(2017-10-23, 06:34 PM)stephenw Wrote: [ -> ]I am not qualified to expound on the subject - but I think you are not aware of the context of Bioinformatics. DNA is just one part of an entire communication system. No one part of bio-communication does it all; and any change to one means they may all are affected. Epigenetic changes are defined as being outside of changes to DNA codon chemistry. You will typically see me refer to DNA/RNA/Ribosomes as a grouping to designate the subject. In my limited understanding, it is in the decoding process of RNA transcription and rDNA where epigenetics communicate with the functional channels that carry signals for protein building.
I read into your responses the materialist worldview where chemistry runs the show. This is not the case, as communication runs the show and presents instructions. The reverse engineering doesn't start with the mechanical "gears" - but with goal-oriented messages. Messages are measured in information theory and in linguistics - neither which are covered in chemical bonding studies. DNA is hardware beloved by materialistic contexts. Behavior, symbolic representation and epigenetic signals are functional as software.
Mind makes a difference. Selections made by minds change real-world probabilities, including adaptive behavior.
The "Weismann barrier" is the fundamental barrier to information transfer from phenotype back to into genotype, or in other words, significant hereditary information moves only from germline cells to somatic cells not the reverse. Significantly, creatively, violating this principle means the impossible requirements for both a reverse-engineering calculation from needed body/behavioral change to the corresponding required DNA changes plus an actual physical mechanism for the results of the calculation to be somehow transformed into the actual DNA changes in gametes.
From a review of Transformations of Lamarckism, at
https://dash.harvard.edu/bitstream/handl...sequence=1 :
Quote:"None of the contributors to ToL defend the kind of hereditary mechanism rejected by Weismann but
some expand Lamarckian inheritance to include all forms of ‘soft inheritance.’ Gissis and Jablonka (#10,
105) adopt Mayr’s definition of soft inheritance as “a gradual change of the genetic material itself, either by
use or disuse, or by some internal progressive tendencies, or through the direct effect of the environment,”
although it is clear that they do not limit the concept to ‘gradual’ changes. Soft inheritance is an elastic
concept but includes mechanisms of cellular epigenetic inheritance such as DNA methylation, self-sustaining
regulatory loops, structural templating, and RNA interference (Jablonka #21).....It seems a matter of personal
preference whether these mechanisms are seen as Lamarckian."
I don't think any of the newly understood mechanisms of "soft inheritance" (including horizontal gene transfer) break the Weismann barrier or incorporate the kind of creativity observed in actual macroevolution. It seems to me that to be credible the "new Lamarckians" would need to show in detail how these "soft inheritance" mechanisms can creatively invent intricate complicated self referent irreducibly complex biological machines like the bacterial flagellum. There seems to be an irreducible requirement for the operation of mind, not mechanism.
Perhaps we agree on this, but disagree on what the nature of that mind must be.
It's interesting that there isn't such a drastic separation between somatic cells and gametes in plants, so that there can be apparent violations of the Weismann barrier in plants (as opposed to animals). At
http://www.frozenevolution.com/weismann-barrier:
Quote:"Because a flower can be formed in a plant through differentiation from somatic tissues, acquired traits can be inherited in plants. For example, if cells better adapted to growth in a certain temperature regime come, in time, to predominate in the tissues of woody species, this property can be transferred to further generations through the seeds from flowers formed by differentiation of these tissues . However, it should be recalled that this is not Lamarckian evolution, as adaptation of cells to a certain temperature regime did not occur through adaptive mutations, which would occur as a reaction to conditions or to the behaviour of the organism, but through the Darwinistic mechanism of survival of those tissue cells (or branches of the tree) that are best adapted to the local environment as a consequence of a random change, somatic mutation, somatic recombination or epigenetic change."
Note that "random change, somatic mutation, somatic recombination or epigenetic change" are all random with respect to fitness.
(2017-10-23, 08:49 PM)nbtruthman Wrote: [ -> ]The "Weismann barrier" is the fundamental barrier to information transfer from phenotype back to into genotype, or in other words, significant hereditary information moves only from germline cells to somatic cells not the reverse. Significantly, creatively, violating this principle means the impossible requirements for both a reverse-engineering calculation from needed body/behavioral change to the corresponding required DNA changes plus an actual physical mechanism for the results of the calculation to be somehow transformed into the actual DNA changes in gametes.
I'm not sure what you're saying about the status of the Weismann barrier, but plants and some animals violate it:
https://en.wikipedia.org/wiki/Weismann_barrier
~~ Paul
(2017-10-23, 08:56 PM)Paul C. Anagnostopoulos Wrote: [ -> ]I'm not sure what you're saying about the status of the Weismann barrier, but plants and some animals violate it:
https://en.wikipedia.org/wiki/Weismann_barrier
~~ Paul
I pointed out how some plants can violate the Weismann barrier. Relatively simple animals like sponges and corals apparently are also exceptions to the rule and do it in roughly the same way, utilizing
stem cell lineages that originate both body cells and gametes. But the mechanism is still random with respect to fitness variations culled by natural selection, with all the limitations of that mechanism. I think the Weismann barrier is still believed to apply to the vast majority of multicellular animals.
(2017-10-23, 11:57 PM)nbtruthman Wrote: [ -> ]I pointed out how some plants can violate the Weismann barrier. Relatively simple animals like sponges and corals apparently are also exceptions to the rule and do it in roughly the same way, utilizing stem cell lineages that originate both body cells and gametes. But the mechanism is still random with respect to fitness variations culled by natural selection, with all the limitations of that mechanism. I think the Weismann barrier is still believed to apply to the vast majority of multicellular animals.
The Wiki article suggests that it may not always be random with respect to fitness.
I won't be surprised if we find this happening in other animals.
~~ Paul
(2017-08-20, 02:41 AM)Kamarling Wrote: [ -> ]For example, I agree with Marshall that consciousness goes all the way down and is, indeed, universal. So the intelligence is in the system right down to the cell level thus there is no (or limited) need to invoke an outside agency. But I agree with Meyer when he says that however you imagine the intelligence, it is still Intelligent Design. In other words, I think he is suggesting that he is not pushing God the designer even though he personally believes that to be the case.
OK - I am back, now that Steve001 has kindly removed his remark about Alex and I from his posts!
I am just reading J Scott Turner's book, which also refers to consciousness (he prefers to call it cognition) going all the way down.
Basically I agree with that idea, but I don't think those who talk that way, quite realise how significant it is - or perhaps they do, but are trying to pick their way through the minefield of academic taboos in this area! When I have finished his book, I am going to try to contact him.
Conventionally consciousness is supposed to be an epiphenomenon of the brain, so accepting it plays a role 'all the way down' is a huge step.
David
(2017-10-23, 08:49 PM)nbtruthman Wrote: [ -> ]From a review of Transformations of Lamarckism, at https://dash.harvard.edu/bitstream/handl...sequence=1 :
I don't think any of the newly understood mechanisms of "soft inheritance" (including horizontal gene transfer) break the Weismann barrier or incorporate the kind of creativity observed in actual macroevolution. It seems to me that to be credible the "new Lamarckians" would need to show in detail how these "soft inheritance" mechanisms can creatively invent intricate complicated self referent irreducibly complex biological machines like the bacterial flagellum. There seems to be an irreducible requirement for the operation of mind, not mechanism.
Perhaps we agree on this, but disagree on what the nature of that mind must be.
Note that "random change, somatic mutation, somatic recombination or epigenetic change" are all random with respect to fitness.
Thanks again for a well thought-out response. Ibid from the review you posted:
Quote: Weismann and his followers rejected the inheritance of acquired characters and promoted the allsufficiency of natural selection. Their strident language provoked a strong response from Darwinian pluralists and from others skeptical of the explanatory power of natural selection. Romanes (1888) wrote “The consequence of this kind of writing is that anyone who, like myself, still retains unmodified the Darwinism of Darwin himself, is ticketed as a follower of Lamarck … The school of Weismann may properly be called Neo-Darwinian: pure Darwinian it certainly is not.” And thus, neo-Darwinism entered the English language. Moreover, the polarizing message of the neo-Darwinists appears to have induced some scientists, who might not otherwise have done so, to identify themselves as latter-day Lamarckists. From a historical perspective, neo-Darwinism can be considered to have lost the argument because, in the ensuing decades, most biologists assigned a relatively modest or negligible role to natural selection in evolutionary change (Bowler 1983).
(bolding is mine)
Haig, who authored the article is promoting his conservative view that bio-evolution is still in the neo-Darwinist camp and can evolve bringing forward most of the recent work. In many ways this is true. From my point of view, however, it cannot do so in context and the thheory must face a complete paradigm shift toward the mental influence of living things in their own construction. Haig makes the same points that I did earlier, without putting Romanes and Darwin in the camp of "mental evolution".
I strongly disagree with the Weismannian bullbleep that "somatic mutation, somatic recombination or epigenetic change" are all random with respect to fitness.
There is logical communication in natural language in biological systems. Humanity included. As we decode this language its functionality in solving problem and taking advantage of benefits offered by their ecological environments is blatantly obvious. It is a "king with no clothes" situation for evolution that is random to information processing fitness.
Quote: "If there were something like a guidebook for living creatures, I think the first line would read like a biblical commandment: Make thy information larger. And next would come the guidelines for colonizing, in good imperialist fashion, the biggest chunk of negative entropy around."
Werner Loewenstein, a cell biologist at Woods Hole Biological Laboratories, has written a remarkably engaging book tying together information theory, thermodynamics, molecular biology, and the structure of cells. The subject is not one to which the human brain is well suited, but with Loewenstein's guidance you may get a better grasp on concepts like entropy than you've ever had before.
https://www.amazon.com/Touchstone-Life-Information-Communication-Foundations/dp/0195140575
Biologist J. Scott Turner’s recent book Purpose and Desire seems to be representative of some of the latest thinking in alternatives to neo-Darwinism.
A few quotes that seem to give the flavor of Turner's thinking (from the review at
https://evolutionnews.org/2017/10/scott-...own-words/):
"I will make a bald assertion: bacteria (or any living system, for that matter) can be agents because they are cognitive beings. Now, before going any further, I need to insert two disclaimers. The first is that I am using “cognition” in the broadest possible sense I can get away with — to mean simply the mapping of information about the external environment onto the cell’s internal workings. The second is that I am distinguishing cognition sharply from consciousness.
......................................
So, it seems to be cognition all the way down to the simplest life forms we know. Since cognition is an important component of agency, it follows that bacteria can be cognitive agents, as can any living system.
......................................
If Biology’s Second Law is true and life is at root an expression of the phenomenon of homeostasis, then the origin of life is tantamount to the origin of homeostasis. Homeostasis demands certain things, however — among them at least rudimentary forms of cognition and intentionality.... intentionality can be defined very broadly. (note: to apply even to simple biological structures like bacterial mats modifying their substrate according to what they "need")"
Comment:
(For eukaryotic organisms especially ) Turner apparently relies on a Lamarckian idea of adaptive homeostasis becoming encoded somehow in another sort of memory system than a genetic one. He offers several alternate reservoirs to DNA for the processing and memory required: membranes, microtubule organizing centers (MTOC), and their cytoskeletons."
I still don't see how these speculations offer a plausible way to supply the evident deep ingenuity of biological nature in designing and implementing things like complicated irreducibly complex structures. To do this absolutely seems to require three basic stages: the analyzing of somatic requirements, then reverse engineering the results of that analysis into the DNA sequence changes and/or whatever extra-DNA encoded information changes that are required to make the needed bodily or behavioral changes (this can include a long complicated developmental pathway), and then physically making the required genetic and/or extra-genetic changes. This is a very high level of intelligent cognition combined with insight and intentionality. No one has proposed yet any actual natural mechanisms that can implement these functional requirements.
I'm not sure at this point that Turner's thinking is limited to it, but he seems to limit the "intelligence" of nature to the definition of simplified cognition previously quoted. I think more is required to have achieved what nature has achieved - it has required the operation of mind. Of course, to propose that would much more strongly violate the methodological materialist taboo against any form of teleology. But it seems clearly necessary to propose it, because of the evident "system requirements" of macroevolution outlined above.
The reviewer's summary:
"Turner’s book is fascinating, stimulating, and befuddling by turns. He has interesting ideas but little to back them up, and in places the prose goes fuzzy, perhaps because there is little to go on. His ideas are only in the beginning stages, and need to be tested and evaluated, because they are controversial."
(2017-10-24, 06:24 PM)nbtruthman Wrote: [ -> ]I still don't see how these speculations offer a plausible way to supply the evident deep ingenuity of biological nature in designing and implementing things like complicated irreducibly complex structures. To do this absolutely seems to require three basic stages: the analyzing of somatic requirements, then reverse engineering the results of that analysis into the DNA sequence changes and/or whatever extra-DNA encoded information changes that are required to make the needed bodily or behavioral changes (this can include a long complicated developmental pathway), and then physically making the required genetic and/or extra-genetic changes. This is a very high level of intelligent cognition combined with insight and intentionality. No one has proposed yet any actual natural mechanisms that can implement these functional requirements.
Why do you think that an "irreducibly complex structure" requires those steps?
~~ Paul
(2017-10-23, 08:49 PM)nbtruthman Wrote: [ -> ]I don't think any of the newly understood mechanisms of "soft inheritance" (including horizontal gene transfer) break the Weismann barrier or incorporate the kind of creativity observed in actual macroevolution. It seems to me that to be credible the "new Lamarckians" would need to show in detail how these "soft inheritance" mechanisms can creatively invent intricate complicated self referent irreducibly complex biological machines like the bacterial flagellum. There seems to be an irreducible requirement for the operation of mind, not mechanism.
I am uncertain about this. epi-genetics means that tags on DNA (methyl or acetyl groups) can be passed down to a child. These effects definitely seem to be real:
https://www.amazon.co.uk/dp/B00JFVOLZK/r...TF8&btkr=1
The problem is that ultimately these tags fall off, and no permanent genetic changes result - but maybe there is a way to make these changes permanent - even so they only affect the frequency of expression of the gene in question.
David
(2017-10-24, 06:24 PM)nbtruthman Wrote: [ -> ]Biologist J. Scott Turner’s recent book Purpose and Desire seems to be representative of some of the latest thinking in alternatives to neo-Darwinism.
A few quotes that seem to give the flavor of Turner's thinking (from the review at https://evolutionnews.org/2017/10/scott-...own-words/):
"I will make a bald assertion: bacteria (or any living system, for that matter) can be agents because they are cognitive beings. Now, before going any further, I need to insert two disclaimers. The first is that I am using “cognition” in the broadest possible sense I can get away with — to mean simply the mapping of information about the external environment onto the cell’s internal workings. The second is that I am distinguishing cognition sharply from consciousness.
......................................
So, it seems to be cognition all the way down to the simplest life forms we know. Since cognition is an important component of agency, it follows that bacteria can be cognitive agents, as can any living system.
......................................
If Biology’s Second Law is true and life is at root an expression of the phenomenon of homeostasis, then the origin of life is tantamount to the origin of homeostasis. Homeostasis demands certain things, however — among them at least rudimentary forms of cognition and intentionality.... intentionality can be defined very broadly. (note: to apply even to simple biological structures like bacterial mats modifying their substrate according to what they "need")"
Comment:
(For eukaryotic organisms especially ) Turner apparently relies on a Lamarckian idea of adaptive homeostasis becoming encoded somehow in another sort of memory system than a genetic one. He offers several alternate reservoirs to DNA for the processing and memory required: membranes, microtubule organizing centers (MTOC), and their cytoskeletons."
I still don't see how these speculations offer a plausible way to supply the evident deep ingenuity of biological nature in designing and implementing things like complicated irreducibly complex structures. To do this absolutely seems to require three basic stages: the analyzing of somatic requirements, then reverse engineering the results of that analysis into the DNA sequence changes and/or whatever extra-DNA encoded information changes that are required to make the needed bodily or behavioral changes (this can include a long complicated developmental pathway), and then physically making the required genetic and/or extra-genetic changes. This is a very high level of intelligent cognition combined with insight and intentionality. No one has proposed yet any actual natural mechanisms that can implement these functional requirements.
I'm not sure at this point that Turner's thinking is limited to it, but he seems to limit the "intelligence" of nature to the definition of simplified cognition previously quoted. I think more is required to have achieved what nature has achieved - it has required the operation of mind. Of course, to propose that would much more strongly violate the methodological materialist taboo against any form of teleology. But it seems clearly necessary to propose it, because of the evident "system requirements" of macroevolution outlined above.
The reviewer's summary: "Turner’s book is fascinating, stimulating, and befuddling by turns. He has interesting ideas but little to back them up, and in places the prose goes fuzzy, perhaps because there is little to go on. His ideas are only in the beginning stages, and need to be tested and evaluated, because they are controversial."
I have just finished this book, and am trying to discuss it with the author. My feeling is that he is picking his way through obvious academic taboos, and that his true position may be quite fluid. I suspect that he really is advocating teleology - otherwise, what is the point of the book?
I am sure he has a whole career of evidence to support his position, and that he hasn't written this book without lots of thought!
David