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Neo-Lamarckian Thoughts

Greetings to all.

I have been interested for some time in the question-begging character of the logic of natural selection. This is old hat, of course, but just in a nutshell: a new well-adapted trait must first exist in an individual before it can be selected, so while natural selection could potentially explain the proliferation of such a trait throughout a population, it could never explain its origin.

Of course, the Darwinist will say, No problem, new traits are thrown up by chance due to random genetic mutation.

There are two things wrong with this reply, however. The first is a conceptual point. Even if it were the case that every mutation at the level of the genome were indeed random, it would still be the case that this genetic change would have to be translated into a new viable phenotype, and the developmental process by which that occurs is itself highly adaptive and functional (i.e., teleological).

One might conceivably still try to claim that the developmental process is just more mechanism put into place by past rounds of selection. However (and this is the second point), there is empirical evidence that this response is inadequate.

One kind of evidence relates to the amazing plasticity of the organism, such as is found in cases like Slijper’s goat and Faith the Dog (one may read about the former case in Mary Jane West-Eberhard’s book, Developmental Plasticity and Evolution; the latter case may be viewed on YouTube). In these cases, quadrupeds born missing their forelimbs have been able to learn to walk upright on their hind limbs, with accompanying extensive remodeling of their skeletons, musculature, and nervous systems. It seems hard to account for this adaptive capacity through standard selectionist reasoning!

Another kind of evidence relates to botany, which I have only learned about recently. There is a school of Botanists (H.R. Lerner and G.N. Amzallag) at the Hebrew University of Jerusalem who are explicitly embracing the neo-Lamarckian idea that plants are able to respond to stress, not only by adapting physiologically, but by restructuring their genomes, such that the adaptive phenotypic responses are heritable.

Lerner pulls no punches in drawing the implications of his research for neo-Darwinism:

“It is difficult to imagine how competition between organisms that
have been disabled by one, or several, mutations(s), such as
exemplified by genetic diseases [references deleted] could possibly be
the mechanism of evolution. Disabling mutations can lead to only
degeneration of organisms less well-equipped to survive than the
nonmutated parents. The whole concept that variation per se, together
with competitive selection, is sufficient to generate evolution is a
hypothesis that is simply not based on facts.”

H.R. Lerner, “Introduction to the Response of Plants to Environmental
Stresses,” in idem, ed., Plant Responses to Environmental Stresses:
From Phytohormones to Genome Reorganization. New York: Marcel Dekker,
1999, pp. 1-26. (Quote is on p. 17.)

On the next page, he also says this:

“It is true that it is not the opinion of the majority of authors, but
science is not a matter of majority, but rather, what is a better
approximation of reality.”

At any rate, all of this obviously raises the question of the source of the inherent adaptive capacity of living systems. Here, I probably part company with most of you in believing that the answer to this question may well lie at a deeper level in the physics of the “living state of matter.”

But be that as it may, we can all agree that there is a lot more going on in living things than meets the Darwinist’s eye.

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38 Responses to Neo-Lamarckian Thoughts

  1. I don’t have the expertise to assess whether there is such a thing as Lamarckian evolution. If there is such a thing it is a challenge for ID. Lamarckism is a natural alternative to Darwinism and the ID folk have not turned their attention to attacking this alternative.

  2. -”But be that as it may, we can all agree that there is a lot more going on in living things than meets the Darwinist’s eye.”

    That’s one of the conclusions I reached when I read about darwinism and partly why I joined this forum.

  3. M.Frank:I don’t have the expertise to assess whether there is such a thing as Lamarckian evolution. …

    An yet, you imagine yourself qualified to be a shill for Darwinism.

  4. Mark Frank-

    “If there is such a thing it is a challenge for ID. Lamarckism is a natural alternative to Darwinism and the ID folk have not turned their attention to attacking this alternative.”

    Actually a Lamarckian mechanism would be in further support of ID as there would have to be some built in response in the genome to the environment. Not only that but this response would have to be coherent and organized in order to react efficiently and “correctly” to a given environmental stress.

  5. Actually a Lamarckian mechanism would be in further support of ID as there would have to be some built in response in the genome to the environment. Not only that but this response would have to be coherent and organized in order to react efficiently and “correctly” to a given environmental stress.

    If you’re saying that Lamarckianism requires some complex fully formed mechanism to be in existence from the very beginning and that’s why ID should like it, I would disagree with that. Its preferable because it makes the time frame for everything happening more tractable.

    If you think about how things in the external environment change the state of internal organs, such that sensory data changes chemical brain states in some determinstic way, to in effect match what is in the environment. Well why couldn’t there be a mechanism where the external environment was modifying genetic information somewhat directly as well, rather than the necessary genetic changes having to happen completely at random.

    It seems that biological cells in general are chemical strutures that match to their physical environment, that somehow mirror their environement in a determinstic by multi-variant way.

    The sort of layman- ish way I think about it is just look at the wildly divergent forms matter can take, even if just looking only at our own solar system (and even by ID’s account occurring completely as a result of natural laws). Well maybe organic compounds, once they come into existence, have very special properties (as pertaining to mirroring their environment and so on.)

  6. Hi Mark!

    I must say that I am very much in favor of a neo-Lamarckian perspective, at least for some of the problems which affect traditional evolutionary thought. I am not so worried that if we understand adaptive processes that will be a problem for ID. Let’s just try and see…

    The simple fact is that the traditional neo-darwinist scenario is wrong. If we could just agree on that, we could probably start asking the right questions, and look for new and better answers. Then, those who find ID is a better paradigm to look for those answers will stick to that paradigm, while those who prefer a non intelligent, non conscious scenario will at least look for new explanations, instead of repeating false theories which cannot explain anything.

    Adaptive scenarios are extremely interesting, and they are certainly abundant in the living world. Bacteria are a very goog starting point for that. I would like to mention, for instance, that the unlucky model of the quick emergence of nylonase by frameshift mutation (one of the boldest darwinist fairy-tales) can and must be replaced by what appears to be a very quick plasmide mediated adaptation to a new environment by slight remodeling of existing information.

    So, let’s keep an open mind and stay tuned to the new perspectives which come from facts. Adaptational scenatios, epigenetic phenomena, network control of biological response, new codes in biological reality, transposons, active genetic remodeling, antibody maturation, are all scenarios which are open to new and fruitful interpretations. I am sure that all new knowledge will favour ID as a general paradigm, but nobody has to share that faith “a priori”. Let’s stay open-minded, and see…

  7. 7

    Hello gpuccio !!!

    Your comments have been sorely missed here. I hope you’ll stay around for a while.

  8. Hi, Upright BiPed!

    Maybe I just needed some rest…

    I’ll do my best to stay, without burning out my limited resources!

  9. JT-

    “If you think about how things in the external environment change the state of internal organs, such that sensory data changes chemical brain states in some determinstic way, to in effect match what is in the environment. Well why couldn’t there be a mechanism where the external environment was modifying genetic information somewhat directly as well, rather than the necessary genetic changes having to happen completely at random.”

    When you say that sensory data is changing chemical states in the brain you are referring to specific chemicals that have specific functions inside the brain. Each chemical sends a different type of signal. It’s not that your brain is “mirroring” the environment, it is using sensory data, provided by incredibly complex sensory organs, via electrical and chemical signals. In order for there to be some kind of one to one transferrence of environmental stressor to genome you have to have some mechanism by which that stressor is translated into some kind of signal that can ultimately be “read” by the genome and then that has to be then somehow converted into information comprising of the 4 bases and then incorporated into DNA in the correct places. This by the way would be what would be necessary for it to be inherited (this would be taking place in the sperm and eggs) by offspring.

  10. JT:

    Well why couldn’t there be a mechanism where the external environment was modifying genetic information somewhat directly as well, rather than the necessary genetic changes having to happen completely at random

    Well, let’s pretend that the external environment should modify genetic information so that a new protein function may arise: a new enzyme. To do that, the external environment should be aware of what function the new enzyme should effect, and of which primary structure (aminoacid sequence) the necessary protein should have, choosing it in a search space of at least 20^100 (for a minimal new protein domain), a task that even modern protein engineering cannot realize. Then the bexternal environment should translate that sequence in the correct nucleotide sequence according to the genetic code, and then in some way synthesize that sequence (or generate it from some pre-existing sequemce by guided mutation), andthen insert it in the correct place in the genome, and then coordinate a new system of regulation of that new gene, in harmony which all that already exists.

    Aren’t you really asking too much of that “external environment”?

    Obviously, the scenario would be very different if the external environment merely gave an input of information, and then an internal complex adaptive mechanism knew how to react to that information through adaptive pathways… But that would probably smell of intelligen design!

  11. #6 Gpuccio – you are back! Always a pleasure to hear from you.

    The simple fact is that the traditional neo-darwinist scenario is wrong. If we could just agree on that, we could probably start asking the right questions, and look for new and better answers.

    You will not be surprised to learn that I don’t agree with the “simple fact” and neither do the majority of biologists. I get the impression that most evolutionary biologists accept that traditional neo-darwinism is not the whole story – other factors such as Lamarckism and epigenetics have a role to play – but neo-darwinism is still a major force.

  12. Mark:

    You will not be surprised to learn that I don’t agree with the “simple fact” and neither do the majority of biologists

    I know, I know… but I’m fine with you just the same! (A little bit less, perhaps, with the majority of biologists).

  13. 13

    gpuccio,

    It’s good to learn that you are still breathing – and typing.

    …and concocting just-so stories.

  14. Anyone else notice this discussion’s tendency to recapitulate intellectual history? Phaedros is playing the role of the Cartesian rationalist; JT is playing the role of the Lockian empiricist; . . . while gpuccio is, I guess, suggesting a Kantian synthesis. At any rate, what is remarkable is that these same positions suggest themselves to us spontaneously as we reflect upon the cell. Perhaps that is the greatest vindication of intelligence at the cellular level of all . . . we simply have no choice but to think of cells in these classical epistemological terms.

  15. gpuccio [10]:

    [JT:]Well why couldn’t there be a mechanism where the external environment was modifying genetic information somewhat directly as well, rather than the necessary genetic changes having to happen completely at random
    [gpuucio] Aren’t you really asking too much of that “external environment”?

    I could have stated that better. Its quite obvious that compared to its immediate environment, the organism is the more complex entity and its probably more appropriate to talk in terms of it being the actor as opposed to the acted upon. It relates somewhat to the current thread where there is a ongoing discussion regarding data being indistinguishable from code. If some tiny piece of data causes a big program to do something drastically different, then you could look at that tiny piece of data as wielding a lot of power. Its just how you look at it. But I could have worded the above better (Not that its a hugely substantive issue.)

    Obviously, the scenario would be very different if the external environment merely gave an input of information, and then an internal complex adaptive mechanism knew how to react to that information through adaptive pathways… But that would probably smell of intelligen design!

    It seems like both you and Phaedros in his post 9 really are strongly implying that fully functional complex integration had to exist in life forms from the very inception of life, or rather that there was some specific preexisting thought out design that some unseen intelligence just brought into existence, maybe not literally instantaneously, but still essentially just fleshing out something quite specific that already existed in his ‘mind’.

    That implies to me some sort of limited focussed perhaps even narrow-minded design project unworthy of the infinite God. As far as humans, we have to specialize, and everyone has their own little niche and their own little world view, and every individual is so proud of their little focussed projects they’ve given their lives to, whether its Ford and his Model T or Van Gogh and his paintings or what have you. But my thinking is that God is infinite. Now if we say that God is infinite, that’s almost like saying he’s nothing, to us, because in our limited capacity we cannot even fathom what infinite intelligence is. But for our own little projects to work, we generally have to plan everything in advance. But I think the true mark of genius is supreme flexibility – throw them in any arbitary scenario and they’ll make something useful out of it (Like MacGruber, Paramount Picture Release, opening this Friday, consult your local newspaper for times and location)

    But from my thinking, to start with nothing and to incrementally build things up from random elements, where at each step there is something more adapted, complex and useful – maybe I can’t do it, maybe you can’t do it, – but I couldn’t say the physical universe and an infinite God can’t do it. And actually I think that somehow life is an equal marriage between Supreme Randomness and Supreme Order, Where at each step randomness throws some pointless monkey-wrench into the works and says, “OK God or Reality or whatever your name is, make something useful with THAT.” And lo and behold he does. (What was the subject again?)

    But to bring it back to Lamarkianism, epigenetics, and so forth I don’t really know much about it, but if DNA determines form, is there a way for form to determine DNA (in sorme sort of reverse-compilation process.) For some reason I am really intrigued with encephalapods of late – and their ability to assume arbitrary form, color, and texture, instantaneously and at will to match their environment. How could such morphological changes become genetic changes. I don’t know.

  16. JT-

    Think of just a single celled organism. Is that not “fully functional complex integration”?

  17. What are you implying?

  18. JT-

    “That implies to me some sort of limited focussed perhaps even narrow-minded design project unworthy of the infinite God.”

    If you consider life “limited” and a practically infinite, although not really, cosmos to be limited then you have a very strange definition of limited in my view. If we play reductionist games, then yes, life can appear to be not all that fantastic. It can seem to be just to be a bunch of matter with complex organization whose “consciousness, if you’d want to call it that under such a scenario, is just a mess of nervous responses to nervous stimuli. However, this kind of reductionism doesn’t hold up when one considers what is needed to be in place just for, say, hearing to work. Matter doesn’t, and can’t, have particular goals in mind, but what is required for hearing are many, many different integrated parts each having specific shapes and functions organized in such a way as to facilitate a common goal, i.e. conducting auditory signals via vibrations to a brain and then to a mind that can differentiate between the various sounds of the world.

  19. Phaedros [17]:

    “what is required for hearing are many, many different integrated parts each having specific shapes and functions organized in such a way as to facilitate a common goal, i.e. conducting auditory signals via vibrations to a brain and then to a mind that can differentiate between the various sounds of the world”

    Compare the goal of one specific 100 word grammatically correct complex sentence vs the goal of ANY 100 word grammatically correct complex sentence. The latter is going to be exceedingly much easier to achieve through random incremental changes, assuming you have an evaluation function that can identify any valid english sentence or phrase (i.e. God) That doesn’t mean the evaluator has to care what sentence is generated, IOW, he doesn’t have to throw out legal phrases that do not get him towards some specific distant end point. So Reality (or God) could be working with whatever was thrown at it.) So whatever the 100 word gramatically correct complex sentence that emerges, that specific sentence needn’t have been the goal at all in order for a such a sentence to realistically emerge.

  20. But I guess the paradox is that at some much deeper level it really was the goal (in that the random element itself could not escape the sovereignty of God, but that needed to be proved.) OK I’ll just say it -is the random element in fact Satan.

  21. That’s speculation – maybe idle speculation.

  22. Phaedros [17]:

    ” If we play reductionist games, then yes, life can appear to be not all that fantastic. It can seem to be just to be a bunch of matter with complex organization whose “consciousness, if you’d want to call it that under such a scenario, is just a mess of nervous responses to nervous stimuli. However, this kind of reductionism doesn’t hold up when one considers what is needed to be in place just for, say, hearing to work”

    I’m saying if that’s all God were capable of it would severely limit him. If there were an infinite number of drastically different projects he could have done, each one equally glorious but still drastically different from the others, that would make him God. And that sort of God can work with any sort of arbitrary garbage you throw at him in any order and make something out of it. That was my point. And all the claims about what randomness cannot achieve are primarily applicable when you limit yourself to one specific goal and one goal only.

  23. But if anyone wants to steer this back to Lamarkianism specifically go ahead.

  24. JT #14:

    Again I appreciate your open discussion about this interesting topic. Some comments about my personal point of view:

    If some tiny piece of data causes a big program to do something drastically different, then you could look at that tiny piece of data as wielding a lot of power.

    This is a common confusing point. A change in some tiny piece of data in the final effector of a complex procedure can certainly ruin the whole procedure, deforming its function or annihilating it. Let’s say you have a cascade of five proteins which performs some function. Well, even a single mutation in one of the proteins can terminate the function (unless it is in some way reduntant), or strongly affect it. Many single mutation diseases are of this kind. Simple mutations in homeobox genes have a great deforming power (whole parts of the body are moved to the wrong place). In some, more constructive cases, simple mutations can slightly modify the affinity of a protein for its target, even increasing it (it’s the case of antibody affinity maturation), or shifting the affinity towards a slightly different target of the same kind (it’s the case of the emergence of nylonase from the penicillinase domain). But a tiny piece of data cannot create a completely new function, which requires a different protein domain with a completely different aminoacid sequence, different folding, different active site, and so on. That “power” can only be exerted by an input of new complex specified information, in other words by conscious intelligent beings.

    It seems like both you and Phaedros in his post 9 really are strongly implying that fully functional complex integration had to exist in life forms from the very inception of life, or rather that there was some specific preexisting thought out design that some unseen intelligence just brought into existence, maybe not literally instantaneously, but still essentially just fleshing out something quite specific that already existed in his ‘mind’.

    Correct. I think that the emergence of new complex specified information in evolution is the effect of “some specific preexisting thought out design”. But I can also believe that Lamarckian adaptation, based on the cooperation of information input from the environment, and a pre-existing, designed, adaptational capacity in the living being, can explain many minor events, which can be regarded as adaptations and not truly new design. Again, antibody affinity maturation is a good example of very intelligently designed adaptation to information input from the environment, and that happens in a few months, and in a single individual. And it does change the genome, although not in a transmissible way.

    So, to sum up, OOL, or the emergence of new phyla (body plans), are extreme examples of what only active design can realize, while antibody maturation, or the plasmid mediated adaptation of pre-existing funcional molecules in bacteria, are a good example of what lamarckian mechanisms can do.

    That implies to me some sort of limited focussed perhaps even narrow-minded design project unworthy of the infinite God.

    That is an old issue. I usually don’t discuss it because, although I do believe in God as the ultimate Designer, my ID approach is really and sincerely limited to a scientific analysis, without any support from faith or philosophy. So, in the ultimate sense, I cannot discuss a priori about the designer being God. From an ID perspective, I can only discuss the qualities of the designer which can be inferred from what we observe and know of the designed objects.

    However, shifting for a moment to another plane of discussion, I must say that I find very strange that religious people consider the continuous acting of God in His creation as a diminutive property of the Divine Being. I really cannot see why God should limit his intervention in creation to, say, before the Big Bang, and then just observe, or only occasionally act in acute miraculous ways. I do believe that God acts in His creation always, and in many different ways. It’s His creation, after all. He is not trying to demonstrate to us that He is clever, and that He can realize even impossible tasks like darwinian evolution. I prefer to think that He is rather pursuing His own goals, which we certainly don’t understand completely, but which are beautiful and glorious.

    So, on a religious plane, I do prefer a God who creates and acts in His creation, with all the modalities He likes. The implementation of design in life is not, IMO, an “acute” miracle, but rather a continuous and exciting miracle, like many other things in creation; but it certainly has some specific characteristics, like the emergence, sometimes rather quickly, of completely new CSI, which no known non-intelligent cause will ever be able to explain.

    But again, I want to reiterate that this is a religious argument, and has nothing to do with ID. For once, I just wanted to comment on that strange argument about God being “smarter” if He does not act in His creation, because it is truly strange for me.

    is there a way for form to determine DNA (in sorme sort of reverse-compilation process.)

    Yes, but it’s not easy, and it requires a complex intelligent machinery designed for that purpose. Again, we have the model of antibody affinity maturation. Here, an external form (that is the antigen which has come in contact with the organism, and which is kept in specialized cells, the antigen presenting cells) is used to realize an intelligent selection of the products of a targeted, highly controlled, random hypermutation (or, at least, that should be the general scenario, until we can understand better how that really happens). And the result is a (slight) modification (usually a few nucleotides) in the DNA of that part of the genes which controls that particular antibody specificity (in that cell clone).

    So, it is possible. But it is not easy, it is not simple, it is not random, it is not automatic. The adepts of neo-neo-darwinism who believe that environmental information can shape the genome by some sort of “magic”, and who speak of tens and tens of supposed engines of variation which can create function, are just building fairy tales, and not trying to explain things.

  25. Phaedros [17]: I don’t think you really understood what I was saying and I didn’t adequately address your misunderstanding.

    I’m not saying at all that life as it exists isn’t marvelous, certainly in comparison to what we’re capable of. But if its all God is capable of, he’s not that great. If Henry Ford were told, “you have to make your cars out of paper mache from now on”, he probably couldn’t manage that. God could. So anyway, the sort of continual random deviations proposed in an evolutionary scenario, he could handle no problem – unless what we see now is all he was ever capable of doing, or planned to do. In that case everything would have to fall into place pretty much from the beginning just like he planned. And also he wouldn’t be all that great.

    Actually I don’t intend to anthropomorphize God by saying ‘He’. I would say God maybe should be conceptualized merely as “Reality”, and he just allows whatever configuration that emerges that is viable to survive. But the range of things that are capable of existing, and the signature of those things that survive and thrive over time, says something about the nature of Reality and of God. I don’t want to commit heresy and say God is not a person. But it seems to me the primary personal manifestation of God is Christ. (But it may in fact be heresy to say God isn’t a person as such but Christ is, even if you say both are God.)

  26. JT:

    I am trying to understand better your point of view form your many posts here (including the last one), and I am not sure I really understand it. It appears that religious implications are very influential for you, and I respect that (although it is not my approach). But some of your statements are truly strange:

    OK I’ll just say it -is the random element in fact Satan.

    Are you saying that the random element is Satan, but that God (or Reality, if you want) is great becuase He can realize glorious things “against” that random “disturb”, even using it for constructive creation? That’s a strange scenario, and certainly npot a darwinist one. In neo darwinism, random variation is the real engine which builds function.

    So, if I understand you well, your scenario is after all an ID scenario. Maybe not the usual one, but ID just the same. In other words, random variation ruins things (genetic entropy?), but a superior principle (I would definitely say a designer) creatively builds up the best from that, even in almost miraculous ways.

    Well, why not? It’s an ID scenario. Unless you think that God (or Reality) is non conscious and non intelligent. But then I have not understood what you are trying to say.

  27. gpuccio [23]:

    [A lot of this off-topic but in response to the above.]

    But a tiny piece of data cannot create a completely new function, which requires a different protein domain with a completely different aminoacid sequence,

    I didn’t mean to imply for example, that if some minor change in a minuscule main process causes a huge section of code that was previously not being executed to start, I’m not saying you give credit to this tiny minuscule change. But as far as the distinction between input and code, you could have input which was quite lengthy and complex and it could have a quite nuanced and complex effect on how the program behaved. The input could even be an actual program, and the program to which it was input merely a universal program that merely executes anything given to it as input. So the predominance of info could be in the input or alternatively in the program, or they could be directly comparable in complexity. Whether we say the program acts upon the input or vice versa is a matter of syntactic convention, unless there is some stipulated requirement that only the more complex and lengthy of the two can be described as “acting”. (I guess with both probably know this.)

    And the analogy of the above to an organism and its environment should be apparent. So the environment would be the input to the organism (and really vice versa because they both change each other.) But I’m not ready to treat the environment as some vastly inferior entity in relation to the organism. Consider how the visual environment of an Octopus drastically shapes his behavior.

    And on a slightly different subject, as I alluded to yesterday, its amazing the wildly divergent forms matter can take in the universe completely via natural laws. The way I look at it is, if the universe created life then the universe equates to life. Just as a image file (plus the decompression algorithm) equates to the actual image they output. Just consider the wildly divergent forms matter takes among the various moons of Jupiter or Saturn for example. My point being, do we treat the universe as so much chopped liver, or the Universe itself as something in essence equating to the life it created. I’m still saying you have an infinite God to make it work, but operating passively with whatever he’s given in this universe.

    That “power” can only be exerted by an input of new complex specified information, in other words by conscious intelligent beings

    I did not realize for a long time the importance given in ID to “consciousness”. Its hard to fathom how you believe that some process has to experience its environment the way people do (what else could “consciousness” mean) in order for it to create complex specified output. Even bodily organs do incredibly complex things, without having to sense or understand the world the way that you or I do.

    The relevant fact for me has always been there has to be comparable levels of information in a process and its output. (But it actually goes further than that, as a completely specified process and its output will always actually equate.) But of course you can’t have a a tiny little program and its given the number 14 as input say, and the output is War and Peace (unless we’re disguising its full input somewhere.) A process and its output may look drastically different from one another – but there has to be comparable levels of information (Because even if the completely specified process is smaller, we can always use it to directly allude to the output. A completely specified process includes both the process (program) and what is input to it.)

    But at any rate, it would never even occur to me for as long as I’ve been thinking about these things to presume ‘consciousness’ is somehow essential. And FYI, my religious beliefs would definitely be considered Orthodox Christianity.

    I think that the emergence of new complex specified information in evolution is the effect of “some specific preexisting thought out design”. But I can also believe that Lamarckian adaptation, based on the cooperation of information input from the environment, and a pre-existing, designed, adaptational capacity in the living being, can explain many minor events, which can be regarded as adaptations and not truly new design.

    I believe you would be coopting the term ‘Lamarckian’ for your own purposes if you did that. I believe you would be doing disservice to the concept to redefine to only allude to minor types of adaptation.

    I do believe in God as the ultimate Designer, my ID approach is really and sincerely limited to a scientific analysis, without any support from faith or philosophy. So, in the ultimate sense, I cannot discuss a priori about the designer being God. From an ID perspective, I can only discuss the qualities of the designer which can be inferred from what we observe and know of the designed objects

    I think that Christians at least are compelled to conceive of the designer as infinite, which would not apply to human designers.

    (I’ll respond to your other post later – haven’t read it yet. I’m a slow writer, and not a particularly good debater.)

  28. gpuccio [24] (cont):

    [JT:] That implies to me some sort of limited focussed perhaps even narrow-minded design project unworthy of the infinite God
    [That is an old issue…He is not trying to demonstrate to us that He is clever, and that He can realize even impossible tasks like darwinian evolution..

    Well that’s what I’m getting at … If God is all powerful then he can do something that would be impossible for us to accomplish (like evolution). Maybe its just now resonating with me since you say its an old issue.

    However, shifting for a moment to another plane of discussion, I must say that I find very strange that religious people consider the continuous acting of God in His creation as a diminutive property of the Divine Being. I really cannot see why God should limit his intervention in creation to, say, before the Big Bang, and then just observe, or only occasionally act in acute miraculous ways. I do believe that God acts in His creation always, and in many different ways. It’s His creation, after all. He is not trying to demonstrate to us that He is clever, and that He can realize even impossible tasks like darwinian evolution. I prefer to think that He is rather pursuing His own goals, which we certainly don’t understand completely, but which are beautiful and glorious.
    So, on a religious plane, I do prefer a God who creates and acts in His creation, with all the modalities He likes. The implementation of design in life is not, IMO, an “acute” miracle, but rather a continuous and exciting miracle, like many other things in creation; but it certainly has some specific characteristics, like the emergence, sometimes rather quickly, of completely new CSI, which no known non-intelligent cause will ever be able to explain.

    My thinking is that if someone is really good at something they can do it in their sleep. It only requires someone’s active engagment if they’re not really skilled at it. If in scripture God is portrayed as seperate and holy, then I’m thinking he may not be directly involved, but instead can operate in a modality similar to autopilot, spin off some instantiation of himself that basically consists of the rules that are essential to his being. And that process is what is monitoring and controlling the unfolding of life and the universe. Anyway that’s a point of view that just came to me now – don’t really espouse it exactly. I’m sort of embarassed to keep peddling this – just trying be engaged in the discussion.

  29. gpuccio [26]:

    OK I’ll just say it -is the random element in fact Satan.
    Are you saying that the random element is Satan, but that God (or Reality, if you want) is great because He can realize glorious things “against” that random “disturb”, even using it for constructive creation? That’s a strange scenario, and certainly not a Darwinist one. In neo Darwinism, random variation is the real engine which builds function.

    I would disagree with your characterization of neo-darwinism. I don’t think it would ever consider random variation in isolation as doing anything. Its inert without selection. the two are always considered together. And that’s where it gets a little tricky (and perhaps pointless) to make the comparison to God and Satan.

    The prime example would be the crucifixion, which led to the eternal glory of the Son and the sanctification of Mankind.
    “if Life gives you Lemon’s make lemon-aid”
    “You can’t make an omelette without breaking a few eggs”
    “The essence of Drama is conflict”
    “You meant it for evil but God meant it for Good”
    And furthermore the observation that indeed innovations seem to arise in nature primarily in response to environmental hazards.

    But as far as the source of random variation, I see unleashed raw energy as creating random variation. You need a lot of energy to create a lot of randomness. But complex meaningful sequences will not be found in monotonic strings, only in the amount of variation provided by randomness.

    But raw energy is also a highly destructive chaotic and undisciplined force, subservient to no one or new thing – it has to be modulated and controlled by order. (So now am I equating energy to Satan – that wasn’t actually my intention.)

    So here’s where I feel like I shouldn’t even be saying this – it implies that God and the Devil are somehow both essential or maybe equal partners, and so what is that – ZoroAsterism [sp]? Or possibly even Taoism or maybe even redolent of Shiva the Destroyer vs. Vishnu the creator in Hinduism So in essence, maybe Satan would like to be given this sort of equal footing with God and I shouldn’t be giving it to him.

    The unsettling part for Satan is that after he’s served his purpose he will be judged and consigned to eternal torment. So the moral God makes use of all his enemies to achieve good out of them and then kills them.

  30. 30

    Just an aside. When reading in “the Descent of man” by Darwin about women’s intelligence he clearly showed he believed traits could be aquired during a lifetime and then later breeding give these traits to off spring. He said that women could biological rise in intelligence to men if in late life women acquire intellectual virtues and then breeding pass them biologically onto the girl babies.
    I suspect he thought lifetime traits acquired do get passed on to offspring.
    Perhaps its known Lamarckin ideas were allowed by Darwin but just a reminder.

  31. JT:

    I find your thoughts interesting and frankly creative, although I don’t agree with many of your conclusions.

    Anyway, I will not comment any more about the religious and philosophical aspects of this debate (I have already made an exception to my rules in my previous post).

    I would rather mention that, judging from your posts, you are probably not well acquainted with ID theory, and I would suggest that you try to read more about it, if you are interested. I would like to just give a few swift suggestions, based on some of your statements.

    1) Neo-darwinism.

    I would disagree with your characterization of neo-darwinism. I don’t think it would ever consider random variation in isolation as doing anything. Its inert without selection. the two are always considered together.

    That is not really correct. In neo darwinism, Rv and NS do act together, but they have separate roles. All the new emerging function must be built by RV, before being selected by NS. NS can only act on exisitng functional information, fixing and expanding it in the population. So, all the search for functional information in the search space is made by RV. RV is not inert in itself: it has to produce completely functional information by itself. It is the only engine of variation in neodarwinian theory. This point is very important, because ID’s main objection to darwinian theory is the simple fact that random variation has not the power to build CSI.

    2) Consciousness and ID.

    I did not realize for a long time the importance given in ID to “consciousness”. Its hard to fathom how you believe that some process has to experience its environment the way people do (what else could “consciousness” mean) in order for it to create complex specified output. Even bodily organs do incredibly complex things, without having to sense or understand the world the way that you or I do.

    Of course consciousness in central in ID theory. ID is about detecting design in things. Design is a process which originates in conscious intelligent beings (the designers). ID affirms that designed objects are recognizable with certainty as such if they exhibit a specific property, CSI. CSI is the main idea in ID. It is objectively recognizable, and in the known world it is always the product of design by an intelligent conscious being (leaving apart biological information, which is the object of the discussion).

    A special subset of CSI, digital functionally specified complex information (or, if you want, dFSCI), is specially useful for the discussion. It is easily definable as any string of digital information with the following properties: complexity higher than 10^150 (that is, length of about 500 bits); non significant compressibility (it cannot be generated through laws of necessity from a simpler string); and a recognizable, objectively definable function.

    That definition is very strong and useful. According to that definition, dFSCI includes language, software and practically all relevant biological information (in particular, the sequences of protein coding genes and the primary sequences of proteins).

    It is easy to show that no example is known of dFSCI (apart from biological information, which is the object of the debate) whic does not originate from a cosncious intelligent being (humans). And our common experience is that consciousness and intelligence are exactly the faculties used by humans in producing dFSCI.

    Biological information is dFSCI (any functional protein is). That’s why ID, with very sound inference based on analogy, assumes that some conscious and intelligent designer is the origin of biological information.

    That is, very quickly, the main idea in ID. Neo-darwinism cannot explain the emergence of dFSCI in living beings. The work of a designer can.

    I would like to mention that dFSCI originates from conscious intelligent beings directly; ot indirectly, through some non conscious machine which has received from an intelligent conscious being the pertinent dFSCI. In other words, Hamlet is dFSCI. Hamlet can be outputted by a PC, but only if someone has inputted it in the software. No computing machine can create Hamlet (or anything equivalent).

    Specification, function and purpose are definable only in relation to consciousness. Only consciousness recognizes them actively. So, consciousness is central to ID. Without consciousness, no function can be recognized. With consciousness, function can be defined, recognized and measured. And function is the only relevant form of specification in biological information.

    To go to your examples, bodily organs do not output dFSCI, even if they do complex things. A mchine can do complex things according to the CSI which has been inputted in the machine, but it cannot generate new dFSCI. The human body as a whole can generate new dFSCI (speaking, writing, programming) only because it is an interface for a conscious intelligent being.

    3) Types of digital information.

    But complex meaningful sequences will not be found in monotonic strings, only in the amount of variation provided by randomness.

    We have three types of digital information:

    a) highly compressible strings, like monotonic strings. These are not dFSCI.

    b) truly random strings (high complexity, no functional specification). These are not dFSCI.

    c) pseudo-random strings, where a recognizable meaning is superimposed to the random structure by an intelligent designer (Hamlet, any software, any long discourse). And, obviouisly, any functional protein. These are dFSCI.

    About that, I would suggest that you read the following paper:

    Three subsets of sequence complexity and their relevance to biopolymeric information

    by David L Abel and Jack T Trevors

    available at the following URL:

    http://www.ncbi.nlm.nih.gov/pm.....MC1208958/

  32. GP: Interesting. G

  33. gpuccio [31]:

    Rv and NS do act together, but they have separate roles. All the new emerging function must be built by RV, before being selected by NS. NS can only act on existing functional information, fixing and expanding it in the population. So, all the search for functional information in the search space is made by RV. RV is not inert in itself: it has to produce completely functional information by itself. It is the only engine of variation in neodarwinian theory. This point is very important, because ID’s main objection to Darwinian theory is the simple fact that random variation has not the power to build CSI.

    I think you’re making a somewhat valid point here, and for the record I have always been receptive to the one specific attribute of I.D. regarding the extreme rarity of compressible strings among the population of all strings and thus there existing the possibility to rule out what pure randomness can accomplish on its own. But actually everyone already basically understands that randomness is never an explanation. There may be the assertion that some slight-of-hand in neodarwinism has always obscured the fact that it really boils down to randomness. But it doesn’t have to actually be proven to anyone that randomness by itself cannot accomplish anything.

    Also, my understanding is that neodarwinian synthesis is quite old now, and really to some extent it seems its always been merely a shorthand to allude to the following: “whatever the full natural processes are that resulted in life, much of which we may not fully understand now.” The work regarding “symbioses” mentioned in another thread started today is very compelling as merely one example, and it is not rejected out of hand by the scientific establishment. Its always seemed to me that for something akin to neodarwinism to work, would require vast quantities of random variations to be accumulated by an organism and carried around as non-functional but neutral for a long time to give a chance for selection to finally produce something.

    Design is a process which originates in conscious intelligent beings (the designers).

    Do you mean that

    a) Design has been repeatedly observed to originate as the result of the activities of what we have to come to label “conscious intelligent beings”

    or

    b) If design is to emerge it can only do so as a result of the activities of “conscious intelligent beings”

    Of course (a) would be contested by no one. It seems in a way you want the second interpretation to gain some legitimacy merely as a result of the legitimacy of (a).

    ID affirms that designed objects are recognizable with certainty as such if they exhibit a specific property, CSI

    What difference would it make what ID “affirms”, honestly?

    CSI is the main idea in ID. It is objectively recognizable, and in the known world it is always the product of design by an intelligent conscious being…Hamlet can be outputted by a PC, but only if someone has inputted it in the software. No computing machine can create Hamlet (or anything equivalent).

    It is not the case that computers programs can only regurgitate some preexisting CSI created by a human. In numerous contexts, programs have generated complex novel output that would have never even occurred to the writer of the program.

    Specification, function and purpose are definable only in relation to consciousness. Only consciousness recognizes them actively.

    A computer program or bodily organ or the like can discern and distinguish some highly specified complex state of affairs existing in some random environment – .e.g. some complex chemical situation, maybe some complex behavior, etc. And we say they “recognize” it because in the presence of this complex specifiable scenario, they “respond” to it, that is they exhibit some specific behavior that can be correlated with the presence of that complex specified scenario. And various processes exhibit that type of recognition all the time, without having the sort of subjective internal sensations that humans experience. So complex recognition and reaction is exhibited by processes that do not have “consciousness” as we construe the term. And the problem is, even we cannot define what we mean by “consciousness.”

    But to return to your example of Hamlet, certainly you recognize that even if some program were just set up to just spit out Hamlet, that in the program, Hamlet could go through all sorts of transformations from one encoding to another before finally being output as Hamlet. It could be merely encrypted, so you would have some encrypted file which would be completely unconnectable to Hamlet by any observer encountering it, and then you have some arcane general purpose disencryption program and together with the encrypted file, Hamlet would be the result.

    But my question to you in this context is, on what basis can we rule out that the physical universe is what created life, just like an encrypted file and disencryption program creates Hamlet. Do you agree that the universe could be capable of that? If your response is, “We have not identified mechanisms in the universe capable of outputting life.” That is in fact an argument from ignorance. You might respond, ‘even if the universe could do that, it implies that some conscious intelligence created the universe. But do you really mean that whatever created the universe is merely “conscious” in the sense that you or I are? That it perceives or thinks about things like you or me? And if the question is, “What can we learn about the physical situation in the universe that led to the emergence of development of life”, why cannot that question be explored apart from the question of what non-physical things, i.e. things that are not physically detectable, might have created the universe.

    And to me when you talk about intelligence and consciousness originating complex things, I would say you have to define intelligence in terms of things that can be potentially observed and quantified. Treating intelligence (or alternatively “conscious intelligence”) As an indivisible metaphysical property that either someone possesses or does not possess and invoke that as an explanation, explains nothing. The sort of intelligence that humans exhibit, is directly connected to things that can be physically described and quantified, having to do with their sensory experience of the world as one example, the fidelity and granularity and complexity of their sense organs, it also has to do with the size and complexity of their brains. There is definitely a necessary correlation between the complexity of a human’s experience of the world, and the complexity of their internal physical makeup, Just as there is a correlation between the complexity of some bodily organ and the complexity of that bodily organ’s behavior and the complexity of the things that it can discern in its environment. We cannot think of the creator of the universe as being quantifiable like that, so how can we even quantify his intelligence. We cannot. So if we cannot quantify his intelligence that property might be considered undefined for him.

    (Maybe someone should steer this back to Lamarkiansm exclusively, and this current discussion brought to a close.)

  34. JT:

    very briefly (it is late):

    Do you mean that

    a) Design has been repeatedly observed to originate as the result of the activities of what we have to come to label “conscious intelligent beings”

    or

    b) If design is to emerge it can only do so as a result of the activities of “conscious intelligent beings”

    I just mean a very simple thing: the word design in our language indicates what is done by conscious intelligent beings. It’s just a question of definition. Here is the definition of “to design” from an online dictionary:

    “de·sign (d-zn)
    v. de·signed, de·sign·ing, de·signs
    v.tr.
    1.
    a. To conceive or fashion in the mind; invent: design a good excuse for not attending the conference.
    b. To formulate a plan for; devise: designed a marketing strategy for the new product.
    2. To plan out in systematic, usually graphic form: design a building; design a computer program.
    3. To create or contrive for a particular purpose or effect: a game designed to appeal to all ages.
    4. To have as a goal or purpose; intend.
    5. To create or execute in an artistic or highly skilled manner.”

    So, when I say “Design is a process which originates in conscious intelligent beings (the designers).”, I am just reminding what “design” means in the english language.

    What difference would it make what ID “affirms”, honestly?

    This is not very fair. I had clearly said that I was just giving a summary of the ID theory. ID affirms that as the result of a detailed theory and analysis, part of which I have anyway briefly mentioned.

    It is not the case that computers programs can only regurgitate some preexisting CSI created by a human. In numerous contexts, programs have generated complex novel output that would have never even occurred to the writer of the program.

    I don’t agree. Programs cannot generate new complex specifications. But that would be a long discussion, and this is not the time.

    A computer program or bodily organ or the like can discern and distinguish some highly specified complex state of affairs existing in some random environment – .e.g. some complex chemical situation, maybe some complex behavior, etc. And we say they “recognize” it because in the presence of this complex specifiable scenario, they “respond” to it, that is they exhibit some specific behavior that can be correlated with the presence of that complex specified scenario.

    Only because the computer or organ has been programmed to “recognize” that information. The necessary specification has been inputted by the programmer, otherwise a computer or organ could recognize nothing. Computers, organs and machines do not recognize, do not have purposes, do not cognize anything. They are not conscious. They just reshuffle information which is in them, or which they receive from outside.

    And the problem is, even we cannot define what we mean by “consciousness.”

    There is no need to define anything. Consciousness is experienced, it is a fact. The only definition we need is something of the type: we use the word consciousness to mean that kind of experience we do inside ourselves any time we experience senastions, or pain, or joy, or thoughts, or any other “subjective” experience. All subjective experiences happen in consciousness. Or are you denying that subjective experiences exist? That each of us knows intuitevely and directly that he exists and perceives? These are empirical realities, facts, not theories.

    But my question to you in this context is, on what basis can we rule out that the physical universe is what created life, just like an encrypted file and disencryption program creates Hamlet.

    I don’t agree. An encrypted file “is” Hamlet, even if written in another symbolic language. An ecrypted file has all the CSI of Hamlet. The physical universe, as we intepret it from the point of view of the laws of physics that we know, has not the CSI of biological information nor can it create it. If the “physical” universe will be shown to contain other forces which are conscious and intelligent, then those forces will have the power to generate CSI. But that universe would be something very different from the physical universe conceived by materialist reductionism. That would be an ID universe.

    I would say you have to define intelligence in terms of things that can be potentially observed and quantified.

    Very easy: those conscious processes which we experience when we produce CSI /when we talk, program, and so on). The conscious processe “can” be observed, and CSI can be observed and measured as a property of the output.

    Treating intelligence (or alternatively “conscious intelligence”) As an indivisible metaphysical property that either someone possesses or does not possess and invoke that as an explanation, explains nothing.

    I have never done such a thing. I have just define intelligence empirically. And according to such definition, there is no doubt that we have intelligence, and non conscious things don’t.

    There is definitely a necessary correlation between the complexity of a human’s experience of the world, and the complexity of their internal physical makeup

    This is certainly true. The physical body is the interface of consciousness. But it is not its cause, nor its explanation.

    We cannot think of the creator of the universe as being quantifiable like that, so how can we even quantify his intelligence. We cannot. So if we cannot quantify his intelligence that property might be considered undefined for him.

    Who wants to quantify it? Not me. Why do you think that a property which is not quantified is “undefined”? Even for human beings, I have just defined consciousness and intelligence, without trying to quantify them. There is no abjective way to quantify love, or hatred, or joy, or pain. Does that mean that those empirical realities are “undefined”? Are you an eliminative materialist? (thank you to the person, I don’t remember who it was, who recently pointed to this definition :) )

  35. JT-

    “But my question to you in this context is, on what basis can we rule out that the physical universe is what created life, just like an encrypted file and disencryption program creates Hamlet.”

    This does not “create” Hamlet, it’s merely converting to different formats or different types of being stored as information. “Disencryption” would only be making the information that ALREADY EXISTS readable to someone that does not understand the encrypted form, albeit no human probably can understand higher levels of encryption.

  36. GP: Well said. G

  37. To steer back to Lamarckism, a brief summary/proposal.

    Three procedures which can modify the genome:

    1) Random Variation + Natural Selection (RV+NS). Traditional neo-darwinist theory. Minimal power (small changes, usually acts mainly through negative NS of non functional mutations, but can fix and expand minimal, non complex mutations which can, in particular contexts, confer some benefits, usually through some concomitant loss of function: example, antibody resistance due to point mutation of target structures).

    2) Adaptation + NS. Adaptation takes place probably through pre-existing structures and algorithms of response which allow the incorporation and utilization of external information to create a selective genome modification. Power: discreet. Possible examples: antibody resistance or other functions obtained through HGT, including the algorithmic tweaking of existing information to accommodate new, slightly different targets (plasmid information, emergence of nylonase from penicillinase); antibody affinity maturation.

    The adaptational algorithms must be already present in the living being. They can be rigidly deterministic, or use partial random search in the context of a deterministic algorithm, and they usually incorporate external information: in antibody affinity maturation, for example, controlled random hypermutation acts on specific segments of the genome, and the information present in the external antigen is used to effect an intelligent selection of the results.

    3) Intelligent design. Power: limited only by the knowledge available to the designer and by his power of implementation. Here the input of information comes from an external source (the designer), who is a conscious intelligent being of some kind. The designer must have previous information about the result to be obtained, and must have access to some modality of manipulation of the physical support of biological information. The information inputted by the designer can be of different kinds (one does not esclude the others):

    a) Previous knowledge of the final information to be implemented (for instance, previous knowledge of the exact sequence of nucleotides/aminoacids which allows the desired function.

    b) Previous knowledge of the desired function, which can be used to effect intelligent selection after a controlled random search, especially if point a) is not available.

    c) Previous knowledge about the search space structure for the desired functional ouptut, which can allow a controlled and more efficient random search by defining specific constraints and procedures.

    In other words, some knowledge of the desired function must always be present (teleologism) for design to be implemented. Knowledge of the detailed information which confers the fucntion can allow a process of direct implementation of that information (point a). On the contrary, knowledge of the function but not of the detailed information needed in the output, and/or knowledge of the structure of the search space, will allow indirect design, with the use of intelligent search algorithms, incorporating possibly controlled random variation, and usually intelligent selection.

    Finally, if the indorect search algorithm is not used directly by the designer, but only incorporated in the genome for future use, if and when new external information will be available, then we are again in point 2, adaptation. In this case the role of the designer is only to design the algorithm, which will automatically produce the necessary output as soon as it is activated by the input of the pertinent external information.

  38. Adel (#13):

    I must confess that I had not seen your post, but thank you for the kind words.

    Regarding just so stories, ever heard of projection?

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