Making new evolutionary innovations (Introduction)
by David Turell 
, Saturday, November 23, 2019, 01:40 (1826 days ago)
A study plays with genes and makes forms change:
https://phys.org/news/2019-11-dung-beetle-discovery-biologists-nature.html
"When studying how organisms evolve, biologists consider most traits, or features, as derived from some earlier version already present in their ancestors. Few traits are regarded as truly "novel."
"Insects were wingless, then winged. Animals were blind, then had eyes.
"And in biology textbooks, novelty has a strict definition: it must have no relationship to any structure found in an ancestor and no relationship to any other body part elsewhere in the organism. By this definition, a dolphin's pectoral fins are not a novelty because they are modified forelimbs that already existed.
"However, some experts argue this creates a problem since it means novelty must seemingly arise from nothing. It must "pop up out of the blue" in evolutionary time.
"Now evidence has emerged—in a study published Nov. 21 in the journal Science—that illuminates how new things can evolve. Moreover, this evidence has come from an unexpected source: the small, yet charismatic dung beetle.
"'Dung beetles are fascinating creatures," said Armin Moczek, the study's senior author and a professor in the IU Bloomington College of Arts and Sciences' Department of Biology. Among their many qualities, one structure has placed them at the forefront of discussions about novelty among researchers. That structure is their thoracic horn, which is regarded as a textbook example of an evolutionary novelty. This is because the thoracic horn is unique to horned beetles, and it appears to have no relationship to any other structure in the animal.
***
"The new IU-led study, which is featured on the journal's cover, provides evidence that the formation of the thoracic horn is instructed by the same core network of genes that led to the evolution of insect wings: flight structures that exist on neighboring thoracic segments. In fact, this ancient gene network predates not just wings and horns; it already existed before there were insects, and in every segment along the entire body.
"'This work forces us to rethink what we mean by 'novelty'", Moczek said. "Each insect segment possesses this gene network, and as such, it is an ancient feature of their makeup. Yet, what each segment does with this network is so strikingly variable that it can yield traits that on the surface seem to have nothing in common, like wings and horns."
***
"In all three species, the researchers were surprised to find that deactivation of genes in the network significantly affected not just the formation of wings, but also thoracic horns, causing them to be reduced or completely absent.
'They also showed that they could manipulate other genes and force the horns to transform into "ectopic" wings—or extra wings on the wrong part of the body—which provided additional evidence that thoracic horns and wings were interchangeable, alternative outputs of the same gene network.
***
"'This new evidence is profound since it suggests that all of this vast diversity, all these novelties, could in fact be enabled by a single gene network that was used millions of years ago to form the flight wings on other body segments.'"
Comment: This did not occur to the scientists, but they acted like God in what they produced in the changes they made. Not new species but large modifications. It fits my concept of God's preplanning an easy way to run evolution.
Making new evolutionary innovations
DAVID: A study plays with genes and makes forms change:
https://phys.org/news/2019-11-dung-beetle-discovery-biologists-nature.html
QUOTES: "When studying how organisms evolve, biologists consider most traits, or features, as derived from some earlier version already present in their ancestors. Few traits are regarded as truly "novel."
And in biology textbooks, novelty has a strict definition: it must have no relationship to any structure found in an ancestor and no relationship to any other body part elsewhere in the organism. By this definition, a dolphin's pectoral fins are not a novelty because they are modified forelimbs that already existed.
"'This work forces us to rethink what we mean by 'novelty'", Moczek said. "Each insect segment possesses this gene network, and as such, it is an ancient feature of their makeup. Yet, what each segment does with this network is so strikingly variable that it can yield traits that on the surface seem to have nothing in common, like wings and horns."
"'This new evidence is profound since it suggests that all of this vast diversity, all these novelties, could in fact be enabled by a single gene network that was used millions of years ago to form the flight wings on other body segments.'"
DAVID: This did not occur to the scientists, but they acted like God in what they produced in the changes they made. Not new species but large modifications. It fits my concept of God's preplanning an easy way to run evolution.
Thank you for this very important article, which both reinforces and explains my own insistence that we cannot draw a firm borderline between adaptation and innovation. (The dolphin example exactly mirrors our own example of the whale.) More importantly, it explains how common descent proceeds – there is some mechanism within the genes (which we may define as “the fundamental units of inheritance and function in a cell”) which enables them to change so radically that they can produce what appears to be every “evolutionary novelty” (Shapiro) leading to speciation. The scientists have simply induced a process which may be perfectly natural. But yes, common descent fits your theory of 3.8 billion years' worth of computer programming as it does Shapiro’s (and my) concept of intelligent cells/cell communities designing their own innovations. The latter theory does not, however, cover the possible origin of the mechanism, which may or may not be your God.
Making new evolutionary innovations
by David Turell , Saturday, November 23, 2019, 18:58 (1825 days ago) @ dhw
DAVID: A study plays with genes and makes forms change:
https://phys.org/news/2019-11-dung-beetle-discovery-biologists-nature.htmlQUOTES: "When studying how organisms evolve, biologists consider most traits, or features, as derived from some earlier version already present in their ancestors. Few traits are regarded as truly "novel."
And in biology textbooks, novelty has a strict definition: it must have no relationship to any structure found in an ancestor and no relationship to any other body part elsewhere in the organism. By this definition, a dolphin's pectoral fins are not a novelty because they are modified forelimbs that already existed.
"'This work forces us to rethink what we mean by 'novelty'", Moczek said. "Each insect segment possesses this gene network, and as such, it is an ancient feature of their makeup. Yet, what each segment does with this network is so strikingly variable that it can yield traits that on the surface seem to have nothing in common, like wings and horns."
"'This new evidence is profound since it suggests that all of this vast diversity, all these novelties, could in fact be enabled by a single gene network that was used millions of years ago to form the flight wings on other body segments.'"
DAVID: This did not occur to the scientists, but they acted like God in what they produced in the changes they made. Not new species but large modifications. It fits my concept of God's preplanning an easy way to run evolution.
dhw: Thank you for this very important article, which both reinforces and explains my own insistence that we cannot draw a firm borderline between adaptation and innovation. (The dolphin example exactly mirrors our own example of the whale.) More importantly, it explains how common descent proceeds – there is some mechanism within the genes (which we may define as “the fundamental units of inheritance and function in a cell”) which enables them to change so radically that they can produce what appears to be every “evolutionary novelty” (Shapiro) leading to speciation. The scientists have simply induced a process which may be perfectly natural. But yes, common descent fits your theory of 3.8 billion years' worth of computer programming as it does Shapiro’s (and my) concept of intelligent cells/cell communities designing their own innovations. The latter theory does not, however, cover the possible origin of the mechanism, which may or may not be your God.
A very fair summary of where we are. There is a firm boundary, if we follow current guidelines in naming new species. Of course it is human judgement as to whether enough adaptations have created a new species, so it can be argued there is some blurring. If speciation can occur naturally by actions of the organisms genome, we've agreed that genome must have a central command post to orchestrate the design changes. I accept a God-given change mechanism, but only with God-given guidelines. Until we find a command post, if it exists, we can only theorize. The only command post may well turn out to be God at work. While we cannot be sure, at this point, my bet is still on God.
Making new evolutionary innovations
dhw: Thank you for this very important article, which both reinforces and explains my own insistence that we cannot draw a firm borderline between adaptation and innovation. (The dolphin example exactly mirrors our own example of the whale.) More importantly, it explains how common descent proceeds – there is some mechanism within the genes (which we may define as “the fundamental units of inheritance and function in a cell”) which enables them to change so radically that they can produce what appears to be every “evolutionary novelty” (Shapiro) leading to speciation. The scientists have simply induced a process which may be perfectly natural. But yes, common descent fits your theory of 3.8 billion years' worth of computer programming as it does Shapiro’s (and my) concept of intelligent cells/cell communities designing their own innovations. The latter theory does not, however, cover the possible origin of the mechanism, which may or may not be your God.
DAVID: A very fair summary of where we are. There is a firm boundary, if we follow current guidelines in naming new species. Of course it is human judgement as to whether enough adaptations have created a new species, so it can be argued there is some blurring.
The article shows clearly that what was once believed to be a complete novelty in fact turns out to be an adjustment of existing structures. What current guidelines are able to tell us whether an apparently new feature is an out-of-the-blue innovation or an adaptation of an existing structure?
DAVID: If speciation can occur naturally by actions of the organisms genome, we've agreed that genome must have a central command post to orchestrate the design changes. I accept a God-given change mechanism, but only with God-given guidelines.
I’m actually hesitant about a “central command post” for the whole genome, though I accepted it earlier. I’d feel safer sticking with the concept of cooperation between intelligent cell communities. The only guidelines you can ever come up with are personal dabbling or a 3.8-billion-year-old computer programme for every change – the very opposite of AUTONOMOUS cells/cell communities which cooperate to produce the changes that allow the organism to adapt or innovate in response to changing conditions.
DAVID: Until we find a command post, if it exists, we can only theorize. The only command post may well turn out to be God at work. While we cannot be sure, at this point, my bet is still on God.
Of course it’s a theory. If it was a fact, there would be no discussion. Once again, I am delighted that at long last you are opening the door to the theory instead of clinging rigidly to your fixed belief in the 3.8-billion-year-old set of programmes for all undabbled innovations etc. which constitutes the God theory you are betting on.
Under “Bacterial chemical communication”:
QUOTE: "'It is quite fascinating for us to see how the bacteria communicate and change behaviour in order for the entire bacterial population to survive. You can almost say that they act as one united organism', says Nina Molin Høyland-Kroghsbo."
DAVID: None of this is surprising. Most antibiotics have been found in nature and then used medically. Bacteriophages are viruses in nature that attack bacteria. It all fits with my comments that bacteria are free-living cells that must have these defenses naturally on board as they appeared at the start of life.
Bacteria communicating, cooperating and changing their behaviour in accordance with whatever new dangers arise from changing conditions fits in with my comments that bacteria are indeed free-living, autonomous cells who use their intelligence to communicate, cooperate and change their behaviour - as opposed to having all the answers prepared for them at the start of life, leaving them only to unconsciously switch on the right one at the right time. And I would suggest that their behaviour is mirrored by that of all the cell communities that make up all bodies: “they act as one united organism”. I’m sure Shapiro would agree.
Making new evolutionary innovations
by David Turell , Sunday, November 24, 2019, 21:20 (1824 days ago) @ dhw
dhw: Thank you for this very important article, which both reinforces and explains my own insistence that we cannot draw a firm borderline between adaptation and innovation. (The dolphin example exactly mirrors our own example of the whale.) More importantly, it explains how common descent proceeds – there is some mechanism within the genes (which we may define as “the fundamental units of inheritance and function in a cell”) which enables them to change so radically that they can produce what appears to be every “evolutionary novelty” (Shapiro) leading to speciation. The scientists have simply induced a process which may be perfectly natural. But yes, common descent fits your theory of 3.8 billion years' worth of computer programming as it does Shapiro’s (and my) concept of intelligent cells/cell communities designing their own innovations. The latter theory does not, however, cover the possible origin of the mechanism, which may or may not be your God.
DAVID: A very fair summary of where we are. There is a firm boundary, if we follow current guidelines in naming new species. Of course it is human judgement as to whether enough adaptations have created a new species, so it can be argued there is some blurring.
dhw: The article shows clearly that what was once believed to be a complete novelty in fact turns out to be an adjustment of existing structures. What current guidelines are able to tell us whether an apparently new feature is an out-of-the-blue innovation or an adaptation of an existing structure?
I've said it is up to human judgement, since we name new species. I still insist, an adaptation is a change in an existing species. Try this:
The following definitions are given by the evolutionary biologist Theodosius Dobzhansky:
1. Adaptation is the evolutionary process whereby an organism becomes better able to live in its habitat or habitats.
2. Adaptedness is the state of being adapted: the degree to which an organism is able to live and reproduce in a given set of habitats.
3. An adaptive trait is an aspect of the developmental pattern of the organism which enables or enhances the probability of that organism surviving and reproducing.
https://en.wikipedia.org/wiki/Adaptation
DAVID: If speciation can occur naturally by actions of the organisms genome, we've agreed that genome must have a central command post to orchestrate the design changes. I accept a God-given change mechanism, but only with God-given guidelines.
dhw: I’m actually hesitant about a “central command post” for the whole genome, though I accepted it earlier. I’d feel safer sticking with the concept of cooperation between intelligent cell communities.
All of the cells in a multicellular organism have assigned duties The command post has to a part of the genome. All the cells have modified DNA to give them their job/purpose. Tell me where your committees exist?
Under “Bacterial chemical communication”:
QUOTE: "'It is quite fascinating for us to see how the bacteria communicate and change behaviour in order for the entire bacterial population to survive. You can almost say that they act as one united organism', says Nina Molin Høyland-Kroghsbo."
DAVID: None of this is surprising. Most antibiotics have been found in nature and then used medically. Bacteriophages are viruses in nature that attack bacteria. It all fits with my comments that bacteria are free-living cells that must have these defenses naturally on board as they appeared at the start of life.
dhw: Bacteria communicating, cooperating and changing their behaviour in accordance with whatever new dangers arise from changing conditions fits in with my comments that bacteria are indeed free-living, autonomous cells who use their intelligence to communicate, cooperate and change their behaviour - as opposed to having all the answers prepared for them at the start of life, leaving them only to unconsciously switch on the right one at the right time. And I would suggest that their behaviour is mirrored by that of all the cell communities that make up all bodies: “they act as one united organism”. I’m sure Shapiro would agree.
That is an exact extrapolation Shapiro uses for his theory of evolution. Bacteria are not multicellular organisms and must have their free-living attributes. Cells in whole multicellular organ isms are fixed in their functions. The genome controls new species, as IDEer's believe by God's manipulation. If not God, materialism must accept the genome itself.
Making new evolutionary innovations; more observations
by David Turell , Monday, November 25, 2019, 01:05 (1824 days ago) @ David Turell
An other source covers the study:
https://cosmosmagazine.com/biology/dung-beetle-s-horns-not-so-novel-after-all?utm_sourc...
"In that respect, the horns of the enigmatic Scarabaeidae dung beetle are popularly showcased as an example of evolutionary novelty, because their ancestors are hornless and the features don’t appear to be related to any other structure in the insect.
"A new study, published in the journal Science, has found otherwise.
"Yonggang Hu and co-authors from Indiana University, US, discovered that the prothoracic horn developed from the same core network of genes as insect wings on neighbouring thoracic segments.
"This ancient network of genes existed before wings, horns and even insects, in every segment along the body.
***
"They also showed that manipulating other genes forced the horns to grow into “ectopic” wings – extra wings on the wrong part of the body – demonstrating that the horns and wings both derived from the same gene network.
“This work forces us to rethink what we mean by ‘novelty’,” says senior author Armin Moczek. “Each insect segment possesses this gene network, and as such, it is an ancient feature of their makeup.
“'This new evidence is profound since it suggests that all of this vast diversity, all these novelties could in fact be enabled by a single gene network that was used millions of years ago to form the flight wings on other body segments.” (my bold)
"In a related commentary, H. Frederik Nijhout from Duke University, US, writes that scientists have long suspected novel features don’t arise from new genetic mutations as hypothesised, but until now, a better explanation was lacking.
"The new discovery builds on insights by modern developmental genetics, which according to Nijhout “reveal[s] that a surprisingly small toolbox of regulatory genes controls the development of exceptionally diverse and seemingly unrelated structures'”.
Comment: note my bolds. It is genes not cell committees that cause major changes, genes that are free from designated restrictions as in multicellular organisms. Further the gene toolbox is setup very early by God to allow Him to manipulate advances easily. Behe thinks is is deletion which causes advances, and he presents lots of evidence from genomic studies of change.
Making new evolutionary innovations
dhw: The article shows clearly that what was once believed to be a complete novelty in fact turns out to be an adjustment of existing structures. What current guidelines are able to tell us whether an apparently new feature is an out-of-the-blue innovation or an adaptation of an existing structure?
DAVID: I've said it is up to human judgement, since we name new species. I still insist, an adaptation is a change in an existing species. Try this:
[…] Theodosius Dobzhansky:
1. Adaptation is the evolutionary process whereby an organism becomes better able to live in its habitat or habitats.
Plus two more. You are missing the point. We know what an adaptation is. What we do not know is the extent to which the mechanics of adaptation may lead to what we believe to be innovation, although the article points out that this may be a restructuring of existing structures:
"However, some experts argue this creates a problem since it means novelty must seemingly arise from nothing. It must "pop up out of the blue" in evolutionary time."
"Now evidence has emerged—in a study published Nov. 21 in the journal Science—that illuminates how new things can evolve.” (dhw’s bold – i.e. be formed out of existing things).
"The new IU-led study […] provides evidence that the formation of the thoracic horn is instructed by the same core network of genes that led to the evolution of insect wings…”
We know what adaptation means, but what appears to be innovation may actually be adaptation.
Now you’ve offered new quotes: 'This new evidence is profound since it suggests that all of this vast diversity, all these novelties could in fact be enabled by a single gene network that was used millions of years ago to form the flight wings on other body segments.” (David’s bold)
"The new discovery builds on insights by modern developmental genetics, which according to Nijhout “reveal[s] that a surprisingly small toolbox of regulatory genes controls the development of exceptionally diverse and seemingly unrelated structures'”. (David’s bold)
DAVID : note my bolds. It is genes not cell committees that cause major changes, genes that are free from designated restrictions as in multicellular organisms. Further the gene toolbox is setup very early by God to allow Him to manipulate advances easily. Behe thinks is is deletion which causes advances, and he presents lots of evidence from genomic studies of change.
You seem to think that genes are somehow separate from cells! Shapiro’s term is “natural genetic engineering”, and specifies that the cells “have the ability to alter their hereditary characteristics”. Of course there must be genes which can be altered, and your bolds simply confirm that the mechanism for common descent consists of a small supply of flexible genes which can be used in an almost infinite variety of ways. But used by what? You say God preprogrammed or personally dabbled every single change, and Behe presumably says all the programmes were present and God simply took away the irrelevant ones. Shapiro proposes that the cells themselves decide how to use their “toolbox” as and when new circumstances arise.
dhw: I’m actually hesitant about a “central command post” for the whole genome, though I accepted it earlier. I’d feel safer sticking with the concept of cooperation between intelligent cell communities.
DAVID: All of the cells in a multicellular organism have assigned duties The command post has to a part of the genome. All the cells have modified DNA to give them their job/purpose. Tell me where your committees exist?
I’ve just said that my cell communities cooperate, and since they are all different, it is fair to assume that they all have their own “command posts” somewhere within the cells themselves. And although the cells/cell communities have assigned duties if the organism is to function, they may be reassigned to different duties (as in the half-brain example) when they are exposed to new conditions or when things go wrong.
dhw: [re bacteria] I would suggest that their behaviour is mirrored by that of all the cell communities that make up all bodies: “they act as one united organism”. I’m sure Shapiro would agree.
DAVID: That is an exact extrapolation Shapiro uses for his theory of evolution. Bacteria are not multicellular organisms and must have their free-living attributes. Cells in whole multicellular organisms are fixed in their functions. The genome controls new species, as IDEer's believe by God's manipulation. If not God, materialism must accept the genome itself.
Please stop pretending that Shapiro only knows about bacteria. See above for “fixed functions”. What do you mean by “manipulation” of the genome? You only offer us a 3.8-billion-year-old set of programmes or personal dabbling as God’s method of making changes. Shapiro’s theory offers autonomy in the form of “natural genetic engineering” in which the cells manipulate the genome themselves. That does not make him a materialist. One can simply argue that instead of your God fiddling with the materials, he created the mechanism enabling the materials to fiddle with themselves.
Making new evolutionary innovations
by David Turell , Tuesday, November 26, 2019, 00:40 (1823 days ago) @ dhw
dhw: Plus two more. You are missing the point. We know what an adaptation is. What we do not know is the extent to which the mechanics of adaptation may lead to what we believe to be innovation, although the article points out that this may be a restructuring of existing structures:
"However, some experts argue this creates a problem since it means novelty must seemingly arise from nothing. It must "pop up out of the blue" in evolutionary time."
"Now evidence has emerged—in a study published Nov. 21 in the journal Science—that illuminates how new things can evolve.” (dhw’s bold – i.e. be formed out of existing things)."The new IU-led study […] provides evidence that the formation of the thoracic horn is instructed by the same core network of genes that led to the evolution of insect wings…”
We know what adaptation means, but what appears to be innovation may actually be adaptation.
Now you’ve offered new quotes: 'This new evidence is profound since it suggests that all of this vast diversity, all these novelties could in fact be enabled by a single gene network that was used millions of years ago to form the flight wings on other body segments.” (David’s bold)"The new discovery builds on insights by modern developmental genetics, which according to Nijhout “reveal[s] that a surprisingly small toolbox of regulatory genes controls the development of exceptionally diverse and seemingly unrelated structures'”. (David’s bold)
DAVID : note my bolds. It is genes not cell committees that cause major changes, genes that are free from designated restrictions as in multicellular organisms. Further the gene toolbox is setup very early by God to allow Him to manipulate advances easily. Behe thinks is is deletion which causes advances, and he presents lots of evidence from genomic studies of change.
dhw: You seem to think that genes are somehow separate from cells! Shapiro’s term is “natural genetic engineering”, and specifies that the cells “have the ability to alter their hereditary characteristics”. Of course there must be genes which can be altered, and your bolds simply confirm that the mechanism for common descent consists of a small supply of flexible genes which can be used in an almost infinite variety of ways. But used by what? You say God preprogrammed or personally dabbled every single change, and Behe presumably says all the programmes were present and God simply took away the irrelevant ones. Shapiro proposes that the cells themselves decide how to use their “toolbox” as and when new circumstances arise.
You persist in skipping over the fact that cells in multicellular organisms are programmed in their DNA for specificity of action. You are suggesting that somehow they have to get together and make decisions for enough changes to become new species. I'm staying with the descision as in the study an agency did the changes, as the study scientists actually did! And it fits what God as agent can do.
dhw: I’m actually hesitant about a “central command post” for the whole genome, though I accepted it earlier. I’d feel safer sticking with the concept of cooperation between intelligent cell communities.DAVID: All of the cells in a multicellular organism have assigned duties The command post has to a part of the genome. All the cells have modified DNA to give them their job/purpose. Tell me where your committees exist?
I’ve just said that my cell communities cooperate, and since they are all different, it is fair to assume that they all have their own “command posts” somewhere within the cells themselves. And although the cells/cell communities have assigned duties if the organism is to function, they may be reassigned to different duties (as in the half-brain example) when they are exposed to new conditions or when things go wrong.
dhw: [re bacteria] I would suggest that their behaviour is mirrored by that of all the cell communities that make up all bodies: “they act as one united organism”. I’m sure Shapiro would agree.
DAVID: That is an exact extrapolation Shapiro uses for his theory of evolution. Bacteria are not multicellular organisms and must have their free-living attributes. Cells in whole multicellular organisms are fixed in their functions. The genome controls new species, as IDEer's believe by God's manipulation. If not God, materialism must accept the genome itself.
dhw: Please stop pretending that Shapiro only knows about bacteria.
That is not what I present to you. He has done a fabulous piece of work. Of course Shapiro knows about genetic biology all over the spectrum. His book is a presentation of his bacterial findings with an attempted extrapolation to the multicellular. His book is filled with references to current research which suggest there is a possibility his findings will in the future, with much more research, have an application. You do not understand his book from the reviews.
Making new evolutionary innovations
dhw: You seem to think that genes are somehow separate from cells! Shapiro’s term is “natural genetic engineering”, and specifies that the cells “have the ability to alter their hereditary characteristics”. Of course there must be genes which can be altered, and your bolds simply confirm that the mechanism for common descent consists of a small supply of flexible genes which can be used in an almost infinite variety of ways. But used by what? You say God preprogrammed or personally dabbled every single change, and Behe presumably says all the programmes were present and God simply took away the irrelevant ones. Shapiro proposes that the cells themselves decide how to use their “toolbox” as and when new circumstances arise.
DAVID: You persist in skipping over the fact that cells in multicellular organisms are programmed in their DNA for specificity of action.
You persist in skipping over the fact that of course they are programmed for specificity once the species has been formed! But speciation involves changes to the programme!
DAVID: You are suggesting that somehow they have to get together and make decisions for enough changes to become new species.
Exactly.
DAVID: I'm staying with the descision as in the study an agency did the changes, as the study scientists actually did! And it fits what God as agent can do.
Yes indeed, the scientists showed that cell communities can change. Shapiro and I suggest that the cells can make their own changes, and you suggest that they can’t and so only God can do it through dabbling or a 3.8-billion-year-old set of computer programmes. That is what we have been arguing about for several years.
dhw: Please stop pretending that Shapiro only knows about bacteria.
DAVID: That is not what I present to you. He has done a fabulous piece of work. Of course Shapiro knows about genetic biology all over the spectrum. His book is a presentation of his bacterial findings with an attempted extrapolation to the multicellular. His book is filled with references to current research which suggest there is a possibility his findings will in the future, with much more research, have an application. You do not understand his book from the reviews.
Thank you for confirming that Shapiro’s theory is just as I have presented it, and that he must have done a lot of research outside his own specialist field. So please stop harping on about the fact that his own research was confined to bacteria. That is irrelevant.
Making new evolutionary innovations
by David Turell , Tuesday, November 26, 2019, 15:51 (1822 days ago) @ dhw
dhw: You seem to think that genes are somehow separate from cells! Shapiro’s term is “natural genetic engineering”, and specifies that the cells “have the ability to alter their hereditary characteristics”. Of course there must be genes which can be altered, and your bolds simply confirm that the mechanism for common descent consists of a small supply of flexible genes which can be used in an almost infinite variety of ways. But used by what? You say God preprogrammed or personally dabbled every single change, and Behe presumably says all the programmes were present and God simply took away the irrelevant ones. Shapiro proposes that the cells themselves decide how to use their “toolbox” as and when new circumstances arise.
DAVID: You persist in skipping over the fact that cells in multicellular organisms are programmed in their DNA for specificity of action.
dhw: you persist in skipping over the fact that of course they are programmed for specificity once the species has been formed! But speciation involves changes to the programme!
The only cells I know of that are pristine are stem cells. How do individual groups of them in different parts of the body communicate to decide on a major change? I still thinks it needs an agent.
DAVID: You are suggesting that somehow they have to get together and make decisions for enough changes to become new species.Exactly.
DAVID: I'm staying with the descision as in the study an agency did the changes, as the study scientists actually did! And it fits what God as agent can do.
Yes indeed, the scientists showed that cell communities can change. Shapiro and I suggest that the cells can make their own changes, and you suggest that they can’t and so only God can do it through dabbling or a 3.8-billion-year-old set of computer programmes. That is what we have been arguing about for several years.
dhw: Please stop pretending that Shapiro only knows about bacteria.
DAVID: That is not what I present to you. He has done a fabulous piece of work. Of course Shapiro knows about genetic biology all over the spectrum. His book is a presentation of his bacterial findings with an attempted extrapolation to the multicellular. His book is filled with references to current research which suggest there is a possibility his findings will in the future, with much more research, have an application. You do not understand his book from the reviews.
dhw: Thank you for confirming that Shapiro’s theory is just as I have presented it, and that he must have done a lot of research outside his own specialist field. So please stop harping on about the fact that his own research was confined to bacteria. That is irrelevant.
It is not irrelevant since he tries to plug it into major evolution processes as you do and it is just a theory that has not received any support I can find. You have a right to support the theory of course.
Making new evolutionary innovations
DAVID: You persist in skipping over the fact that cells in multicellular organisms are programmed in their DNA for specificity of action.
dhw: you persist in skipping over the fact that of course they are programmed for specificity once the species has been formed! But speciation involves changes to the programme!
DAVID: The only cells I know of that are pristine are stem cells. How do individual groups of them in different parts of the body communicate to decide on a major change? I still thinks it needs an agent.
Stem cells may well be the key to the whole evolutionary process. Cell communities would communicate in the same way as when they decide on a minor change. Why do you think cells are incapable of communication when all the articles you have presented here illustrate that very process?
DAVID: That is not what I present to you. He has done a fabulous piece of work. Of course Shapiro knows about genetic biology all over the spectrum. His book is a presentation of his bacterial findings with an attempted extrapolation to the multicellular. His book is filled with references to current research which suggest there is a possibility his findings will in the future, with much more research, have an application. You do not understand his book from the reviews.
dhw: Thank you for confirming that Shapiro’s theory is just as I have presented it, and that he must have done a lot of research outside his own specialist field. So please stop harping on about the fact that his own research was confined to bacteria. That is irrelevant.
DAVID: It is not irrelevant since he tries to plug it into major evolution processes as you do and it is just a theory that has not received any support I can find. You have a right to support the theory of course.
He obviously plugs it into major evolution processes using the research of others (“references to current research”) who are as convinced as he is that cells are cognitive, sentient, intelligent beings. The rest of his theory (and mine) grows from this one basic premise, and the fact that his personal research is confined to bacteria does not invalidate the argument. Of course it is “just a theory”, as is the existence of your God, and your belief in a 3.8-billion-year-old set of programmes for all undabbled innovations. We can only test the feasibility of each theory that is proposed. I do not regard the theorist’s main field of research as relevant to the reasonableness of his theory.
Making new evolutionary innovations
by David Turell , Wednesday, November 27, 2019, 15:40 (1821 days ago) @ dhw
DAVID: You persist in skipping over the fact that cells in multicellular organisms are programmed in their DNA for specificity of action.
dhw: you persist in skipping over the fact that of course they are programmed for specificity once the species has been formed! But speciation involves changes to the programme!
DAVID: The only cells I know of that are pristine are stem cells. How do individual groups of them in different parts of the body communicate to decide on a major change? I still thinks it needs an agent.
dhw: Stem cells may well be the key to the whole evolutionary process. Cell communities would communicate in the same way as when they decide on a minor change. Why do you think cells are incapable of communication when all the articles you have presented here illustrate that very process?
Of course I know cells communicate in their daily duties in my articles. We know of nothing further. How they can arrange to design is my issue.
DAVID: That is not what I present to you. He has done a fabulous piece of work. Of course Shapiro knows about genetic biology all over the spectrum. His book is a presentation of his bacterial findings with an attempted extrapolation to the multicellular. His book is filled with references to current research which suggest there is a possibility his findings will in the future, with much more research, have an application. You do not understand his book from the reviews.dhw: Thank you for confirming that Shapiro’s theory is just as I have presented it, and that he must have done a lot of research outside his own specialist field. So please stop harping on about the fact that his own research was confined to bacteria. That is irrelevant.
DAVID: It is not irrelevant since he tries to plug it into major evolution processes as you do and it is just a theory that has not received any support I can find. You have a right to support the theory of course.
dhw: He obviously plugs it into major evolution processes using the research of others (“references to current research”) who are as convinced as he is that cells are cognitive, sentient, intelligent beings. The rest of his theory (and mine) grows from this one basic premise, and the fact that his personal research is confined to bacteria does not invalidate the argument. Of course it is “just a theory”, as is the existence of your God, and your belief in a 3.8-billion-year-old set of programmes for all undabbled innovations. We can only test the feasibility of each theory that is proposed. I do not regard the theorist’s main field of research as relevant to the reasonableness of his theory.
The reason I explained his field is to show how he developed his theory, and I do not know if it can be applied to multicellular evolution. However his research is an important addition to all the research. Note it also helped to destroy most of the Darwin theory.
Making new evolutionary innovations
DAVID: The only cells I know of that are pristine are stem cells. How do individual groups of them in different parts of the body communicate to decide on a major change? I still thinks it needs an agent.
dhw: Stem cells may well be the key to the whole evolutionary process. Cell communities would communicate in the same way as when they decide on a minor change. Why do you think cells are incapable of communication when all the articles you have presented here illustrate that very process?
DAVID: Of course I know cells communicate in their daily duties in my articles. We know of nothing further. How they can arrange to design is my issue.
So why did you ask how they communicate? I know you don’t think they are capable of cooperating in order to design something new, but communication is not an issue.
Making new evolutionary innovations
by David Turell , Thursday, November 28, 2019, 18:27 (1820 days ago) @ dhw
DAVID: The only cells I know of that are pristine are stem cells. How do individual groups of them in different parts of the body communicate to decide on a major change? I still thinks it needs an agent.
dhw: Stem cells may well be the key to the whole evolutionary process. Cell communities would communicate in the same way as when they decide on a minor change. Why do you think cells are incapable of communication when all the articles you have presented here illustrate that very process?
DAVID: Of course I know cells communicate in their daily duties in my articles. We know of nothing further. How they can arrange to design is my issue.
dhw: So why did you ask how they communicate? I know you don’t think they are capable of cooperating in order to design something new, but communication is not an issue.
Since you think the cells communicate their so-called intelligence, I asked you how they do it, at that intellectual level in order to design. We know how they communicate during daily work.
Making new evolutionary innovations
DAVID: The only cells I know of that are pristine are stem cells. How do individual groups of them in different parts of the body communicate to decide on a major change? I still thinks it needs an agent.
dhw: Stem cells may well be the key to the whole evolutionary process. Cell communities would communicate in the same way as when they decide on a minor change. Why do you think cells are incapable of communication when all the articles you have presented here illustrate that very process?
DAVID: Of course I know cells communicate in their daily duties in my articles. We know of nothing further. How they can arrange to design is my issue.
dhw: So why did you ask how they communicate? I know you don’t think they are capable of cooperating in order to design something new, but communication is not an issue.
DAVID: Since you think the cells communicate their so-called intelligence, I asked you how they do it, at that intellectual level in order to design. We know how they communicate during daily work.
You are trying to conflate two issues. You do not accept that cells have the intelligence to do their own designing. This has nothing whatsoever to do with communication, because they would use exactly the same means of communicating innovative “thoughts” as they use to communicate adaptive “thoughts” and the “thoughts” required for their everyday work. This is a non-discussion.
Making new evolutionary innovations
by David Turell , Friday, November 29, 2019, 19:59 (1819 days ago) @ dhw
DAVID: The only cells I know of that are pristine are stem cells. How do individual groups of them in different parts of the body communicate to decide on a major change? I still thinks it needs an agent.
dhw: Stem cells may well be the key to the whole evolutionary process. Cell communities would communicate in the same way as when they decide on a minor change. Why do you think cells are incapable of communication when all the articles you have presented here illustrate that very process?
DAVID: Of course I know cells communicate in their daily duties in my articles. We know of nothing further. How they can arrange to design is my issue.
dhw: So why did you ask how they communicate? I know you don’t think they are capable of cooperating in order to design something new, but communication is not an issue.
DAVID: Since you think the cells communicate their so-called intelligence, I asked you how they do it, at that intellectual level in order to design. We know how they communicate during daily work.
dhw: You are trying to conflate two issues. You do not accept that cells have the intelligence to do their own designing. This has nothing whatsoever to do with communication, because they would use exactly the same means of communicating innovative “thoughts” as they use to communicate adaptive “thoughts” and the “thoughts” required for their everyday work. This is a non-discussion.
No, I'm not conflating. We only know how cells communicate during daily work. You suppose another line of design communication that has no current evidence. I prefer to work with theory from existing evidence.
Making new evolutionary innovations
DAVID: The only cells I know of that are pristine are stem cells. How do individual groups of them in different parts of the body communicate to decide on a major change? I still thinks it needs an agent.
dhw: Stem cells may well be the key to the whole evolutionary process. Cell communities would communicate in the same way as when they decide on a minor change. Why do you think cells are incapable of communication when all the articles you have presented here illustrate that very process?
DAVID: Of course I know cells communicate in their daily duties in my articles. We know of nothing further. How they can arrange to design is my issue.
dhw: So why did you ask how they communicate? I know you don’t think they are capable of cooperating in order to design something new, but communication is not an issue.
DAVID: Since you think the cells communicate their so-called intelligence, I asked you how they do it, at that intellectual level in order to design. We know how they communicate during daily work.
dhw: You are trying to conflate two issues. You do not accept that cells have the intelligence to do their own designing. This has nothing whatsoever to do with communication, because they would use exactly the same means of communicating innovative “thoughts” as they use to communicate adaptive “thoughts” and the “thoughts” required for their everyday work. This is a non-discussion.
DAVID: No, I'm not conflating. We only know how cells communicate during daily work. You suppose another line of design communication that has no current evidence. I prefer to work with theory from existing evidence.
What on earth is design communication? All organisms have their own means of communication. Cells communicate through chemical signals. Whether they communicate everyday tasks, adaptive tasks or innovative tasks, they will still communicate through chemical signals. But you do not believe they are capable of innovative tasks. A non-discussion which we should end.
Making new evolutionary innovations
by David Turell , Saturday, November 30, 2019, 20:59 (1818 days ago) @ dhw
DAVID: The only cells I know of that are pristine are stem cells. How do individual groups of them in different parts of the body communicate to decide on a major change? I still thinks it needs an agent.
dhw: Stem cells may well be the key to the whole evolutionary process. Cell communities would communicate in the same way as when they decide on a minor change. Why do you think cells are incapable of communication when all the articles you have presented here illustrate that very process?
DAVID: Of course I know cells communicate in their daily duties in my articles. We know of nothing further. How they can arrange to design is my issue.
dhw: So why did you ask how they communicate? I know you don’t think they are capable of cooperating in order to design something new, but communication is not an issue.
DAVID: Since you think the cells communicate their so-called intelligence, I asked you how they do it, at that intellectual level in order to design. We know how they communicate during daily work.
dhw: You are trying to conflate two issues. You do not accept that cells have the intelligence to do their own designing. This has nothing whatsoever to do with communication, because they would use exactly the same means of communicating innovative “thoughts” as they use to communicate adaptive “thoughts” and the “thoughts” required for their everyday work. This is a non-discussion.
DAVID: No, I'm not conflating. We only know how cells communicate during daily work. You suppose another line of design communication that has no current evidence. I prefer to work with theory from existing evidence.
dhw:What on earth is design communication? All organisms have their own means of communication. Cells communicate through chemical signals. Whether they communicate everyday tasks, adaptive tasks or innovative tasks, they will still communicate through chemical signals. But you do not believe they are capable of innovative tasks. A non-discussion which we should end.
We agree that cells communicate chemically in their everyday tasks. Those simple signals are go or no go. 'Design communication' is what is required in exchanging design concepts, something that requires a designing mind or minds ( like at Volvo), not extrapolation of poor Shapiro's theoretical extensions of his bacterial research.
Making new evolutionary innovations
dhw: You are trying to conflate two issues. You do not accept that cells have the intelligence to do their own designing. This has nothing whatsoever to do with communication, because they would use exactly the same means of communicating innovative “thoughts” as they use to communicate adaptive “thoughts” and the “thoughts” required for their everyday work. This is a non-discussion.
DAVID: No, I'm not conflating. We only know how cells communicate during daily work. You suppose another line of design communication that has no current evidence. I prefer to work with theory from existing evidence.
dhw: What on earth is design communication? All organisms have their own means of communication. Cells communicate through chemical signals. Whether they communicate everyday tasks, adaptive tasks or innovative tasks, they will still communicate through chemical signals. But you do not believe they are capable of innovative tasks. A non-discussion which we should end.
DAVID: We agree that cells communicate chemically in their everyday tasks. Those simple signals are go or no go. 'Design communication' is what is required in exchanging design concepts, something that requires a designing mind or minds ( like at Volvo), not extrapolation of poor Shapiro's theoretical extensions of his bacterial research.
You do not believe that cells are capable of designing innovations because you do not believe that they have designing minds. That is the nub of the matter. If they do have designing minds, they must use the same chemical means of communication as they use in performing their everyday tasks and their adaptations. I don’t know why the Shapiro you praised so highly in your book is now “poor” Shapiro, and I don’t know why you have gone back to pretending that he knows nothing about cellular behaviour, when you have acknowledged the research he has called upon. This discussion is becoming sillier and sillier.
Making new evolutionary innovations
by David Turell , Sunday, December 01, 2019, 15:39 (1817 days ago) @ dhw
dhw: You are trying to conflate two issues. You do not accept that cells have the intelligence to do their own designing. This has nothing whatsoever to do with communication, because they would use exactly the same means of communicating innovative “thoughts” as they use to communicate adaptive “thoughts” and the “thoughts” required for their everyday work. This is a non-discussion.
DAVID: No, I'm not conflating. We only know how cells communicate during daily work. You suppose another line of design communication that has no current evidence. I prefer to work with theory from existing evidence.
dhw: What on earth is design communication? All organisms have their own means of communication. Cells communicate through chemical signals. Whether they communicate everyday tasks, adaptive tasks or innovative tasks, they will still communicate through chemical signals. But you do not believe they are capable of innovative tasks. A non-discussion which we should end.
DAVID: We agree that cells communicate chemically in their everyday tasks. Those simple signals are go or no go. 'Design communication' is what is required in exchanging design concepts, something that requires a designing mind or minds ( like at Volvo), not extrapolation of poor Shapiro's theoretical extensions of his bacterial research.
dhw: You do not believe that cells are capable of designing innovations because you do not believe that they have designing minds. That is the nub of the matter. If they do have designing minds, they must use the same chemical means of communication as they use in performing their everyday tasks and their adaptations. I don’t know why the Shapiro you praised so highly in your book is now “poor” Shapiro, and I don’t know why you have gone back to pretending that he knows nothing about cellular behaviour, when you have acknowledged the research he has called upon. This discussion is becoming sillier and sillier.
Shapiro did fabulous work. He is a wonderful scientist. You have made him 'poor' by what I think is misusing his theories , and you haven't read the book, only reviews. He also published some lay articles which l have read, if I remember correctly the Atlantic, but no one else has picked his approach up and run with it that I can find. From his work we only know free-living bacteria can manipulate their genome, but after that all we have is possible unproven theory. We do know that in multicellular organisms, stem cells adjust DNA to make many different functioning styles of cells with different jobs. This is an exact replica of what bacteria do and therefore they are a forerunner of that stem cell ability! And that may be all that Shapiro has shown. That is not in any way the solution to the problem of speciation.
Making new evolutionary innovations
dhw: You do not believe that cells are capable of designing innovations because you do not believe that they have designing minds. That is the nub of the matter. If they do have designing minds, they must use the same chemical means of communication as they use in performing their everyday tasks and their adaptations. I don’t know why the Shapiro you praised so highly in your book is now “poor” Shapiro, and I don’t know why you have gone back to pretending that he knows nothing about cellular behaviour, when you have acknowledged the research he has called upon. This discussion is becoming sillier and sillier.
DAVID: Shapiro did fabulous work. He is a wonderful scientist. You have made him 'poor' by what I think is misusing his theories, and you haven't read the book, only reviews.
You have quoted him abundantly in your own book, and his theory is that “living cells are cognitive (sentient) entities that act and interact purposefully…”, they “have the ability to alter their hereditary characteristics”, and “evolutionary novelty arises from the prosecution of new cell and multicellular structures as a result of cellular self-modification”. That IS his theory. How am I misusing it?
DAVID: He also published some lay articles which l have read, if I remember correctly the Atlantic, but no one else has picked his approach up and run with it that I can find. From his work we only know free-living bacteria can manipulate their genome, but after that all we have is possible unproven theory.
Yes, it is as unproven as every other theory. If it was proven, it would be a fact. What is your point?
DAVID: We do know that in multicellular organisms, stem cells adjust DNA to make many different functioning styles of cells with different jobs. This is an exact replica of what bacteria do and therefore they are a forerunner of that stem cell ability! And that may be all that Shapiro has shown. That is not in any way the solution to the problem of
speciation.
It is a theory concerning how speciation may have occurred. If it’s true, it solves the problem. You can say the same about any theory, including your own. All of this flannelling serves only to distract attention from your silly question: “How do individual groups of [cells] in different parts of the body communicate to decide on a major change?” Answer: they would communicate in exactly the same way as they communicate on everyday tasks and adaptation – by chemical signals. Now we have the equally silly argument that an unproven theory to explain how speciation may happen does not prove how speciation happens. What next?
Making new evolutionary innovations
by David Turell , Tuesday, December 03, 2019, 01:03 (1816 days ago) @ dhw
DAVID: Shapiro did fabulous work. He is a wonderful scientist. You have made him 'poor' by what I think is misusing his theories, and you haven't read the book, only reviews.
dhw: You have quoted him abundantly in your own book, and his theory is that “living cells are cognitive (sentient) entities that act and interact purposefully…”, they “have the ability to alter their hereditary characteristics”, and “evolutionary novelty arises from the prosecution of new cell and multicellular structures as a result of cellular self-modification”. That IS his theory. How am I misusing it?
As I have over the years my concepts have altered. I should have emphasized that his work on
bacteria was something he tried to extrapolate to further understanding of the genetic role in further evolution/speciation. He was not discussing the everyday function of multicellular cells.
DAVID: He also published some lay articles which l have read, if I remember correctly the Atlantic, but no one else has picked his approach up and run with it that I can find. From his work we only know free-living bacteria can manipulate their genome, but after that all we have is possible unproven theory.dhw: Yes, it is as unproven as every other theory. If it was proven, it would be a fact. What is your point?
you have grabbed and run with his theories when I don't think from my readings of his articles that he would agree with your conclusions.
DAVID: We do know that in multicellular organisms, stem cells adjust DNA to make many different functioning styles of cells with different jobs. This is an exact replica of what bacteria do and therefore they are a forerunner of that stem cell ability! And that may be all that Shapiro has shown. That is not in any way the solution to the problem of
speciation.dhw: It is a theory concerning how speciation may have occurred. If it’s true, it solves the problem. You can say the same about any theory, including your own. All of this flannelling serves only to distract attention from your silly question: “How do individual groups of [cells] in different parts of the body communicate to decide on a major change?” Answer: they would communicate in exactly the same way as they communicate on everyday tasks and adaptation – by chemical signals. Now we have the equally silly argument that an unproven theory to explain how speciation may happen does not prove how speciation happens.
What next?
I'll continue: the chemical signals represent information/instructions, not thought in design or planning design. Cell A might ask cell B to produce something which B knows how to do from the instructions it carries. You made no comment abut my idea that stem cells might represent Shapiro's bacterial work as part of how evolution produced complexity in organisms.
Making new evolutionary innovations: butterfly study
by David Turell , Wednesday, December 11, 2019, 18:38 (1807 days ago) @ David Turell
Their so called species interbreed:
http://nautil.us/blog/do-butterflies-challenge-the-meaning-of-species
"Researchers recently analyzing the genomes of every butterfly species in the United States and Canada—845 in total—have revealed that at critical evolutionary intervals, butterfly species have crossed the reproductive barrier, mating with other species of butterfly and thereby transferring genes from one species to another. Hybridization, it turns out, plays a pivotal role in how life forms evolve. The tree of life may never look the same.
***
"Traditional taxonomy had outlined an ancestral tree for butterflies, discerning family, tribe, genus, and species based on the overall body shape of the butterfly and wing-pattern. By sequencing the genomes of all 845 butterfly species, Grishin and colleagues were able to work out a genomic family tree that in large part agreed with the existing one based on anatomy. But it also showed more. “People thought butterflies were closely related based on what they look like, but genomically, we saw something else.” Grishin’s group reclassified 40 species and suggested several new genus levels.
"Analyzing the genes of multiple species added a huge new dimension to the idea of “butterflies,” because it revealed not just the species themselves but also the relationships between them. Going back 70 million years, a burst of diversification ensued. Butterfly subfamilies appeared with major evolutionary inventions as a result of high positive selection (the tendency of beneficial traits to increase in a population), which is the overall driving force of adaptive evolution. Another burst, an explosive radiation in butterfly species, came about five million years ago
“'One surprise is that there are so many diversifications,” Grishin told me. “We see lots of rapid radiation in some groups—with many species forming in short periods of time. We didn’t understand the degree to which interbreeding was driving genetic transfer.” The hybridization tends to happen in “younger” species, many of which will eventually die off. Grishin explains it this way: “There are patterns of a cycle in butterfly evolution. Diversification, radiation, introgression, extinction, and repeat.” The timing, duration, and character of this pattern depend foundationally on geological change. “Butterflies exchange these genes and some of them can spread because they have beneficial genes” that aid in adapting to new conditions.
"It may be that the species paradigm needs a big overhaul if seemingly well-separated animals can actually interbreed. The revelations of butterflies are informing long-standing questions about Homo sapiens, for example. We have ancient DNA that may or may not have come by way of our ancestors mating with Neanderthals. “It’s possible we received genes from Neanderthals that enabled us to move out of Africa and into cooler climates,” Grishin said.
"As the picture of life gets longer and deeper thanks to genetic analysis, so too the humble arts play their part. Grishin and Cong are both computational scientists who work in the lab and not in the field. Yet Grishin credits Cong and colleagues with becoming stellar amateur lepidopterists in the course of their research. Instead of flying to conferences, they would drive, stopping by the side of the road to collect butterflies. Cong told me that their research adds to those with similar ambitions, “to obtain genomes of every species on Earth. These genomes are gifts from millions of years of evolution. Nature did the experiments, and we are trying to check the results.'”
Comment: We still do not understand speciation and morphological comparisons are not as good as genome studies in analyzing evolutionary relationships.
Making new evolutionary innovations: butterfly study
QUOTE: By sequencing the genomes of all 845 butterfly species, Grishin and colleagues were able to work out a genomic family tree that in large part agreed with the existing one based on anatomy. But it also showed more. “People thought butterflies were closely related based on what they look like, but genomically, we saw something else.” Grishin’s group reclassified 40 species and suggested several new genus levels.
This whole study is based on the narrowest possible view of speciation. All of these butterflies remain butterflies, and the variations may be attributed to interbreeding and adaptation. The mystery of evolution lies in the innovations that have resulted in the broader concept of “species”, i.e. ants as opposed to sharks as opposed to eagles as opposed to lions as opposed to humans.
Making new evolutionary innovations: butterfly study
by David Turell , Thursday, December 12, 2019, 19:29 (1806 days ago) @ dhw
QUOTE: By sequencing the genomes of all 845 butterfly species, Grishin and colleagues were able to work out a genomic family tree that in large part agreed with the existing one based on anatomy. But it also showed more. “People thought butterflies were closely related based on what they look like, but genomically, we saw something else.” Grishin’s group reclassified 40 species and suggested several new genus levels.
dhw: This whole study is based on the narrowest possible view of speciation. All of these butterflies remain butterflies, and the variations may be attributed to interbreeding and adaptation. The mystery of evolution lies in the innovations that have resulted in the broader concept of “species”, i.e. ants as opposed to sharks as opposed to eagles as opposed to lions as opposed to humans.
You are right. Adds nothing to the concept of advancing evolution and speciation, but the key point is genome studies must classify.
Making new evolutionary innovations: latest butterfly study
by David Turell , Wednesday, February 14, 2024, 23:54 (281 days ago) @ David Turell
Pushes origin back millions of years:
https://www.smithsonianmag.com/science-nature/where-did-butterflies-come-from-scientist...
"This past May, working with nearly 90 co-authors from six continents, he published the results of a massive global study of butterfly evolution, based on DNA samples from 2,300 butterfly species. Not only does it fill in the gaps on the phylogeny chart he saw as a child, but it also presents a completely new origin story for these charismatic insects. Most scientists thought they evolved in Australasia, but it seems most likely that the first butterflies appeared in North and Central America. The ancestor of butterflies was a nocturnal moth that became day-flying here, 101.4 million years ago. (my bold)
***
"Moths were the focus of Kawahara’s early career. He remains fascinated by them and likes to point out that butterflies are basically just moths that fly by day. Approximately half of moths have hearing abilities, and he’s particularly interested in a group that can hear bat sonar and make acoustic signals to “jam” the sonar and escape predation.
***
"The result is a beautiful, elaborate diagram that looks more like a wheel than a tree. Besides the breakthrough discoveries into where and when butterflies originated, it demonstrates that 36 tribes of butterflies need to be reclassified—and supports Kawahara’s 2019 hypothesis on how and why moths started flying in the day. Since the oldest intact fossilized butterfly was 55 million years old, and bats evolved in the same era, many scientists had thought that a group of moths became day-flying to escape bat predation. Now we know, thanks in large part to Kawahara’s revelatory work, that butterflies originated over 100 million years ago—some 35 million years before bats. Kawahara thinks that it was bees, not bats, that caused the advent of day-flying moths.
***
"By assigning a geographic area to every species in the study, and then using the DNA tree and supercomputers to calculate the probability that their ancestors were there in the past, researchers were able to form a hypothesis about the spread of butterflies around the world. First they fluttered east across North America and down into South America. Then they dispersed in waves to Australia, Asia, India, Africa and finally, around 30 million years ago, to Europe. Today there are an estimated 19,500 species, distributed all over the world except Antarctica, even on remote and isolated islands.
"By assigning a geographic area to every species in the study, and then using the DNA tree and supercomputers to calculate the probability that their ancestors were there in the past, researchers were able to form a hypothesis about the spread of butterflies around the world. First they fluttered east across North America and down into South America. Then they dispersed in waves to Australia, Asia, India, Africa and finally, around 30 million years ago, to Europe. Today there are an estimated 19,500 species, distributed all over the world except Antarctica, even on remote and isolated islands.
***
"Asked why some butterflies became so beautifully colored, Kawahara offers three generally agreed-upon reasons. “They’re displaying their chemical defense to predators, so birds and lizards, when they see a bright red butterfly, they think, ‘No, I’m not going to eat this thing because it’s toxic.’ Then there’s mimicry. Many butterflies look like the brightly colored toxic ones, but they’re not chemically defended. And lastly for mating. They use their colors to flash and display to the opposite sex.'”
Comment: so, butterflies came from moths that knew the dinosaurs. They pollinate which mean their arrival helped flowering plants which had recently arrived. Their fabulous coloration may be explained as above.
Making new evolutionary innovations efficiently
by David Turell , Monday, January 20, 2020, 00:03 (1768 days ago) @ David Turell
Patterns of vascular structures are evolved efficiently:
https://phys.org/news/2020-01-biology-networks-cheap-robust-efficient.html
"A new study shows how a wide variety of vascular networks can be created by changing only a small number of a network's attributes. Published in Physical Review Letters, the work of two physicists, former Penn postdoc Henrik Ronellenfitsch and professor Eleni Katifori, shows that vascular networks evolve through a tradeoff between how well the network can transport fluid, a network's "cost," or how many cells it takes to build the network, and its robustness, or how well the system works if part of the structure is damaged.
"This research builds off Katifori and Ronellenfitsch's previous work on "adaptation equations," mathematical models of systems that are good at a specific function, such as moving fluid. In this study, they wanted to see if their adaptation equation could get vascular networks to "self-organize" into the most efficient structure possible.
***
"When researchers want to analyze the costs and benefits of different trade-offs, they rely on a concept known as Pareto efficiency. As an example, in renovating a house with new insulation under a limited budget, one can either spend a lot of money and have a house that is well-insulated, or spend less money and do little to improve the insulation. The most efficient set of options, on the spectrum of low to high cost and from few to many renovations in the illustrative example, is known as the Pareto frontier. Using this approach, Ronellenfitsch was able to see which attributes were the most important to create efficient vascular networks. "The networks that we identify are those where you cannot improve any of these requirements without getting worse at one of the others," he says.
"The researchers found that vascular network efficiency was driven by how robust the network was to damage and how "expensive" it was to build. Across a spectrum of changes to these two attributes, researchers could create a wide variety of structures from intricately interwoven networks that were robust against damage to simpler designs that wouldn't stand up to breakage.
"But how does nature know how to balance cost with robustness? By simulating fluctuations, or changes in the average amount of fluid that moved through parts of the network, they found that changes in flow rates impact whether a network should be robust or not. "If you want something that is cheap but not robust, you'd better not have a lot of fluctuations," says Katifori.'
Comment: It takes a good designer to find just the right mix of attributes. It doesn't happen by trial and error, as proposed BY Darwin.
Making new evolutionary innovations: a neutral view of ID
by David Turell , Monday, March 30, 2020, 19:41 (1697 days ago) @ David Turell
This author does not take sides:
https://www.researchgate.net/publication/317332700_Intelligent_Design_Maybe_True_Maybe_...
"I do not wish to argue that intelligent design is true. I don't know if it's true. I also
do not wish to argue that it is a scientific position. I believe that it is not, but is instead an empirically undecidable, metaphysical one. I wish only to argue, contrary to the current intellectual zeitgeist, that it is neither stupid nor ridiculous either to believe in it or to entertain it as a possibility. I am referring here, not to a version of intelligent design that claims that the world was created 6000 years ago just as we find it today, but to one stating simply that there is now, or may have been at some time in the past, an ordering
intelligence behind the structure of the universe and its contents. I also want to argue that the position most commonly posed in opposition to it at the cosmic level (which is where
I will focus), which I shall refer to as "accidentalism," is not, as many would have it,
itself a scientifically open and shut case.
***
"Albert Einstein, a secular Jew who repeatedly affirmed his disbelief in a personal god, stated that, "The scientist's religious feeling takes the form of a rapturous amazement at the harmony of natural law, which reveals an intelligence of such superiority that, compared with it, all the systematic thinking and acting of human beings is an utterly insignificant reflection." Other great scientifically informed minds from the past (e.g., Galileo, Kepler, and Maxwell) as well as the present time (e.g., Francis Collins, Fred Hoyle, and Alan Sandage) have expressed essentially the same belief. My admittedly ad hominem point here is simply this: Whether intelligent design is true or not, if people with relevantly informed minds of this caliber -- some of them the greatest minds in scientific history -- believe in it, it seems unreasonable simply to dismiss it as a ridiculous position with no merit whatsoever.
***
"The foregoing discussion is not proffered as an argument for intelligent design. It
is, rather, an objection directed at those who, in response to any suggestion that intelligent design beliefs may have some merit, blithely assert that, "We have no need for that hypothesis. We have it all covered scientifically." Aside from the fact that, properly
understood, there is no conflict between science and intelligent design, it is simply not
true that "we have it all covered scientifically." As M.I.T. physicist Alan Lightman reports
in his fascinating article, "The Accidental Universe," there remain very deep and
unresolved questions about the extraordinary improbabilities in our cosmos.
"I do not claim to have a settled answer for myself. I just don't know. Intelligent design may or may not be the case -- I believe we will not, indeed cannot, ever know for sure -- but it is hard for me to dismiss as merely foolish Einstein's conjecture that there may exist "an intelligence of such superiority that, compared with it, all the systematic thinking and acting of human beings is an utterly insignificant reflection." At the end of the day, the existence or non-existence of such an intelligence cannot be established empirically, is not a matter for science, and should not be taught in science courses. It is a matter for belief, and I have tried here only to argue that such belief, at least in certain of its forms, is not unreasonable, ought not to be unreflectively branded "creationism", and should not be viewed with contempt. The possibility of intelligent design falls in the realm covered by Wittgenstein's famous assertion that "even when all possible scientific questions have been answered, the problems of life remain completely untouched.'"
Comment: The whole neutral article is a good read. Of course design is required. God comes with the establishment of faith.
Making new evolutionary innovations: symmetry
by David Turell , Thursday, April 07, 2022, 01:45 (960 days ago) @ David Turell
Why symmetry is explained in this paper:
http://www.sci-news.com/biology/mother-nature-symmetry-simplicity-10690.html
"Biological structures frequently exhibit modularity and symmetry, but the origin of such trends is not well understood. It can be tempting to assume — by analogy to engineering design — that symmetry and modularity arise from natural selection. However, evolution, unlike engineers, cannot plan ahead, and so these traits must also afford some immediate selective advantage which is hard to reconcile with the breadth of systems where symmetry is observed. In a new paper, published in the Proceedings of the National Academy of Sciences, scientists introduce an alternative hypothesis based on an algorithmic picture of evolution; it suggests that symmetric structures preferentially arise not just due to natural selection but also because they require less specific information to encode and are therefore much more likely to appear as genetic variation through random mutations. (my bold)
"From snowflakes to sunflowers, starfish to sharks, symmetry is everywhere in nature.
"Not just in the body plans which govern shape and form, but right down to the microscopic molecular machines keeping cells alive.
Although there is a larger collection of asymmetrical forms in the natural world, symmetrical patterns seem to occur more often than you would expect if due to sheer random chance.
***
"At this stage, it is useful to remind ourselves that there are two stages in evolutionary development.
"The first is the genetic mutation that causes a variation in a particular physical characteristic (a phenotype) and the second is the natural selection that leads to some traits dominating over others.
“'Most evolutionary theory concentrates on the second ‘survival of the fittest’ step,” said University of Oxford’s Professor Ard Louis.
“'But what if the first ‘arrival of variation’ step is highly biased towards phenotypes high in symmetry or modularity. Could that lead to the bias towards these traits that we observe in nature.”
***
"The study authors looked to computer science for the secret behind nature’s sleight of hand as they continued their investigation into the bias.
"In algorithmic information theory (AIT), the complexity of an object is measured by the length of its shortest description. (my bold)
"For example, a sequence of the letters AB a million times could be described as either a million repetitions of AB or the full sequence of ABABAB in its entirety.
"The shorter description is less complex and considerably more efficient — 28 characters, rather than a million characters. A random sequence with no possible ‘shorthand’ to describe it would be truly complex.
“'It’s much more efficient to follow an instruction that says, ‘do this, and then repeat it x times,’ than to follow all the detailed instructions required for a more complex asymmetrical shape,” Professor Louis said.
"The idea that nature often follows a less complex set of instructions, which are simpler to follow, is behind the paper’s key message — the notion of a distinct developmental bias. (my bold)
"The scientists suggest that the idea of a deck stacked with shapes as prescribed by shorter, simpler ‘instructions’ at the point of phenotype variation offers a much better explanation for the statistical improbability of so many symmetrical shapes in nature.
“'The question of whether or not bias in the arrival of variation has an impact on evolutionary outcomes has been highly contested for many decades,” Professor Louis said.
“'Our examples are simple enough to allow us to address this question head-on, with clear results pointing towards the critical importance of such bias.
Comment: that nasty word 'information' is back to the fore. Information in the DNA code makes everything. The authors are Darwinists relying on random mutations and natural selection, but I view it as God simplifying things for Himself. Why use complex information if simple will do, as the article notes.
Making new evolutionary innovations: bacteria create soil
by David Turell , Tuesday, May 05, 2020, 02:07 (1662 days ago) @ David Turell
It is well known lichens break down rock, but bacteria are also very active in the process:
https://blogs.scientificamerican.com/artful-amoeba/scientists-waited-two-and-a-half-yea...
"It’s long been assumed that life is somehow involved (on Earth, there is very little in which life is not involved), and scientists have demonstrated that it is theoretically possible. But no one had ever actually observed this in common types of iron-silicate continental rocks, likely due to the distressingly large gap in weathering’s reaction velocity relative to scientists’ career velocity.
***
"One way was to find rock that weathers fast. The Rio Blanco Quartz Diorite bedrock beneath the Rio Icacos watershed in Puerto Rico weathers exceptionally fast, making it a tempting target for an experiment conducted on a publishable timescale. The scientists took samples of pure bedrock from a roadcut as well as long tubes of soil and rock drilled into the formation from above. Included in these cores was the transition zone where fractured bedrock alternates with veins of newborn soil, a region is somewhat oddly called the “rindlet” zone (which sadly does not yield anything crunchy and delicious sold in 99-cent bags).
***
"All living beings juggle electrons, usually by stripping them from sugars and other reduced organic compounds (stuff we call “food”) and using those electrons to power their cells through cellular respiration. But some microbes can use simple inorganic compounds or atoms as electron sources. The ones that can use stone as a source of electrons are called lithotrophs. They eat rocks.
"Minerals rich in reduced iron like pyrite (fool’s gold), biotite, and hornblende are potential bacteria chow. The physical changes to these minerals wrought by electron stripping should initiate the process of their chemical dissolution — that is, weathering. This should be visible under the microscope as some sort of physical alteration.
"So the scientists took their highly weather-able rock and microbe-laced soil back home and accelerated the proceedings further by grinding the rock, increasing its surface area. They mixed crushed rock with microbes.
***
"After 30 months, they put their samples under the microscope. The minerals incubated with microbes appeared ragged or pitted — as if they had been dipped in acid, not bacteria — after their 864-day incubation. The sterile control minerals, by contrast, retained sharp, smooth edges.
***
"The lithotrophic bacteria they did find have a special power: the ability to harvest electrons from iron atoms outside their bodies. That is, they can eat without swallowing their food. The bacteria “ingest” the electrons in a technique called external electron transfer. This is vital because the iron atoms are part of the mineral and the bacteria have no crow bars or other means with which to pry them loose. But there is another advantage to doing it this way: if the iron atoms were ingested before oxidation, the microbes would fill with rust, a potentially lethal and definitely embarrassing situation.
"So, bacteria indeed appear able to initiate and accelerate the dirt-making process. On land, dirt supports plants, which support most everything else. In this way among many others, life feeds back, yielding the planet we see today in which no surface remains uncolonized, and the height and depth at which life vanishes remain unknown."
Comment: I've described the Earth as being evolved by God's creations in life. Starting with bacteria as God's workhorses, our Earth beautifully supports all sorts of life in a vast necessary bush of life. Analyzed this way God's methods for His purposes are easy to understand.