Automatic cell activity (Introduction)
by David Turell 
, Monday, April 22, 2013, 16:22 (4234 days ago)
An example, one molecule in control:-http://phys.org/news/2013-04-cell-molecule-on-off.html-Another example: choice through feedback loops.-http://phys.org/news/2013-04-code-bacteria.html-And it even fits Darwin as this response is reaction to environmental stress, and present in an ancient form of life, probably present from the beginning of life.
Automatic cell activity
DAVID: An example, one molecule in control: http://phys.org/news/2013-04-cell-molecule-on-off.html Another example: choice through feedback loops. http://phys.org/news/2013-04-code-bacteria.html And it even fits Darwin as this response is reaction to environmental stress, and present in an ancient form of life, probably present from the beginning of life.-Thank you for these enlightening articles. I did not find the word "automatic" in either of them. On the contrary, as the following quotes vividly illustrate, the researchers emphasize the degree of independent intelligence involved:-1) Individual freedom and social responsibility may sound like humanistic concepts, but an investigation of the genetic circuitry of bacteria suggests that even the simplest creatures can make difficult choices that strike a balance between selflessness and selfishness. 2) "Our findings suggest new principles for collective decisions that allow both random behavior by individuals and nonrandom outcomes for the population as a whole," said study co-author Eshel Ben-Jacob, a senior investigator at CTBP and adjunct professor of biochemistry and cell biology at Rice. 3) Years of studies have determined that each individual constantly senses its environment and continuously sends out chemical signals to communicate with its neighbors about the choices it is making. Experimental studies have revealed dozens of regulatory genes, signaling proteins and other genetic tools that cells use to gather information and communicate with one another.-4) Individual bacteria weigh their decisions carefully, taking into account the stress they are facing, the situation of their peers, the statistics of how many cells are sporulating and how many are choosing competence, Onuchic said. Each bacterium in the colony communicates via chemical "tweets" and performs a sophisticated decision-making process using a specialized complex gene network comprised of many genes connected via complex circuitry.-It would seem, then, that like humans bacteria use their materials, instead of their materials using them. They take individual decisions, communicate and cooperate. At the very least this should make you pause before you go on insisting that the cell IS an automaton, and it provides ample reason for you once more to heed McClintock's call for more research into how much knowledge cells have of themselves. Come out of your box, David!
Automatic cell activity
by David Turell , Tuesday, April 23, 2013, 15:40 (4233 days ago) @ dhw
> dhw; It would seem, then, that like humans bacteria use their materials, instead of their materials using them. They take individual decisions, communicate and cooperate. At the very least this should make you pause before you go on insisting that the cell IS an automaton, and it provides ample reason for you once more to heed McClintock's call for more research into how much knowledge cells have of themselves. Come out of your box, David!-You can anthropomorphize bacteria all you wish but they still are automatons, responding to chemical signals automatically. Why not recognize a God who can give bacteria such marvelous protections, they can live their lives, as they have for 3.5 billion years without having a thought or an organ of thought. I haven't met a thoughtful molecule yet. But they certinaly have reactions, none of them mental or emotional. To paraphrase G. Stein: a molecule is a molecule is a molecule; a string of atoms with electrical characteristics acting in a quantum fashion. No more, no less. Your lack of understanding organic chemistry has your reasoning in a box.
Automatic cell activity
dhw: It would seem, then, that like humans bacteria use their materials, instead of their materials using them. They take individual decisions, communicate and cooperate. At the very least this should make you pause before you go on insisting that the cell IS an automaton, and it provides ample reason for you once more to heed McClintock's call for more research into how much knowledge cells have of themselves. Come out of your box, David!-DAVID: You can anthropomorphize bacteria all you wish but they still are automatons, responding to chemical signals automatically. Why not recognize a God who can give bacteria such marvelous protections, they can live their lives, as they have for 3.5 billion years without having a thought or an organ of thought. -There is a dislocation in this argument. If I believed in God and if I believed in the "intelligent cell", I would say to you: "Why not recognize a God who can give bacteria and his other inventions the ability to think and make their own decisions?" You seem to take this hypothesis as an argument against God, but just like Darwin's theory, it is perfectly compatible with belief in him. -DAVID: I haven't met a thoughtful molecule yet. But they certainly have reactions, none of them mental or emotional. To paraphrase G. Stein: a molecule is a molecule is a molecule; a string of atoms with electrical characteristics acting in a quantum fashion. No more, no less. Your lack of understanding organic chemistry has your reasoning in a box.-Yes, I lack understanding of organic chemistry, which is why I depend on experts for my information. You have drawn attention to the work of several such experts, only to find that one (Talbott) explicitly says that cells are not automatons, while a Nobel Prize-winning geneticist (McClintock) calls for research into "the extent of cellular self-knowledge". Why, then, must I accept your view that cells are automatons? Similarly, I take it seriously when a team of experts inform us that bacteria have individual freedom, make difficult choices between selfish and selfless behaviour, communicate with their neighbours about their choices, weigh their decisions carefully. These are not metaphors, and the findings could hardly offer clearer evidence of individual intelligence. The fact that bacteria do not show human emotions, and that you have never met a thoughtful molecule, does not make me want to dismiss Talbott, McClintock or the researchers from Rice and Tel Aviv Universities and the Harvard Medical School. Even you agreed that McClintock "is right to ask for that study of cellular self-knowledge." If it is right for her, why is not right for me? But perhaps I'm able to take these ideas seriously because my reasoning is NOT in a box. I have not made up my mind, and so I'm reluctant to dismiss the work of scientists who do understand organic chemistry, even if their ideas run contrary to those of my science mentor!
Automatic cell activity
by David Turell , Wednesday, April 24, 2013, 17:31 (4232 days ago) @ dhw
edited by unknown, Wednesday, April 24, 2013, 17:44
DAVID: You can anthropomorphize bacteria all you wish but they still are automatons, responding to chemical signals automatically. Why not recognize a God who can give bacteria such marvelous protections, they can live their lives, as they have for 3.5 billion years without having a thought or an organ of thought. > > dhw:There is a dislocation in this argument. If I believed in God and if I believed in the "intelligent cell", I would say to you: "Why not recognize a God who can give bacteria and his other inventions the ability to think and make their own decisions?" You seem to take this hypothesis as an argument against God, but just like Darwin's theory, it is perfectly compatible with belief in him. -I disagree. You are inventing intelligence in bacteria, where none exists except the information coded into DNA. I have described this as a two-step mechanism. A superior intelligene invented DNA and coded it so that bacteria could respond automatically and act as if they had intelligence. > > DAVID: I haven't met a thoughtful molecule yet. But they certainly have reactions, none of them mental or emotional. To paraphrase G. Stein: a molecule is a molecule is a molecule; a string of atoms with electrical characteristics acting in a quantum fashion. No more, no less. Your lack of understanding organic chemistry has your reasoning in a box. > > dhw: Yes, I lack understanding of organic chemistry, which is why I depend on experts for my information. You have drawn attention to the work of several such experts, only to find that one (Talbott) explicitly says that cells are not automatons, -Talbott is a philosoher, not an expert in organic chemistry. He is the frustrated one who cannot find a way out of his box.-> dhw: while a Nobel Prize-winning geneticist (McClintock) calls for research into "the extent of cellular self-knowledge". Why, then, must I accept your view that cells are automatons? Similarly, I take it seriously when a team of experts inform us that bacteria have individual freedom, make difficult choices between selfish and selfless behaviour, communicate with their neighbours about their choices, weigh their decisions carefully. These are not metaphors, and the findings could hardly offer clearer evidence of individual intelligence. -The intelligence is the the coder of the DNA. The DNA responses are automatic.- > dhw: Even you agreed that McClintock "is right to ask for that study of cellular self-knowledge." If it is right for her, why is not right for me?-Her's is a reasonable request. Since the bacteria are so thoughtful, let's check and make sure there isn't evidence for intelligence at the cellular level. But her comment is ancient history, expressed many years ago before all the recent discoveries with fluorsecent molecules wandering throughthe cell acting like nano-machines. None of the authors of those studies imply thinking molecules in their discussions of the findings. It is all automatisms. -> dhw: But perhaps I'm able to take these ideas seriously because my reasoning is NOT in a box. I have not made up my mind, and so I'm reluctant to dismiss the work of scientists who do understand organic chemistry, even if their ideas run contrary to those of my science mentor!-The box is yours, boxed into non-decision making between chance and design, just like Talbott.-Taken from uncommon descent website:-" We know the Omega watch exists. Anyone who admits that the Omega watch needs any intelligent design at all should be a believer in Intelligent Design. Evolution ( uppercase E ) is the belief that everything in the world evolved by blind chance. evolution ( lowercase e ) is the belief that some things evolve over time by blind chance. Intelligent Design ( uppercase ID ) is the belief that the universe was created by a Designer (uppercase D ). intelligent design ( lowercase id ) is the belief that some things in the universe ( like the Omega watch ) were created by a designer. The interesting thing is that if you are truly honest: -ID being true allows both e, and id to take place. E being true disallows id and only allows e. So if E is true, the Omega watch was made by pure chance."
Automatic cell activity
by David Turell , Wednesday, April 24, 2013, 20:39 (4232 days ago) @ David Turell
> > dhw: Yes, I lack understanding of organic chemistry, which is why I depend on experts for my information. You have drawn attention to the work of several such experts, only to find that one (Talbott) explicitly says that cells are not automatons, > > DAvid: Talbott is a philosoher, not an expert in organic chemistry. He is the frustrated one who cannot find a way out of his box.-Addendum: I went back and re-read Talbott's four articles, the main point of which is life is an emergent property from a mass of organized organic chemicals and we are just beginning to recognize that it is difficult to analyze life's 'specialism'. At no point does he look at the DNA coding and what might be its source of origin. The 'specialism' is in the emerging complexity of the genome and all its layers of control. It is from there that life's special quality begins. Like Nagel, he presents the problem for philosophy, but offers no solution.-" If the world is indeed intelligible — if it speaks meaningfully, as must be assumed by every scientist who tries to capture that meaning in revelatory words and ideas — then the place where we find it speaking most fully and explicitly is presumably the place where we will find its fundamental truths most fully declared. And that is in the living organism. The "difficulty" of the organism is really just the difficulty of reducing it to mere physics and chemistry. Yes, very difficult indeed — but that's because the organism is alive, as we are alive, and because every biologist instinctively understands this life as offering more than lessons in physics and chemistry. As for the "nonliving" world: we imagine it is simpler to understand only because we are bewitched by the precision and predictability of the physical laws we find implicit in things — things of whose nature we know almost nothing." (final article)
Automatic cell activity
I have covered most of this post in my entry under "Cell response", and what is not covered only repeats the points of possible disagreement between us. However, you have quoted a silly syllogism from the uncommon descent website, which demands to be demolished:-We know the Omega watch exists. Anyone who admits that the Omega watch needs any intelligent design at all should be a believer in Intelligent Design.-Abandon reason all ye who enter here.-Evolution (uppercase E ) is the belief that everything in the world evolved by blind chance.-Evolution is not a belief, but let that pass. It's the theory that describes the process by which living organisms have developed from earlier ancestral forms. It has nothing to do with the creation of man-made objects. How the process works is the subject of ongoing research, but many religious people believe that their god started and even directed it (= design), and Darwin himself emphasized that his theory was compatible with religion (though of course it is incompatible with Creationism). -evolution ( lowercase e ) is the belief that some things evolve over time by blind chance.-See above. -Intelligent Design (uppercase ID ) is the belief that the universe was created by a Designer (uppercase D).-OK.-intelligent design (lowercase id ) is the belief that some things in the universe ( like the Omega watch) were created by a designer.-OK.-The interesting thing is that if you are truly honest: ID being true allows both e, and id to take place.-It also allows E. unless by ID he means Creationism.-E being true disallows id [ID?] and only allows e.-No it doesn't (see above).-So if E is true, the Omega watch was made by pure chance.-As explained above, the theory of evolution / Theory of Evolution has nothing whatsoever to do with Omega watches or any other man-made design. Nor does it preclude belief in ID or id. The author didn't need any of the in-between stuff. His false definition of E would have sufficed, because any false premise will lead to a false conclusion: if "everything in the world evolved by blind chance", then of course his Omega watch evolved by blind chance. And if God made everything in the world, then God made my supper, so why should I thank my wife?-If these are the intellectual depths to which uncommon descent descends, David, you should cancel your subscription immediately (assuming they have the cheek to charge you). But thanks for the entertainment!-*******-I note your comment on Talbott. He has made a detailed study of the genome, and I presume you cannot find fault with it. You only find fault with his conclusion that the cell is not an "automatism", and with the fact that he does not try to solve one mystery (intricacies of life) by embracing another (your God). *******-You have raised an important point under "Energy from AtP" which I will discuss tomorrow.
Automatic cell activity
by David Turell , Thursday, April 25, 2013, 15:43 (4231 days ago) @ dhw
> Evolution (uppercase E ) is the belief that everything in the world evolved by blind chance. > > Evolution is not a belief, but let that pass. It's the theory that describes the process by which living organisms have developed from earlier ancestral forms. - Your interpretation of Evolutonary theory is wrong. As I interpret the purveyors of a strictly Darwin-style of evolutionary theory, it is a "belief" that the whole process is constructed from a chance mechanism. Dawkins hangs his hat on chance. That means atheism is OK, since all evolution is a natural chance process. But it looks too complex to me to be entirely by chance. That is why I believe in theistic evolution. And that is why your interpretation above is wrong. Theory is a form of belief, and it does not 'describe' an accurate process. It proposes a process to be investigated, which is then open for research. Chance mutation and natural selection now appear to be a tiny part of the process, and machinations within the genome are discovered to be a major portion of the process. -I interpret this as a degree of complexity that disallows chance and introduces the theory that Darwin's theory is not a natural process.