A third bacterial motor (Introduction)
by David Turell 
, Thursday, February 05, 2015, 05:13 (3579 days ago)
All rotary, all highly complex:-http://www.cell.com/current-biology/abstract/S0960-9822%2814%2901506-1-"Cells of Flavobacterium johnsoniae, a rod-shaped bacterium devoid of pili or flagella, glide over glass at speeds of 2-4 ?m/s [ 1 ]. Gliding is powered by a protonmotive force [ 2 ], but the machinery required for this motion is not known. Usually, cells move along straight paths, but sometimes they exhibit a reciprocal motion, attach near one pole and flip end over end, or rotate. This behavior is similar to that of a Cytophaga species described earlier [ 3 ]. Development of genetic tools for F. johnsoniae led to discovery of proteins involved in gliding [ 4 ]. These include the surface adhesin SprB that forms filaments about 160 nm long by 6 nm in diameter, which, when labeled with a fluorescent antibody [ 2 ] or a latex bead [ 5 ], are seen to move longitudinally down the length of a cell, occasionally shifting positions to the right or the left. Evidently, interaction of these filaments with a surface produces gliding. To learn more about the gliding motor, we sheared cells to reduce the number and size of SprB filaments and tethered cells to glass by adding anti-SprB antibody. Cells spun about fixed points, mostly counterclockwise, rotating at speeds of 1 Hz or more. The torques required to sustain such speeds were large, comparable to those generated by the flagellar rotary motor. However, we found that a gliding motor runs at constant speed rather than at constant torque. Now, there are three rotary motors powered by protonmotive force: the bacterial flagellar motor, the Fo ATP synthase, and the gliding motor."-And all invented by chance.
Bacterial motors carefully studied
by David Turell , Wednesday, March 30, 2016, 01:35 (3160 days ago) @ David Turell
edited by David Turell, Wednesday, March 30, 2016, 01:46
Using very advanced techniques a lab has delineated a grappling hook type motor and the workings of a flagellum type:-http://phys.org/news/2016-03-up-close-view-bacterial-motors.html-"Jensen and his colleagues used a technique called electron cryotomography to study the complexity of these cell motility nanomachines. The technique allows them to capture 3-D images of intact cells at macromolecular resolution—specifically, with a resolution that ranges from 2 to 5 nanometers (for comparison, a whole cell can be several thousand nanometers in diameter). First, the cells are instantaneously frozen so that water molecules do not have time to rearrange to form ice crystals; this locks the cells in place without damaging their structure. Then, using a transmission electron microscope, the researchers image the cells from different angles, producing a series of 2-D images that—like a computed tomography, or CT, scan—can be digitally reconstructed into a 3-D picture of the cell's structures.-***-"The Caltech team used this technique to analyze the cell motility machinery that involves a structure called the type IVa pilus machine (T4PM). This mechanism allows a bacterium to move through its environment in much the same way that Spider-Man travels between skyscrapers; the T4PM assembles a long fiber (the pilus) that attaches to a surface like a grappling hook and subsequently retracts, thus pulling the cell forward.-***-"In this study, we revealed the beautiful complexity of this machine that may be the strongest motor known in nature. The machine lets M. xanthus, a predatory bacterium, move across a field to form a 'wolf pack' with other M. xanthus cells, and hunt together for other bacteria on which to prey," Jensen says.-"Another way that bacteria move about their environment is by employing a flagellum—a long whiplike structure that extends outward from the cell. The flagellum is spun by cellular machinery, creating a sort of propeller that motors the bacterium through a substrate. However, cells that must push through the thick mucus of the intestine, for example, need more powerful versions of these motors, compared to cells that only need enough propeller power to travel through a pool of water.-"In a second paper, published in the online early edition of the Proceedings of the National Academy of Sciences (PNAS) on March 14, Jensen and his colleagues again used electron cryotomography to study the differences between these heavy-duty and light-duty versions of the bacterial propeller. The 3-D images they captured showed that the varying levels of propeller power among several different species of bacteria can be explained by structural differences in these tiny motors.-"In order for the flagellum to act as a propeller, structures in the cell's motor must apply torque—the force needed to cause an object to rotate—to the flagellum. The researchers found that the high-power motors have additional torque-generating protein complexes that are found at a relatively wide radius from the flagellum. This extra distance provides greater leverage to rotate the flagellum, thus generating greater torque. The strength of the cell's motor was directly correlated with the number of these torque-generating complexes in the cell."-Comment: These nanomotors are so complex they have to be developed all at once. Half a motor or less is useless. Darwin doesn't work here. As Darwin's theory collapses, it has just been reported that epigenetic changes can be inherited across generations guided by small RNA's.-http://www.cell.com/cell/abstract/S0092-8674(16)30207-0?_returnURL=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867416302070%3Fshowall%3Dtrue-"In C. elegans, small RNAs enable transmission of epigenetic responses across multiple generations.......We now show that exposure to dsRNA activates a feedback loop whereby gene-specific RNAi responses dictate the transgenerational duration of RNAi responses mounted against unrelated genes, elicited separately in previous generations. RNA-sequencing analysis reveals that, aside from silencing of genes with complementary sequences, dsRNA-induced RNAi affects the production of heritable endogenous small RNAs, which regulate the expression of RNAi factors. Manipulating genes in this feedback pathway changes the duration of heritable silencing. Such active control of transgenerational effects could be adaptive, since ancestral responses would be detrimental if the environments of the progeny and the ancestors were different."
Bacterial motors carefully studied
DAVID: Using very advanced techniques a lab has delineated a grappling hook type motor and the workings of a flagellum type:-http://phys.org/news/2016-03-up-close-view-bacterial-motors.html-David's comment: These nanomotors are so complex they have to be developed all at once. Half a motor or less is useless. Darwin doesn't work here. As Darwin's theory collapses, it has just been reported that epigenetic changes can be inherited across generations guided by small RNA's.-Thank you for another marvellous piece. However, it is unworthy of you to join the fundamentalists of both sides who use exaggerated language to discredit one another. Darwin's theory of evolution is not “collapsing”, and you know it. What has long since “collapsed” - and was already regarded as a weakness in his own time - is his gradualistic explanation of the innovations that drive evolution. You and I and many others also reject the theory of random mutations, but there is no “collapse” in the basic theory of common descent or of natural selection as the process which results in the survival or extinction of organs and organisms. As for epigenetic changes, once more the question is whether the same mechanisms that power those smaller modifications might also be capable of innovation when the environment undergoes major changes that allow for new patterns.
Bacterial motors carefully studied
by David Turell , Wednesday, March 30, 2016, 15:52 (3160 days ago) @ dhw
> dhw: Thank you for another marvellous piece. However, it is unworthy of you to join the fundamentalists of both sides who use exaggerated language to discredit one another. Darwin's theory of evolution is not “collapsing”, and you know it. What has long since “collapsed” - and was already regarded as a weakness in his own time - is his gradualistic explanation of the innovations that drive evolution. You and I and many others also reject the theory of random mutations, but there is no “collapse” in the basic theory of common descent or of natural selection as the process which results in the survival or extinction of organs and organisms. - It is a good Englishman who defends his countryman. My view of Darwin is very different. Evolution was recognized well before Chuck. He provided a theoretical natural mechanism which you and I both think is incorrect. That was his contribution. Natural selection is a logical tautology. Of course there will be competition between variations, and small variations was his prime theme. Today we are well beyond Darwin in trying to reach answers. - > dhw: As for epigenetic changes, once more the question is whether the same mechanisms that power those smaller modifications might also be capable of innovation when the environment undergoes major changes that allow for new patterns. - Epigenetics is now being shown to be a more powerful heritable mechanism than previously thought. Perhaps it will turn out to be so powerful as to create species, but I doubt it. Just thinking of the issues involved in a giraffe neck make me pause. Same seven vertebrae (patterns), tremendous blood pressure, and did the acacia trees start short and as they grew taller the giraffes stretched heir necks? Kipling! Not to mention leather-like tongues to handle the thorns that are like daggers.
Bacterial motors carefully studied
dhw: Thank you for another marvellous piece. However, it is unworthy of you to join the fundamentalists of both sides who use exaggerated language to discredit one another. Darwin's theory of evolution is not “collapsing”, and you know it. […] DAVID: It is a good Englishman who defends his countryman. My view of Darwin is very different. Evolution was recognized well before Chuck. - Nothing to do with Darwin being an Englishman, and the fact that other people (especially your favourite Wallace) had also worked on the idea of evolution does not mean the theory is now collapsing, so why mention it? - DAVID: He provided a theoretical natural mechanism which you and I both think is incorrect. That was his contribution. - His major contribution was to make the concept of common descent so convincing that even many religious folk now accept the theory, as opposed to that of separate creation. The evidence he accumulated for this theory, in the form of basic patterns, remains just as valid today as it was then. DAVID: Natural selection is a logical tautology. Of course there will be competition between variations, and small variations was his prime theme. Today we are well beyond Darwin in trying to reach answers. - Agreed. My objection is not to your individual criticisms of Darwinism but to the misleading use of language which is common to both sides. Just as an atheist would be delighted to hear from Dawkins that natural selection “explains the whole of life”, your Creationist would leap with joy at hearing that the theory of evolution is collapsing. But it isn't. It is the explanation of how evolution works - the theory of random mutations and gradualism - which in your view and mine is collapsing. - DAVID: Epigenetics is now being shown to be a more powerful heritable mechanism than previously thought. Perhaps it will turn out to be so powerful as to create species, but I doubt it. Just thinking of the issues involved in a giraffe neck make me pause. Same seven vertebrae (patterns), tremendous blood pressure, and did the acacia trees start short and as they grew taller the giraffes stretched their necks? Kipling! Not to mention leather-like tongues to handle the thorns that are like daggers. - All the theories so far seem like “just-so” stories if we tell them that way. There was once an eternal spirit who came down to earth and pulled a spotty animal's neck to make it as tall as a tree. There was once an eternal computer geek who planted a programme in a cell, and a couple of thousand million years later, the programme switched itself on and a spotty animal's neck suddenly shot up as tall as a tree. There was once a spotty animal who wanted to eat the top of a tree, and its cells said: “Yeah, yeah, guys an' dolls, let's do it!” And they worked out a new formula to make its neck as tall as a tree. Once upon a time a spotty animal with a normal neck had a genetic accident and gave birth to a spotty animal with a longer neck, and longer necks became fashionable (or useful) and gradually sort of…well…got longer, y'know whadImean?
Bacterial motors carefully studied
by David Turell , Thursday, March 31, 2016, 19:10 (3158 days ago) @ dhw
> dhw; His major contribution was to make the concept of common descent so convincing that even many religious folk now accept the theory, as opposed to that of separate creation. The evidence he accumulated for this theory, in the form of basic patterns, remains just as valid today as it was then.-You are correct, as far as that goes as a popularizer. As to methodology, no. > > DAVID: Natural selection is a logical tautology. Of course there will be competition between variations, and small variations was his prime theme. Today we are well beyond Darwin in trying to reach answers. > > dhw: Agreed. My objection is not to your individual criticisms of Darwinism .... It is the explanation of how evolution works - the theory of random mutations and gradualism - which in your view and mine is collapsing. -Agreed.-> > DAVID: Epigenetics is now being shown to be a more powerful heritable mechanism than previously thought. Perhaps it will turn out to be so powerful as to create species, but I doubt it. Just thinking of the issues involved in a giraffe neck make me pause. Same seven vertebrae (patterns), tremendous blood pressure, and did the acacia trees start short and as they grew taller the giraffes stretched their necks? Kipling! Not to mention leather-like tongues to handle the thorns that are like daggers. > > dhw: All the theories so far seem like “just-so” stories if we tell them that way. -Skipped the just-so's which are wonderfully inventive. But the giraffe series shows the usual jumps, nothing in tiny changes:-http://phenomena.nationalgeographic.com/2015/10/07/how-giraffes-became-winners-by-a-neck/-"But even though the earliest giraffes already had slightly-elongated neck bones, there was no “March of Progress” towards towering heights. At least one - and possibly more - giraffe lineages reverted to abbreviated necks hung around stout vertebrae. Giraffokeryx was among the earliest of the short-necked giraffes, browsing low-lying foliage around 12 million years ago, and within the last three million years Sivatherium, Bramatherium, and the okapi followed suit. The short-necks proliferated alongside their lankier relatives, which is why we still have both short- and long-necked giraffes today. But even though the earliest giraffes already had slightly-elongated neck bones, there was no “March of Progress” towards towering heights. At least one - and possibly more - giraffe lineages reverted to abbreviated necks hung around stout vertebrae. Giraffokeryx was among the earliest of the short-necked giraffes, browsing low-lying foliage around 12 million years ago, and within the last three million years Sivatherium, Bramatherium, and the okapi followed suit. The short-necks proliferated alongside their lankier relatives, which is why we still have both short- and long-necked giraffes today.-"Truly long-necked giraffes didn't evolve until about 7.5 million years ago. Samotherium, Palaeotragus, Bohlinia, the extinct Giraffa sivalensis and the living Giraffa camelopardalis preserve enough transitional features to let Danowitz and colleagues reconstruct how this stretching occurred. It wasn't simply a matter of drawing out their vertebrae as if they were in some sort of anatomical taffy pull. The front half of the neck vertebrae became elongated in Samotherium and Palaeotragus, generating forms intermediate between today's Giraffa and their foreshortened predecessors. Then, within the last two millions years or so, the lineage leading up to the modern Giraffa elongated the back half of their neck vertebrae, giving them even more reach and making them literally at the top of their class."-Comment: No just-so here! Only jumps in phenotype.
Bacterial motors carefully studied
I am telescoping three different posts here, as they all deal mainly with the same argument.-dhw (under “cavefish”): I can only respond to what you tell me about his [Denton's] book, so perhaps this response is unfair. DAVID: Not unfair. dhw: Then it would seem, alas, that Denton has taught us nothing new.-DAVID: Only to help destroy Darwin's gradualist approach and bring back a consideration of structure first for an initial methodology for evolution. To me that offers God first with my favorite pre-planning concept, i.e., God set up initial patterns of form in living animals and plants, and designed organic chemistry in planned molecules for easier methods for advances appearing.-Since even Huxley expressed his doubts, and punctuated equilibrium has been on the table since 1972, I'm surprised anyone needs more help in opposing gradualism. I discussed structuralism and functionalism in my last post, but am interested in your “planned molecules for easier methods for advances appearing”. Easier than what? (See below) I presume this simply means God preprogrammed the molecules/cells with every single evolutionary innovation, lifestyle and natural wonder.-dhw: All the theories so far seem like “just-so” stories if we tell them that way. DAVID: Skipped the just-so's which are wonderfully inventive. But the giraffe series shows the usual jumps, nothing in tiny changes:-http://phenomena.nationalgeographic.com/2015/10/07/how-giraffes-became-winners-by-a-neck/ David's comment: No just-so here! Only jumps in phenotype.-We have made a giant saltation from bacteria to giraffes! Once again, I can only point out that all such examples suggest independent evolution, with organisms devising their own structural variations and innovations which survive if they work. The idea that ALL of these “jumps” were preprogrammed in the very first cells, or your God personally organized every one of them - not to mention that he did so in order to produce or feed humans, and not to mention the fact that the programme would have to cope with every environmental change - does not sound like an “easier method” to me. There is a similar problem with your post on fish filters:-http://www.nature.com/ncomms/2016/160329/ncomms11092/full/ncomms11092.html-David's comment: A very complex engineering article which basically says directed vortices of water flow keep the filters clean, a system better than current human inventions for filtering. How is a natural process of evolution able to invent such complex solutions better than thinking humans seem able to do? Possibly a better mind behind it all.-Not necessarily a better mind, but perhaps different minds. Same problem as with the giraffe. I find it hard to imagine a less “easy” method than the programme decribed above. If you want an “easier method”, and discounting the ability of blind chance to produce such complex mechanisms, individual inventive intelligences - perhaps originally created by your God and left to do their OWN thing for their OWN purposes - will fit the bill. Yes, we've been over this again and again, but so long as you revert to your favourite divine "pre-planning concept", I will revert to my alternative! It's called an “agnostic balance of nature”.
Bacterial motors carefully studied
by David Turell , Friday, April 01, 2016, 16:37 (3158 days ago) @ dhw
DAVID: To me that offers God first with my favorite pre-planning concept, i.e., God set up initial patterns of form in living animals and plants, and designed organic chemistry in planned molecules for easier methods for advances appearing.[/i] > > dhw: I discussed structuralism and functionalism in my last post, but am interested in your “planned molecules for easier methods for advances appearing”. Easier than what? (See below) ......-Without getting into the intricacies of organic chemistry, remember that proteins vital to life are large collections of amino acids folded certain ways. It appears those folds and shapes follow certain patterns which make it easier to modify the proteins necessary for change as new adaptations appear. The landscapes of probably useful proteins runs to hundreds of thousands. But only a relatively few are chosen and can be altered in patterns. The idea of looking at a landscape is a favorite thought of ID folks. Just image an inventor looking out at a landscape of proteins and wondering which one to precisely pick for the next improvement. This is why they quote such big odds, but with patterns in the molecules the odds are much lower to find the 'right' molecule. The Denton argument gets back to structuralism theory. He spends four dense pages on this point. To me it fits the idea that God started with easy plans and patterns.- > David's comment: How is a natural process of evolution able to invent such complex solutions better than thinking humans seem able to do? Possibly a better mind behind it all. > > dhw: Not necessarily a better mind, but perhaps different minds. .....Yes, we've been over this again and again, but so long as you revert to your favourite divine "pre-planning concept", I will revert to my alternative! It's called an “agnostic balance of nature”.-Yes, over again and again. I am incredulous that evolution can advance because the organisms are so inventive in and of themselves. This is why I constantly present newly-discovered amazing inventions of nanomachines, etc., and other anatomic structures. But I've run into your brick wall. You are convinced that such complexities can be easily invented by the organisms themselves. I'm convinced it ain't so easy! Denton is like you. He wants 'laws of nature' to do it. Each of you agnostics look for 'outs'. And then you give the opinion Denton hasn't added anything! But neither have you. I'm sure you like answers just as I do. You just won't take (faith) the logical one. Remember no proof is allowed!
Bacterial motors carefully studied
by BBella , Friday, April 01, 2016, 22:22 (3157 days ago) @ David Turell
Just image an inventor looking out at a landscape of proteins and wondering which one to precisely pick for the next improvement. This is why they quote such big odds, but with patterns in the molecules the odds are much lower to find the 'right' molecule. The Denton argument gets back to structuralism theory. He spends four dense pages on this point. To me it fits the idea that God started with easy plans and patterns.-And for me it fits the idea that each inventor looking out at a landscape of choices has the intelligence (wisdom) of the ages guiding their choices in that moment.
Bacterial motors carefully studied
by David Turell , Saturday, April 02, 2016, 01:43 (3157 days ago) @ BBella
David: Just image an inventor looking out at a landscape of proteins and wondering which one to precisely pick for the next improvement. This is why they quote such big odds, but with patterns in the molecules the odds are much lower to find the 'right' molecule. The Denton argument gets back to structuralism theory. He spends four dense pages on this point. To me it fits the idea that God started with easy plans and patterns. > > BBella: And for me it fits the idea that each inventor looking out at a landscape of choices has the intelligence (wisdom) of the ages guiding their choices in that moment.-Ah, but who is the inventor?
Bacterial motors carefully studied
David: Just image an inventor looking out at a landscape of proteins and wondering which one to precisely pick for the next improvement. This is why they quote such big odds, but with patterns in the molecules the odds are much lower to find the 'right' molecule. The Denton argument gets back to structuralism theory. He spends four dense pages on this point. To me it fits the idea that God started with easy plans and patterns.-BBella: And for me it fits the idea that each inventor looking out at a landscape of choices has the intelligence (wisdom) of the ages guiding their choices in that moment.-DAVID: Ah, but who is the inventor?-If I understand BBella correctly, each organism can call on the knowledge and experience gained by its predecessors. Remember, we are dealing here with Chapter 2 in the history of life.
Bacterial motors carefully studied
by David Turell , Saturday, April 02, 2016, 16:14 (3157 days ago) @ dhw
David: Just image an inventor looking out at a landscape of proteins and wondering which one to precisely pick for the next improvement. This is why they quote such big odds, but with patterns in the molecules the odds are much lower to find the 'right' molecule. The Denton argument gets back to structuralism theory. He spends four dense pages on this point. To me it fits the idea that God started with easy plans and patterns. > > BBella: And for me it fits the idea that each inventor looking out at a landscape of choices has the intelligence (wisdom) of the ages guiding their choices in that moment. > > DAVID: Ah, but who is the inventor? > > dhw: If I understand BBella correctly, each organism can call on the knowledge and experience gained by its predecessors. Remember, we are dealing here with Chapter 2 in the history of life.-You've got it wrong. If you are looking at several hundred thousand protein molecules to wonder which one to use next, they don't come labeled! You must find the one with the right number of amino acids and the correct 3-D form to perform the function desired. No human organic chemist can do this. We discover all the function qualities of certain molecules by working backwards from living organisms. I'm also in Chapter 2 and again who is the inventor who knows the specific function of each molecule in advance?
Bacterial motors carefully studied
David's comment: How is a natural process of evolution able to invent such complex solutions better than thinking humans seem able to do? Possibly a better mind behind it all. dhw: Not necessarily a better mind, but perhaps different minds. .....Yes, we've been over this again and again, but so long as you revert to your favourite divine "pre-planning concept", I will revert to my alternative! It's called an “agnostic balance of nature”.-DAVID: Yes, over again and again. I am incredulous that evolution can advance because the organisms are so inventive in and of themselves. This is why I constantly present newly-discovered amazing inventions of nanomachines, etc., and other anatomic structures. But I've run into your brick wall. You are convinced that such complexities can be easily invented by the organisms themselves. I'm convinced it ain't so easy! Denton is like you. He wants 'laws of nature' to do it. Each of you agnostics look for 'outs'. And then you give the opinion Denton hasn't added anything! But neither have you. I'm sure you like answers just as I do. You just won't take (faith) the logical one. Remember no proof is allowed!-By editing my post, you have subtly changed the subject, so let me restore the section you left out, which refers to your God's 3.8-billion-year-old computer programme for every innovation, lifestyle and natural wonder throughout the history of evolution: Dhw: “I find it hard to imagine a less “easy” method than the programme described above. If you want an “easier method”, and discounting the ability of blind chance to produce such complex mechanisms, individual inventive intelligences - perhaps originally created by your God and left to do their OWN thing for their OWN purposes - will fit the bill.” (My new bold)-The discussion concerns how evolution works. This has absolutely nothing to do with agnosticism. The alternative that I have presented to your preprogramming is that your God may have given organisms the intelligence to do their own inventing, and therefore pursue their own purposes. You surely won't deny your God's ability to invent such a mechanism, which although hypothetical at least has the feasibility granted by existing mechanisms for adaptation and by the claims of some scientists that cells are sentient, cognitive, intelligent beings. However, the hypothesis is anathema to you because it goes against your theory that God's evolutionary purpose was to produce or feed humans, although you freely admit that you don't know how the purpose and the history fit together. Of course there is no proof either way, but it is extremely naughty of you to pretend that my hypothesis is looking for an ‘out'. It is an explanation for the higgledy-piggledy history of evolution, and it allows for your God. It just doesn't allow for your personal reading of your God's mind and evolutionary method.
Bacterial motors carefully studied
by David Turell , Saturday, April 02, 2016, 20:06 (3156 days ago) @ dhw
> dhw: By editing my post, you have subtly changed the subject, so let me restore the section you left out, which refers to your God's 3.8-billion-year-old computer programme for every innovation, lifestyle and natural wonder throughout the history of evolution: > Dhw: “I find it hard to imagine a less “easy” method than the programme described above. If you want an “easier method”, and discounting the ability of blind chance to produce such complex mechanisms, individual inventive intelligences - perhaps originally created by your God and left to do their OWN thing for their OWN purposes - will fit the bill.” (My new bold)-The real reason I edited your post is that you keep reverting to the 3.8 billion year programming as though I believe this thought. I don't. In the past, repeatedly, I have stated hat I believe God guided evolution but I have no idea how He did it. Programming and dabbling were two alternatives I stated as possibilities, and I accepted your inventive on-board mechanism might be the way, but you would never accept my proviso that God would monitor it so that evolution progressed as He wished. Thus we go round and round. This statement of my thoughts is exactly where I still am and will stay. -> > dhw: The discussion concerns how evolution works. This has absolutely nothing to do with agnosticism. The alternative that I have presented to your preprogramming is that your God may have given organisms the intelligence to do their own inventing, and therefore pursue their own purposes.-Of course your agnosticism is in play. Note your IM remains independent of God's guidance, which, believing in God, I insist must be part of an IM.-> dhw; You surely won't deny your God's ability to invent such a mechanism, which although hypothetical at least has the feasibility granted by existing mechanisms for adaptation and by the claims of some scientists that cells are sentient, cognitive, intelligent beings. -Of course, God could invent and grant such a mechanism to organisms, but with guidance.-> dhw: However, the hypothesis is anathema to you because it goes against your theory that God's evolutionary purpose was to produce or feed humans, although you freely admit that you don't know how the purpose and the history fit together.-The history does fit! We are here with our giant brains, that are not needed for survival, as proven by other primates who are here also over 7-10 million years. -> dhw: Of course there is no proof either way, but it is extremely naughty of you to pretend that my hypothesis is looking for an ‘out'. It is an explanation for the higgledy-piggledy history of evolution, and it allows for your God. It just doesn't allow for your personal reading of your God's mind and evolutionary method.-Your views are exactly as I noted above. When you think about God you read Him from your agnostic point of view, nothing like my point of view. Are humans an accident as Gould claims, arriving by Darwin's theory? They look like a saltation to me. God did it. Simple logic.
Bacterial motors carefully studied
by BBella , Saturday, April 02, 2016, 20:56 (3156 days ago) @ David Turell
edited by BBella, Saturday, April 02, 2016, 21:02
dhw; You surely won't deny your God's ability to invent such a mechanism, which although hypothetical at least has the feasibility granted by existing mechanisms for adaptation and by the claims of some scientists that cells are sentient, cognitive, intelligent beings. > > Of course, God could invent and grant such a mechanism to organisms, but with guidance.-So what you are saying (altho you can't be sure of course - but using the weaver bird for an example), is that the weaver bird is looking out onto the landscape of choices and at that very moment God decides suddenly the weaver bird must have a different, more innovative nest than any before. So into the weaver birds imagination pops a new innovative idea to tie knots - altho it had previously never tied a knot before? Really?-For me, it has to be because the bird has the ability to do almost anything within certain bounds, it just works with what it knows in creating its nest with what seems to work or look better, no different than this guy in this video: -http://www.viralvo.com/honey-badger/
Bacterial motors carefully studied
by David Turell , Saturday, April 02, 2016, 22:14 (3156 days ago) @ BBella
BBella: So what you are saying (altho you can't be sure of course - but using the weaver bird for an example), is that the weaver bird is looking out onto the landscape of choices and at that very moment God decides suddenly the weaver bird must have a different, more innovative nest than any before. So into the weaver birds imagination pops a new innovative idea to tie knots - altho it had previously never tied a knot before? Really?-In landscapes I'm discussing protein molecules and function only, and the molecules are not tagged with possible function labels. So how does one know which one to pick to create a new invention of form?-With the weavers, I just don't think they invented those knots. They seem as complex as the ones boy scouts learn. Those nests are very protective of the birds and their chicks Why wouldn't God help them with protection? > > BBella: For me, it has to be because the bird has the ability to do almost anything within certain bounds, it just works with what it knows in creating its nest with what seems to work or look better, no different than this guy in this video: > > http://www.viralvo.com/honey-badger/-I loved the video. Our raccoons are somewhat like the badger.
Bacterial motors carefully studied
David: Just image an inventor looking out at a landscape of proteins and wondering which one to precisely pick for the next improvement. [..] To me it (|Denton's structuralism] fits the idea that God started with easy plans and patterns. BBella: And for me it fits the idea that each inventor looking out at a landscape of choices has the intelligence (wisdom) of the ages guiding their choices in that moment. DAVID: Ah, but who is the inventor? dhw: If I understand BBella correctly, each organism can call on the knowledge and experience gained by its predecessors. Remember, we are dealing here with Chapter 2 in the history of life.-DAVID: You've got it wrong. If you are looking at several hundred thousand protein molecules to wonder which one to use next, they don't come labeled! You must find the one with the right number of amino acids and the correct 3-D form to perform the function desired. […] who is the inventor who knows the specific function of each molecule in advance?-If you believe in common descent, all innovations have to take place within existing organisms. They are not looking out onto an endless landscape, but make internal adjustments to an already functioning mechanism that needs to adapt or has the opportunity to improve. Without your 3.8 billion-year computer programme, you are left with your God directly adjusting existing cell communities to produce every innovation/lifestyle/natural wonder. My alternative theistic hypothesis is that God gave them the means of making those adjustments autonomously. Either he was capable of giving them that ability or he was not. Your response seems to suggest that he was not. They all had to be “guided”
avid: Of course, God could invent and grant such a mechanism to organisms, but with guidance. BBELLA: So what you are saying (altho you can't be sure of course - but using the weaver bird for an example), is that the weaver bird is looking out onto the landscape of choices and at that very moment God decides suddenly the weaver bird must have a different, more innovative nest than any before. So into the weaver birds imagination pops a new innovative idea to tie knots - altho it had previously never tied a knot before? Really? DAVID: In landscapes I'm discussing protein molecules and function only, and the molecules are not tagged with possible function labels. So how does one know which one to pick to create a new invention of form?-On landscapes, see above. On God's special guidance for all innovations, lifestyles and natural wonders, see below.-BBELLA: For me, it has to be because the bird has the ability to do almost anything within certain bounds, it just works with what it knows in creating its nest with what seems to work or look better, no different than this guy in this video: http://www.viralvo.com/honey-badger/-Amazing video. And I could not agree more. But we are all arguing now from the viewpoint of incredulity. Like you, BBella, I cannot believe that God had to personally “guide” the weaverbird or the monarch, wasp, spider or cuttlefish etc. to work out their own modes of survival/improvement, and in addition I do not believe such wonders are geared to “balancing nature” for the sake of humans. It may well be that we can get no further than this, since David can't believe that organisms are intelligent enough to work out improvements, or that his God is capable of giving them such intelligence without their having to be “guided” by him.
Bacterial motors carefully studied
by David Turell , Sunday, April 03, 2016, 15:34 (3156 days ago) @ dhw
dhw: If I understand BBella correctly, each organism can call on the knowledge and experience gained by its predecessors. Remember, we are dealing here with Chapter 2 in the history of life.-I know her point. At issue is her inference that animals can make adaptations, epigenetics, and I agree. But what we see in evolution is large gaps between phenotypes as animal series develop (whale as example). This requires new protein molecules acting in their specific ways, with prior knowledge of their functionalities not labeled on the molecules. Thus the landscape probability issue. > > dhw: If you believe in common descent, all innovations have to take place within existing organisms. They are not looking out onto an endless landscape, but make internal adjustments to an already functioning mechanism that needs to adapt or has the opportunity to improve.-Directly opposite to my comment above. You are discussing epigenetics, not the gaps.-> dhw: My alternative theistic hypothesis is that God gave them the means of making those adjustments autonomously. Either he was capable of giving them that ability or he was not. Your response seems to suggest that he was not. They all had to be “guided”:-Built-in guidance solves your objection.-> http://www.viralvo.com/honey-badger/ > > Amazing video. -I loved the video, but don't you realize it was put-up job? The badger is bright, but his tools for escape were obviously provided. We had a horse who constantly got his mother out of her locked stall. It took me three attempts to solve the problem, but I beat him at his game. Animals ain't stupid. Currently we have to tie our show guy in. He can flip a lever with his tongue.-> dhw: And I could not agree more. But we are all arguing now from the viewpoint of incredulity. Like you, BBella, I cannot believe that God had to personally “guide” the weaverbird or the monarch, wasp, spider or cuttlefish etc. to work out their own modes of survival/improvement, and in addition I do not believe such wonders are geared to “balancing nature” for the sake of humans. It may well be that we can get no further than this, since David can't believe that organisms are intelligent enough to work out improvements, or that his God is capable of giving them such intelligence without their having to be “guided” by him.-You are still thinking at the gradual epigenetic level, not the major gaps of evolution.
Bacterial motors carefully studied
dhw: If I understand BBella correctly, each organism can call on the knowledge and experience gained by its predecessors. Remember, we are dealing here with Chapter 2 in the history of life. DAVID: I know her point. At issue is her inference that animals can make adaptations, epigenetics, and I agree. -According to her post, BBella's point and mine is that the weaverbird has the intelligence to build its own nest. You disagree: you say God had to guide it. -DAVID: But what we see in evolution is large gaps between phenotypes as animal series develop (whale as example). This requires new protein molecules acting in their specific ways, with prior knowledge of their functionalities not labeled on the molecules. Thus the landscape probability issue.-I have always distinguished between adaptations and innovations (= large gaps). NOBODY knows how the latter took place. Your theory is that God did it but you don't know how (maybe preprogramming, maybe dabbling). My proposal is that the cell communities did it, and your God may have given them the ability to do it autonomously. But I can understand why you prefer to duck away from the weaverbird issue by concentrating on the far greater complexity of molecules. dhw: If you believe in common descent, all innovations have to take place within existing organisms. They are not looking out onto an endless landscape, but make internal adjustments to an already functioning mechanism that needs to adapt or has the opportunity to improve. DAVID: Directly opposite to my comment above. You are discussing epigenetics, not the gaps.-Innovations must also take place within existing organisms if you accept common descent, and I am offering a hypothesis to explain the hitherto unexplained gaps/saltations/innovations.-DAVID: I loved the video, but don't you realize it was put-up job? The badger is bright, but his tools for escape were obviously provided. -Yes of course the tools were provided. The whole point is that the badger has the intelligence to work out how to use whatever materials are available. And the same formula may apply to other organisms using whatever materials are available in order to adapt and innovate. dhw: It may well be that we can get no further than this, since David can't believe that organisms are intelligent enough to work out improvements, or that his God is capable of giving them such intelligence without their having to be “guided” by him. DAVID: You are still thinking at the gradual epigenetic level, not the major gaps of evolution.-No, you are the one who insists on sticking at the gradual epigenetic level, because you are not prepared to consider the possibility that your God gave organisms the autonomous ability to innovate as well as to adapt. I include the weaverbird's nest, the monarch's lifestyle, the wasp's egg-laying etc. in the category of innovations.
Bacterial motors carefully studied
by David Turell , Monday, April 04, 2016, 18:21 (3154 days ago) @ dhw
> dhw: I have always distinguished between adaptations and innovations (= large gaps). NOBODY knows how the latter took place. ...I can understand why you prefer to duck away from the weaverbird issue by concentrating on the far greater complexity of molecules.-Because innovations, which is how evolution really advances requires finding new molecules with unknown unlabeled underlying functional capacities from a group of possibilities. You don't like the landscape concept because it challenges your concept of how common descent must advance, and it cannot be through organismal planning. Since the phenotypical advances are huge gaps, the new molecules used for those advances must have functions known in advance. If not, back to hunt and peck, trying to figure it out. Simple logic. Weaver nests are adaptations, no molecules, much simpler. We don't know how speciation occurs, but new molecules are required.-> > dhw: Innovations must also take place within existing organisms if you accept common descent, and I am offering a hypothesis to explain the hitherto unexplained gaps/saltations/innovations.-Look at landscapes and defend your hypothesis!- > dhw: No, you are the one who insists on sticking at the gradual epigenetic level, because you are not prepared to consider the possibility that your God gave organisms the autonomous ability to innovate as well as to adapt. I include the weaverbird's nest, the monarch's lifestyle, the wasp's egg-laying etc. in the category of innovations.-Watch your definitions: innovations=gaps, not the adaptations you list above, all possibly epigenetic.
Bacterial motors carefully studied
dhw: I have always distinguished between adaptations and innovations (= large gaps). NOBODY knows how the latter took place. ...I can understand why you prefer to duck away from the weaverbird issue by concentrating on the far greater complexity of molecules. DAVID: Because innovations, which is how evolution really advances requires finding new molecules with unknown unlabeled underlying functional capacities from a group of possibilities. You don't like the landscape concept because it challenges your concept of how common descent must advance, and it cannot be through organismal planning. Since the phenotypical advances are huge gaps, the new molecules used for those advances must have functions known in advance. If not, back to hunt and peck, trying to figure it out. Simple logic. Weaver nests are adaptations, no molecules, much simpler. We don't know how speciation occurs, but new molecules are required. -This is not in dispute. But you insist that weavers do not have the intelligence to build their own nests, and so God must have preplanned them or intervened. It stands to reason, then, that if organisms can't perform such relatively simple tasks, they won't be able to perform the more complicated tasks of rearranging their own cells and giving them new forms. But this creates a dilemma for you. If you grant other organisms the intelligence to work out their own lifestyles and natural wonders, maybe they can do more. It IS a maybe. Since we don't know how speciation occurs, and we don't know how cell communities transform themselves, we can only speculate. There is no dispute over what has to be done. The dispute is over the capacity of organisms to do it through their own intelligence, or even apparently the capacity of your God to give them such intelligence. dhw: Innovations must also take place within existing organisms if you accept common descent, and I am offering a hypothesis to explain the hitherto unexplained gaps/saltations/innovations. DAVID: Look at landscapes and defend your hypothesis!-There is no landscape. Each organism has its own cell communities, and if you believe in common descent, each new cell community has arisen from its predecessors. The whole question is the extent to which these cell communities can rearrange and transform themselves. We don't know the extent of their intelligence, just as we don't know how speciation occurs. And “God did it” still doesn't tell us how speciation occurs. He could have done it through an autonomous IM.-dhw: No, you are the one who insists on sticking at the gradual epigenetic level, because you are not prepared to consider the possibility that your God gave organisms the autonomous ability to innovate as well as to adapt. I include the weaverbird's nest, the monarch's lifestyle, the wasp's egg-laying etc. in the category of innovations. DAVID: Watch your definitions: innovations=gaps, not the adaptations you list above, all possibly epigenetic.-One could argue that the first nest, the first migration, the first parasitic egg-laying were innovations, but that really isn't the point. You use “epigenetic” as if somehow that removed these phenomena from the discussion, but according to you it makes not the slightest difference! Because you say the weaver, monarch and wasp are incapable of working these procedures out for themselves, whether you call them innovations or adaptations. That is why I focus on the weaverbird as a prime example of the gaps in your hypotheses.
Bacterial motors carefully studied
by David Turell , Wednesday, April 06, 2016, 01:28 (3153 days ago) @ dhw
David: Simple logic. Weaver nests are adaptations, no molecules, much simpler. We don't know how speciation occurs, but new molecules are required. > [/i] > > dhw" This is not in dispute. But this creates a dilemma for you If you grant other organisms the intelligence to work out their own lifestyles and natural wonders, maybe they can do more. It IS a maybe. Since we don't know how speciation occurs, and we don't know how cell communities transform themselves, we can only speculate.-You are mixing apples and oranges. I'm discussing the new molecules needed for speciation, not adaptations. You are using the ability to create adaptations to try to presume that can lead to picking out new organic molecular arrangements for a new species! My dog can adapt. I can adapt, but I have no idea how to create a new species of me, even with my superior ability to conceive and plan. Genetic changes are not open to us living folks to fiddle with voluntarily, except on animals in a lab, note, again a third person approach.. -> > dhw: Innovations must also take place within existing organisms if you accept common descent, and I am offering a hypothesis to explain the hitherto unexplained gaps/saltations/innovations. > DAVID: Look at landscapes and defend your hypothesis! > > dhw: There is no landscape.-Yes, there is. It is a conceptual landscape which I have described. A new species needs new molecular combinations and arrangements. this fact is beyond question. The big mystery is how those molecules and arrangements get picked out when the possible combinations are so big and the types of molecules are so varied. -> dhw: No, you are the one who insists on sticking at the gradual epigenetic level, because you are not prepared to consider the possibility that your God gave organisms the autonomous ability to innovate as well as to adapt. I include the weaverbird's nest, the monarch's lifestyle, the wasp's egg-laying etc. in the category of innovations.-Sorry. To me innovations are new species. Nests and life styles are adaptations when considering how to advance evolution from simple to complex. Same as the discussion about 'degree' and 'kind'. Adaptations are 'degree', new species are changes in 'kind'.-> dhw: One could argue that the first nest, the first migration, the first parasitic egg-laying were innovations, but that really isn't the point. You use “epigenetic” as if somehow that removed these phenomena from the discussion, but according to you it makes not the slightest difference! Because you say the weaver, monarch and wasp are incapable of working these procedures out for themselves, whether you call them innovations or adaptations. That is why I focus on the weaverbird as a prime example of the gaps in your hypotheses.-My thesis remains the same. God guided evolution. The details you want answered are secondary.
Bacterial motors carefully studied
dhw: But your anthropocentric hypothesis still leaves us with the problem of 3.(whatever) billion years of dabbled or (for you too, unbelievably) preprogrammed innovations, lifestyles and natural wonders all somehow geared to the production of us! DAVID: It is only a problem for you, not for me. There are only three possibilities for how evolution works, as discussed before: Natural chance, strict creation step by step (tony) or a process with guidelines. Without purpose and with purpose.-The fourth possibility for how evolution works (as opposed to how it all started) - which you now refuse even to include in your list - is that organisms have the autonomous power, whether God-given or not, to innovate, their purpose being to survive and/or improve.-David: Simple logic. Weaver nests are adaptations, no molecules, much simpler. We don't know how speciation occurs, but new molecules are required. dhw: This is not in dispute. But this creates a dilemma for you If you grant other organisms the intelligence to work out their own lifestyles and natural wonders, maybe they can do more. It IS a maybe. Since we don't know how speciation occurs, and we don't know how cell communities transform themselves, we can only speculate.-DAVID: You are mixing apples and oranges. I'm discussing the new molecules needed for speciation, not adaptations. You are using the ability to create adaptations to try to presume that can lead to picking out new organic molecular arrangements for a new species! My dog can adapt. I can adapt, but I have no idea how to create a new species of me, even with my superior ability to conceive and plan. Genetic changes are not open to us living folks to fiddle with voluntarily, except on animals in a lab, note, again a third person approach.-Yes, the nest and the kidney are apples and oranges, but according to you, God had to “guide” (= preprogramme or personally organize) every innovation, lifestyle and natural wonder throughout the history of evolution. Whether you call the first weaver nest or the first monarch migration an adaptation or innovation therefore makes no difference: God did it all. However, there are different types of adaptation and innovation. The nest and migration are external adaptations/innovations, whereas cuttlefish camouflage or fish adaptation to pollution requires adjustments from the inside, and that is where I would suggest a possible link between evolutionary adaptation (preserving the status quo) and innovation (the unexplained process of speciation), since both processes entail adjustments made within the cell communities. The link is a hypothesis based on the fact that we know cell communities make changes to themselves (adaptation), and some scientists tell us cells are intelligent beings. But there is no presumption.-The remainder of your post deals with the same point, and culminates in the following conclusion: “My thesis remains the same. God guided evolution. The details you want answered are secondary.” Wanting to know how a hypothesis fits the facts it is meant to explain does not seem to me to be secondary, and I think you are quite right to query the likelihood of my own hypothesis on the grounds that we have no evidence to prove that cell communities are intelligent enough to fill the major gaps that are involved in speciation. Of course I could say to you: “My thesis remains the same. Autonomously intelligent cell communities guided evolution. The details you want answered are secondary.” But I shan't. If there are flaws in a hypothesis, one should acknowledge them.
Bacterial motors carefully studied
by David Turell , Wednesday, April 06, 2016, 21:26 (3152 days ago) @ dhw
David: There are only three possibilities for how evolution works, as discussed before: Natural chance, strict creation step by step (tony) or a process with guidelines. Without purpose and with purpose.[/i] > > The fourth possibility for how evolution works (as opposed to how it all started) - which you now refuse even to include in your list - is that organisms have the autonomous power, whether God-given or not, to innovate, their purpose being to survive and/or improve.-That possibility I've agreed to but I view it as part of God's guidance because I only see it as having guidelines > > DAVID: You are mixing apples and oranges. I'm discussing the new molecules needed for speciation, not adaptations. > > dhw:... Whether you call the first weaver nest or the first monarch migration an adaptation or innovation therefore makes no difference: God did it all. However, there are different types of adaptation and innovation. The nest and migration are external adaptations/innovations, whereas cuttlefish camouflage or fish adaptation to pollution requires adjustments from the inside, and that is where I would suggest a possible link between evolutionary adaptation (preserving the status quo) and innovation (the unexplained process of speciation), since both processes entail adjustments made within the cell communities. The link is a hypothesis based on the fact that we know cell communities make changes to themselves (adaptation), and some scientists tell us cells are intelligent beings. But there is no presumption.-What a mixed up bit of reasoning. You admit that major changes as in cuttlefish require 'adjustment on the inside' but refuse to accept the difficulty in that major step. It will require changed molecular reactions in the skin. In planning for it, what new molecules and what molecular interactions should be chosen from possibilities of thousands? THIS is why we don't understand speciation. In the whale series (my favorite)there are giant phenotypic changes requiring much more complex molecular choices and rearrangements. The genome is getting very complex from the discoveries made, but nothing has been found to explain the changes required for a new species form. Simply proposing 'fish adaptation to pollution' is equivalent is totally unreasonable. We are back to a gap like degree and kind. If God gave organisms an IM it must be highly complex and some hint of it should have been spotted by now. It is either deeply hidden or God directly dabbles. > > dhw: Wanting to know how a hypothesis fits the facts it is meant to explain does not seem to me to be secondary, and I think you are quite right to query the likelihood of my own hypothesis on the grounds that we have no evidence to prove that cell communities are intelligent enough to fill the major gaps that are involved in speciation. -I'm working backward from the problems I see in speciation. You appear to be working in the opposite direction, throwing out hypothetical mechanisms without recognizing the planning problems, which are real, not hypothetical. Once again I see an agnostic mind saying 'anything but God', while admitting God might do it..
Bacterial motors carefully studied
Dhw: The fourth possibility for how evolution works (as opposed to how it all started) - which you now refuse even to include in your list - is that organisms have the autonomous power, whether God-given or not, to innovate, their purpose being to survive and/or improve. DAVID: That possibility I've agreed to but I view it as part of God's guidance because I only see it as having guidelines.-The fourth possibility is WITHOUT guidelines. The fact that you disagree with it (just as you disagree with the chance hypothesis) does not mean you can leave it out!-DAVID: […] You admit that major changes as in cuttlefish require ‘adjustment on the inside' but refuse to accept the difficulty in that major step. […] Simply proposing 'fish adaptation to pollution' is equivalent is totally unreasonable. We are back to a gap like degree and kind. If God gave organisms an IM it must be highly complex and some hint of it should have been spotted by now. It is either deeply hidden or God directly dabbles.-I did not say fish adaptation to pollution was equivalent. I suggested a “possible link”, since these processes of adaptation and innovation both require internal change (as opposed to the external adaptations/innovations of weaverbirds). Nor have I suggested that such a mechanism would not be highly complex. So would the mechanism you are prepared to agree to WITH guidelines. And I do not refuse to accept the difficulties in any of the major steps. On the contrary, you have even quoted my acknowledgement of these in the next part of your post:-dhw: Wanting to know how a hypothesis fits the facts it is meant to explain does not seem to me to be secondary, and I think you are quite right to query the likelihood of my own hypothesis on the grounds that we have no evidence to prove that cell communities are intelligent enough to fill the major gaps that are involved in speciation. -DAVID: I'm working backward from the problems I see in speciation. You appear to be working in the opposite direction, throwing out hypothetical mechanisms without recognizing the planning problems, which are real, not hypothetical. Once again I see an agnostic mind saying 'anything but God', while admitting God might do it. -Of course the problems are real, and that is why my autonomous inventive mechanism remains a hypothesis, just like chance, separate creation, and your divine “guidance” (= preprogramming and/or dabbling). There is no evidence for any of them. The admission that God might do it is hardly “anything but God”. I see a theistic mind saying 'nothing but MY god', while not admitting that God might think differently!
Bacterial motors carefully studied
by David Turell , Friday, April 08, 2016, 02:49 (3151 days ago) @ dhw
Dhw: The fourth possibility for how evolution works (as opposed to how it all started) - which you now refuse even to include in your list - is that organisms have the autonomous power, whether God-given or not, to innovate, their purpose being to survive and/or improve. > DAVID: That possibility I've agreed to but I view it as part of God's guidance because I only see it as having guidelines. > > dhw: The fourth possibility is WITHOUT guidelines. The fact that you disagree with it (just as you disagree with the chance hypothesis) does not mean you can leave it out!-Well you agree with the chance issue, but refuse to look closely at the 'landscape' problem of how to pick out the right new molecules and the right arrangement of those molecules. Either the IM must know them in advance or be instructed about them in advance. Your hypothesis just assumes there is a mechanism that can handle this issue. There is no way around this objection. But something must solve it for species to advance to the next step of complexity. For me that is implanted guidance.-> > dhw: Of course the problems are real, and that is why my autonomous inventive mechanism remains a hypothesis, just like chance, separate creation, and your divine “guidance” (= preprogramming and/or dabbling). There is no evidence for any of them. The admission that God might do it is hardly “anything but God”. I see a theistic mind saying 'nothing but MY god', while not admitting that God might think differently!-I come back to the same problem: who or what picks the new molecules/arrangement for the new species? The gaps are there. For me if God doesn't do it or arrange for it, it can't happen (the gaps). I don't see the comment about God thinking having validity beyond His choice of using evolution or creating humans.
Bacterial motors carefully studied
dhw: The fourth possibility [an autonomous inventive mechanism] is WITHOUT guidelines. The fact that you disagree with it (just as you disagree with the chance hypothesis) does not mean you can leave it out! DAVID: Well you agree with the chance issue, but refuse to look closely at the 'landscape' problem of how to pick out the right new molecules and the right arrangement of those molecules. Either the IM must know them in advance or be instructed about them in advance. Your hypothesis just assumes there is a mechanism that can handle this issue. There is no way around this objection. But something must solve it for species to advance to the next step of complexity. For me that is implanted guidance.-I don't know how cell communities manage to reorganize themselves in order to produce something new. You don't know how your God manages to “guide” cell communities into producing something new (you don't believe in your own 3.8-billion-year programme hypothesis, and you don't know how God does his dabbles). And yet although we have both admitted our ignorance of how the process actually works, you still focus on what I don't know as if somehow that made what you don't know less of a problem than mine. To sum it up: nobody knows how speciation takes place. That is why people come up with different theories. dhw: Of course the problems are real, and that is why my autonomous inventive mechanism remains a hypothesis, just like chance, separate creation, and your divine “guidance” (= preprogramming and/or dabbling). There is no evidence for any of them. The admission that God might do it is hardly “anything but God”. I see a theistic mind saying 'nothing but MY god', while not admitting that God might think differently!-DAVID: I come back to the same problem: who or what picks the new molecules/arrangement for the new species? The gaps are there. For me if God doesn't do it or arrange for it, it can't happen (the gaps). I don't see the comment about God thinking having validity beyond His choice of using evolution [f]or creating humans.-See above for the “same problem” of innovation. And I know you can't see beyond your own interpretation of God's thinking. It is apparently inconceivable for you that God might have used evolution as an experiment to see what would happen if he set in motion a free-for-all. That need not preclude the occasional dabble (perhaps to create a creature with self-awareness), but it does preclude your hypothesis that every single innovation, lifestyle and natural wonder in the history of evolution was “guided” (i.e. preprogrammed and/or personally dabbled) for the sake of humans. Since the latter is your fixed belief, of course you can't imagine any other hypothesis having validity.
Bacterial motors carefully studied
by David Turell , Friday, April 08, 2016, 15:36 (3151 days ago) @ dhw
> dhw: I don't know how cell communities manage to reorganize themselves in order to produce something new. ... To sum it up: nobody knows how speciation takes place. That is why people come up with different theories.-You are again ignoring a non-theoretical point. The 'landscape concept' must enter into thinking about how speciation occurs. We are allowed to think about it. Speciation must involve new molecules and new arrangements, and planning. But it involves putting together a jig-saw puzzle with no picture to guide you and pieces with fuzzy edges. All of this is not a theory, but a salient point as to how difficult speciation is, and therefore some mechanism must exist to solve the problem. You and I can argue about the possibilities of mechanism, but 'landscape' never goes away. > > dhw: And I know you can't see beyond your own interpretation of God's thinking..... Since the latter is your fixed belief, of course you can't imagine any other hypothesis having validity.-You are still arguing mechanism. I'm simply presenting a legitimate issue on the point that a speciation mechanism must not be blinded but somehow forward looking, nothing further. Once that is noted, then mechanism can be hypothesized.
Bacterial motors carefully studied
dhw: I don't know how cell communities manage to reorganize themselves in order to produce something new. ... To sum it up: nobody knows how speciation takes place. That is why people come up with different theories. DAVID: You are again ignoring a non-theoretical point. The 'landscape concept' must enter into thinking about how speciation occurs. We are allowed to think about it. Speciation must involve new molecules and new arrangements, and planning. But it involves putting together a jig-saw puzzle with no picture to guide you and pieces with fuzzy edges. All of this is not a theory, but a salient point as to how difficult speciation is, and therefore some mechanism must exist to solve the problem. You and I can argue about the possibilities of mechanism, but 'landscape' never goes away.-I keep pointing out that speciation is so difficult that NOBODY knows how it happens, and I keep agreeing with you that it involves new molecules (though I prefer to talk more generally about cells) and new arrangements, and innovation by definition cannot have a pre-existing picture, and thank you for acknowledging that some mechanism must exist to solve the problem. That is my whole point. There has to be a mechanism, but we don't know what it is. You think your God personally “guided” (by preprogramming or direct dabbling) every single innovation, new lifestyle and new natural wonder, all for the sake of humans. I suggest he may have created an autonomous inventive mechanism. Those are alternative solutions to the problem. Why do you have to keep telling me there is a problem?-dhw: And I know you can't see beyond your own interpretation of God's thinking..... Since the latter is your fixed belief, of course you can't imagine any other hypothesis having validity.-DAVID: You are still arguing mechanism. I'm simply presenting a legitimate issue on the point that a speciation mechanism must not be blinded but somehow forward looking, nothing further. Once that is noted, then mechanism can be hypothesized. -It has been noted. Many times. And having noted it, I have hypothesized an autonomous, intelligent, inventive mechanism, possibly designed by your God, as opposed to the preprogramming/dabbling hypothesis summarized above.
Bacterial motors carefully studied
by David Turell , Saturday, April 09, 2016, 16:27 (3150 days ago) @ dhw
dhw: I keep pointing out that speciation is so difficult that NOBODY knows how it happens, and I keep agreeing with you that it involves new molecules (though I prefer to talk more generally about cells) and new arrangements, and innovation by definition cannot have a pre-existing picture, and thank you for acknowledging that some mechanism must exist to solve the problem. That is my whole point. There has to be a mechanism, but we don't know what it is. -Agreed. I've simply used a new tack to go one layer of complexity deeper than 'cells'. We've now discussed choosing new molecules and molecular arrangements. I understand that this is still insufficient evidence for you.
Bacterial motors carefully studied
dhw: I keep pointing out that speciation is so difficult that NOBODY knows how it happens, and I keep agreeing with you that it involves new molecules (though I prefer to talk more generally about cells) and new arrangements, and innovation by definition cannot have a pre-existing picture, and thank you for acknowledging that some mechanism must exist to solve the problem. That is my whole point. There has to be a mechanism, but we don't know what it is. -DAVID: Agreed. I've simply used a new tack to go one layer of complexity deeper than 'cells'. We've now discussed choosing new molecules and molecular arrangements. I understand that this is still insufficient evidence for you.-We need to be clear about evidence for what. The complexity of the cell is mind-boggling, and it is fair enough to break it down to its individual components in order to emphasize just how mind-boggling it is. I have long ago accepted this as evidence for design, and hence a powerful argument against atheism. But that is not the subject we have been discussing, which is the question of how speciation takes place. We know that cells and their component parts must undergo radical changes in order to produce innovations. The complexity of the process provides no “evidence” for your hypothetical explanation (preprogramming and/or dabbling) or for mine (an autonomous IM, possibly God-given). But since yours goes so far as to demand God's active participation even in matters of lifestyle (the monarch) and natural wonders (the weaverbird's nest) - regardless of cellular complexity, and apparently all for the sake of humans - it is not just a matter of "evidence". I simply find my hypothesis more cohesive than yours!
Bacterial motors carefully studied
by David Turell , Monday, April 11, 2016, 00:54 (3148 days ago) @ dhw
> We need to be clear about evidence for what. The complexity of the cell is mind-boggling, and it is fair enough to break it down to its individual components in order to emphasize just how mind-boggling it is. ... But that is not the subject we have been discussing, which is the question of how speciation takes place. ... The complexity of the process provides no “evidence” for your hypothetical explanation (preprogramming and/or dabbling) or for mine (an autonomous IM, possibly God-given).-But in my mind it does. First, are the advances at random or with purpose? Can you pick one? Or do you find a third choice? I don't. If you don't accept chance advances, and you've said you don't, what else is there but purpose and design. Once that issue is settled the complexity of advances (try whales again) requires planning. Complex planning which only minds can do. Read about whales if you don't believe me.-> dhw: But since yours goes so far as to demand God's active participation even in matters of lifestyle (the monarch) and natural wonders (the weaverbird's nest) - regardless of cellular complexity, and apparently all for the sake of humans - it is not just a matter of "evidence". I simply find my hypothesis more cohesive than yours!-The things in the above paragraph that disturb you are extrapolations of mine from the basic observations about speciation problems. You've invented an IM that glosses over all of these considerations.
Bacterial motors carefully studied
Dhw: We need to be clear about evidence for what. The complexity of the cell is mind-boggling, and it is fair enough to break it down to its individual components in order to emphasize just how mind-boggling it is. ... But that is not the subject we have been discussing, which is the question of how speciation takes place. ... The complexity of the process provides no “evidence” for your hypothetical explanation (preprogramming and/or dabbling) or for mine (an autonomous IM, possibly God-given).-DAVID: But in my mind it does. First, are the advances at random or with purpose? Can you pick one? Or do you find a third choice? I don't. If you don't accept chance advances, and you've said you don't, what else is there but purpose and design. Once that issue is settled the complexity of advances (try whales again) requires planning. Complex planning which only minds can do. Read about whales if you don't believe me.-I do reject chance, and I accept purpose and design, but that is the whole point of my hypothesis: that instead of design being “guided” by God, it is carried out by autonomous, intelligent cell communities (perhaps invented by God), and the purpose is self-improvement, not the production and feeding of humans. Every new organ required - past tense, because we have not witnessed innovations ourselves - not only inventiveness but also the cooperation of all the other cell communities in the organism in which the innovation took place. That would also be the case if your God preprogrammed or dabbled. I agree that only minds could do it, and so the question is: do cells have minds? Not human minds, but cell minds that are sentient, cognitive, communicative, cooperative, and capable of taking decisions. You say no, and others say yes. Even the yes, however, does not guarantee that those cell minds are capable of such complex innovations. I have never denied the problem of complexity. That is why my hypothesis is just that - a hypothesis, and not a belief. -dhw: But since yours goes so far as to demand God's active participation even in matters of lifestyle (the monarch) and natural wonders (the weaverbird's nest) - regardless of cellular complexity, and apparently all for the sake of humans - it is not just a matter of "evidence". I simply find my hypothesis more cohesive than yours! DAVID: The things in the above paragraph that disturb you are extrapolations of mine from the basic observations about speciation problems. You've invented an IM that glosses over all of these considerations.-The complexity is the consideration, as above, but your “large organisms chauvinism” will not even allow the monarch or the weaverbird the intelligence to devise their own lifestyle or design their own nest. Instead, God must plan everything, and we had better “gloss over” the claim that all such lifestyles and wonders are somehow linked to the production or feeding of humans. Both our hypotheses come up against questions they cannot answer, and there is no “evidence” for divine preprogramming or dabbling or autonomous cell communities producing innovations. But at least my proposal offers a cohesive explanation of the higgledy-piggledy history of evolution.
Bacterial motors carefully studied
by David Turell , Monday, April 11, 2016, 15:37 (3148 days ago) @ dhw
> dhw: I do reject chance, and I accept purpose and design, but that is the whole point of my hypothesis: that instead of design being “guided” by God, it is carried out by autonomous, intelligent cell communities (perhaps invented by God), and the purpose is self-improvement, not the production and feeding of humans.... I agree that only minds could do it, and so the question is: do cells have minds? Not human minds, but cell minds that are sentient, cognitive, communicative, cooperative, and capable of taking decisions. You say no, and others say yes. Even the yes, however, does not guarantee that those cell minds are capable of such complex innovations. I have never denied the problem of complexity.-I don't think that you have any notion of the complexity of living organic chemistry.-> > dhw: The complexity is the consideration, .... Both our hypotheses come up against questions they cannot answer, and there is no “evidence” for divine preprogramming or dabbling or autonomous cell communities producing innovations. But at least my proposal offers a cohesive explanation of the higgledy-piggledy history of evolution.-If I can cajole you, please watch the first 15 or so minutes of this lecture by a Rice U. professor who makes synthetic organic molecules as is profession, in a discussion of origin of life. But what he describers goes on every day in the living body after life starts:-http://www.uncommondescent.com/origin-of-life/james-tour-on-the-hypocrisy-of-origin-of-life-conjectures/-I apologize that he is a terrible lecturer, but the point he makes about the intricacies of protein production in living tissues is right on. Your cell committees have no chance of ever making a major modification of form, style or structure in speciation. My large organism chauvinism is valid!
Bacterial motors carefully studied
dhw: I do reject chance, and I accept purpose and design, but that is the whole point of my hypothesis: that instead of design being “guided” by God, it is carried out by autonomous, intelligent cell communities (perhaps invented by God), and the purpose is self-improvement, not the production and feeding of humans.... I agree that only minds could do it, and so the question is: do cells have minds? Not human minds, but cell minds that are sentient, cognitive, communicative, cooperative, and capable of taking decisions. You say no, and others say yes. Even the yes, however, does not guarantee that those cell minds are capable of such complex innovations. I have never denied the problem of complexity. (New bold) DAVID: I don't think that you have any notion of the complexity of living organic chemistry.-You need to be an organic chemist to understand the complexity of organic chemistry. I'm not a physicist, cosmologist, botanist, chemist, or quantum theorist either. So what are you saying? Does every organic chemist, physicist etc. tell us that God “guided” (i.e. preprogrammed or personally directed) every single innovation, lifestyle and natural wonder in the history of evolution, all in order to produce and/or feed humans? And does my not being an organic chemist invalidate my acknowledgement, repeated ad nauseam, of the complexity of the cell and the process that leads to innovation? DAVID: If I can cajole you, please watch the first 15 or so minutes of this lecture by a Rice U. professor who makes synthetic organic molecules as is profession, in a discussion of origin of life. But what he describers goes on every day in the living body after life starts: http://www.uncommondescent.com/origin-of-life/james-tour-on-the-hypocrisy-of-origin-of-... I apologize that he is a terrible lecturer, but the point he makes about the intricacies of protein production in living tissues is right on. Your cell committees have no chance of ever making a major modification of form, style or structure in speciation. My large organism chauvinism is valid!-I waited in vain for him to shout at me that God “guided” every molecule throughout every step of evolution, from bacteria to humans, or even that cells are automatons - though I admit that I switched him off after half an hour of his ranting. However, we are informed by the blurb that “most scientists do not understand how evolution could explain the existence of life”, and the heading tells us that this is an attack on origin of life hypocrisy. Yet again: Evolution is not a theory designed to explain the origin of life. “There's no scientist alive today who understands macroevolution.” Correct. How often do we have to repeat this? That is why we have different theories. Under "Immunity" you wrote: “As Prof. Tour points out, the complexity of evolutionary advancement is mind-boggling, but perhaps not for a certain mind.” I too regard the complexity of evolutionary advancement as mind-boggling, and I don't know how it happened. Nor does he and nor do you. And if we ever do find out how, the answer may be as mind-boggling as your hypothesis or mine.
Bacterial motors carefully studied
by David Turell , Tuesday, April 12, 2016, 19:00 (3146 days ago) @ dhw
> dhw: You need to be an organic chemist to understand the complexity of organic chemistry. I'm not a physicist, cosmologist, botanist, chemist, or quantum theorist either. So what are you saying? > > I waited in vain for him to shout at me that God “guided” every molecule throughout every step of evolution, from bacteria to humans, or even that cells are automatons - though I admit that I switched him off after half an hour of his ranting. However, we are informed by the blurb that “most scientists do not understand how evolution could explain the existence of life”, and the heading tells us that this is an attack on origin of life hypocrisy.... I too regard the complexity of evolutionary advancement as mind-boggling, and I don't know how it happened. Nor does he and nor do you. And if we ever do find out how, the answer may be as mind-boggling as your hypothesis or mine.-I am not communicating properly, I think, for I find your remarks about Dr. Tour entirely off the mark. I asked for 15 minutes to get a flavor of his point of view. God was never at issue. First of all his lecture is not to organic chemistry students. It is a philosophic address about his difficulties in making organic molecules as compared to how easily the living cell does it. And secondly, how he has been persecuted for his honest view. You do not need any knowledge of organic chemistry to follow his discussion. What he points out is that as he proceeds step by step he has to clean up a mess each stepwise reaction causes, while the cell does it automatically. -In the Miller-Urey lightning-in-a-bottle experiment all they got in the bottom of the jar was a tarry goo which then had to be laboriously separated to see what they had gotten. This is typical in organic chemistry, and you don't need to be a student of OC to understand this. I mentioned it in my first book.-Whether you like it or not these OC problems affect how research is done with both origin of life and evolution of life, because the presence of life is a continuum of the same organic chemistry process from its origin to the complex organisms seen now. The fact that Darwin skipped the origin problem is of no consequence in the thinking about how OC plays a role in all of this. You have always tried to separate out origin, but in matter of fact you can't. Dr. Tour is telling you that what he finds as a professional manufacturer of organic molecules is that it is damned complicated arduous work that living cells, as built, do easily. -Now I'm sure you understand that Dr. Tour is a confirmed Christian believer, which explains his unbridled passion in his lecture. But that cannot honestly reduce the import of his discussion. Don't hide behind the fact that you do not know organic chemistry. You don't need to know it. Tour's objection to the glib approach to OOL is right on, and all of us who do know organic chemistry are fully aware of it, as he points out. But grantesmanship (in which I have had a role years ago) requires that superficiality if any money is to appear, although I don't think my grant request was superficial.
One does not admit to the theoretical problems with any hope of success if you want the money.-Don't hide behind your ignorance. The folks at the lecture were just like you.
Bacterial motors carefully studied
dhw: You need to be an organic chemist to understand the complexity of organic chemistry. I'm not a physicist, cosmologist, botanist, chemist, or quantum theorist either. So what are you saying? […] I waited in vain for him (Prof. Tour] to shout at me that God “guided” every molecule throughout every step of evolution, from bacteria to humans, or even that cells are automatons - though I admit that I switched him off after half an hour of his ranting. However, we are informed by the blurb that “most scientists do not understand how evolution could explain the existence of life”, and the heading tells us that this is an attack on origin of life hypocrisy. Yet again: Evolution is not a theory designed to explain the origin of life… I too regard the complexity of evolutionary advancement as mind-boggling, and I don't know how it happened. Nor does he and nor do you. And if we ever do find out how, the answer may be as mind-boggling as your hypothesis or mine.-DAVID: I am not communicating properly, I think, for I find your remarks about Dr. Tour entirely off the mark. I asked for 15 minutes to get a flavor of his point of view. God was never at issue [...] Whether you like it or not these OC problems affect how research is done with both origin of life and evolution of life [….] Don't hide behind the fact that you do not know organic chemistry. You don't need to know it. Tour's objection to the glib approach to OOL is right on, and all of us who do know organic chemistry are fully aware of it, as he points out […] Don't hide behind your ignorance. The folks at the lecture were just like you. -I deny all charges, my lord. After I had defended my hypothesis while also acknowledging its flaws, the plaintiff's response was to accuse me of not understanding organic chemistry! The plaintiff has therefore placed the above remarks in an entirely false context. Herewith the correct context: dhw: I do reject chance, and I accept purpose and design, but that is the whole point of my hypothesis: that instead of design being “guided” by God, it is carried out by autonomous, intelligent cell communities (perhaps invented by God), and the purpose is self-improvement, not the production and feeding of humans.... I agree that only minds could do it, and so the question is: do cells have minds? Not human minds, but cell minds that are sentient, cognitive, communicative, cooperative, and capable of taking decisions. You say no, and others say yes. Even the yes, however, does not guarantee that those cell minds are capable of such complex innovations. I have never denied the problem of complexity. -DAVID: I don't think that you have any notion of the complexity of living organic chemistry. (My very bold bold)-In response, I pointed out that my ignorance of organic chemistry did not mean that organic chemists all supported the plaintiff's hypothesis, and it did not stop me from recognizing the enormous complexity of the cell and of the process of innovation (the plaintiff has omitted all of these comments). He referred me to Prof. Tour's lecture, as if this would somehow support his hypothesis against mine. It doesn't. However, we agree on the whole subject of complexity, and we agree that Tour's “objection to the glib approach to OOL is right on” (how often do I have to repeat that I don't believe in chance?), and we agree that nobody can explain evolutionary innovations. Would the plaintiff therefore please inform the jury as to exactly what I was hiding when I agreed with him that I am not an organic chemist? -As regards the origin itself, David, you wrote: “The fact that Darwin skipped the origin problem is of no consequence in the thinking about how OC plays a role in all this.” Despite my ignorance, I am fully aware that OC "plays a role" in both the origin of life and the course of evolution - they could hardly take place without it! That does not mean that OC supports your hypothesis that God "guided" (= personally preprogrammed or directly organized) every step in evolution, plus every lifestyle and natural wonder, all for the sake of humans. And that is the issue under discussion.
Bacterial motors carefully studied
by David Turell , Wednesday, April 13, 2016, 15:21 (3146 days ago) @ dhw
dhw: In response, I pointed out that my ignorance of organic chemistry did not mean that organic chemists all supported the plaintiff's hypothesis, and it did not stop me from recognizing the enormous complexity of the cell and of the process of innovation (the plaintiff has omitted all of these comments). He referred me to Prof. Tour's lecture, as if this would somehow support his hypothesis against mine. It doesn't. However, we agree on the whole subject of complexity, and we agree that Tour's “objection to the glib approach to OOL is right on” (how often do I have to repeat that I don't believe in chance?), > > As regards the origin itself, David, you wrote: “The fact that Darwin skipped the origin problem is of no consequence in the thinking about how OC plays a role in all this.” Despite my ignorance, I am fully aware that OC "plays a role" in both the origin of life and the course of evolution - they could hardly take place without it! That does not mean that OC supports your hypothesis that God "guided" (= personally preprogrammed or directly organized) every step in evolution, plus every lifestyle and natural wonder, all for the sake of humans. And that is the issue under discussion.-Tour's discussion of his difficulties in manufacturing organic molecules simply becomes an argument from incredulity that nature could do this on its own. It seems to me you believe it can. I don't. And I cannot explain the arrival of unique organisms, humans, as the result of a free-flowing complexity mechanism that has no need to respond to nature's challenges, but makes giant leaps such as the Cambrian or human consciousness for seemingly no good natural reason.
Bacterial motors carefully studied: Addendum
by David Turell , Wednesday, April 13, 2016, 18:39 (3145 days ago) @ David Turell
Tour's incredulity comes from more than his problems with protein synthesis. A living cell, whether by itself or part of a body is constantly active in production of proteins or it dies. Either as a necessary product required at the moment, a replacement part, or the production of necessary energy from food sources, it cannot stop or it dies. Since it is unstoppable, it has built-in processes for death at the right moment, if multicellular (apoptosis); if single-celled splitting in two, a very complex process all its own. The human body is about 65% water, as bacteria are, so all of this occurs in a watery environment. However, water is very detrimental to protein synthesis and attempts at polymerization and other protein forms won't occur without very large, highly complex enzymes present to hold everything together and to speed the process to milliseconds so that the fully formed product can resist water. Protein molecules actually have both hydrophilic and hydrophobic parts to them. These processes throw off gooey, gunky byproducts, so there must be a garbage reduction system, also acting in milliseconds to keep the cell environment clean at all times. -It is this picture which creates Tour's wonderment. Did the first life start with all of this onboard? How could it be developed without the full arrangement? And with evolution after life started, how did new forms set themselves up, while continuously keeping every process going under the old system while trying out the new one. When thinking about sponges pooping out simple waste, to Cambrian kidneys controlling several levels of several items at once, and no in-between precursors, the enormity of the gap becomes very apparent.-I'm with Tour. His problems in the lab make the case: life in improbably complex, and could not have started by chance.
Bacterial motors carefully studied: Addendum
Re the OC case of Turell v dhw: owing to the failure of the plaintiff to appear before the court on the third day of the hearing, the jury has been instructed to dismiss all charges and award damages to the defendant. The damages will be specified at a later date.-DAVID: Tour's discussion of his difficulties in manufacturing organic molecules simply becomes an argument from incredulity that nature could do this on its own. It seems to me you believe it can. I don't. -Tour attacks the theory of abiogenesis. You have merely substituted “nature” for “chance”. How often do I have to repeat that I do not believe chance could have created life or the mechanism for evolution? However, I see no reason why you should believe your God to have been incapable of creating an evolutionary mechanism that would function without his preprogrammed or personal “guidance”. DAVID: And I cannot explain the arrival of unique organisms, humans, as the result of a free-flowing complexity mechanism that has no need to respond to nature's challenges, but makes giant leaps such as the Cambrian or human consciousness for seemingly no good natural reason.-Nobody can explain innovations, or the Cambrian, or any sort of consciousness, human or otherwise. Nobody can explain your God either. That is why we have so many different theories. However, “responding to nature's challenges” may not be the only natural spur for evolution: I don't know why it should be deemed unnatural, or "no good reason", for some intelligent organisms to exploit nature's opportunities in order to improve themselves (remember, my hypothesis allows for your God endowing them with their intelligence). But I accept the reasons for your questioning the concept of an autonomous inventive mechanism. I only remain surprised by your unwillingness to question the hypothesis that an individual, unknown, sourceless, superintelligent mind deliberately and personally organized every single innovation, lifestyle and natural wonder (including the weaverbird's nest) throughout the history of evolution in order to produce and feed humans.-DAVID: Tour's incredulity comes from more than his problems with protein synthesis etc. etc. […] I'm with Tour. His problems in the lab make the case: life is improbably complex, and could not have started by chance.-I also share Tour's incredulity. How often do I have to repeat that I do not believe in chance? How often do I have to repeat…? How often do…? That is one of the main reasons why I am not an atheist. I may have said that before too. However, that does not mean God personally organized every single innovation, lifestyle etc. etc. as per your own personal theory of evolution. I may have said… Furthermore, I have similar problems of incredulity regarding a single, unknown, sourceless, superintelligent mind creating billions of solar systems that come and go for no apparent reason...etc. etc. That is one of the main reasons why I am not a theist. I may have...zzzzz...
Bacterial motors carefully studied: Addendum
by David Turell , Thursday, April 14, 2016, 18:04 (3144 days ago) @ dhw
> dhw: I see no reason why you should believe your God to have been incapable of creating an evolutionary mechanism that would function without his preprogrammed or personal “guidance”.-I think he is perfectly capable of it with preprogrammed guidance. > > dhw: Nobody can explain innovations, or the Cambrian, or any sort of consciousness, human or otherwise. Nobody can explain your God either.-Why is it then that all civilizations have suggested that there must be God/gods?. It is an idea built into our consciousness, as a recognition that the mysteries of nature and life require a mind to plan it.-> dhw: I don't know why it should be deemed unnatural, or "no good reason", for some intelligent organisms to exploit nature's opportunities in order to improve themselves (remember, my hypothesis allows for your God endowing them with their intelligence).-They can, but only if God gives them planning ability.- > dhw: But I accept the reasons for your questioning the concept of an autonomous inventive mechanism. I only remain surprised by your unwillingness to question the hypothesis that an individual, unknown, sourceless, superintelligent mind deliberately and personally organized every single innovation, lifestyle and natural wonder (including the weaverbird's nest) throughout the history of evolution in order to produce and feed humans.-Simple answer. Why are humans here? An extremely improbable event. > > DAVID: Tour's incredulity comes from more than his problems with protein synthesis etc. etc. […] I'm with Tour. His problems in the lab make the case: life is improbably complex, and could not have started by chance. > > dhw: I also share Tour's incredulity. How often do I have to repeat that I do not believe in chance? ...However, that does not mean God personally organized every single innovation, lifestyle etc. etc. as per your own personal theory of evolution. .... I have similar problems of incredulity regarding a single, unknown, sourceless, superintelligent mind creating billions of solar systems. That is one of the main reasons why I am not a theist. I may have...zzzzz...-And so to sleep with a dead end in your thinking. Perchance to dream....
Bacterial motors carefully studied: Addendum
dhw: I see no reason why you should believe your God to have been incapable of creating an evolutionary mechanism that would function without his preprogrammed or personal “guidance”. DAVID: I think he is perfectly capable of it with preprogrammed guidance.-Otherwise not capable, then. And yet according to you he IS capable of creating autonomous, inventive minds (free will) in humans and to a lesser degree in other large organisms. He just can't do it with small organisms, to enable them to control how they combine to form new, larger organisms. A strange gap in his almighty powers. dhw: Nobody can explain innovations, or the Cambrian, or any sort of consciousness, human or otherwise. Nobody can explain your God either. DAVID: Why is it then that all civilizations have suggested that there must be God/gods? It is an idea built into our consciousness, as a recognition that the mysteries of nature and life require a mind to plan it.-See the God thread (more suitable than bacterial motors).-dhw: I don't know why it should be deemed unnatural, or "no good reason", for some intelligent organisms to exploit nature's opportunities in order to improve themselves (remember, my hypothesis allows for your God endowing them with their intelligence). DAVID: They can, but only if God gives them planning ability.-I would subsume planning ability under the heading of an autonomous inventive mechanism, but apparently your God's powers are too limited for him to provide organisms with that. However, thank you for now accepting that evolution might advance through a natural drive for improvement. Another problem solved. dhw: But I accept the reasons for your questioning the concept of an autonomous inventive mechanism. I only remain surprised by your unwillingness to question the hypothesis that an individual, unknown, sourceless, superintelligent mind deliberately and personally organized every single innovation, lifestyle and natural wonder (including the weaverbird's nest) throughout the history of evolution in order to produce and feed humans. DAVID: Simple answer. Why are humans here? An extremely improbable event.-All of life is an extremely improbable event, and every innovation, lifestyle and natural wonder is an extremely improbable event. That still doesn't tell us why God had to design the monarch's migration, the weaverbird's nest and the duck-billed platypus in order to produce/feed humans.-DAVID: Tour's incredulity comes from more than his problems with protein synthesis etc. etc. […] I'm with Tour. His problems in the lab make the case: life is improbably complex, and could not have started by chance. dhw: I also share Tour's incredulity. How often do I have to repeat that I do not believe in chance? ...However, that does not mean God personally organized every single innovation, lifestyle etc. etc. as per your own personal theory of evolution. .... I have similar problems of incredulity regarding a single, unknown, sourceless, superintelligent mind creating billions of solar systems. That is one of the main reasons why I am not a theist. I may have...zzzzz...-DAVID: And so to sleep with a dead end in your thinking. Perchance to dream...-A superb answer, totally apt on all levels, and it made me laugh out loud! Thank you.
Bacterial motors carefully studied: Addendum
by David Turell , Friday, April 15, 2016, 15:57 (3144 days ago) @ dhw
DAVID: They can, but only if God gives them planning ability. > > dhw: I would subsume planning ability under the heading of an autonomous inventive mechanism, but apparently your God's powers are too limited for him to provide organisms with that. However, thank you for now accepting that evolution might advance through a natural drive for improvement. Another problem solved.-That is a stretch of my comments. There is obviously some sort of 'drive to complexity', for that is what we see. I would dispute that it is 'natural', but instead state that it is guided.-> DAVID: Simple answer. Why are humans here? An extremely improbable event. > > All of life is an extremely improbable event, and every innovation, lifestyle and natural wonder is an extremely improbable event. That still doesn't tell us why God had to design the monarch's migration, the weaverbird's nest and the duck-billed platypus in order to produce/feed humans.-With all the extremely improbables, and lets add the sudden origin of our fine-tuned universe to the list, I don't see why you can't accept the idea of God running everything. Something is a first cause.
Bacterial motors carefully studied: Addendum
Dhw: I don't know why it should be deemed unnatural, or “no good reason”, for some intelligent organisms to exploit nature's opportunities in order to improve themselves… DAVID: They can, but only if God gives them planning ability. dhw: I would subsume planning ability under the heading of an autonomous inventive mechanism, but apparently your God's powers are too limited for him to provide organisms with that. However, thank you for now accepting that evolution might advance through a natural drive for improvement. Another problem solved.-DAVID: That is a stretch of my comments. There is obviously some sort of 'drive to complexity', for that is what we see. I would dispute that it is 'natural', but instead state that it is guided.-For those who believe in common descent, the drive to complexity - or to improvement - is limited to those individual organisms in which the innovations take place. The rest remain the same (or go extinct). In my hypothesis the innovators use their (God-given?) intelligence to exploit opportunities offered by the environment. An analogy would be individual humans using their (God-given?) intelligence inventively. You have now told us your God is incapable not only of giving other organisms the intelligence to improve themselves (he is only “capable of it with preprogrammed guidance”), but he can't even give them the intelligence to want to improve. I am astonished that you can impose such limitations on your God's capabilities - or is this another case of your not quite making yourself clear? Out of interest, do you regard the will to survive as “natural”, or does God have to guide individual organisms to want to survive and then guide them into finding out how to do it? DAVID: ...Why are humans here? An extremely improbable event. Dhw: All of life is an extremely improbable event, and every innovation, lifestyle and natural wonder is an extremely improbable event. That still doesn't tell us why God had to design the monarch's migration, the weaverbird's nest and the duck-billed platypus in order to produce/feed humans. DAVID: With all the extremely improbables, and lets add the sudden origin of our fine-tuned universe to the list, I don't see why you can't accept the idea of God running everything. Something is a first cause.-Once again: your first cause is a sourceless, unknown, unknowable, conscious, single mind that deliberately creates billions of solar systems that come and go for no apparent reason etc. (Do I need to repeat the etc.?) This is so irrational that you yourself have said many times that it requires a gigantic leap of faith - just like the faith needed to believe that the mechanism for life, reproduction and evolution could assemble itself by chance. And we still don't know why your God had to design the nest etc. in order to produce/feed humans.
Bacterial motors carefully studied: Addendum
by David Turell , Saturday, April 16, 2016, 15:54 (3143 days ago) @ dhw
dhw: You have now told us your God is incapable not only of giving other organisms the intelligence to improve themselves (he is only “capable of it with preprogrammed guidance”), but he can't even give them the intelligence to want to improve....Out of interest, do you regard the will to survive as “natural”, or does God have to guide individual organisms to want to survive and then guide them into finding out how to do it?-If you could tell us where God would put 'intelligence' into bacteria, or into animals who only understand danger of injury as prey animals, I would agree. In bacteria I only see automaticity. In animals fear, n ot the ability to plan new species improvements. -> DAVID: With all the extremely improbables, and lets add the sudden origin of our fine-tuned universe to the list, I don't see why you can't accept the idea of God running everything. Something is a first cause. > > dhw: Once again: your first cause is a sourceless, unknown, unknowable, conscious, single mind that deliberately creates billions of solar systems that come and go for no apparent reason etc. (Do I need to repeat the etc.?) This is so irrational that you yourself have said many times that it requires a gigantic leap of faith - just like the faith needed to believe that the mechanism for life, reproduction and evolution could assemble itself by chance.-Of course, faith requires a leap. Do you ever think positively about not 'how' but 'why' humans exist?
Bacterial motors carefully studied: Addendum
dhw: You have now told us your God is incapable not only of giving other organisms the intelligence to improve themselves (he is only “capable of it with preprogrammed guidance”), but he can't even give them the intelligence to want to improve....Out of interest, do you regard the will to survive as “natural”, or does God have to guide individual organisms to want to survive and then guide them into finding out how to do it? DAVID: If you could tell us where God would put 'intelligence' into bacteria, or into animals who only understand danger of injury as prey animals, I would agree. In bacteria I only see automaticity. In animals fear, not the ability to plan new species improvements.-If you could tell us where God put his 3.8-billion-year computer programme into bacteria (though not even you believe he did), or - the only remaining alternative you have mentioned so far - exactly how and why he personally “guided” chosen individual organisms into multicellularity and then into producing every single innovation, lifestyle and natural wonder in the history of evolution all for the sake of humans, I would agree that your own hypothesis is feasible. Why do you confine animals to fear, when every post you offer us - including Frans de Waal's - emphasizes the vast range of their cognitive abilities? But of course there is no evidence that they can plan new species improvements. Yet again: NOBODY knows how innovations took place. Meanwhile, how about the will to survive - natural or unnatural?-DAVID: With all the extremely improbables, and lets add the sudden origin of our fine-tuned universe to the list, I don't see why you can't accept the idea of God running everything. Something is a first cause. dhw: Once again: your first cause is a sourceless, unknown, unknowable, conscious, single mind that deliberately creates billions of solar systems that come and go for no apparent reason etc. (Do I need to repeat the etc.?) This is so irrational that you yourself have said many times that it requires a gigantic leap of faith […] DAVID: Of course, faith requires a leap. Do you ever think positively about not 'how' but 'why' humans exist?-You could not see why I didn't accept “the idea of God running everything”. If the answer is so blindingly obvious, I wonder why you asked the question. In response to your new question, I have previously suggested that if your God exists, he may have created life and humans in order to relieve his eternal boredom. “Positive” enough? You didn't like that, though, because although you regard humans as being in God's image, you don't like to see him as being anything like humans. Why do YOU think he created humans?
Bacterial motors carefully studied: Addendum
by David Turell , Sunday, April 17, 2016, 15:07 (3142 days ago) @ dhw
> dhw: If you could tell us where God put his 3.8-billion-year computer programme into bacteria (though not even you believe he did), or - the only remaining alternative you have mentioned so far - exactly how and why he personally “guided” chosen individual organisms into multicellularity and then into producing every single innovation, lifestyle and natural wonder in the history of evolution all for the sake of humans, I would agree that your own hypothesis is feasible.-If the program exists, it is in the layers of DNA modification mechanisms and its controls. If 'dabbles' exist, He rearranges the genome controls.- > dhw: Meanwhile, how about the will to survive - natural or unnatural? Built-in instinct.-> dhw: because although you regard humans as being in God's image, you don't like to see him as being anything like humans. Why do YOU think he created humans?-Our mind is only a small reproduction of the complexity of His mind, a minor reflection of His mind. We are created to respond to Him and relate to him.
Bacterial motors carefully studied: Addendum
David: If the program exists, it is in the layers of DNA modification mechanisms and its controls. If 'dabbles' exist, He rearranges the genome controls.-If cellular intelligence exists, it is what you call the controls. If ‘dabbles' exist, of course they are rearrangements. The question is how and why your God picks on individual organisms and physically rearranges their genome to produce a nose, a kidney, a wing, or mentally guides them to fly to warmer climes or to tie complicated knots.-PS: Re our previous exchange, animal cognition is not confined to fear, and PPS: Do you think the will to survive is “natural” or can only be “guided” by God?-dhw: …because although you regard humans as being in God's image, you don't like to see him as being anything like humans. Why do YOU think he created humans?-DAVID: Our mind is only a small reproduction of the complexity of His mind, a minor reflection of His mind. We are created to respond to Him and relate to him.-Difficult to respond and relate to someone who deliberately remains hidden, but in any case, why would he create us in order to have us respond and relate to him? Is he lonely? Bored?
Bacterial motors carefully studied: Addendum
by David Turell , Monday, April 18, 2016, 18:05 (3140 days ago) @ dhw
> dhw:If cellular intelligence exists, it is what you call the controls. If ‘dabbles' exist, of course they are rearrangements. The question is how and why your God picks on individual organisms and physically rearranges their genome to produce a nose, a kidney, a wing, or mentally guides them to fly to warmer climes or to tie complicated knots. - It is all the process of God-driven evolution. We see evolution start with bacteria and end up with us. Success! Why bother with questions about the roadmap? > > DAVID: Our mind is only a small reproduction of the complexity of His mind, a minor reflection of His mind. We are created to respond to Him and relate to him. > > dhw: Difficult to respond and relate to someone who deliberately remains hidden, but in any case, why would he create us in order to have us respond and relate to him? Is he lonely? Bored? - Apparently He treasures faith.
cellular motors carefully studied
by David Turell , Saturday, November 10, 2018, 00:30 (2205 days ago) @ dhw
An interesting interview with someone who is studying the automatic reactions and responses of cell molecules
https://oscillations.net/2018/11/06/on-the-frontline-allen-liu-the-mechanome-and-synthe...
“'The design of biological motors can be classified by cataloging the motor’s general structural features, fuel type, stepping distance, stall force, and other mechanical parameters. Detailed measurements of the motility cycles and underlying mechanisms for motility also provide information about how these mechanisms work. Ultimately ‘sequencing’ the mechanome will lead to the discovery of the design features of biological motors in general, enabling us to catalogue them and outline the rules that govern their behavior.”
***
"I think Matt had an important insight that if we measure the forces and displacements of proteins under forces, we may be able to decipher the design principle of molecular machines. If you think about all the proteins that sense or respond to forces, one can argue that in principle all proteins are sensitive to forces. This is because proteins are folded into three-dimensional structures by non-covalent interactions. And if you apply a force by grabbing onto a single molecule and extend it, the protein will unfold. So by their nature, all proteins are sensitive to forces.
"The key thing the field is trying to understand now is that if a force is applied, how does it change the energy landscape of the molecular interactions. How does that force facilitate binding or unbinding to other molecular entities? We still don’t know which proteins have cryptic sites that open upon physiological force applications. To a certain extent, we have not identified all the key molecular players in force transduction.
***
"An artificial cell that does not have any encoded components. It can still come from purifying a protein out of a host cell like E. coli. A major approach is based on protein reconstitution.
"The way that this could work is—if you think about the cells in our bodies that do not have a nucleus, like red blood cells and platelets. Although these cells do not have a nucleus, they perform very sophisticated functions. For instance, a platelet is just ~2-3 microns in size, yet it has all the protein machinery enclosed within its own cell membrane and can function in blood coagulation without having any genetically encoded components.
Comment: I think of this scientist as viewing the cell as I do. Where in the platelet is the intelligence to run its functions? The interview is about a ten minute read and opens up a new area of cell research looking at how the cell's automatic reactions are controlled in part by physical forces.
Bacterial motors carefully studied
DAVID: The real reason I edited your post is that you keep reverting to the 3.8 billion year programming as though I believe this thought. I don't. In the past, repeatedly, I have stated that I believe God guided evolution but I have no idea how He did it. Programming and dabbling were two alternatives I stated as possibilities, and I accepted your inventive on-board mechanism might be the way, but you would never accept my proviso that God would monitor it so that evolution progressed as He wished…-You are assuming he did not wish it to progress unmonitored! I am surprised but pleased to hear that you don't believe in your hypothesis of a 3.8-billion-year computer programme after all. But since you insist on God's “guidance”, even down to the building of the weaverbird's nest, this leaves you with nothing but divine dabbling (unless you can think of an alternative means of “guidance”) to account for every innovation, lifestyle and natural wonder. For more on this, see my second post.-dhw: The discussion concerns how evolution works. This has absolutely nothing to do with agnosticism… DAVID: Of course your agnosticism is in play. Note your IM remains independent of God's guidance, which, believing in God, I insist must be part of an IM.-Once more: your insistence that God guided every evolutionary development is your own theistic version; my theistic alternative of God inventing an autonomous mechanism has nothing to do with agnosticism, and everything to do with the history of evolution and different interpretations of God's intentions and methods. -dhw: You surely won't deny your God's ability to invent such a mechanism […] DAVID: Of course, God could invent and grant such a mechanism to organisms, but with guidance.-Why could he not have invented a mechanism to function without his guidance? -dhw: However, the hypothesis is anathema to you because it goes against your theory that God's evolutionary purpose was to produce or feed humans, although you freely admit that you don't know how the purpose and the history fit together.-DAVID: The history does fit! We are here with our giant brains, that are not needed for survival, as proven by other primates who are here also over 7-10 million years. -As agreed a thousand times, the survival of bacteria shows that no further developments were “needed for survival”. It is the special creation of the weaverbird's nest (plus a few million other examples) that doesn't fit your anthropocentric theory. But I am not hell-bent on denying a special place for humans, or even the possibility of a (comparatively) late divine dabble. My objection is to your insistence that all innovations etc. are “guided” by God, and are/were geared to humans right from the start. Maybe the weaverbird designed its own nest for its own purposes. (See my second post.)-DAVID: When you think about God you read Him from your agnostic point of view, nothing like my point of view. Are humans an accident as Gould claims, arriving by Darwin's theory? They look like a saltation to me. God did it. Simple logic.-Lots of theists read God (the gods) differently from your point of view. Indeed, you yourself reject many views of the organized religions. When I think about him, I try to envisage him in the light of the world he created, and I do not think your panentheism gives you more authority than my agnosticism to speculate on his motives, nature and methods. My hypothesis actually allows for humans not being an accident, for their being a saltation (like every other innovation), for a God, and even for a God intervening. What it does not allow for is every innovation, lifestyle and natural wonder depending on God's guidance, and for his anthropocentric starting-point.
Bacterial motors carefully studied
by David Turell , Sunday, April 03, 2016, 15:17 (3156 days ago) @ dhw
> dhw: You are assuming he did not wish it to progress unmonitored! I am surprised but pleased to hear that you don't believe in your hypothesis of a 3.8-billion-year computer programme after all. But since you insist on God's “guidance”, even down to the building of the weaverbird's nest, this leaves you with nothing but divine dabbling (unless you can think of an alternative means of “guidance”) to account for every innovation, lifestyle and natural wonder.-Again a misinterpretation of my thinking: the 3.8 billion year program and the dabble are two alternative ways God guided evolution. The key starting point of my reasoning is God invented and guided evolution. Since guidance is a key, an IM is guided also. I believe in guidance, method unknown.-> > dhw: Why could he not have invented a mechanism to function without his guidance?-He could have with all the guidance built in. > dhw: My objection is to your insistence that all innovations etc. are “guided” by God, and are/were geared to humans right from the start. Maybe the weaverbird designed its own nest for its own purposes. -Design involves visualizing the purpose in the present for the future. Bird brains can conceptualize? I see trial and error for those birds. If nests fossilized we might find a trail of changes. > > DAVID: When you think about God you read Him from your agnostic point of view, nothing like my point of view. Are humans an accident as Gould claims, arriving by Darwin's theory? They look like a saltation to me. God did it. Simple logic. > > dhw: My hypothesis actually allows for humans not being an accident, for their being a saltation (like every other innovation), for a God, and even for a God intervening. What it does not allow for is every innovation, lifestyle and natural wonder depending on God's guidance, and for his anthropocentric starting-point.-So God intervenes on and off when He feels like it? If He bothered to start a universe and life, why wouldn't He have an intense continuous interest?
Bacterial motors carefully studied
DAVID: The real reason I edited your post is that you keep reverting to the 3.8 billion year programming as though I believe this thought. I don't. In the past, repeatedly, I have stated that I believe God guided evolution but I have no idea how He did it. dhw: I am surprised but pleased to hear that you don't believe in your hypothesis of a 3.8-billion-year computer programme after all. But since you insist on God's “guidance”, even down to the building of the weaverbird's nest, this leaves you with nothing but divine dabbling (unless you can think of an alternative means of “guidance”) to account for every innovation, lifestyle and natural wonder.-DAVID: Again a misinterpretation of my thinking: the 3.8 billion year program and the dabble are two alternative ways God guided evolution. The key starting point of my reasoning is God invented and guided evolution. Since guidance is a key, an IM is guided also. I believe in guidance, method unknown.-It is your starting point of “guidance” that is the great divide between us, and the weaverbird is the example that epitomizes the gaps in your hypotheses: God had to “guide” the weaverbird - you don't know how - in order to “balance nature” - you don't know how - in order to produce or feed humans, but you can't explain the connection.-dhw: Why could he not have invented a mechanism to function without his guidance? DAVID: He could have with all the guidance built in.-If you accept common descent, built-in guidance can only be your 3.8-billion-year computer programme or dabbling! You know very well that I am proposing a mechanism that works without guidance - i.e. an autonomous intelligence that makes its own decisions. You believe your God gave humans the intelligence to make their own decisions. So why could he not have done the same with other organisms? (Some scientists tell us they do have such intelligence, but you prefer to dismiss their findings.) DAVID: Design involves visualizing the purpose in the present for the future. Bird brains can conceptualize? I see trial and error for those birds. If nests fossilized we might find a trail of changes.-Even humans have to combine conceptualization with trial and error when they create something new. Nobody knows to what extent other organisms have originally achieved their wonders in the same way.-dhw: My hypothesis actually allows for humans not being an accident, for their being a saltation (like every other innovation), for a God, and even for a God intervening. What it does not allow for is every innovation, lifestyle and natural wonder depending on God's guidance, and for his anthropocentric starting-point.-DAVID: So God intervenes on and off when He feels like it? If He bothered to start a universe and life, why wouldn't He have an intense continuous interest?-Perhaps because instead of starting out with the purpose of creating humans, he started out with the purpose of seeing what would happen if he set evolution in motion. You don't like to speculate on why he would have created humans, but whatever the reason, it can be applied to the rest of “creation”. Possibly as an entertainment to relieve his eternal boredom.
Bacterial motors carefully studied
by David Turell , Monday, April 04, 2016, 18:08 (3154 days ago) @ dhw
> dhw; You believe your God gave humans the intelligence to make their own decisions. So why could he not have done the same with other organisms? (Some scientists tell us they do have such intelligence, but you prefer to dismiss their findings.)-You forget human intelligence is so different from animal intelligence. We can reason and plan. Can animals to any important degree? No. > > dhw: Even humans have to combine conceptualization with trial and error when they create something new. Nobody knows to what extent other organisms have originally achieved their wonders in the same way.-Yes, we do not know the extent of animal advanced planning. It doesn't seem to be much.-> > dhw: Perhaps because instead of starting out with the purpose of creating humans, he started out with the purpose of seeing what would happen if he set evolution in motion. You don't like to speculate on why he would have created humans, but whatever the reason, it can be applied to the rest of “creation”. Possibly as an entertainment to relieve his eternal boredom.-Again interpreting God's mind, while I shouldn't. I feel He wanted to create a thinking being to respond to Him, which we have done. We think like He does, only to a much less degree. Remember we are made in His image, at the mental level.
Bacterial motors carefully studied
Dhw: You believe your God gave humans the intelligence to make their own decisions. So why could he not have done the same with other organisms? (Some scientists tell us they do have such intelligence, but you prefer to dismiss their findings.) DAVID: You forget human intelligence is so different from animal intelligence. We can reason and plan. Can animals to any important degree? No.-That is the whole issue! Where do you draw the line between a degree and an important degree? We design a thousand different types of home; the weaverbird designs one. dhw: Even humans have to combine conceptualization with trial and error when they create something new. Nobody knows to what extent other organisms have originally achieved their wonders in the same way. DAVID: Yes, we do not know the extent of animal advanced planning. It doesn't seem to be much.-It doesn't seem to be much compared to our scale of advanced planning. But it seems to be enough for their purposes. -dhw: Perhaps because instead of starting out with the purpose of creating humans, he started out with the purpose of seeing what would happen if he set evolution in motion. You don't like to speculate on why he would have created humans, but whatever the reason, it can be applied to the rest of “creation”. Possibly as an entertainment to relieve his eternal boredom. DAVID: Again interpreting God's mind, while I shouldn't. -You asked me why God would only intervene on and off. You can hardly complain if I give you a possible answer.-DAVID: I feel He wanted to create a thinking being to respond to Him, which we have done. We think like He does, only to a much less degree. Remember we are made in His image, at the mental level.-I don't have a problem with that, except that I'm not sure what you mean by “respond to him”. Response usually entails the other party making the first move, whereas you have always claimed that God deliberately hides himself from us. You have often accused me of anthropomorphizing God when I talk of boredom and entertainment, so I'm glad you now accept that if we think like him, he must think like us. I wrote that whatever reason he had for creating us could be applied to the rest of creation. Well, how much more entertaining to watch a thinking, questioning, ever expanding intelligence, rather than the endless comings and goings of organisms only bent on their own physical survival/improvement. But your anthropocentric hypothesis still leaves us with the problem of 3.(whatever) billion years of dabbled or (for you too, unbelievably) preprogrammed innovations, lifestyles and natural wonders all somehow geared to the production of us!
Bacterial motors carefully studied
by BBella , Tuesday, April 05, 2016, 20:56 (3153 days ago) @ dhw
You asked me why God would only intervene on and off. You can hardly complain if I give you a possible answer. > > DAVID: I feel He wanted to create a thinking being to respond to Him, which we have done. We think like He does, only to a much less degree. Remember we are made in His image, at the mental level. > > I don't have a problem with that, except that I'm not sure what you mean by “respond to him”. Response usually entails the other party making the first move, whereas you have always claimed that God deliberately hides himself from us. You have often accused me of anthropomorphizing God when I talk of boredom and entertainment, so I'm glad you now accept that if we think like him, he must think like us. I wrote that whatever reason he had for creating us could be applied to the rest of creation. Well, how much more entertaining to watch a thinking, questioning, ever expanding intelligence, rather than the endless comings and goings of organisms only bent on their own physical survival/improvement. But your anthropocentric hypothesis still leaves us with the problem of 3.(whatever) billion years of dabbled or (for you too, unbelievably) preprogrammed innovations, lifestyles and natural wonders all somehow geared to the production of us!-I agree with dhw on this. If God wanted to create beings to "respond" to him, then why do we (those who supposedly have been created for that purpose) have to argue, fight and kill over what we believe about his intentions? And what kind of "relationship" can any of us really have anyway - at least until the afterlife? Certainly, while in this life, none of us have a face to face relationship with God - so is there really a relationship at all - doesnt a relationship at least take two? -If we have been created just to respond to him or to be his entertainment (like a movie - only more real to us that are playing the parts), then God would obviously not only have a very great ego, he would also be quite a sadistic voyeur as well. Which we humans consider a person like that very base and the lowest of low life's.-On the other hand, putting myself into the place of ONE such eternal being with all power to create - instead of creating life, and becoming a watcher and a fiddler of it - I would become life itself. Become it in such a multitude of ways as to experience any and every possible way of being and experience it all fully. But the only way to do that, to truly experience ALL things exclusively as one thing, I would have to close the door to the true knowledge of who - I AM. -If you took a moment and put yourself in that ONE eternal being billions of years ago, you would do the same. Of course we cannot know anything for sure - but doesnt that kinda make this hypothesis more credible? We can know NOTHING for sure, but - I AM.
Bacterial motors carefully studied
by David Turell , Wednesday, April 06, 2016, 01:34 (3153 days ago) @ BBella
BBella: If you took a moment and put yourself in that ONE eternal being billions of years ago, you would do the same. Of course we cannot know anything for sure - but doesnt that kinda make this hypothesis more credible? We can know NOTHING for sure, but - I AM.-Yes, Just as God answered Abraham, 'I am who I am'. The voyeur part of dhw's proposal just having entertainment watching us is out and out wrong. God created us for a relationship, but He chooses to remain concealed so as to require faith.
Bacterial motors carefully studied
by David Turell , Wednesday, April 06, 2016, 01:06 (3153 days ago) @ dhw
> DAVID: I feel He wanted to create a thinking being to respond to Him, which we have done. We think like He does, only to a much less degree. Remember we are made in His image, at the mental level. > > dhw: I don't have a problem with that, except that I'm not sure what you mean by “respond to him”. -I meant 'response' in the sense that humans setup religions.->dhw: But your anthropocentric hypothesis still leaves us with the problem of 3.(whatever) billion years of dabbled or (for you too, unbelievably) preprogrammed innovations, lifestyles and natural wonders all somehow geared to the production of us!-It is only a problem for you, not for me. There are only three possibilities for how evolution works, as discussed before: Natural chance, strict creation step by step (tony) or a process with guidelines. Without purpose and with purpose.
Bacterial motors carefully studied: flagellum
by David Turell , Sunday, September 11, 2016, 00:16 (2995 days ago) @ dhw
A careful study of the flagellum and how it is composed by various molecules. This is what the ID folks thinks is irreducible complexity: - https://www.sciencedaily.com/releases/2016/09/160907113352.htm - "Researchers used biochemical techniques and electron microscopy to uncover the structure of the bacterial MotA protein, which forms part of the propeller motor (flagellum). Three-dimensional analysis found it is composed of a transmembrane component and cytoplasmic domain, while MotA molecules were shown to form stable tetramer complexes with other MotA molecules. These findings will aid understanding of the mechanism underlying energy conversion during bacterial movement. - Heading under the diagram: "The three-dimensional structure of a complex of MotA and the flagellar motor structure in a bacterial cell. Many motile bacteria have rotating fiber (flagellum) generating from a cell surface which functions like a screw and create a driving force to move or swim. At the proximal end of flagellum there is a rotary motor which is composed of a rotor and a stator and ions, Na+ or H+, flow into cells by way of the stator. The flows of ions are converted into a rotational force by the interaction between the stator and the rotor. The three-dimensional structure of the MotA complex has been determined from a large number of electron microscope images in this report. - *** - " They found that it can form a structure of four MotA molecules (called a tetramer), which differs in shape from the previously predicted complex. - *** - "The MotA protein spans the bacterial membrane, and has previously been shown to form a tetramer complex with another transmembrane protein, MotB, creating the stator. In this latest work, MotA was expressed and purified from A. aeolicus, and found to be structurally stable. Assessment of its interactive potential revealed it can form a tetramer even in the absence of MotB. - "Electron microscopy showed that the elongated top part of the MotA complex matches the size of the lipid bilayer of the bacterium, suggesting that it represents the transmembrane component. "This region has a globular shape that corresponds to a MotA tetramer fitted inside an aggregate of detergent molecules which were used to purify the protein," first author Norihiro Takekawa says. - "The lower part of the complex has two arch-like regions with spiky projections. "These match the cytoplasmic domain of the MotA protein," corresponding author Michio Homma says. "We predict that its structure will change with the movement of ions through the stator channel and in association with the stator-motor interaction." The shape of the complex differs from that reported for a related protein complex in another bacterium." - Comment: This article and the diagram show how it is impossible to believe this sort of motor developed stepwise. Darwin theory cannot explain this. All the Darwin folks can do is point to precursor parts that were modified.
Bacterial motors carefully studied:flagellum complexity
by David Turell , Wednesday, November 16, 2016, 21:09 (2928 days ago) @ David Turell
A very careful study which shows the various protein molecules that make up a flagellum. Since this provides motility, when the organism appeared this had to be an initial part:
http://www.nature.com/articles/ncomms13425#f2
Abstract: "The bacterial flagellar hook is a tubular helical structure made by the polymerization of multiple copies of a protein, FlgE. Here we report the structure of the hook from Campylobacter jejuni by cryo-electron microscopy at a resolution of 3.5 Å. On the basis of this structure, we show that the hook is stabilized by intricate inter-molecular interactions between FlgE molecules. Extra domains in FlgE, found only in Campylobacter and in related bacteria, bring more stability and robustness to the hook. Functional experiments suggest that Campylobacter requires an unusually strong hook to swim without its flagella being torn off. This structure reveals details of the quaternary organization of the hook that consists of 11 protofilaments. Previous study of the flagellar filament of Campylobacter by electron microscopy showed its quaternary structure made of seven protofilaments. Therefore, this study puts in evidence the difference between the quaternary structures of a bacterial filament and its hook."
***
"Flagella are found in both gram-positive and gram-negative bacteria. Although flagellar hooks appear identical at first sight, the diversity of flagellar hook proteins suggests that the hooks have diverged to specifically fit the motility requirements of each bacterium.
***
"Flagella, although macroscopically similar, have evolved features that will make them specially adapted to particular tasks. The intestinal jejunum is a viscous environment where C. jejuni is adapted for swimming25,26. The results shown here tend to support the idea that additional strengthening of the hook in C. jejuni is necessary to enable motility in this viscous environment."
Comment: Please look at the diagrams and illustrations in the article. That is the easiest way to understand the enormous complexity of this bacterial motor. Bacteria did not self-invent these motors. That is self-evident.
Bacterial motors carefully studied:flagellum complexity
by David Turell , Tuesday, April 18, 2017, 15:06 (2776 days ago) @ David Turell
The latest findings:
https://www.sciencedaily.com/releases/2017/04/170413141058.htm
"The bacterial flagellum is one of nature's smallest motors, rotating at up to 60,000 revolutions per minute. To function properly and propel the bacterium, the flagellum requires all of its components to fit together to exacting measurements. In a study published in Science, University of Utah researchers report the eludication of a mechanism that regulates the length of the flagellum's 25 nanometer driveshaft-like rod and answers a long-standing question about how cells are held together.
"While the biomechanical controls that determine the dimensions of other flagellar components have already been determined, the control of the length of the rod, a rigid shaft that transfers torque from the flagellar motor in the interior of the cell to the external propeller filament, were unknown. "Since the majority of the machine is assembled outside the cell there have to be mechanisms for self-assembly and also to determine optimal lengths of different components," says biology professor Kelly Hughes. "How does it do that?"
"Eli Cohen pursued the question of rod length control in Salmonella enterica using genetic tools with slow progress until, in one of his courses, he heard about the concept of the outer membrane tethering protein Lpp, that physically links the outer membrane to the cell wall. The Salmonella envelope is composed of an inner membrane and an outer membrane that interacts with the outside world. Between the two membranes is a space containing a cell wall called the periplasm. Cell biologists previously didn't know whether the LppA protein propped up the cell wall, like pillars prop up a roof, or whether the outer membrane was tethered to the cell wall.
"Cohen, Hughes, and their colleagues engineered strains of Salmonella to determine if LppA acted as a tether for the outer membrane and whether or not the outer membrane influenced flagellar rod length. They found that varying the length of the LppA protein varied the width of the periplasm along with the length of the rod.
"'The rod needs to touch the inside of the outer membrane," Cohen says. "So, if the outer membrane is farther away, the rod has to grow there to meet it."
"'This work ended up showing that it actually is a tether holding the outer membrane down," Hughes adds. "If you don't tether it down, the outer membrane explodes away from the cell.'"
Comment: There is no way chance mutations could produce this mechanism. Only a designing mind can do it. It has to be put together all at once.
Bacterial motors carefully studied:flagellum enzymes
by David Turell , Tuesday, September 12, 2017, 18:21 (2628 days ago) @ David Turell
Found on the surface of flagella, this enzyme can attack the organism the bacterium is infecting. This adds to the complexity of the flagellum which is a tiny motor:
https://www.sciencedaily.com/releases/2017/09/170912093059.htm
"Researchers have discovered a new class of enzymes in hundreds of bacterial species, including some that cause disease in humans and animals. The discovery provides new insights into how bacteria invade their hosts.
***
"'What we found in this case is that many bacteria have repurposed their flagella to function as protein-degrading enzymes. There are thousands of these enzymes, making this potentially one of the largest enzyme structures known."
"Bacterial flagella are filaments composed of around 20,000 proteins that link up together and form structures about 10 micrometers long -- roughly one-tenth the width of a human hair. While they can differ structurally, most flagella help with propulsion, and in some cases, they can attach bacteria to host cells. The discovery of flagella as enzymes means that some of them can also break down tough bonds in cells and tissues.
"We think that these enzymatic flagella may help some bacteria degrade and move through viscous environments. Interestingly, scientists have tried engineering flagella with this functionality before, but until now, we didn't know that nature already did this," said Doxey, a member of the Centre for Bioengineering and Biotechnology at Waterloo.
"To test whether these new enzymatic flagella are active, scientists examined Clostridium haemolyticum, a pathogen that's highly fatal in cows and sheep, and isolated the flagella. This pathogen has numerous flagella on one cell. They found that the flagella are capable of breaking down proteins found in cow liver -- precisely where the organism infects.
"The researchers also found the enzymes in bacteria that inhabit the human gut. Further research is needed to determine whether they play a beneficial or harmful role in humans."
Conclusion from the study: http://www.nature.com/articles/s41467-017-00599-0
"our findings provide a fascinating and multilayered story of molecular evolution, involving not only protein domain recombination, but also lateral gene transfer. First, a collagenase-related gene appears to have inserted into a flagellin hypervariable region, presumably within a collagenase-containing lineage such as Clostridium. This is consistent with numerous studies that have documented intragenic recombination in flagellins, which serves as a mechanism for antigenic diversification. It is reasonable to assume that this domain insertion likely happened after the evolution of microbial collagenase and MMP-like proteins. The proteolytic flagellin gene then spread to other microorganisms through lateral transfer "
Comment: Enzymes are giant complex molecules. This one contains zinc. This adds to the known complexity of flagella. It cannot have developed by chance evolution, as it is irreducibly complex.
Bacterial motors carefully studied:flagellum video
by David Turell , Tuesday, September 12, 2017, 19:37 (2628 days ago) @ David Turell
Bacterial motors carefully studied:flagellum video
DAVID: Here it is:
Too complex for anything but a designer
Superb! Thank you. I don’t know why some folk think it’s a slap in the face for Darwinism, but I would certainly acknowledge that it is a problem for atheism.
Bacterial motors carefully studied:flagellum sequence
by David Turell , Saturday, April 28, 2018, 05:21 (2401 days ago) @ dhw
It takes 70+ specific genes to make a flagellum:
https://phys.org/news/2018-04-bacterial-propeller.html
"Many bacteria are equipped with a flagellum, a helical propeller that allows bacteria to travel. The flagellum is assembled in a highly organized manner involving the stepwise addition of each of its internal parts. However, there are many open questions as to how this orderly construction is achieved.
***
"'Flagellar assembly is a complex process involving more than 70 genes," lead author Naoya Terahara explains. "First, the basal motor is assembled, followed by the hook, and finally the helical filament. Each structure is built by sending a unique set of proteins to the site of assembly. The cell can somehow sense when each structure is complete, triggering a switch to export the next series of proteins. We wanted to develop a more detailed picture of how this switching occurs.
"The export machinery sits at the base of the flagellum, and is made from nine copies of a protein that form a ring. The ring acts like a gatekeeper, selecting which proteins will travel out to the growing flagellum. The ring is incredibly small—mere nanometers in diameter—making precise analysis relatively difficult. To gain insight into this machinery, the researchers used high-speed atomic force microscopy. The approach, conducted through a collaborative effort with researchers at Kanazawa University, allowed the team to directly visualize the ring. By then making mutations in the ring, they could pinpoint which regions were responsible for triggering the export switch.
***
"'Our findings suggest that subtle changes in the ring's shape determine which proteins are exported to the growing flagellum," lead investigator Tohru Minamino explains. "Once the hook has been assembled, contact points in the ring shift slightly, altering the ring's shape and allowing helical filament proteins to travel through."
"The proposed model may have a significant impact on research into bacterial infections: the flagellum shares many similarities to the injectisome, a needle-like structure used by infectious bacteria to deliver proteins to their host. The study may thus serve as a map to better guide infectious disease research."
Comment: Of course atheists believe this all happened by chance. Doesn't seem reasonable to me. 70+ genes just got together naturally. Really?
Bacterial motors carefully studied:vital flagellum protein
by David Turell , Sunday, May 13, 2018, 20:27 (2385 days ago) @ David Turell
A specialized protein must be present in sperm flagella for proper function:
https://www.sciencedaily.com/releases/2018/05/180511102316.htm
"The group led by ICREA Research Professor Cayetano Gonzalez at the Institute for Research in Biomedicine (IRB Barcelona), in collaboration with Giuliano Callaini's team at the University of Siena in Italy, has published a study in The Journal of Cell Biology that identifies the critical role played by a protein called CENTROBIN in sperm tail development.
"In flies, as in humans, the sperm cell (spermatozoon) is made up of the cell body proper, also referred to as the sperm "head," and the flagellum. The flagellum, also called the sperm "tail," is a slender lash-like appendage that protrudes from the cell body. By beating their tails, sperm cells swim to the female reproductive cell (oocyte) and fertilise it. A bundle of microtubules that span the entire length of the tail is critical for flagellar beating. These microtubules are arranged in a characteristic radial symmetry that has been conserved throughout evolution and is templated by a small organelle called the basal body, which sits at the base of the flagellum.
"Using the vinegar fly Drosophila melanogaster as a model to study how the sperm tail develops, Gonzalez's Cell Division Lab has found that CENTROBIN plays a critical role in the assembly of a subset of microtubules within basal bodies. In the absence of CENTROBIN, basal bodies lack these microtubules, as do the non-motile tails that they template. Consequently, CENTROBIN mutant males are sterile.
***
"In summary, the recent article demonstrates that CENTROBIN, which is well conserved between humans and flies, is a positive regulator of normal flagellum development. Remarkably, a previous study by the same group showed that CENTROBIN exerts a negative effect in the development of primary cilia. Primary cilia are a shorter version of flagella that are present in certain neurons in the fly and in many cell types in humans, where they function as sensors of external stimuli. Like flagella, primary cilia contain a microtubule array that is templated by the basal body.
"Taken together, these results reveal the multifunctional nature of CENTROBIN, a protein that plays opposing roles in distinct cell types in the same organism.
Once again evolution must find just the right specialized protein for a specific function and this protein has two different functions in flagella and cilia. A chance form of evolution has little likelihood of finding just the right protein molecule. a
Bacterial motors and other organelles
by David Turell , Friday, June 28, 2019, 21:11 (1974 days ago) @ David Turell
Bacteria are highly complex with specific organelles. Although without a specific nucleus they have specific functional areas:
https://www.quantamagazine.org/bacterial-organelles-revise-ideas-about-which-came-first...
"for the past few decades, researchers have been quietly uncovering many complex structures within prokaryotes, including membrane-bound organelles. In contrast to eukaryotes, which all have a suite of organelles in common, different groups of prokaryotes showcase their own specialized compartments.
***
"And that list is only growing as scientists discover more and more compartments within supposedly simple bacterial cells. “Bacteria are a lot more complex, in other words, and may have a lot more similarities in their biology to eukaryotes than people have assumed in the past,” said John Fuerst, a microbiologist at the University of Queensland in Australia. The very existence of organelles in these bacteria, coupled with intriguing parallels to the more familiar ones that characterize eukaryotes, has prompted scientists to revise how they think about the evolution of cellular complexity — all while offering new ways to probe the basic principles that underlie it.
***
“'Historically, people have known about compartments in bacterial cells that carry out specific functions for a long, long time, going back to the 1800s,” said Arash Komeili, a microbiologist at the University of California, Berkeley. Yet, while eukaryotic organelles have been studied in great detail for many decades, it has only recently become possible to do so in prokaryotes. Bacteria are tiny: orders of magnitude smaller than typical eukaryotic cells, and sometimes even smaller than eukaryotes’ organelles. That made it extremely difficult to isolate and analyze bacterial compartments to get a sense of what they were — and what they were doing.
***
"A couple of decades ago, two-dimensional imaging by Fuerst and others seemed to indicate that the DNA of the bacterium Gemmata obscuriglobus was surrounded by a membrane, instantly raising comparisons to the eukaryotic nucleus. Those results have been called into question — imaging seems to indicate that the compartment isn’t entirely closed, meaning it does not satisfy the definition of an organelle — but experts remain excited about these bacteria. They have the most complex internal membrane system seen in prokaryotes to date, and they contain proteins that structurally resemble those that shape and maintain eukaryotic membranes. They also seem capable of processes that were thought to be unique to eukaryotes, such as digesting nutrients inside their cells and synthesizing molecules called sterols.
“'The problem is, we basically don’t know anything about [this membrane system],” said Damien Devos,
***
"Bacteria also seem to have a wide variety of enclosed structures that are bound not by a lipid membrane but by a protein coat. Take carboxysomes, which evolved in bacteria twice, independently, to fix carbon. They and smaller, self-assembling nanocompartments have a polyhedral structure that looks shockingly like a viral capsid, the protein shell that encloses viral genomic material.
"The catalog keeps getting longer: Komeili and his colleagues recently discovered a new lipid-bound organelle that accumulates iron, which they’ve dubbed the ferrosome. Bacteria seem to have a cornucopia of such organelles, with more waiting to be discovered."
Comment: These studies raise the issue of just how complex was original life if it started with so-called simple bacteria. Perhaps not so simple and required a designer.
Bacterial motors carefully studied
by David Turell , Sunday, July 04, 2021, 14:57 (1238 days ago) @ dhw
A new engineering study, first part of three:
https://bio-complexity.org/ojs/index.php/main/article/view/BIO-C.2021.1/BIO-C.2021.1
"Systems biology [1] employs methodology and techniques typical of systems engineering. Similarly, reverse engineering the features of biological organisms leverages both biology and engineering disciplines. Specifically, the systems engineering perspective on bacterial motility detailed in Parts 1, 2 and 3 studies the purpose, functions, components, and structure of a typical bacterial flagellum and the flagellum’s assembly stages. The dynamic operation and control of this motility organelle is also studied. This study takes two essentially independent approaches below. One is a constructive approach, which this
Part 1 covers; the other is an analytical approach to be covered in Part 2. The first, constructive approach is a top-down specification. It starts with specifying the purpose of a bacterial motility organelle, the environment of a bacterium, its existing resources, its existing constitution, and its physical limits, all within the relevant aspects of physics and molecular chemistry. From that, the constructive approach derives the logically necessary
functional requirements, the constraints, the assembly needs, and the hierarchical relationships within the functionality. The functionality must include a control subsystem, which needs to properly direct the operation of a propulsion subsystem. Those functional requirements and constraints then suggest a few—and only a few—viable implementation schemata for a bacterial propulsion system. The entailed details of one configuration
schema are then set forth. This constructive approach is analogous to how a myriad of
theorems, definitions, and constructions of plane geometry are derived from the few basic axioms and the rules of logic. A sincere attempt has been made to keep the elaboration of this constructive approach logical and as independent as possible from knowledge of the actual flagellar structure. The analytic approach of this study will be covered in Part 2 and is a bottom-up deconstruction of a typical flagellum. The bacterial flagellum is a well-researched molecular subsystem, and Part 2 draws its information from many cited papers. It documents the known 40+ protein components and the observed and inferred structure, assembly, and control of a typical flagellum. However, in Part 2 the protein and assembly relationships will be illustrated graphically in a form and detail not found in any previous paper. After the constructive and analytic approaches are presented, they will be compared in Part 3 along with a set of fresh concluding observations. The comparison is appropriate, because engineers regularly specify and design systems top-down, but they construct those systems bottom-up. Then the resulting implemented system is evaluated against the specification."
***
OBSERVATIONS
"Regarding the foregoing derivation of requirements and Figures 2 to 4, we see intricate coherence which is essentially irreducible. It is hard to imagine that a motility system (comprising control, propulsion, and redirection subsystems) could function at all without each of those details present. Current evolutionary biology proposes that the flagellum
could have been “engineered” naturalistically by cumulative mutations, by horizontal gene transfer, by gene duplication, by co-option of existing organelles, by self-organization, or
by some combination thereof [10, p. 210]. See the summary and references by Finn Pond [11]. Yet to date, no scenario in substantive detail exists for how such an intricate propulsion
system could have evolved naturalistically piece by piece. Can any partial implementation of a motility system be even slightly advantageous to a bacterium? Examples of a partial system might lack sensors, lack decision logic, lack control messages, lack a rotor or stator, lack sealed bearings, lack a rod, lack a propeller, or lack redirection means. Would such partial systems be preserved long enough for additional cooperating components to evolve? Further observations will conclude Parts 2 and 3. They will include suggestions for further research into the molecular details of proteins composing the bacterial flagellum, as detailed in Part 2."
Comment: I just copied out the beginning and the end of an enormous technical engineering can analysis of the flagellum. Note my bolds. The point of this paper is always the same as the poster child for design. There must be an engineering designer.
Bacterial motors carefully studied
by David Turell , Monday, July 05, 2021, 16:55 (1236 days ago) @ David Turell
The function of sensory cilia desscribed:
https://www.cell.com/current-biology/fulltext/S0960-9822(21)00454-1#tbox1
"Summary
Cells need to be able to sense different types of signals, such as chemical and mechanical stimuli, from the extracellular environment in order to properly function. Most eukaryotic cells sense these signals in part through a specialized hair-like organelle, the cilium, that extends from the cell body as a sort of antenna. The signaling and sensory functions of cilia are fundamental during the early stages of embryonic development, when cilia coordinate the establishment of the internal left–right asymmetry that is typical of the vertebrate body. Later, cilia continue to be required for the correct development and function of specific tissues and organs, such as the brain, heart, kidney, liver, and pancreas. Sensory cilia allow us to sense the environment that surrounds us; for instance, we see as a result of the connecting cilia of photoreceptors in our retina, we smell through the sensory cilia at the tips of our olfactory neurons, and we hear thanks to the kinocilia of our sensory hair cells. Motile cilia, which themselves have sensory functions, also work as propeller-like extensions that allow us to breathe because they keep our lungs clean, to reproduce because they propel sperm cells, and even to properly reason because they contribute to the flow of cerebrospinal fluid in our brain ventricles. Not surprisingly, defects in the assembly and function of these tiny organelles result in devastating pathologies, collectively known as ciliopathies (Box 1). Thus, the proper function of cilia is fundamental for human health."
From Evolution News:
https://evolutionnews.org/2021/06/cilium-and-intraflagellar-transport-more-irreducibly-...
"Consider first how many players are needed to build a cilium. Pigino’s parts list begins with microtubules in a 9+2 arrangement going up the cilium from base to tip. The two center microtubules are singlets; the outer ring of 9 are in doublet pairs. Riding on those rails are two engines: kinesin-2, which travels from base to tip (anterograde), and dynein-2, which goes from tip back to the base. Kinesin-2 has a head, stalk, hinge and two “feet” (called heads) that walk on the microtubule while carrying a load; the engine contains six protein subunits. Dynein-2 also has a motor, stalk, linker and tail, and is powered by two AAA+ domains that spend ATP for power. Those are the two engine types, and they work in teams along the microtubules.
"IFT proteins are numbered, such as IFT8 and IFT176. IFT complexes, such as IFT-A, is composed of six IFT proteins. IFT-B, with 16 IFT proteins is another complex. These ride along the trains to the tip, acting as adaptors for the cargo, which include tubulin proteins, dynein parts, membrane proteins and other IFT proteins.
"At the base, a basal body structure called the BBSome forms out of eight BB proteins. It functions as the cargo adaptor for the anterograde train. It authenticates other molecules trying to enter the cilium and moves cargo exiting the retrograde train. Overall, “About 24 different proteins constitute the theoretical minimal functional unit of IFT,” Pigino says, although much needs to be learned.
***
"A precise sequence of amino acids is required for each protein’s function, and the longer the protein, the more improbable that chance could get it right. IFT proteins are large. For instance, BBS1 in the BBSome has 593 amino acid residues; IFT172 (part of the IFT-B complex) has 1,749. The improbability is exacerbated when proteins have to work together. It’s not necessary to belabor the point again, but it’s instructive that Pigino never mentions evolution in her article.
"Moving cargo up and down the cilium takes place in five steps. First, the train assembles at the base. Kinesins line up along a microtubule doublet, their “heads” touching the tracks. Parts of dynein (the return engine) are loaded so as not to touch the tracks, avoiding a “tug-of-war” between the engines. Membrane parts and other cargoes are loaded with the help of IFT-A and IFT-B. Like a well-organized monorail car, the completed train “walks” up the track aided by multiple kinesin-2 engines powered by ATP.
"At the tip, the third phase begins. Cargo is unloaded and ferried to the growing cilium (microtubules and membrane). Concurrently, the dynein engines are assembled in an “open configuration as an intermediate state to ensure a controlled activation.” The kinesins are disassembled for transport back to the base. The fourth stage activates the dyneins and starts the train moving, carrying both IFT complexes and waste products to the base. The fifth and final stage unloads the cargo, disassembles the retrograde train and recycles the parts. If you conceive of railcars in a narrow mine shaft carrying tools needed by miners at the far end, and returning the carts with waste products, the analogy seems apt — only the cell’s actions are all automated."
Comment: the study of the bacterial flagellum all over again evolved into helpful celia/hairs that are vital to health. Pure irreducible complexity requiring a designer.
Bacterial motors carefully studied
by David Turell , Tuesday, August 09, 2022, 22:47 (836 days ago) @ David Turell
Cell control by Kinesin-8 which motors molecules around the cell and controls it shape and
length of microtubules:
https://phys.org/news/2022-08-motor-proteins-cells.html
"With the help of the Canadian Light Source (CLS) at the University of Saskatchewan, a research team led by John Allingham from Queen's University and Hernando Sosa from the Albert Einstein College of Medicine has shed light on a protein that regulates the intricate microscopic networks that give cells their shape and helps ship important molecules to diverse locations.
***
"n their published work, they are the first group to clearly describe the mechanism of action of a tiny motor protein called Kinesin-8 that enables it to control the structures of microtubule fiber networks inside the cell.
"Our recent paper in Nature Communications, co-first authored by Byron Hunter and Matthieu Benoit, shows how this specific type of kinesin motor protein has developed the ability to use microtubules as tracks for movement, guiding transport of cargo within the cell," said Dr. John Allingham, a professor at the Queen's School of Medicine, "in addition to being able to disassemble these tracks, controlling their length and location in cells."
"The Kinesin-8 proteins ensure that a cell's cargo is in the right place during cellular division and help to regulate cellular networks, making sure the microtubules do not grow too long."
Comment: this precision in delivery control of cellular protein products can only result from a carefully designed controlled process. Compare it to Amazon Prime receiving a Monday order and delivering it precisely on Tuesday.
Bacterial motors carefully studied; rapid repairs
by David Turell , Thursday, November 24, 2022, 18:59 (729 days ago) @ David Turell
They are so vital they can be repaired quickl
https://phys.org/news/2022-11-uncovers-bacteria-ancient-mechanisms-self-repair.html
"The findings, published today in Science Advances, show how the flagellar—the ancient motor that powers the swimming ability of bacteria—can also help these tiny organisms adjust to conditions where their motility is impaired.
***
"The researchers from the School of Biotechnology and Biomolecular Sciences are the first in the world to use CRISPR gene-editing technology to alter a flagellar motor. They used synthetic biology techniques to engineer a sodium motor onto the genome to create a sodium-driven swimming bacteria. They then tested and tracked the bacteria's ability to adapt when the environment was starved of sodium.
"Sodium is an ion, which means that it carries a charge. It is this charge that powers the flagellar motor via stators, or ion channels.
"The team found that the stators were able to rapidly self-repair the flagellar motor and restore movement. These findings could lead to new advances across the biological and medical science fields.
"'We showed that environmental changes can cause ion channels to react quickly," said lead author of the paper Dr. Pietro Ridone."
Comment: this shows active immediate adaptation. a must for a single cell organism. When bacteria first appeared this vital mechanism had to be present. Only by design.
Bacterial motors carefully studied; the latest
by David Turell , Saturday, May 27, 2023, 01:55 (546 days ago) @ David Turell
Highly complex methods revealed latest findings:
https://inference-review.com/article/bacterial-swimming
"STUDIES OF THE bacterial flagellar motor were some of the first to take advantage of cryo-EM. David DeRosier and Keiichi Namba used cryo-EM to study the basal body and the flagellar filament, respectively.10 Structural insight into the stator units around the basal body was restricted to negative-stain reconstructions, again with limited resolution.11 Tomography gave additional insight into their organization,12 but the limited resolution of these reconstructions prevented detailed molecular understanding of torque generation.
***
"To our great surprise, we found that the stator unit is a complex with a stoichiometry of 5:2 MotA:MotB, and not 4:2 as previously believed.16 This ratio introduces an asymmetry, as 4:2 stoichiometry would most likely have been symmetric. MotA has four helices spanning the inner membrane and a cytoplasmic domain. The part of this domain most distal from the membrane is well conserved and binds the rotor. The five MotA molecules make a nearly symmetric, ringlike structure surrounding the N-terminal helices of two MotB molecules, which contain a universally conserved aspartate residue. Each of the MotB N-terminal helices is followed by a plug helix that lies between two MotA molecules. The two plugs cross over and are thought, based on prior experiments, to block activity of the stator unit. As expected, the channel appears in closed conformation.
***
"...result can be explained if it is the rotation of MotA around MotB that drives the rotation of the motor. We proposed that one of the two MotB aspartates—call it MotB1—is protonated and anchored to MotA. This is a high-energy state for MotB1, which would drive MotA rotation were it not for the aspartate of MotB2. This aspartate is both negatively charged and unprotonated: the neutral surface of MotA cannot rotate across it. But when MotB2 accepts a proton from the periplasm, it is neutralized, and rotation of the hydrophobic MotA surface across the neutralized MotB2 aspartate can now occur. After rotation, MotB2 grabs on to MotA in this new position, and MotB1 releases its proton. MotB1 then waits at the cytoplasmic side to pick up a new proton. After these steps, a 36º rotation of the MotA ring around the MotB dimer has occurred. The whole structure is in the same state as before, except that MotB1 and MotB2 have switched roles, so the cycle can begin again.
***
"How does this miniature MotAB rotary motor power the rotation of a large flagellum? Upon incorporation in the motor, the C-terminal domains of MotB dimerize and bind to the peptidoglycan layer that forms part of the cell envelope. Peptidoglycan binding is accompanied by the unplugging of the MotAB ion channel, which allows ions to flow from the periplasm to the cytoplasm. Upon ion flow, MotA rotates clockwise around MotB. Given normal swimming conditions, the rotor is engaged at the proximal side of the MotA ring, and the clockwise rotation of MotA rotates the rotor counterclockwise. When all flagella spin counterclockwise, they form a bundle and swim in a straight line.
"Upon chemotactic signaling, a whole signaling cascade takes place and results in the phosphorylation of CheY. Phosphorylated CheY binds to the rotor and switches its conformation. The rotor now interacts with the distal side of the MotA ring. The same clockwise rotation of MotA around MotB induces a clockwise rotation in the motor. One or several flagella change their rotation direction, breaking up the flagellar bundle. The bacterium starts tumbling, until CheY is dephosphorylated and gets released from the rotor and all flagella again spin in the same counterclockwise direction and the bundle reforms.
"Researchers have come a long way since Antonie van Leeuwenhoek observed moving bacteria several centuries ago. They now know bacteria swim using long filaments powered by a bidirectional, rotary proteinaceous motor. They know the molecular makeup of the rotary motor, and that this bidirectional motor is itself driven by unidirectional miniature rotary motors. Yet several unanswered questions still remain. What is the exact energy consumption of the motor—how many ions are used per rotation of MotA around MotB? How can the motor use several stator units? Do they need to act cooperatively, or can single stator units drive rotation even in the presence of other bound but non-active stator units? A combination of single-molecule light microscopy, biophysical experiments, and cryo-electron tomography is likely necessary to answer these questions."
Comment: a microscopic bacterial motor just like the ones we make macroscopically, down to what each molecule does. This is the favorite ID example of what must be designed by a mind. The quality of design is the equal of what we create. If bacteria came first, can you imagine how complex first life was in the very beginning? Remember Archaea came first and they had flagella.
Bacterial motors carefully studied Archaea included
by David Turell , Sunday, October 02, 2022, 17:58 (782 days ago) @ David Turell
A comparison between bacterial flagella and Archaea's
https://www.sciencedaily.com/releases/2022/09/220927111326.htm
"It has been known that the propeller in bacteria is quite different than similar propellers used by hearty one-celled organisms called archaea. Archaea are found in some of the most extreme environments on Earth, such as in nearly boiling pools of acid, the very bottom of the ocean and in petroleum deposits deep in the ground.
"Using cryo-EM, Egelman and his team found that the protein that makes up the flagellum can exist in 11 different states. It is the precise mixture of these states that causes the corkscrew shape to form.
"Egelman and colleagues used cryo-EM to examine the flagella of one form of archaea, Saccharolobus islandicus, and found that the protein forming its flagellum exists in 10 different states. While the details were quite different than what the researchers saw in bacteria, the result was the same, with the filaments forming regular corkscrews. They conclude that this is an example of "convergent evolution" -- when nature arrives at similar solutions via very different means. This shows that even though bacteria and archaea's propellers are similar in form and function, the organisms evolved those traits independently.
"'As with birds, bats and bees, which have all independently evolved wings for flying, the evolution of bacteria and archaea has converged on a similar solution for swimming in both," said Egelman,"
Comment: it is not surprising that the flagella of bacteria and Archaea are similar. Similar
solutions abound in evolution.
Bacterial motors carefully studied: in salmonella
by David Turell , Wednesday, May 08, 2024, 18:15 (198 days ago) @ David Turell
Two studies:
https://www.chemistryworld.com/news/ultracold-snapshots-reveals-in-exquisite-detail-how...
"A series of highly detailed images of the structures found in the whirling flagellum that powers a bacterium’s movement has revealed new insights about how microbes get to where they want to be.
"Using cryo-electron microscopy (cryo-EM) two different groups have uncovered the molecular architecture of, and interactions between, key components of the bacterial motor that powers bidirectional rotation of the flagellum.
‘The whole concept of chemotaxis is the ability to move away from danger and towards food sources and many bacteria are able to do this via the flagellum … either by changing the direction in which the flagellum rotates or by stopping it completely,’ explains Steven Johnson, staff scientist at the National Cancer Institute (NCI)...
***
‘'[Salmonella] has a very simple system of turn counterclockwise to go in a straight line, turn clockwise to just start tumbling on the spot, and by combining those two different modes of operation, you can bias the direction in which the bacteria is walking,’ Johnson explains.
"The motor in the flagellum is composed of multiple rings, one of which is the cytoplasmic ring (C-ring), or ‘switch’, which is responsible for switching the rotation of the flagellum between counterclockwise and clockwise.
***
‘'It has been known for decades that the rotation direction did change and … that it’s this giant [C-]ring structure in the cytoplasm of the cell that’s responsible for that change and … that there’s a whole host of signalling receptors that respond to the external signals that then signal for this one particular molecule which combines to the C-ring motor and changes the direction the rotation occurs,’ Johnson says. ‘We also know that this rotation was partly being driven by small external stators … we learned a couple of years ago that that’s likely due to a mechanism by which the stators themselves have tiny little rotary motors…. This led to the hypothesis that the tiny rotary motors on the outside are driving this giant cog on the inside.’
"However, Johnson says what they didn’t know was how to alter the C-ring and change the direction it rotates relative to these tiny external motors, because they’re rotating in one direction.
***
"They looked at both the clockwise and the counterclockwise rotating forms and were able to define a huge structural conformational change in the C-ring, enabling directional switching.
‘'This essentially means that these little rotating motors move from being on the outside [of the big cog] to the inside, so the direction in which they drive it is reversed because essentially there is a 180° swap in conformation,’ explains Susan Lea, chief of the Center for Structural Biology at the NCI, who led the team of researchers. ‘It’s this humungous change which really extends our understanding of how big a conformational change proteins are able to make,’ she adds.
***
"However, Iverson says the questions they were trying to answer evolved over the course of the study. ‘The first questions that we had seem so trivial now – which is that this motor is powered by a gradient across the membrane of protons – a proton flux. It’s a current that runs down, transverses the membrane and can turn the rotor one way or the other. In this case, the current that goes one way can turn the motor either way and so we asked, how do you have something that’s reversible? That really wasn’t understood.’
‘'What we see after this study is almost a trivial explanation, which is you have this giant motor and a piece of the motor that responds to the current just flips around to reverse the motor.’
"Morgan Beeby, a structural biologist at Imperial College London, in the UK, welcomed the findings of the two studies. ‘Both papers determine the actual molecular architecture of a part of the motor we call the rotor – the cytoplasmic ring … the rotor component is interesting because it can also switch from rotating clockwise to counterclockwise and that’s the basis for how bacteria navigate… The key insight is a very clear, molecular rationale for how the rotor rings switches between a clockwise and counterclockwise conformation.’
‘'In isolation this result may not be that exciting, but because we’ve now got the structure of the stator component as well … we can now start saying something quite intelligent about how the thing actually works.'’
Comment: this is a highly complex reversible rotary motor powered by a proton flow. See the videos to understand how mind boggling this motor is. And it appeared with bacteria early in evolution. We generally characterize evolution as developing from simple to complex. Not so according to this study. We are seeing highly designed motors from early on. Only a designer mind fits the issue of the source..
Bacterial motors carefully studied; a review of kinesins
by David Turell , Wednesday, October 09, 2024, 19:11 (44 days ago) @ David Turell
Kinesins are amazingly complex:
https://evolutionnews.org/2024/10/kinesins-nanoscale-molecular-motors-each-built-for-a-...
"Typically, kinesins are built with 1) a set of motor domains responsible for harnessing the energy from ATP and generating force, 2) a central stalk domain that holds the motor domains together, and 3) a tail domain with specialized functions for binding different cargo.
"What is amazing about kinesins is they all get their energy from the same place (ATP hydrolysis), but they seem to use it differently for different tasks inside the cell. Some kinesins are power walkers (like the one in the video above) — taking hundreds of steps along the microtubule before falling off. Others are hoppers — only taking a few steps before letting go of the track. Some kinesins walk forward, some walk backward, and some walk in both directions (trust me…this observation is still quite puzzling from a biophysical perspective). Other kinesins don’t walk at all, but somehow use their ATP energy to trigger the microtubule track to fall apart underneath them.
"Are these differences in function a result of random haphazardness — stochastic tweaking of gene sequences to give infinitesimally small perturbations of amino acids within the motor to eventually (over billions and billions of years) produce a smorgasbord of elegant machines like the kinesin family? Many in the scientific community have faith in this hopeless Darwinian theory. Thankfully, there are a number of scientists who view the nanoscale world with wonder and are open to the idea that molecular machines reflect purpose and design. They see molecular motors as intelligently designed for a reason. These machines must function properly for cells to divide, for essential cargo to be delivered, for biochemical energy to be converted from chemical gradients into stored energy for metabolism, for the propulsion of a cell in a given direction to avoid danger."
Comment: there are many videos available to see kinesins in action walking along the tubules while carrying a cargo. All constructed from amino acids in various folding patterns. dhw to the contrary, this is the proper level for discussion of cellular activity.