Extended Evolutionary Synthesis (Introduction)
by George Jelliss 
, Crewe, Thursday, August 06, 2015, 14:47 (3396 days ago)
According to Indiana University an 'Extended Evolutionary Synthesis' is developing. -http://phys.org/news/2015-08-theory-evolution.html?utm_source=menu&utm_medium=link&utm_campaign=item-menu-In other words the theory of evolution evolves.
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GPJ
Extended Evolutionary Synthesis
by David Turell , Thursday, August 06, 2015, 17:20 (3396 days ago) @ George Jelliss
George: According to Indiana University an 'Extended Evolutionary Synthesis' is developing. > > http://phys.org/news/2015-08-theory-evolution.html?utm_source=menu&utm_medium=link&... > In other words the theory of evolution evolves.-Thanks again for an interesting entry. We have been discussing patterns of development in evolution and the place for epigenetics. From the article:-" The authors discuss the way an organism's growth from egg to adult influences species' evolution. The field of evolutionary developmental biology, or "evo-devo," has found that highly different organisms—from sea urchins to insects and mammals—use the same "building blocks" to grow their bodies during development. This shared "toolbox" enables unrelated organisms to evolve strikingly similar structures over time—the independent evolution of eyes in insects and vertebrates, for example.-"These same building blocks may also be re-used in different ways. Moczek's research, for example, shows that genes and developmental pathways that originally gave rise to legs and other appendages were later re-used to create beetles' extravagant horn-like structures.-"Moczek and colleagues also argue that the role of "plasticity"—or the ability of many organisms to adjust their growth and development in response to environmental changes over their lifetime—has been overlooked in evolutionary theory. They cite growing evidence that novel traits prompted by the environment may be genetically fixed in subsequent generations.-"Lastly, the scientists say evolutionary theory should expand to consider how organisms systematically modify their own environment, such as building nests or burrows; change the atmosphere or soil; or create cultures. And they show that factors beyond genetic inheritance influence species across generations, including prenatal hormones, care after birth and learning.-"Traditional evolutionary biology emphasizes a single direction: Genes give rise to observable traits, such as its physical characteristics, biological processes or behaviors. The environment may favor certain traits but in the process remains external from the organism.-"'We're arguing for a reciprocal model, one in which genes not only contribute to an organism's observable traits, but also where an organisms' own traits, behaviors and actions significantly impact the rate and direction of evolutionary change," Moczek said."
Extended Evolutionary Synthesis; another view
by David Turell , Friday, August 07, 2015, 21:10 (3395 days ago) @ David Turell
By a philosopher of genetic science:-http://www.huffingtonpost.com/suzan-mazur/guenther-witzany-modern-s_b_7947442.html-Günther Witzany: I've known the scientific papers of University of Chicago microbiologist James Shapiro going back decades. Jim Shapiro has a perspective about how the genetic component in organisms evolved or disorganized that I find interesting. So I invited him for a congress in Salzburg in 2008 on "natural genetic engineering." This is Shapiro's term natural genetic engineering. ( my bold)-" "Natural genome editing" is the term I coined in 2008 at Salzburg. A lot of other scientists attended our meeting. We discussed how genetic order in organisms is organized. It was clear to those of us gathered that this was different from the Modern Synthesis, where the idea is that genetic content is a result of chance mutations and selection of chance mutations.-*** " My point is if we look at the genetic code, we think first of DNA. But if we integrate the role of viruses and virus-derived parts, such as mobile genetic elements, or endogenous retroviruses, it becomes clear that most of the DNA serves as a house, a habitat for its RNA inhabitants. . . . -"Viruses are so abundant on this planet, in each ecological niche, that there is no organism independent of the influence of viruses and their genetic content. . . .-"The other point is that the genetic code is really a code, it is a natural code. This means it's a natural language, so we must assume there are code users because no natural language speaks itself as no natural code codes itself. It is always competent users that produce sequences for transport of meaning or content. . . . -***-"I found that coordination of living agents, whether they are cells or viruses or parts of cells -- coordination of behavior in organisms needs and must have signaling. Without signaling you can't have transport of information and you can't really get coordination of two participating agents. This is the main principal of communication. Communication means sign-mediated interactions or signal-mediated interactions. . . .-"But the signals are not the agents. There are living agents that use signals and generate signals to transport meaning and content and information-***-"There are four levels of communication in the biosphere. First is signaling within an organism -- mitochondria, chloroplast, cell nucleus, etc. This is intra-organismic communication, within a cell. -"Second, we have the inter-organismic communication process, the signaling between cells of an organism like in an organ or tissue. Specialized communication between the participating cells with the same and related cells. -"Third is the trans-organismic communication level, which is where organisms communicate, signal other organisms not of the same species as we can find it in symbiotic processes. -"The fourth level is sensing and differentiation of indices. They serve as abiotic information for living organisms. . . . -***-"The older concepts we have now for a half century cannot sufficiently explain the complex tendency of the genetic code. They can't explain the functions of mobile genetic elements and the endogenous retroviruses and non-coding RNAs. Also, the central dogma of molecular biology has been falsified -- that is, the way is always from DNA to RNA to proteins to anything else, or the other "dogmas," e.g., replication errors drive evolutionary genetic variation, that one gene codes for one protein and that non-coding DNA is junk. All these concepts that dominated science for half a century are falsified now." (my bold)
Extended Evolutionary Synthesis; another view
by Balance_Maintained , U.S.A., Saturday, August 08, 2015, 00:50 (3395 days ago) @ David Turell
*** > " My point is if we look at the genetic code, we think first of DNA. But if we integrate the role of viruses and virus-derived parts, such as mobile genetic elements, or endogenous retroviruses, it becomes clear that most of the DNA serves as a house, a habitat for its RNA inhabitants. . . . > - This is similar in nature to a programming function within a class. The Genome acts as a class, the RNA as a function. - > "Viruses are so abundant on this planet, in each ecological niche, that there is no organism independent of the influence of viruses and their genetic content. . . . > > "The other point is that the genetic code is really a code, it is a natural code. This means it's a natural language, so we must assume there are code users because no natural language speaks itself as no natural code codes itself. It is always competent users that produce sequences for transport of meaning or content. . . . > - No natural code codes itself... that is pretty much to the point, isn't it? And if no natural language exists without a reader, than naturalism ends up with a chicken and egg problem. Which came first, the intelligent coder/reader, or the code to create the coder/reader?- > *** > > "I found that coordination of living agents, whether they are cells or viruses or parts of cells -- coordination of behavior in organisms needs and must have signaling. Without signaling you can't have transport of information and you can't really get coordination of two participating agents. This is the main principal of communication. Communication means sign-mediated interactions or signal-mediated interactions. . . . > -> "Third is the trans-organismic communication level, which is where organisms communicate, signal other organisms not of the same species as we can find it in symbiotic processes. > -Flowers and bees anyone? How did they communicate to organize their communication?
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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.
Extended Evolutionary Synthesis; another view
by David Turell , Saturday, August 08, 2015, 04:17 (3395 days ago) @ Balance_Maintained
> > > "Third is the trans-organismic communication level, which is where organisms communicate, signal other organisms not of the same species as we can find it in symbiotic processes. > > > > Tony; Flowers and bees anyone? How did they communicate to organize their communication?-Exactly.
Extended Evolutionary Synthesis; another view
DAVID and TONY: (quoting James Shapiro) "I found that coordination of living agents, whether they are cells or viruses or parts of cells -- coordination of behavior in organisms needs and must have signaling. Without signaling you can't have transport of information and you can't really get coordination of two participating agents. This is the main principal of communication. Communication means sign-mediated interactions or signal-mediated interactions. . . .-"Third is the trans-organismic communication level, which is where organisms communicate, signal other organisms not of the same species as we can find it in symbiotic processes. -TONY: Flowers and bees anyone? How did they communicate to organize their communication?-Once again, David, thank you for a fascinating article. Almost as interesting as the article is the choice of sections we would all choose to highlight. Here's the one that grabs me:-“But the signals are not the agents. There are living agents that use signals and generate signals to transport meaning and content and information.” -If we bear in mind that Shapiro, a bacterial geneticist, firmly believes that bacteria are sentient, cognitive, intelligent beings, the answer to your question, Tony, might be that all organisms are possessed of an intelligence different from ours. They have their own ways of thinking and communicating. I don't have a problem if theists argue that God created this intelligence (and you might possibly even lean towards this idea yourself - I'm not quite sure of your views on this question.) I only have a problem if folk of all creeds insist that other organisms, apart from ourselves and to a lesser degree some of our fellow animals, are mere automatons. --
Extended Evolutionary Synthesis; another view
by David Turell , Saturday, August 08, 2015, 14:27 (3394 days ago) @ dhw
> dhw: Once again, David, thank you for a fascinating article.-Thank you. > > dhw: “But the signals are not the agents. There are living agents that use signals and generate signals to transport meaning and content and information.” > > If we bear in mind that Shapiro, a bacterial geneticist, firmly believes that bacteria are sentient, cognitive, intelligent beings, the answer to your question, Tony, might be that all organisms are possessed of an intelligence different from ours. They have their own ways of thinking and communicating.....I only have a problem if folk of all creeds insist that other organisms, apart from ourselves and to a lesser degree some of our fellow animals, are mere automatons.-But I will continue to make the point: from outside the organism one cannot tell the difference between some type of mental action or automatism. I have my choice.
Extended Evolutionary Synthesis; another view
by Balance_Maintained , U.S.A., Saturday, August 08, 2015, 23:34 (3394 days ago) @ David Turell
> > dhw: Once again, David, thank you for a fascinating article. > > Thank you. > > > > dhw: “But the signals are not the agents. There are living agents that use signals and generate signals to transport meaning and content and information.” > > > > If we bear in mind that Shapiro, a bacterial geneticist, firmly believes that bacteria are sentient, cognitive, intelligent beings, the answer to your question, Tony, might be that all organisms are possessed of an intelligence different from ours. They have their own ways of thinking and communicating.....I only have a problem if folk of all creeds insist that other organisms, apart from ourselves and to a lesser degree some of our fellow animals, are mere automatons. > >David: But I will continue to make the point: from outside the organism one cannot tell the difference between some type of mental action or automatism. I have my choice.-I don't doubt that organisms have intelligence. I doubt the degree of that intelligence. Some intelligence is obviously needed for survival, but interspecies communication, planning, and coordination all take a level of communication that I've seen no evidence for.
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What is the purpose of living? How about, 'to reduce needless suffering. It seems to me to be a worthy purpose.
Extended Evolutionary Synthesis; another view
by David Turell , Sunday, August 09, 2015, 00:20 (3394 days ago) @ Balance_Maintained
> Tony: I don't doubt that organisms have intelligence. I doubt the degree of that intelligence. Some intelligence is obviously needed for survival, but interspecies communication, planning, and coordination all take a level of communication that I've seen no evidence for.-And I think they contain intelligent information for guidance wich they use automatically when stimulated in various ways.
Extended Evolutionary Synthesis; another view
SHAPIRO: “But the signals are not the agents. There are living agents that use signals and generate signals to transport meaning and content and information.” -TONY: Flowers and bees anyone? How did they communicate to organize their communication?-DHW: If we bear in mind that Shapiro, a bacterial geneticist, firmly believes that bacteria are sentient, cognitive, intelligent beings, the answer to your question, Tony, might be that all organisms are possessed of an intelligence different from ours. They have their own ways of thinking and communicating. I don't have a problem if theists argue that God created this intelligence (and you might possibly even lean towards this idea yourself - I'm not quite sure of your views on this question.) I only have a problem if folk of all creeds insist that other organisms, apart from ourselves and to a lesser degree some of our fellow animals, are mere automatons. -DAVID: But I will continue to make the point: from outside the organism one cannot tell the difference between some type of mental action or automatism. I have my choice.-Indeed you do, but if one cannot tell the difference from outside, and one can't get inside, the only means of access is through testing and observing. I don't know how many years of your life you have devoted to testing and observing the behaviour of bacteria, but I doubt if they extend long enough for you to reject outright the findings of Shapiro and the many other experts who share his conclusions. Are you really so convinced that they are all deluded? -TONY: I don't doubt that organism have intelligence. I doubt the degree of that intelligence. Some intelligence is obviously needed for survival, but interspecies communication, planning, and coordination all take a level of communication that I've seen no evidence for.-The evidence is in the symbiosis itself. What evidence have you seen that God preprogrammed the various prototypes so that certain descendants (ah, common descent again!) would automatically communicate, plan and coordinate?
Extended Evolutionary Synthesis; another view
by David Turell , Sunday, August 09, 2015, 17:37 (3393 days ago) @ dhw
dhw: if one cannot tell the difference from outside, and one can't get inside, the only means of access is through testing and observing..... Are you really so convinced that they are all deluded? -Not deluded, just a different interpretation of the known facts. > > TONY: I don't doubt that organism have intelligence. I doubt the degree of that intelligence. Some intelligence is obviously needed for survival, but interspecies communication, planning, and coordination all take a level of communication that I've seen no evidence for. > > dhw: The evidence is in the symbiosis itself. What evidence have you seen that God preprogrammed the various prototypes so that certain descendants (ah, common descent again!) would automatically communicate, plan and coordinate?-Chicken and egg problem. The complicated relationships of symbiosis cannot develop by chance. Each organism has to plan its response in advance of the experimental relationship. The negotiations of the biochemical relationship would be as complex as the US-Iran 'deal'.
Extended Evolutionary Synthesis; another view
dhw: ...if one cannot tell the difference from outside, and one can't get inside, the only means of access is through testing and observing..... Are you really so convinced that they are all deluded? DAVID: Not deluded, just a different interpretation of the known fact-“Deluded” = believing something that is not true. Since you are convinced that bacteria are automatons, you believe that Shapiro believes something that is not true. Dawkins believes that people who believe in God are deluded. You are - thank heavens! - more polite than Dawkins, but perhaps my use of the word will make you hesitate to dismiss completely the many years of research into what after all is a highly specialized subject. I am not denying your right to your opinion - I just wish it was a little less firm!-TONY: I don't doubt that organism have intelligence. I doubt the degree of that intelligence. Some intelligence is obviously needed for survival, but interspecies communication, planning, and coordination all take a level of communication that I've seen no evidence for. dhw: The evidence is in the symbiosis itself. What evidence have you seen that God preprogrammed the various prototypes so that certain descendants (ah, common descent again!) would automatically communicate, plan and coordinate?-DAVID: Chicken and egg problem. The complicated relationships of symbiosis cannot develop by chance. Each organism has to plan its response in advance of the experimental relationship. The negotiations of the biochemical relationship would be as complex as the US-Iran 'deal'.-I like the example of the Egyptian plover and the Nile crocodile because it doesn't involve biochemical relationships - only communication and cooperation between the two organisms. Not so complex, but perhaps a guide as to how the process develops. Yes, all symbiotic relationships raise the chicken and egg problem, but I don't agree that each organism has to plan its response in advance of the experiment. I don't see why they shouldn't (sometimes) follow the same path as we often do, when we set out to see what will happen if....The first step might simply be communication and an agreement to cooperate. Tony's explanation (if he rejects autonomous intelligence) apparently entails God's preprogramming both variations of their respective prototypes at the same time, which at least is not quite so convoluted as your hypotheses that each programme for the organisms themselves and their symbiotic relationship was passed down by the first living cells (whose purpose was to create humans), or was the result of a personal dabble by God (whose purpose was to create humans).
Extended Evolutionary Synthesis; another view
by David Turell , Monday, August 10, 2015, 17:08 (3392 days ago) @ dhw
dhw: You are - thank heavens! - more polite than Dawkins, but perhaps my use of the word will make you hesitate to dismiss completely the many years of research into what after all is a highly specialized subject. I am not denying your right to your opinion - I just wish it was a little less firm!-But I've read Shapiro's book and still have the same conclusion. > > dh: I like the example of the Egyptian plover and the Nile crocodile because it doesn't involve biochemical relationships - only communication and cooperation between the two organisms.-Of course you like it. Cooperating animals are light years apart from symbiotic biochemical relationships.-> dhw: Not so complex, but perhaps a guide as to how the process develops. Yes, all symbiotic relationships raise the chicken and egg problem, but I don't agree that each organism has to plan its response in advance of the experiment. I don't see why they shouldn't (sometimes) follow the same path as we often do, when we set out to see what will happen if....The first step might simply be communication and an agreement to cooperate. Tony's explanation (if he rejects autonomous intelligence) apparently entails God's preprogramming both variations of their respective prototypes at the same time,-I'll buy Tony's approach, but not yours which uses comparisons to how humans approach the problem. The symbiosis involves intricately planned biochemical interactions.