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We know taht evolution can be rapid, when dangers confront a species. The NY Times has an article which discusses the 50 year change in an endangered fish in the Hudson river from PCB contamination. A block of six bases was deleted from one gene to accomplish the feat. The mechanism for the gene change is not known.-http://green.blogs.nytimes.com/2011/02/18/speedy-evolution-indeed/

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BBella has been asking some searching questions about the Cambrian debate, and as they tie in with David's post about rapid evolution, I'm combining both threads.
 
DAVID: We know that evolution can be rapid, when dangers confront a species. The NY Times has an article which discusses the 50 year change in an endangered fish in the Hudson river from PCB contamination. A block of six bases was deleted from one gene to accomplish the feat. The mechanism for the gene change is not known.-http://green.blogs.nytimes.com/2011/02/18/speedy-evolution-indeed/-The article goes out of its way to specify that a rare genetic mutation allowed the species to thrive, and although this is a clear example of adaptation and natural selection at work, it's an equally clear example of evolution preserving the status quo. The Atlantic tomcod remained an Atlantic tomcod. At the risk of boring everyone to tears, let me reiterate that adaptation is not the same as innovation, i.e. the survival of a species does not lead to new species. This brings us to the next point :-D AVID: A new entry in the Cambrian debate. Plankton caused the huge jump in oxygen in the atmosphere:-http://wattsupwiththat.com/ 2/22/11-BBELLA: I read this article and it seems to say that upheavals in the earths crust (volcanic activity/earthquakes?) is what created the increase in plankton that caused more oxygen. Does this then mean when we have earthquakes and volcanic activity now more oxygen is a by-product? We sure could use more O2!-A lovely observation! What interests me, though, is that everyone seems to be concerned about what caused the jump in oxygen. Is anyone asking how a jump in oxygen could result in new species? On the not unreasonable assumption that each generation descends from the preceding generation, and bearing in mind the example of the Atlantic tomcod (or Darwin's finches if you like), why should changes in the atmosphere result in existing creatures changing into different creatures? In other words, what evidence is there that micro-evolution can, even over millions of years, lead to macro-evolution? Epigenetics may explain the former, but it certainly doesn't explain the latter. As always, I'm not questioning whether evolution happened. I'm asking for help in understanding the innovations that led to speciation.

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David's post of 26 February at 05.21 under "AI and wiring of the brain" has alerted us yet again to the astonishing complexity of the brain. I was particularly struck by a quote from Jean Goodwin ... though I don't know why the observation is limited to brain cells ... and wonder if we can't expand it. That's why I'm shifting it to this evolutionary thread. The quote:-"Each point in the brain, each brain cell, contains all the genetic information necessary to produce the entire organism. A brain cell is not a switch. It has a memory; it can be subtle. Each brain cell is like a computer. The brain is like a hundred million computers all connected together."-Can we perhaps link this to the problem of innovation in evolution (new organs, new species)? The quotation suggests to me that every living organism is a society of organisms. We are the macro-being, composed of billions of micro-beings in which each cell acts both socially and individually (like bees and ants). If each cell has a memory and can be subtle, why should not each cell or, even better, each collection of cells also have the potential for building on its memory? We know for a fact that different parts of our body ... each agglomeration of cells ... perform immensely complex tasks of which we are not even conscious; they direct themselves. Apparently groups of cells in some creatures are also able to transform themselves in response to environmental changes, whereas less "gifted" cells can't, and the species dies out. What I'm getting at is that cells themselves may come up with new combinations that result in new organs and faculties ... not by chance, as in random mutations, and not solely by reaction (epigenetics), but also by experiment. And every so often a cell or a group of cells comes up with something special, which it passes on to succeeding generations for further development. This would be neither chance nor pre-programming, but a form of creative intelligence. Instead of the selfish gene, perhaps we should talk of the intelligent cell. Is this any more far-fetched than some of the theories we're being bombarded with?

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"Each point in the brain, each brain cell, contains all the genetic information necessary to produce the entire organism."-> Can we perhaps link this to the problem of innovation in evolution (new organs, new species)? If each cell has a memory and can be subtle, why should not each cell or, even better, each collection of cells also have the potential for building on its memory? -Not really. The original cells, after the sperm and egg get together form a ball, the blastocyst. These blast or stem cells are pluripotential, and can make everything. But once they have made everything, they are generally turned off, and under control not to take off and make something uncontrolled like a cancer.There are still adult stem cells which can be called upon, but generally everything is under tight control. Yet you are correct. Every cell has the same DNA.-> And every so often a cell or a group of cells comes up with something special, which it passes on to succeeding generations for further development.-Again, no. The passing on of 'something special' has to occur in the germ cells, those guys who make sperm or egg.-> This would be neither chance nor pre-programming, but a form of creative intelligence. Is this any more far-fetched than some of the theories we're being bombarded with?-Way more far-fetched. As an author, playwright, translator, website leader, sometime poet and punner, you obviously have much more imagination than the rest of us put together! And a nod to Matt who is struggling with his novel. The germ cells have to have the mutation, the epigenetic effect, the transposition, the duplication, etc. for changes to occur. -Yet you have made an amazing point: in histology I learned to identify organs by the microscopic slice. Liver cells don't look like kidney. Lung is nothing like an adrenal gland. Lymph nodes are not anything like skin cells. And the brain can only be brain, the spinal cord has its own pattern. The body IS a community of organs, all functioning in great cooperation. A community of communities, like London and its suburbs. But everyone of these cells has the same DNA! And George tells us it all came from inorganic chemicals that fell together by chance.

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Following on from various articles David has alerted us to, I suggested a revolutionary concept: the intelligent cell which, in combination with its fellow cells, is able to innovate and pass on its innovations. The Nobel Prize was beckoning, only to be snatched from my grasp by a scientist who, unlike me, knows what he's talking about.-DAVID: These blast or stem cells are pluripotential, and can make everything. But once they have made everything, they are generally turned off, and under control not to take off and make something uncontrolled like a cancer.-I am now genuinely asking for enlightenment here, so please correct me wherever I go wrong. The common explanation for innovations is that they are caused by beneficial mutations, i.e. beneficial changes in the DNA sequence of a cell's genome. (Epigenetics may explain adaptations, but not innovations, because the species remain the same.) Such mutations are generally attributed to chance. Your own theory, however, as I understand it, is that the relevant cells were pre-programmed by a UI to produce these beneficial changes. My question, then, is why should they not be the result of intelligent experimentation by the cells themselves instead of by chance, or through pre-programming? -You may of course be right that this is the product of a runaway imagination, but let me try your patience a little further. We know already that intelligence is not confined to our human concept of it. Once upon a time, people would have laughed at the idea of intelligent animals and birds. We now know better. Your UI would be a form of intelligence which is independent of the human brain, and for which there is no evidence except the existence of mechanisms too complex to have come about by chance. Microscopic organisms show signs of intelligence which we believe to be merely mechanical, but how do we know that there isn't more to it than blind instinct? New organs and new species have come into existence somehow, and whether it's by chance or by pre-programming, the process is the same ... genetic mutation: a new sequence, survival and development via natural selection. And so let me ask again: instead of by chance (far-fetched), or through the planning of some unknown outside intelligence (equally far-fetched), why not an inside intelligence? What would be the difference in procedure and outcome between chance or pre-programmed mutations and self-initiated mutations?-(N.B. This would not, of course, solve the problem of the origin of life or of the mechanisms themselves. I am focusing only, and very narrowly, on the problem of innovations.)

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why not an inside intelligence? What would be the difference in procedure and outcome between chance or pre-programmed mutations and self-initiated mutations?-This suggestion is not really different from my theory that the UI has put into the evolutionary code, all the advanced planning for evolutionary complexity, to be tested against the geochemical change as the Earth also evolves.
> 
> (N.B. This would not, of course, solve the problem of the origin of life or of the mechanisms themselves. I am focusing only, and very narrowly, on the problem of innovations.)-See the following article, a primer on epigenetics:-http://www.the-scientist.com/2011/3/1/32/1/-These changes are inheritable. As are mutations caused by cosmic waves, or mistakes, or transposition, reduplications, or epigentic methylations, etc. But how to we suddenly have entirely new species? Darwin's guess is not supported in the fossil record as Gould has shown. Your focus on innovation is extremely important to the current discussions in science. And this is why Darwin may be totally wrong except for the modification of existing species to new environmental challenges.

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dhw: why not an inside intelligence? What would be the difference in procedure and outcome between chance or pre-programmed mutations and self-initiated mutations?-DAVID: This suggestion is not really different from my theory that the UI has put into the evolutionary code, all the advanced planning for evolutionary complexity, to be tested against the geochemical change as the Earth also evolves.-I'm still confining myself to innovation, and for me testing against geochemical changes means adaptation. You move onto epigenetics again before returning to what I see as the crucial question: How do we suddenly have entirely new species? "Darwin's guess is not supported in the fossil record as Gould has shown. Your focus on innovation is extremely important to the current discussions in science. And this is why Darwin may be totally wrong except for the modification of existing species to new environmental challenges."-If my suggestion (that innovation is powered by intelligent cells) is not really different from your theory (that cells are pre-programmed to innovate), may I take it that there is no scientific objection? If so, it frees me to pursue further non-scientific speculations. Each body is a community. In the human community, every so often an inventor comes up with something new. Ditto the body community. The human invention can only function within its social context. Ditto the body invention. A new organ, even in its most rudimentary state, must be integrated into the rest of the body: a rudimentary eye would be no use if it was disconnected! And so just as human society connects with the new invention (if it is to survive), the body society adjusts to it. And from this new invention spring further inventions. From the wheel in due course there developed a million different species of machine. From legs there developed a million different species of animal. But the machines didn't develop by chance ... each one needed intelligence: a deliberate adjustment of existing technology to produce new technology. Perhaps it's been the same with "mutations" ... that the cells themselves work on what they have, to produce something new. Far less intensively than in human society, almost certainly less self-consciously, but following the same principle.-My suggestion would actually support Darwin's theory, with the important exception of his gradualism. New inventions (self-engineeered mutations) would be sudden, even in their most rudimentary form, and there could be golden ages of inventiveness (e.g. the Cambrian Explosion ), perhaps inspired by major changes in the environment. Hence "punctuated equilibrium". But otherwise, the theory stands: a few forms to begin with, innovations that natural selection allows to survive and develop, more innovations leading to ever increasing complexity ... just like human society and human technology. The intelligent cell or community of cells therefore adapts (epigenetics), invents (self-engineered mutations), and survives while the not-so-intelligent cell communities perish (natural selection).-What, then, is the advantage of this suggestion? It doesn't solve the mystery of how "intelligent", "inventive" cells originated, but it does explain the origin of new species. Such cells also eliminate the need for chance in the assembly of complex mechanisms, which removes one layer of improbability (random but functioning mutations) from the atheist scenario. They also eliminate the need for pre-planning, since just like humans they would forge their own destiny. They invent what they invent. Out goes the anthropocentric teleology of religion, and in comes the unpredictable unfolding of history that marks just about every phase and every aspect of existence on Earth. Still too far-fetched?

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dhw: why not an inside intelligence? What would be the difference in procedure and outcome between chance or pre-programmed mutations and self-initiated mutations?
> 
> DAVID: This suggestion is not really different from my theory that the UI has put into the evolutionary code, all the advanced planning for evolutionary complexity, to be tested against the geochemical change as the Earth also evolves.
> 
> I'm still confining myself to innovation, and for me testing against geochemical changes means adaptation. You move onto epigenetics again before returning to what I see as the crucial question: How do we suddenly have entirely new species? "Darwin's guess is not supported in the fossil record as Gould has shown. Your focus on innovation is extremely important to the current discussions in science. And this is why Darwin may be totally wrong except for the modification of existing species to new environmental challenges."
> 
> If my suggestion (that innovation is powered by intelligent cells) is not really different from your theory (that cells are pre-programmed to innovate), may I take it that there is no scientific objection? -Yes, objections. It seems as though you are picking my brain with knife and fork. Let's define what we are discussing. All cells have the same DNA, but cells are differentiated into unchanging cell types for the different organs in complex eukaryotes (CE). The only cells allowed by biochemical controls in that CE to further differentiate are adult stem cells, and they are meant for repair. Thus we are left with germ cells making sperm or egg. They can mutate or change epigenetically and then can carry forward some change in the CE, usually small. If somatic cells, those of the various organs, decide to change, what we see clinically is that now you are dealing with cells out of control and creating a cancer originating in the particular organ. -So our discussion is confined to germ cells, and they can change endogenously by epigentic adaptation mechanisms, some of which I listed in my last entry, or exogenously by cosmic rays, or transcription errors, etc. It would be neat to satisfy our curiosity about macroevolution, by your fuzzy theories, but they won't work, based on the enumerated controls. We have not researched all 'junk' DNA, and as it is picked apart it reveals more and more code or control mechanisms. The 'drive to complexity' may turn up there if I am correct or DOC may be hidden in histones, around which DNA is carefully wrapped. We just don't know enough as yet. So we remain where we started: Darwin does describe microevolution, but has no answers for macroevolution. But neither do we, as yet, the skeptics.

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I asked David if there were scientific objections to my suggestion that innovations might be powered by intelligent cells.-DAVID: Yes, objections. It seems as though you are picking my brain with knife and fork. Let's define what we are discussing. All cells have the same DNA, but cells are differentiated into unchanging cell types for the different organs in complex eukaryotes (CE). The only cells allowed by biochemical controls in that CE to further differentiate are adult stem cells, and they are meant for repair. Thus we are left with germ cells making sperm or egg. They can mutate or change epigenetically and then can carry forward some change in the CE, usually small. If somatic cells, those of the various organs, decide to change, what we see clinically is that now you are dealing with cells out of control and creating a cancer originating in the particular organ. -So our discussion is confined to germ cells, and they can change endogenously by epigenetic adaptation mechanisms, some of which I listed in my last entry, or exogenously by cosmic rays, or transcription errors, etc. It would be neat to satisfy our curiosity about macroevolution, by your fuzzy theories, but they won't work, based on the enumerated controls. We have not researched all 'junk' DNA, and as it is picked apart it reveals more and more code or control mechanisms. The 'drive to complexity' may turn up there if I am correct or DOC may be hidden in histones, around which DNA is carefully wrapped. We just don't know enough as yet. So we remain where we started: Darwin does describe microevolution, but has no answers for macroevolution. But neither do we, as yet, the skeptics.-My apologies for making a meal of your grey cells, but thank you for this comprehensive answer, the sting of which lies scorpion-like in the tail. It appears that no cells are capable of major beneficial innovations, but no-one can explain macroevolution. At least that puts me in good company! I agree with you that my suggestion ... I wouldn't dare call it a theory ... is fuzzy (nice word!) but is it any fuzzier than the proposition that an unknown and unknowable super-intelligence pre-programmed an as yet unknown mechanism to produce new organs and species?
 
However, you have a more concrete proposition, if I've understood you correctly: the innovative mechanism lies in 'junk' DNA, or possibly in histones, and presumably in the germ cells, which makes perfect sense anyway, since an existing creature is hardly likely suddenly to sprout a new organ. Initially in your post you confine the endogenous changes to epigenetic adaptation (and suggest that exogenous changes are deleterious?) though even this can imply a form of intelligence. Many organisms fail to adapt, so in those that do, there is some sort of superiority inherent in the mechanism. But ... if my interpretation is correct ... you also believe that this same mechanism is pre-programmed to produce innovations when conditions are right. So please indulge me in my fuzziness, my ignorance, and also my repetitiveness, and let me ask again: what would be the difference in procedure and outcome between, on the one hand, a UI pre-programming a mechanism within the germ cells to produce the innovations and, on the other, the same mechanism responding to the right conditions and producing the innovations on its own intelligent, inventive initiative?

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> However, you have a more concrete proposition, if I've understood you correctly: the innovative mechanism lies in 'junk' DNA, or possibly in histones, and presumably in the germ cells, which makes perfect sense anyway, since an existing creature is hardly likely suddenly to sprout a new organ. But ... if my interpretation is correct ... you also believe that this same mechanism is pre-programmed to produce innovations when conditions are right. What would be the difference in procedure and outcome between, on the one hand, a UI pre-programming a mechanism within the germ cells to produce the innovations and, on the other, the same mechanism responding to the right conditions and producing the innovations on its own intelligent, inventive initiative?-If the drive to complexity, to advance evolution, is part of the genome complex, and is coded in advance, then we can imagine that it is in direct drive, and must happen, but is coded in bush form, the pattern of the 'tree' we see,. The other way, your descripion, is under less control, relies more on itself, and is more likely to make mistakes, and automatically will be in bush form. However, we do not know if the evolution of the Earth, adding water, adding plasmatismals, adding atmosphere, having continental plate movement and subduction, etc. is under control or on its own. If on its own even a very guided evolution may make mistakes, not timing itself with geologic changes. Since I propose a UI, I think my proposal for the evolutionary mechanism is more likely. But either way, evolution gets to where we are.

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I'm not sure if this video is rellevant to the discussion here,
it's an example of how something completely new can evolve:-http://www.bbc.co.uk/news/uk-wales-12615888-Research in Oxford has shown that the trumpet of the Daffodil
is a newly evolved flower part - neither petals nor stamen.

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GPJ

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it's an example of how something completely new can evolve:
> 
> http://www.bbc.co.uk/news/uk-wales-12615888
> 
> Research in Oxford has shown that the trumpet of the Daffodil
> is a newly evolved flower part - neither petals nor stamen.-What is described in the video certainly shows evolution by the daffodil, but not the 'how', although I suspect that is not the way George meant the use of the word 'how'. I wonder, was there any purpose in the additional part or was there a necessary environmental pressure to which this is a response? Or did it happen for no particular reason, an unrequired change?

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GEORGE: I'm not sure if this video is rellevant to the discussion here,
it's an example of how something completely new can evolve:-http://www.bbc.co.uk/news/uk-wales-12615888-Research in Oxford has shown that the trumpet of the Daffodil
is a newly evolved flower part - neither petals nor stamen.-Thank you for this, George. Unfortunately, my computer won't show it unless I download some new software, and when I tried to do so, it warned me that my anti-virus software might be disabled, the Earth might turn a somersault, and the solar system might collapse. I suspect, from David's response, that the daffodil's trumpet won't summmon up a final judgement on this issue, but I wonder what you yourself think.

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Sounds like you've stopped evolving. -Here's more examples of evolution in action, gleaned from facebook.-More brain-controlling zombie ant parasitic fungi - cordyleps-http://scienceblogs.com/neurophilosophy/2011/03/return_of_the_brain-manipulating_zombie-ant_parasitic_fungi.php-This is just a bit of fun, another video:-http://www.milkmatters.co.uk/cats/-Cats with thumbs!

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GPJ

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Sounds like you've stopped evolving. 
> 
> Here's more examples of evolution in action, gleaned from facebook.
> 
> More brain-controlling zombie ant parasitic fungi - cordyleps
> 
> http://scienceblogs.com/neurophilosophy/2011/03/return_of_the_brain-manipulating_zombie... 
> This is just a bit of fun, another video:
> 
> http://www.milkmatters.co.uk/cats/
> 
> Cats with thumbs!-Goerge: the cats are really funny ,but I appreciate the ant-parasitc fungi site. I have shown one of those earlier here. Just fascinating. thanks.

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GEORGE (to dhw): Sounds like you've stopped evolving.-Technologically stuck, biologically going backwards.-GEORGE: Here's more examples of evolution in action, gleaned from facebook.
More brain-controlling zombie ant parasitic fungi ... cordyleps***-http://scienceblogs.com/neurophilosophy/2011/03/return_of_the_brain-manipulating_zombie...
 
***Cordyceps, George. A slight cordy-leps in concentration there. Ah, revenge for the evolutionary dig!-You and David are developing an unhealthy obsession with zombie ants. David, was the cordyceps pre-corded? -GEORGE: This is just a bit of fun, another video:-http://www.milkmatters.co.uk/cats/-Cats with thumbs!-Hilarious! Many thanks.

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> GEORGE: Here's more examples of evolution in action, gleaned from facebook.
> More brain-controlling zombie ant parasitic fungi ... cordyleps***
> 
> http://scienceblogs.com/neurophilosophy/2011/03/return_of_the_brain-manipulating_zombie... You and David are developing an unhealthy obsession with zombie ants. David, was the cordyceps pre-corded? -Here's more info on zombie ants and their fungus controllers. Probably enough material for a chiller- thriller scary movie:-http://www.physorg.com/news/2011-03-parasitic-fungi-ants-zombies.html

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DAVID: If the drive to complexity, to advance evolution, is part of the genome complex, and is coded in advance, then we can imagine that it is in direct drive, and must happen, but is coded in bush form, the pattern of the 'tree' we see,. The other way, your description, is under less control, relies more on itself, and is more likely to make mistakes, and automatically will be in bush form. However, we do not know if the evolution of the Earth, adding water, adding plasmatismals, adding atmosphere, having continental plate movement and subduction, etc. is under control or on its own. If on its own even a very guided evolution may make mistakes, not timing itself with geologic changes. Since I propose a UI, I think my proposal for the evolutionary mechanism is more likely. But either way, evolution gets to where we are.-This exchange is probably far more interesting and fruitful for someone who has not made up his mind than for someone who has, but I do hope you will stay with me. Your comment that "we do not know if the evolution of the Earth [...] is under control or on its own" is just as applicable to the evolution of life, and if my proposal (an intelligent mechanism within the germ cells that produces innovations) is less controlled and more self-reliant, that certainly doesn't make it either more or less likely. Even if you believe in a UI, the "likelihood" will depend on whether you think the UI did or did not start out with a plan. I'm surprised that you link direct drive to a bush form. As I have no sense of direction, that is frequently the pattern of our excursions, but by direct drive I would understand the shortest possible route. The bush seems to me to support the suggestion of no plan or ... as in my case ... bad plan, or plan gone wrong. -Still in the context of this discussion, I was struck by an unrelated but, in the wider context, extremely relevant comment in the article on consciousness: -"One of Damasio's favourite words is "image", which gets 34 entries in the book's index. Images are the basis of first-person being and hence, according to him, consciousness. Yet at the same time they are for the most part not experienced at all, and unconscious minds, such as those of insects, are seething with them."-I don't want to get side-tracked by attempting to define intelligence or consciousness (though we've had long discussions on this subject), but we do not actually know how intelligent/conscious other forms of life are. However, we do know that insects are capable of building astoundingly intricate structures and performing tasks that require detailed planning. Think of termite mounds. I do not believe that the first termites were shown how to do it by clever old Adam. No matter what evolutionary stages their mound-building went through, each one was decided by the termites themselves. Within our bodies are even more complex structures, and many of them function independently of our own conscious minds. If all life is descended from a few simple forms, then those structures (which contribute to what you call the 'drive to complexity') have resulted from innovations within organisms. We are an assembly of such structures and, as with insects, we do not know how intelligent is the internal mechanism that "invented" them. All three of our general options ... (1) pre-planning by a UI, (2) no planning by a UI, (3) no UI ... take evolution "to where we are". The question is the degree of chance involved. My suggestion increases it in relation to (1), and reduces it in relation to (2) and (3).

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However, we do not know if the evolution of the Earth, adding water, adding plasmatismals, adding atmosphere, having continental plate movement and subduction, etc. is under control or on its own.-Sometimes my typing doesn't listen to my brain. In the above it should be PLANETISMALS. Sorry. -> I'm surprised that you link direct drive to a bush form. As I have no sense of direction, that is frequently the pattern of our excursions, but by direct drive I would understand the shortest possible route.-No, the 'bush' comment is due to direct observation. the so-called tree of life is really a bush. Look at it. Why that form? The organisms have epigenetic responses to many threats and respond to htem, creating the bush.- 
> Still in the context of this discussion, I was struck by an unrelated but, in the wider context, extremely relevant comment in the article on consciousness: 
 
> Think of termite mounds. I do not believe that the first termites were shown how to do it by clever old Adam. No matter what evolutionary stages their mound-building went through, each one was decided by the termites themselves. Within our bodies are even more complex structures, and many of them function independently of our own conscious minds. -We don't know how those termite activities arose. Possibly invented by the bugs, and by the way both of us have seen those structures in Africa. Humongous! But we also don't know how instinct is carried: is it coded in the DNA? Was it pre-coded? That sounds like a stretch. All the animals in the ant family do this burrowing. Some ancestor started it and it became automatic instinct. We literally don't know how this works. Consciousness? No way. It was coded in by epigenetics and carried forward genetically.-As far as our automatic function go, do you really want to have to think to breathe? But each of us can become conscious of our breathing. Renal function hepatic function, oxygen exchange all go on automatically. Heart beating. I can take my pulse, but if I get very quiet and concentrate I can feel my body pulse.-Those functions have no relation to consciousness. I don't really know why you related them to the consciousness discussion. They sure suggest design to me.

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dhw: I'm surprised that you link direct drive to a bush form. [...] By direct drive I would understand the shortest possible route.-DAVID: No, the 'bush' comment is due to direct observation. The so-called tree of life is really a bush. Look at it. Why that form? The organisms have epigenetic responses to many threats and respond to them, creating the bush.-A misunderstanding. I'm not disputing the bush pattern. I'm disputing your identification of the bush with a direct drive to what you regard as the end product ... humans. One would have expected pre-planning to be direct, but direct is NOT bush-form. As you rightly pointed out, my proposal (without pre-planning) "automatically will be in bush form". One up, I think, for my proposal.-DAVID: We don't know how those termite activities arose. Possibly invented by the bugs [...] But we also don't know how instinct is carried: is it coded in the DNA? Was it pre-coded? That sounds like a stretch. All the animals in the ant family do this burrowing. Some ancestor started it and it became automatic instinct. -Exactly. It began with an intelligent innovation which was passed on. I'm using this as an analogy for all evolutionary innovations: within the organisms themselves is a mechanism capable of invention, leading to new organs and new species. That mechanism has to be there. The question is whether it's 1) a machine pre-programmed by a UI (your version), 2) has some form of "intelligence" which ... like the ancestral mound-builder ... invents and passes on its invention (my suggestion), or 3) has no "intelligence" of its own and invents solely by way of random mutations (atheist version).
 
DAVID: We literally don't know how this works. Consciousness? No way. It was coded in by epigenetics and carried forward genetically.-As I said before, I don't want to get sidetracked into definitions of intelligence/ consciousness. Just as your UI would be a form of intelligence we don't understand, I'm using the word because we don't have any other. As for epigenetics, it may explain adaptation, but not (so far) innovation.-DAVID: Those [bodily] functions have no relation to consciousness. I don't really know why you related them to the consciousness discussion. They sure suggest design to me.-Another misunderstanding. I quoted the passage about consciousness because of its assumption that insects are unconscious. I used it to draw the analogy described above between the termite mound and the complex structures in our bodies. The outcome of the three "theories" is the same, and of course we're still faced with the problem of the origin of the mechanism, but whether the latter was designed or not, I think my suggestion provides a more convincing explanation of evolution's comings and goings and general meanderings (your bush pattern), and it reduces the Darwinian dependence on chance (the sheer luck of random mutations) for innovations. It is also a challenge to the anthropocentric interpretation of evolution, which may be why you don't like it!

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> A misunderstanding. I'm not disputing the bush pattern. I'm disputing your identification of the bush with a direct drive to what you regard as the end product ... humans. One would have expected pre-planning to be direct, but direct is NOT bush-form. As you rightly pointed out, my proposal (without pre-planning) "automatically will be in bush form". One up, I think, for my proposal.
> -Not one-up. You are theorizing completely. I have presumed a directed pattern. then I look and see the adaptation abilities with directed allow for any sudden environmedtal or preditory dangers. A wise director made this kind of direct plan. Wa la! bush. Your bush comes from a diffferent source and mechanism, and the bushes will be similar in overall appearance and different in internal pattern. We are all even! 
> 
> As I said before, I don't want to get sidetracked into definitions of intelligence/ consciousness. -My poodle is very intelligent. He is conscious and aware of what he needs to do, or keep from doing, like peeing on the rug. But he is not 'aware that he is aware'. Neither were the termites who took to build big mounds. My fire ants, no thanks to Africa, make very tiny mounds. They are tiny, termites are big, so big mounds. Those insects have no consciousness, but like the poodle are conscious and aware of proper things to do, by instinct.
> 
> Another misunderstanding. I quoted the passage about consciousness because of its assumption that insects are unconscious. It is also a challenge to the anthropocentric interpretation of evolution, which may be why you don't like it!-Insects are conscious, as I stated above. The anthropocentric interpretation of evolution is from the conclusion that DNA and its layers of control cannot have been developed by chance. There is no code we know of within human endeavor that is not created by intellect. This code in DNA is extremely efficient, transmits extrordinary amounts of information, and information cannot be created by chance. Try monkeys, a typewriter and a Shakespeare sonnet.

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I have suggested that innovations may be produced by internal mechanisms that have some form of intelligence of their own, as opposed to being programmed by a UI to lead evolution to humanity, or being thrown up by random mutations.-DAVID: You are theorizing completely. I have presumed a directed pattern. Then I look and see the adaptation abilities with directed allow for any sudden environmental or predatory dangers. A wise director made this kind of direct plan. Wa la! bush. Your bush comes from a different source and mechanism, and the bushes will be similar in overall appearance and different in internal pattern. We are all even!-I am indeed theorizing, and your presuming carries no more authority than my theorizing. My focus is on innovation, not adaptation, but it makes no difference here, as I'm NOT excluding your "wise director". We're talking about the SAME bush, but your mechanism is pre-programmed and mine has a degree of autonomy ... see below.
 
DAVID: My poodle is very intelligent. He is conscious and aware of what he needs to do. [...] But he is not 'aware that he is aware'. Neither were the termites who took to build big mounds. [...] Those insects have no consciousness, but like the poodle are conscious and aware of proper things to do, by instinct.-I'm happy to accept the oxymoron of unconscious consciousness. Using your terminology (termitology?), here is my version: somewhere within DNA lurks a mechanism ... perhaps deliberately created by a UI ... which, like your poodle and my termites, is "very intelligent", has "no consciousness", but is conscious and able to invent every so often a new, inheritable organ (just as the ancestor termite invented the first mound). Your version (correct me if I'm wrong): somewhere within DNA lurks a mechanism ... deliberately created by a UI ... which, unlike your poodle and my termites, has no intelligence or unconscious consciousness, but has been programmed to invent every so often a new, inheritable organ. Same result: new organs, new species, the evolutionary bush.-DAVID: Insects are conscious, as I stated above. The anthropocentric interpretation of evolution is from the conclusion that DNA and its layers of control cannot have been developed by chance. There is no code we know of within human endeavor that is not created by intellect. This code in DNA is extremely efficient, transmits extraordinary amounts of information, and information cannot be created by chance. Try monkeys, a typewriter and a Shakespeare sonnet.-I have frequently mounted precisely the same argument against chance, and my suggestion encompasses the possible deliberate creation by a UI. Your anthropocentric version, as opposed to my let's-see-what-it-comes-up-with version, is therefore derived solely from your presumption of a pattern directed towards the goal of humanity. I admit that my suggestion is pure speculation, but so is yours. (Of course, I think mine fits in far better with the higgledy-piggledy, hello-goodbye, where's-this-leading evolutionary bush, not to mention the UI's apparent absence of interest in what you believe to be the main object of his attentions. But hey, I'll still grant your speculation equality with mine!)

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I admit that my suggestion is pure speculation, but so is yours. (Of course, I think mine fits in far better with the higgledy-piggledy, hello-goodbye, where's-this-leading evolutionary bush, not to mention the UI's apparent absence of interest in what you believe to be the main object of his attentions. But hey, I'll still grant your speculation equality with mine!)-I think we are close enough to each other to agree that DNA seems to have a mechanism for increasing complexity, however it got there. Gould's opinion that evolution could only work in one direction because it started with such simple bacteria makes no sense. Bacteria started it and are still here. With that kind of success, the biggest biomass on Earth, why bother with complexity?

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> I think we are close enough to each other to agree that DNA seems to have a mechanism for increasing complexity, however it got there.-Latest discoveries in evolution showing deletion of non-coding segments of DNA evolved humans away from other primates. Regulators of genes are removed for this to occur.-http://www.physorg.com/news/2011-03-dna-human.html

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> Latest discoveries in evolution showing deletion of non-coding segments of DNA evolved humans away from other primates. Regulators of genes are removed for this to occur.
> 
> http://www.physorg.com/news/2011-03-dna-human.html-In all the major science blogs I follow this is the story of the week. The article in Nature has been widely accepted as a carefully done, elegent study. The researchers were able to show that deletion of long segments of modifying DNA, that is, non-gene segments that controlled gene expression, possitively or negatively, enhanced human development from the common primate ancestor of six million years ago. Thus mutations may make changes, as originally proposed by Neo-Darwinism, but a deletion in the so-called 'junk DNA' can also accomplish major changes, perhaps more rapidly than mutations can. Most mutations are deleterious, some neutral and a few are helpful. Using mutations alone reasonably might take much longer than six million years. Whatever mechanism caused the deletions to occur, they seemed to have speeded the evolutionary developments that were identified: genital and neural/ brain. Wow! Lose DNA and get a much bigger brain!

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This seems to be the same research-http://www.nature.com/news/2011/110309/full/news.2011.148.html-But presented more popularly: "How the penis lost its spikes".-None of this is contrary to the modern understanding of evolution,
combining Darwin's insights with Mendel and all the discoveries in 
molecular genetics over the last hundred years.

--
GPJ

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I have suggested that innovations may be produced by internal mechanisms that have some form of intelligence of their own, as opposed to being programmed by a UI to lead evolution to humanity, or being thrown up by random mutations.
> 
> DAVID: You are theorizing completely. I have presumed a directed pattern. -The following looks like directed pattern. Slime mold single-celled organisms, can group together, form a stalk with protein seen in multicellular organisms. One research person comments that genes can be adapted to new functions, and multicellularity may have been an easy jump! Looks like directed evolution, pre-planning, to me:-http://www.the-scientist.com/news/display/58047/

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Insects can have rapid evolution, after invasion by Ricketsia ( a tiny form of bacteria):-http://www.the-scientist.com/news/display/58109/

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> I'm still confining myself to innovation, and for me testing against geochemical changes means adaptation. You move onto epigenetics again before returning to what I see as the crucial question: How do we suddenly have entirely new species? "Darwin's guess is not supported in the fossil record as Gould has shown.-There is a marvelous old video starring Eldridge and Gould on puntuated equilibrium with an explanation of their version of the theory: stasis and then a burst of new branching, bush style over 50-100 thousand years, on blog Sandwalk, today.-http://sandwalk.blogspot.com/

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DAVID: There is a marvelous old video starring Eldridge and Gould on punctuated equilibrium with an explanation of their version of the theory: stasis and then a burst of new branching, bush style over 50-100 thousand years, on blog Sandwalk, today.-http://sandwalk.blogspot.com/-I find the argument for punctuated equilibrium very convincing, but in the context of innovations and the development of new species, evolutionists always talk of thousands of years as being a short period. Of course it is, by comparison with 2 billion years or 3.7 billion years of life (whichever is correct), but thousands of years cover hundreds of generations, and I find something odd about this. Perhaps you or someone else can clarify the thinking for me by commenting on what follows:-Epigenetics explains adaptation, and you gave us an example not long ago of a fish which over a period of just a few years adapted to a dramatic environmental change. That makes perfect sense to me. Without swift adaptation, the species would have died out. But the species remained the same. And so my first question is whether there is any evidence that adaptation can lead to NEW species as opposed to variations on existing species. In this context, it's also worth noting that "bursts of new branching" are often associated with catastrophes like volcanic eruptions and meteorite collisions, but these are also dramatically sudden, and again survival would depend on swift adaptation. -Secondly, Darwinism presumes that innovations are caused by random mutations. A mutation has to take place within an existing creature, and although it may be passed on to subsequent generations, it will not survive unless it conveys some kind of advantage (= natural selection). Why, then, would it take thousands of years (hundreds of generations) for new species to develop? Darwin's explanation of the absence of "intermediate links" was the imperfection of the geological record. Although it's claimed that links have been found (e.g. the horse, archaeopteryx), they are few and far between and open to different interpretations. Besides, who knows which of today's facts may turn into tomorrow's fictions? Is it not possible that the still "imperfect" geological record might indicate that there are no "intermediate links", and that new species can form over a much shorter period ... perhaps, like the adapting fish, just a few generations, as innovations "bed in"? Is there evidence to disprove such a theory? In other words, I'm looking for a parallel between swift adaptation and swift innovation, on the grounds that in both cases the changes must begin with one generation and must function straight away in order to survive.

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A new botanical report suggests a kind of punctuated equilibrium in flowering plants: -http://www.sciencedaily.com/releases/2011/03/110329134343.htm

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DAVID: A new botanical report suggests a kind of punctuated equilibrium in flowering plants:
 
http://www.sciencedaily.com/releases/2011/03/110329134343.htm-In addition to the evidence for punctuated equilibrium, this seems to me once more to point to intelligent and inventive mechanisms within the organisms themselves ... my counter to David's theory of pre-programming: -"Just as a company creates new, better versions of a product to increase market share and pad its bottom line, an international team of researchers led by Brown University has found that plants tinker with their design and performance before flooding the environment with new, improved versions of themselves."-"Smith believes some triggers for the speciation explosion could have been internal, such as building a better flower or learning how to grow faster and thus outcompete other plants. The winning edge could also have come from the arrival of pollinating insects or changes in climate. The team plans to investigate these questions."-It's the reference to "internal triggers" that particularly intrigues me. I'd suggested an analogy with the intelligence of insect colonies, and by coincidence yesterday's Guardian carried a tiny article:-"Bees are taking emergency measures to protect their hives from pesticides, according to experts. The creatures are sealing up hive cells full of pollen to put them out of use and protect the rest from their contents. The pollen in the sealed-up cells has been found to contain much higher levels of pesticides and other potentially harmful chemicals than the pollen stored in neighbouring cells, which is used to feed young bees."-This will not, of course, lead to innovation, but my comparison here is with intelligent cooperation WITHIN organisms, which may lead to adaptations or innovations. I'm fully aware that such inventive, intelligent mechanisms are highly unlikely to come into existence by chance. My tentative suggestion is that in the course of evolution they do not follow a pre-ordained programme (David's version) and they do not depend on random mutations (the Darwinian version), but themselves initiate and develop changes from within.

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> This will not, of course, lead to innovation, but my comparison here is with intelligent cooperation WITHIN organisms, which may lead to adaptations or innovations. I'm fully aware that such inventive, intelligent mechanisms are highly unlikely to come into existence by chance. My tentative suggestion is that in the course of evolution they do not follow a pre-ordained programme (David's version) and they do not depend on random mutations (the Darwinian version), but themselves initiate and develop changes from within.-In this article bacteria create a new chemical way to methylate DNA and become resistant to seen classees of antibiotics. This is epigenetics at its best. You misunderstand my 'pre-ordained' theory of evolution. Part of the theory that evolution has built in directionality includes giving organisms the ability to protect themselves from sudden environmental changes within the framework of driving evolution to create humans. It is quite clear that epigenetic changes are a powerful evolutionary tool.-http://www.physorg.com/news/2011-04-bacteria-evolved-unique-chemical-mechanism.html

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DAVID: In this article bacteria create a new chemical way to methylate DNA and become resistant to seen classes of antibiotics. This is epigenetics at its best. You misunderstand my 'pre-ordained' theory of evolution. Part of the theory that evolution has built in directionality includes giving organisms the ability to protect themselves from sudden environmental changes within the framework of driving evolution to create humans. It is quite clear that epigenetic changes are a powerful evolutionary tool.-http://www.physorg.com/news/2011-04-bacteria-evolved-unique-chemical-mechanism.html-Fascinating stuff, as is your later post on possible communications between bacteria, though it was much too technical for me and I'm grateful for your summary. I would regard it as supporting the suggestion that cells may have an intelligence of their own that is responsible for innovations.-I have absolutely no problem with the idea that the mechanisms of epigenetics enable organisms to protect themselves against environmental changes, but firstly these mechanisms, as far as we know, do not change organisms into different species ... they result in adaptations not innovations. Secondly, it's your preordained "framework of driving evolution to create humans" that I find unconvincing in the light of the higgledy-piggledy evolutionary bush of species which come and go. Adaptation to change does not indicate that bacteria are preordained to evolve into humans! On the contrary, their being "programmed" to remain as bacteria suggests to me that they are an end in themselves.

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I have absolutely no problem with the idea that the mechanisms of epigenetics enable organisms to protect themselves against environmental changes, but firstly these mechanisms, as far as we know, do not change organisms into different species ... they result in adaptations not innovations. Secondly, it's your preordained "framework of driving evolution to create humans" that I find unconvincing in the light of the higgledy-piggledy evolutionary bush of species which come and go. Adaptation to change does not indicate that bacteria are preordained to evolve into humans! On the contrary, their being "programmed" to remain as bacteria suggests to me that they are an end in themselves.--If the are 'programmed' to remain bacteria, then evolution between species, and in particular from vastly less complicated to vastly more complicated would not occur. What I find even more intriguing is the method of their communication, which directly ties one of the four basic forces directly to life. i.e. Electromagnetism.

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Secondly, it's your preordained "framework of driving evolution to create humans" that I find unconvincing in the light of the higgledy-piggledy evolutionary bush of species which come and go. Adaptation to change does not indicate that bacteria are preordained to evolve into humans! On the contrary, their being "programmed" to remain as bacteria suggests to me that they are an end in themselves.-BUT, view it a different way: bacteria are very successful, as shown that they have survived for 3.6 billion years or so. But somehow or other they became multicellular also, and that set of organisms became more and more complex. They invented sex which made the dispersal of various types of organisms even more complex and more varied as a wider range of DNA became more and more mixed together. From this process humans arrived. Some branches of organisms ran out of steam and stopped but stayed around in stasis. Others, less successful, diappeared completely. But humans did arrive, and that suggests directionality built into evolution. See Michael Denton's book : Nature's Destiny, 1998. No one has said that directionality has only one road to follow. As Yogi Berra once said, "if you come to a fork in the road, take it!"

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Except that we have no clear examples of a single celled organism, or group there of, communicating with each other and deciding to form together to become a multi-cellular organism... and on and on. Yes, this accounts for variety, no, it does not account for speciation.

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Except that we have no clear examples of a single celled organism, or group there of, communicating with each other and deciding to form together to become a multi-cellular organism... and on and on. Yes, this accounts for variety, no, it does not account for speciation.-Nothing proves speciation is a result of chance, in fact, we have no idea how it occurs.

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> Yet you have made an amazing point: in histology I learned to identify organs by the microscopic slice. Liver cells don't look like kidney. Lung is nothing like an adrenal gland. Lymph nodes are not anything like skin cells. And the brain can only be brain, the spinal cord has its own pattern. The body IS a community of organs, all functioning in great cooperation. A community of communities, like London and its suburbs. But everyone of these cells has the same DNA! And George tells us it all came from inorganic chemicals that fell together by chance.-How epigenetics help the different kinds of cells (about 200) stay the same and maintain their identity:-http://www.the-scientist.com/article/display/58007/

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Darwin's finches can change year by year, but are still finches. Epigentics in action:-http://www.nytimes.com/2014/08/05/science/in-darwins-footsteps.html?emc=edit_th_20140805&nl=todaysheadlines&nlid=60788861&_r=0

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We know that evolution can be rapid, when dangers confront a species. The NY Times has an article which discusses the 50 year change in an endangered fish in the Hudson river from PCB contamination. A block of six bases was deleted from one gene to accomplish the feat. The mechanism for the gene change is not known.-
James Shapiro is coming out with his book on his approach to evolution. Don't expect Darwin!!-http://www.amazon.com/Evolution-View-Century-James-Shapiro/dp/0132780933/ref=sr_1_1?ie=UTF8&s=books&qid=1308156663&sr=1-1

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