biology is quite indifferent to the loss of millions of organisms so that the one can survive, so the notion that the process is more proactive, has little evidence to support it.

    I have a problem with the assertion that this is all an intelligent process that is directed by the organism to control its own evolution through self-engineering.  In my view that's nonsense.
    Mundus vult decipi
    Keep adjusting your story to fit what you can no longer object to of mine and you might get somewhere. But not with the following:

    "The point being that mutations [not random, but rather increased rates of] are certainly sufficient to satisfy the "trial and error" aspects of "solving a problem" and it doesn't need to be any more specifically directed than that."


    Not random but rather increased rates of?  How does an increase of rates decrease the randomness?
    And what is increasing the rates in any case but a purposive trial by what you see as a non-intelligent and purposeless organism?  In your view is that not nonsense, or the nonsense that would beget what you call my nonsense?

    "Biology is quite indifferent to the loss of millions of organisms so that the one can survive, so the notion that the process is more proactive, has little evidence to support it."



    That's meaningless.  You've given biology a purpose by taking away the intelligence necessary  to any purpose.  Laughable.
    Gerhard Adam
    I'm hardly adjusting my story, and certainly not in support of your ideas.

    However, as I said, you can argue all you like.  You've provided no evidence, you've provided nothing to support your idea other than your assertion that somewhere in the jumble of what you've posted, there's supposed to be a reference someplace.

    I give up.  Do what you like. 
    Mundus vult decipi
    Thanks, I will.
    We prepare strategies all the time, and more with our unconscious systems than the conscious.  And our bodies have a myriad of other calculative systems that we can hypothesize about but not consciously monitor.  In short we operate with and by intelligent processes that for their purposes are smarter than we like to think our rational systems are.  We also know, or assume we know, that these processes are predictive and anticipatory.  So assuming as I do that we are a self engineering system, we can expect that we've anticipated the need to prepare for alternate solutions to expected future problems.  And I expect living creatures have found the need to do that to competitively survive for the longer terms that some are wont to do.  But as I said, at this point it's my speculation, based on my belief that we operate with intelligent purposes as opposed to the common belief that junk DNA could  not have a purpose because for one reason it's stochastically produced.
    Bonny Bonobo alias Brat
    We prepare strategies all the time, and more with our unconscious systems than the conscious. And our bodies have a myriad of other calculative systems that we can hypothesize about but not consciously monitor.

    I have to only partly agree with you there Roy. For a start I have a stygmatism on my eyes and sometimes I wonder if that is one of my most beneficial traits or faults, because my eyeballs are not completely symmetrical my brain has been trained from birth to make a constant adjustment for a constant warp in my perception. Then when i get tired my usually 20/20 vision suddenly fails, like now! My brain can no longer make the adjustment and everything suddenly becomes blurred and difficult to perceive even though nothing has really changed, just my tired brain's ability to make the adjustment and calculations.

    Therefore, I think that I can hypothesize about many of my other conscious and unconscious cognitive processes and calculative systems that work on a similar premise but because I feel that I'm a trained athlete in warped perspectives, I can sometimes consciously monitor and be aware of my many other warped perspectives that I think I have developed from the crazy society I live in and from other warped  cognitive behavioural conditionings, that I also misinterpret through my many other warped cognitive processes and perceptions.

    It has been quite a liberating, obvious flaw and compensating skill to develop, understanding that I have my own myriad of warped, often unconscious, flawed perspectives and calculative systems, if you get what I mean?
    My latest forum article 'Australian Researchers Discover Potential Blue Green Algae Cause & Treatment of Motor Neuron Disease (MND)&(ALS)' Parkinsons's and Alzheimer's can be found at http://www.science20.com/forums/medicine
    Helen, I'm not sure we have any significant disagreement there.  The more astute among us are aware of a lot of what our bodies are doing and can make a conscious effort to control these less conscious processes, which are, ironically, more conscious of what they're doing than our so-called conscious self is.  We know that we can talk to our intelligently operated functions and tell them to shape up.  We don't know that thy hear us, but occasionally they seem to.
    We know that we can talk to our intelligently operated functions and tell them to shape up. We don't know that thy hear us, but occasionally they seem to.
     That also applies to science bloggers...
     
    Bonny Bonobo alias Brat
    Ha ha Derek, you are so funny!
    My latest forum article 'Australian Researchers Discover Potential Blue Green Algae Cause & Treatment of Motor Neuron Disease (MND)&(ALS)' Parkinsons's and Alzheimer's can be found at http://www.science20.com/forums/medicine
    When somebody can BS about a hypothetical life form and just for kicks create it and release it and see it successfully compete in the wild, preferably with language culture and technology at its command, then I will believe that somebody sort of understands life. Not before.

    The thing I note about dna is that rna/dna seems an irreplaceable common attribute of Earthly life, so that all by itself makes it of great interest. The other factors mentioned would be present with other sorts of living beings which lacked rna/dna…

    Junk DNA, is there no such thing?
    Three questions... answer the first two, the third will blow your mind.
    1st
    You put a strip of duck tape on a wart that causes the immune system to attack and in the process kills the wart.
    What do you put on a Psoriasis scab to trick the immune system into not attacking the skin cells?

    Yea, take your time, it's a hard one.