Sunday, June 5, 2011

Biological Control of Cell Membrane Structural Properties

You learned about DNA and proteins in your high school biology class, but you may not remember much about the cell’s membrane which is based on a dynamic, fluctuating sandwich structure. This cellular envelope controls what chemicals enter and exit the cell, partly due to molecular machines such as channels and pumps in the membrane, and partly due to the sandwich structure itself. This sandwich structure is a barrier to certain types of chemicals. But the membrane permeability and the operation of the molecular machines depend on the details of the sandwich structure. And as recent research has been finding, contra evolutionary expectations, organisms actively maintain and fine-tune the sandwich structure in response to environmental challenges.

The cell membrane’s sandwich structure consists of two layers facing away from each other. Each layer is made up of an array of phospholipid molecules lined up next to each other. Phospholipid molecules consist of a water-loving (or hydrophilic) head, a phosphate group, and two oily (or hydrophobic) hydrocarbon tails.

The two layers face away from each other in a tail-to-tail arrangement. This creates a very oily, low dielectric, interior of the sandwich. While small oily molecules are able to pass through this membrane structure, it is difficult for any water-loving molecule, including water itself, to pass through the barrier. So when this sandwich structure forms a closed sphere surrounding the cell, the inside compartment is separated and protected from the outer aqueous environment. But the sandwich structure is not a simple, rigid, structure. It fluctuates, and this influences the membrane performance.

At lower temperatures the sandwich structure has a more rigid, gel, phase and at higher temperatures it has a less rigid, fluid phase. As with the freezing and melting of water there is a distinct phase change, between the gel and fluid phases of the sandwich structure, which occurs over a rather narrow temperature range. This melting point temperature is strongly influenced by the degree of attraction between the adjacent phospholipid tails. Depending on the temperature and this degree of attraction, the sandwich structure may be like a gel or like a fluid, and this is important because the phase influences the membrane permeability and the membrane’s molecular machines.

Within the membrane sandwich structure, the phospholipid tails are attracted to each other via the weakest chemical force, van der Waals interactions. Unlike the stronger chemical bonds, van der Waals interactions do not arise from the trading or sharing of electrons. So how do these interactions work?

Consider two neighboring atoms. As the electrons quickly move about, uneven charge distributions can occur across the atom. One side of an atom may temporarily be positively charged, and the other side negatively charged. Such charges influence the neighboring atom. For instance, a negative charge will tend to repel the electrons of the neighboring atom causing an attractive, uneven charge distribution in that atom. The two atoms can then continue with synchronized, fluctuating charge distributions. But all of this depends greatly on the distance between the two neighboring atoms. If they are too far apart (or too close together), the entire interaction, weak as it is, becomes insignificant.

The distance between adjacent phospholipid tails depends on their shape. If the tails have two hydrogen atoms for each carbon atom, then there are no double bonds. Such saturated chains have a consistent, linear, shape and they pack tightly together at the van der Waals preferred distance.

Unsaturated chains, on the other hand, have double bonds which cause structural kinks, loose packing and therefore weaker van der Waals interactions. And the particular location of the double bond is important, as some locations disrupt the van der Waals interactions more than others.

So all of this means that the number and location of hydrogen atoms in the phospholipid tails is an important tuning parameter (there are other tuning strategies as well), determining the phase of the sandwich structure and, in turn, the cell’s membrane performance. This is particularly important for organisms that are subject to greater temperature variations, such as poikilotherms. Such temperature variations can cause unwelcome phase changes in the membrane’s sandwich structure.

Physiological response to temperature change


Years ago it was thought that the various protein machines in the cell’s membrane were more or less randomly distributed. It is yet another example of the influence of evolutionary thinking on biology. If the biological world is a fluke, then aren’t biological designs, such as the cell’s membrane architecture, random?

Now we know better. The cell membrane architecture is anything but random. In fact, the attention to detail is enormous. This includes the phase of the sandwich structure and its tuning mechanisms, such as the degree to which the phospholipid tails are saturated. Here are quotes from representative research papers discussing how organisms monitor and control their membrane fluidity, particularly in response to temperature variations:

E. coli incorporates increasing proportions of saturated and long-chain fatty acids into phospholipids as growth temperature is increased. It was found that this compositional variation results in the biosynthesis of phospholipids that have identical viscosities at the temperature of growth of the cells. [link to paper]

Numerous studies have shown that fluidity is an important factor in the function of biological membranes. Changes in fluidity affect the activity of membrane-bound enzymes and the activity of transporters, as well as the permeability of membranes to nonelectrolytes, water, and cations. Given that temperature has profound effects on membrane fluidity, it is not surprising that poikilotherms adjust the composition of their membranes in ways that defend fluidity in the face of changes in body temperature. …

Although the ways in which membrane composition is altered in response to temperature are not always consistent among species, tissues, cells, or even organelles, a few important trends have emerged. One prominent response to a decrease in the body temperature of poikilotherms is an increase in the percentage of unsaturated fatty acids that make up the phospholipids. … Phospholipids with saturated fatty acids pack readily into bilayers, whereas phospholipids with unsaturated (and therefore, kinked) acyl chains tend to disrupt hydrophobic interactions among acyl chains of adjacent phospholipids. An increase in the proportion of unsaturated fatty acids thus results in an increase in membrane disorder and fluidity, which tends to oppose the ordering effect of a drop in temperature. [link to paper]

The phospholipid composition of plasma membranes from the kidney of rainbow trout, Salmo gairdneri, was determined over a period of 21 days as fish were acclimating between temperatures of 5 and 20 degrees C. Proportions of phosphatidylethanolamine (PE) were significantly higher (29.03 vs. 23.26%) in membranes of 5 degrees C- than 20 degrees C-acclimated trout [link to paper]

Our observations suggest that a physical parallel to the changes of lipid composition is the maintenance of an optimal lipid order in the hydrophobic core of the cytoplasmic membranes. It can be interpreted as a tendency of Bacillus subtilis to keep the lateral pressure in its membranes at an optimal value, independent of the temperature of cultivation. [link to paper]

Not only is the cell membrane intricate and complex (and certainly not random), but it has tuning parameters such as the degree to which the phospholipid tails are saturated. It is another example of a sophisticated biological design about which evolutionists can only speculate. Random mutations must have luckily assembled molecular mechanisms which sense environmental challenges and respond to them by altering the phospholipid population in the membrane in just the right way. Such designs are tremendously helpful so of course they would have been preserved by natural selection. It is yet another example of how silly evolutionary theory is in light of scientific facts.

141 comments:

  1. Years ago it was thought that the various protein machines in the cell’s membrane were more or less randomly distributed. It is yet another example of the influence of evolutionary thinking on biology. If the biological world is a fluke, then aren’t biological designs, such as the cell’s membrane architecture, random?

    Who were the doofuses that equated random mutation with respect to function with random distribution of components in a membrane? That wouldn’t be a failed prediction, that would be stupidity.

    References, please.

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  2. Random mutations must have luckily assembled molecular mechanisms which sense environmental challenges and respond to them by altering the phospholipid population in the membrane in just the right way.

    Some mothers have healthy babies, some mothers have babies with fatal genetic disorders. Design or luck?

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  3. This comment has been removed by the author.

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  4. "Who were the doofuses that equated random mutation with respect to function with random distribution of components in a membrane?"

    Clearly if any part of a system is random, then every aspect of it is necessarily random. It's just like the lottery. Since it's determined by a random set of random numbers, if you win you get a random amount of money comprised of random denominations in a random currency that you must pick up from a random location at a random time. It's really fun to see someone win 10 Mmbul that they have to pick up from Al Hudaydah, Yemen at midnight on Christmas Eve. That's what makes the lottery so much fun!

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  5. Cornelius Hunter said...

    If the biological world is a fluke, then aren’t biological designs, such as the cell’s membrane architecture, random?


    How many hours per night do you think CH lies awake in bed , scheming up new and different ways to make himself look totally clueless on actual evolutionary biology?

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  6. Venture free:

    Clearly if any part of a system is random, then every aspect of it is necessarily random.

    Ergodic systems "forget" their initial conditions. In other words, from any random starting point the system will converge to the same "attractor".

    Try it out for yourself: iterate the map x' -> 2x(1-x) for random starting conditions between 0 and 1. You'll find that x -> 0.5 regardless.

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  7. Another 'what came first the chicken or the egg' problem for evolutionists. What came first, the DNA that codes for the proteins of the cell membrane or the cell membrane? The DNA that codes for the membrane, needs the membrane to function. Gradual evolutionary steps can not explain how DNA began to code for a structure that it needs to function in the first place. It's an integrated system and a property of design.

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  8. Turns out that fatty acids can spontaneously assemble into a vesicle.
    http://exploringorigins.org/fattyacids.html

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  9. Tedford the Idiot said...

    Another 'what came first the chicken or the egg' problem for evolutionists. What came first, the DNA that codes for the proteins of the cell membrane or the cell membrane? The DNA that codes for the membrane, needs the membrane to function. Gradual evolutionary steps can not explain how DNA began to code for a structure that it needs to function in the first place. It's an integrated system and a property of design.


    Psst...hey idiot...Behe's "irreducible complexity" argument was shot down in flames years ago.

    Do try and keep up.

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  10. Zachriel said, "Turns out that fatty acids can spontaneously assemble into a vesicle."

    This is not anywhere sufficient to explain the critical membrane proteins which are coded by the DNA. Your still left with the chicken and egg problem.

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  11. Tedford the Idiot said...

    Your still left with the chicken and egg problem.


    Damn Tedford, it's bad enough you have the scientific acumen of dog doo, but at least learn the difference between "your" and "you're".

    ReplyDelete
  12. Thorton

    "Behe's "irreducible complexity" argument was shot down in flames years ago."

    Who did it? Maybe I missed something.

    ReplyDelete
  13. I understand the problem of irreducible complexity was addressed by suggesting the possibility of functional intermediates. How would that work in this case?

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  14. natschuster said...

    I understand the problem of irreducible complexity was addressed by suggesting the possibility of functional intermediates. How would that work in this case?


    Nat, go be a disingenuous ass somewhere else.

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  15. So the problem of irreducible complexity was not addressed with functional intermiates? Or is it that functional intermidiates are obvious in this case? I'm trying to unbdetstand why I'm a gluteal region. Or do yuo mean equus africanus? Anyway, I'm not leaving anytime soon. I have too much fun here.

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  16. Zachriel: Turns out that fatty acids can spontaneously assemble into a vesicle.

    Neal Tedford: This is not anywhere sufficient to explain the critical membrane proteins which are coded by the DNA. Your still left with the chicken and egg problem.

    It solves the chicken and egg problem.

    natschuster: I understand the problem of irreducible complexity was addressed by suggesting the possibility of functional intermediates. How would that work in this case?

    Because the vesicle forms a primitive barrier sufficient for segregation, the primary purpose of the membrane.

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  17. natschuster said...

    I like being a disingenuous ass


    Got it.

    ReplyDelete
  18. "How many hours per night do you think CH lies awake in bed , scheming up new and different ways to make himself look totally clueless on actual evolutionary biology? "

    Why does thorton feel it is so very important to be here everyday "scheming up new and different ways to himself look totally clueless on actual evolutionary biology" by futile ad homs against CH while never quite understanding a single thing CH ever says?

    It's only 99% of Darwinists that give a bad reputation to the rest ... as utterly incompetent thinkers.

    Thank thorton for proving this once again.

    Should I bring Hoyle in here again?
    Sure, it's simply irresistible:

    "Older folk in the know told me that selection didn't operate to make complicated things out of complicated things, only to make complex things out of simple ones. I couldn't understand how anything of the sort could be true, because, unlikely as it was, it would surely be less difficult to make a rabbit out of a potato than to make a rabbit out of sludge, which is what people said had happened, people with line after line of letters after their names who should have known what they were talking about, but obviously didn't." (Hoyle, F., Mathematics of Evolution

    "Because the old believers said that God came out of the sky, thereby connecting the Earth with events outside it, the new believers were obliged to say the opposite and to do so, as always, with intense conviction. Although the new believers had not a particle of evidence to support their statements on the matter, they asserted that the rabbit producing sludge (called soup to make it sound more palatable) was terrestrially located and that all chemical and biochemical transmogrifications of the sludge were terrestrially inspired. Because there was not a particle of evidence to support this view, new believers had to swallow it as an article of faith, otherwise they could not pass their examinations or secure a job or avoid the ridicule of their colleagues. So it came about from 1860 onward that new believers became in a sense mentally ill, or, more precisely, either you became mentally ill or you quitted the subject of biology, as I had done in my early teens. The trouble for young biologists was that, with everyone around them ill, it became impossible for them to think they were well unless they were ill, which again is a situation you can read all about in the columns of Nature [magazine]."

    Hoyle owned the Darwinians - no contest.

    ;-)

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  19. Zachriel:

    A cell membrane has to let stuff in as well. How could a simple lipid vesicle do that? Or did early cells not need to metabolize or polymerize.

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  20. Pedant:

    "Who were the doofuses that equated random mutation with respect to function with random distribution of components in a membrane? That wouldn’t be a failed prediction, that would be stupidity."
    ===

    I believe your own Church invented this cult following worldview to begin with. Of course, I understand you reserve the right to evolve it at any time as needed.
    ---

    natchuster:

    "A cell membrane has to let stuff in as well. How could a simple lipid vesicle do that? Or did early cells not need to metabolize or polymerize."
    ===

    You don't exactly expect a real world answer from this thing do you ??? Half these gamers live in multiple virtual universe worlds to numerous to number. At best, you'll get nothing more than the usual authoritative faith-based statement from this particular self-promoting neighbourhood intellect with the usual dogmatically defending it as a fact ploy. This followed by more and more word definition shell games until the O.P. becomes totally obliterated under a sea of illusion. It's their world, let'em play in it for a while longer.

    For many here it's all the life and purpose they have, since the real world rejected them long ago! Let them enjoy it in peace. Oh wait a minute, that's not exactly what they want either. Okay, for the time that's reduced, let'em have their chaos. *smile*

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  21. natschuster: A cell membrane has to let stuff in as well. How could a simple lipid vesicle do that?

    Fatty acid vesicles can be semi-permeable to small molecules. If we have a vesicle containing an RNA replicator, the membrane would allow nucleotides to enter, but prevent the polymer from leaving. Also, there's a natural process of cleaving when the vesicle reaches a certain size.

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  22. "Ergodic systems "forget" their initial conditions. In other words, from any random starting point the system will converge to the same "attractor".

    Try it out for yourself: iterate the map x' -> 2x(1-x) for random starting conditions between 0 and 1. You'll find that x -> 0.5 regardless."

    I have no idea what you are talking about, but since you seem to be disagreeing with me then obviously you are wrong. If you start with any random number then the result of any function will be random. I can prove it.

    If that weren't true then you would be right. If you were right, then I would be wrong. Since I am not wrong, then logically you must not be right, thereby proving that anything with a random component can only possibly have random results because that's what I'm not wrong about.

    It's called logic, of which I am a master.

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  23. Zachriel said, "Because the vesicle forms a primitive barrier sufficient for segregation, the primary purpose of the membrane."

    Cellular reproduction begins within the cell and is tightly controlled from within the cell. It's not like a house that is put together in a certain way with external materials like siding and roofing brought in from an external source and added to the structure. Cellular components do not add themselves together to form a whole, but rather progressively differentiate themselves out of the existing parent cell, including the cellular membrane. Fatty acids are not added like siding to a house to form the membrane.

    In an imagined scenario where a lipid monolayer bubble in a warm little pond surrounds a supposed RNA molecule you have a fortunate molecule that just had exterior "plywood" and "siding" added. This is not a living cell. A living cell membrane is tightly integrated from its formation to maturity from within the cell, with its vital membrane proteins coded by the information within the cell. You haven't explained how the supposed primitive vesicle becomes fully integrated into the whole with the proto-cell being able to replicate the vesicle barrier.

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  24. Venture Free:

    If you start with any random number then the result of any function will be random. I can prove it.

    Please do so. I could be wrong, but, um, the function f(x)=1 is a counterexample. You see, any random input x gives the same result, namely 1, which isn't terribly random.

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  25. troy

    I've already proven it over and over again. It's somewhere in one of my previous comments on this site or one of the multitude of other sites that I frequent. If you're unwilling to search through every comment on every one of these sites to verify my claim that's your problem.

    Besides, anything with a random component can only possibly have random results. This simple fact completely dismantles your entire argument.

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  26. Neal Tedford: Fatty acids are not added like siding to a house to form the membrane.

    Your original contention concerned the chicken and egg problem regarding cell membranes. The fact that semipermeable membranes can spontaneously assemble resolves that conundrum.

    By the way, that sort of negative argument is not scientifically valid. It's like concluding that planetary movements are under the auspices of angels simply because you don't what else could cause them.
    http://www.zachriel.com/images/AngelsCranking.gif

    ReplyDelete
  27. Zachriel said, "The fact that semipermeable membranes can spontaneously assemble resolves that conundrum. "

    Were talking about origin of life, right?

    You didn't answer question... You haven't explained how the supposed primitive vesicle becomes fully integrated into the whole with the proto-cell being able to replicate the vesicle barrier.

    Neither have you explained how the complex proteins that are vital for real cellular membranes assembled in your scenario.

    Life comes from life (no angels necessary), and the origin of life comes from the Creator.

    A cell membrane is much more than self-assembling fatty acids. If this was an exam question on a test and you were being graded on completeness of your answer, you'd get a 1% on your exam if I was feeling generous.

    I'm not claiming that angels assemble cellular membranes, so you're attacking a strawman and not answering the questions.

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  28. Neal Tedford: Were talking about origin of life, right?

    We're talking about this specific claim:

    Neal Tedford: Another 'what came first the chicken or the egg' problem for evolutionists. What came first, the DNA that codes for the proteins of the cell membrane or the cell membrane?

    As a semipermeable membrane can spontaneously assemble, that resolves the problem of chicken or egg.

    Neal Tedford: You haven't explained how the supposed primitive vesicle becomes fully integrated into the whole with the proto-cell being able to replicate the vesicle barrier... A cell membrane is much more than self-assembling fatty acids.

    We're not talking about a modern cell, but a semipermeable membrane that is sufficient for a primitive cell.

    Neal Tedford: Life comes from life (no angels necessary), and the origin of life comes from the Creator... If this was an exam question on a test and you were being graded on completeness of your answer, you'd get a 1% on your exam if I was feeling generous.

    We don't even need 1%, as ignorance is not evidence. Even if we had no plausible understanding of how a primitive membrane may have formed, that doesn't support the claim that life was the result of special creation. In any case, we do have some idea of how a primitive membrane could form. This resolves the chicken and egg problem you noted above. It doesn't require a preexisting and complex mechanism to form a membrane.

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  29. Zach:"If we have a vesicle containing an RNA replicator, the membrane would allow nucleotides to enter, but prevent the polymer from leaving. Also, there's a natural process of cleaving when the vesicle reaches a certain size."

    In your imagination. Which concentration of nucleotides you need outside the membrane to get inside, by passive diffusion as you do not have the active channels, you need in order to allow the self replicator RNA replicat himself?
    I would consider more probable see angels pushing planets.

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  30. I've already proven it over and over again. It's somewhere in one of my previous comments on this site or one of the multitude of other sites that I frequent. If you're unwilling to search through every comment on every one of these sites to verify my claim that's your problem.

    Yeah right. Argumentum ad Fermatum. Fine, if you don't want to show your "proof", perhaps you can explain where my counterexamples go wrong? Remember, all it takes is a single valid counterexample to invalidate a conjectured theorem.

    zzzzzzzzzzzzz

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  31. Zachriel said, "In any case, we do have some idea of how a primitive membrane could form. "

    You're still ignoring the question. The primitive fatty acid bubble is not integrated with the RNA molecule any more than the air conditioned room I'm in now is integrated with my DNA/RNA. What does your happy RNA molecule do next?

    You said, "a semipermeable membrane that is sufficient for a primitive cell"

    That has not been established. See the question by Blas.

    You said, "Even if we had no plausible understanding of how a primitive membrane may have formed, that doesn't support the claim that life was the result of special creation."

    I would agree with the first part. You have given no plausible explanation as the fatty acid self-assembly is not enough. You have neither a chicken nor an egg in your scenario.

    Since purely natural processes look incapable of forming an integrated and viable cellular membrane you will be forever pleading ignorance while ignoring that the best explanation for an integrated system that looks designed is because it was designed. Again, we are not basing design on ignorance, but rather out of knowledge.

    We know out of common knowledge that a Mt Rushmore was not created by wind, lightning and other natural forces. We would know this even if we did not know any of the history about it. We live out our lives in the elements and know what wind, lightning, etc is capable of. So its a no-brainer to say it was designed.

    The microscopic forces at the cellular level are not so familar to us. But that is changing. Evolutionists can't forever use ignorance to argue their point against design.

    I wish you would, at a minimum, address the question about how your fatty acid bubble becomes integrated with the RNA and cellular reproduction.

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  32. Blas: Which concentration of nucleotides you need outside the membrane to get inside, by passive diffusion as you do not have the active channels, you need in order to allow the self replicator RNA replicat himself?

    Though a fatty acid vesicle is stable, the individual fatty acid molecules flip incessantly, a process which can allow small molecules to pass through the membrane. It can also allow for an energy gradient for a primitive metabolism.

    Neal Tedford: The primitive fatty acid bubble is not integrated with the RNA molecule any more than the air conditioned room I'm in now is integrated with my DNA/RNA. What does your happy RNA molecule do next?

    Replicate.

    Neal Tedford: You have given no plausible explanation as the fatty acid self-assembly is not enough.

    It answers the original chicken and egg concern, where a membrane requires a complex assembly process, but the complex assembler requires a membrane.

    Neal Tedford: I wish you would, at a minimum, address the question about how your fatty acid bubble becomes integrated with the RNA and cellular reproduction.

    A vesicle containing RNA replicase is "integrated." (Incidentally, fatty acid vesicles and RNA sequences are both catalyzed by montmorillonite clay.)

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  33. Does the repicator keep on replicating until it fills the vesicle, and then the vesicles splits?
    I would expect it to burst under thoise ocnditions. Or does the replicator replicate once, then the vesicle splits? Or does the timing of the replicating and the splitting of the vesicle just happen to coincide? Did we just get really, really lucky?

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  34. Zachriel, said "It answers the original chicken and egg concern"

    No, you don't have a chicken nor an egg! You have a few hypothetical components that lack integration. The fatty acid bubble is not under the control of the RNA molecule, does not signal the molecule, nor do membrane proteins exist. You actually don't even have a proto-cell.

    What you described is neither the chicken nor the egg.

    You said, "A vesicle containing RNA replicase is "integrated."

    How so?

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  35. natschuster: I would expect it to burst under thoise ocnditions. Or does the replicator replicate once, then the vesicle splits?

    As the replicase multiplies, the vesicle expands by incorporating more fatty acids. When the vesicle reaches a certain size, it becomes unstable and cleaves. Those proto-cells that are the most efficient at taking up resources from the environment will out-compete those which are less efficient.

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  36. Neal Tedford: No, you don't have a chicken nor an egg! You have a few hypothetical components that lack integration. The fatty acid bubble is not under the control of the RNA molecule, does not signal the molecule, nor do membrane proteins exist. You actually don't even have a proto-cell.

    As the replicases increase in number, the vesicle grows, then divides. That's all the integration you need to resolve the chicken and egg conundrum. It's primitive, yes. That's the point.

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  37. Zachriel:"Though a fatty acid vesicle is stable, the individual fatty acid molecules flip incessantly, a process which can allow small molecules to pass through the membrane."

    They can pass if there is a differential of concentration, and you need an impossible concentration outside to get nucleotides enough nucleotides inside to make the replication starts.

    "It can also allow for an energy gradient for a primitive metabolism. "


    Again your imagination, in which way you can transform the concentration differential in to chemical energy?

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  38. Zachriel:

    Are you sure the vesicle wouldn't burst as it got too big, and spill ouit all its contents? When a cell divides, its division is closely
    coordinated, so it doesn't just burst. Cna the same thing be said of a vesicle?

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  39. natschuster: Are you sure the vesicle wouldn't burst as it got too big, and spill ouit all its contents?

    Szostak's group has shown that vesicles can grow and divide. An alternative method would be excrusion through porous rocks.

    Chen & Szostak, A Kinetic Study of the Growth of Fatty Acid Vesicles, Biophysical Journal 2004.

    Blas: They can pass if there is a differential of concentration, and you need an impossible concentration outside to get nucleotides enough nucleotides inside to make the replication starts.

    The differential occurs because the free nucleotides in the proto-cell are incorporated into polymers.

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  40. Zachriel said, "Szostak's group has shown that vesicles can grow and divide. An alternative method would be excrusion through porous rocks"

    With RNA molecules intact in both the parent and new vesicle?

    Sure bubbles can grow and divide, Mr. Bubble bath can do that! But what of the RNA in all the new bubbles?

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  41. Neal Tedford: With RNA molecules intact in both the parent and new vesicle?

    Yes. It's not posited that they are like modern chromosomes, but more like a loose collection of molecules.

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  42. Zachriel said, "Yes. It's not posited that they are like modern chromosomes, but more like a loose collection of molecules. "


    Your not saying that a copy of the parent RNA is in the child bubbles are you?

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  43. Neal Tedford: Your not saying that a copy of the parent RNA is in the child bubbles are you?

    Yes.

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  44. Zachriel:

    The vesicles will grow and divide if empty. But if they explode because they are full of a polymer molecules, will they reform into vesicles, and atill hold their contents?

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  45. natschuster: The vesicles will grow and divide if empty. But if they explode because they are full of a polymer molecules, will they reform into vesicles, and atill hold their contents?

    The vesicles don't explode. They divide. The replicases would be randomly divided between daughter cells.

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  46. Hanczyc & Szostak, Replicating vesicles as models of primitive cell growth and division, Chemical Biology 2004.

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  47. Neal Tedford:

    "Zachriel said, "The fact that semipermeable membranes can spontaneously assemble resolves that conundrum. "

    Were talking about origin of life, right?
    ===

    The political ideologue you're attempting to have discussion with is referencing the magic of clay bubbles magically forming membranes over supposed already existing RNA and the brilliant encoded information it contains and now you expect you to believe that those bubbles competed with each other in the evolutionary fitness game? Back in reality world however, bubbles couldn’t give a tinker's damn if they win the race or pop, but "IT" apparently figures you're dumb enough to be taken in by the fairytale given enough intellect speak loaded into the storyline.

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  48. Blas:

    Zachriel:
    "If we have a vesicle containing an RNA replicator, the membrane would allow nucleotides to enter, but prevent the polymer from leaving. Also, there's a natural process of cleaving when the vesicle reaches a certain size."

    Hanczyc & Szostak, Replicating vesicles as models of primitive cell growth and division, Chemical Biology 2004."
    ---

    Blas:
    "In your IMAGINATION. Which concentration of nucleotides you need outside the membrane to get inside, by passive diffusion as you do not have the active channels, you need in order to allow the self replicator RNA replicate himself?
    ===

    I believe you hit the proverbial nail on the head here with the word IMAGINATION. Take a good look at an opening line in the link above that IT referenced:

    "Introduction
    Several distinct pathways can be imagined for the replication
    of primitive vesicles"

    What more needs to be said. Any further attempt at dialogue on this subject is nothing more than debating science fiction.
    -----------

    Zachriel:
    "It's like concluding that planetary movements are under the auspices of angels simply because you don't what else could cause them."

    Blas:
    "I would consider more probable see angels pushing planets."
    ===

    Careful, This Astrologer has the uncanny mystic ability to read codes in Stars. I think you're out of your league on this one. *wink*

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  49. Zachriel:"The differential occurs because the free nucleotides in the proto-cell are incorporated into polymers."

    You need an internl concentration of nucleotides before they can be incorported in the polymers, so you need the gradient before the polymerization starts.

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  50. Neal Tedford:

    "Zachriel said,
    "Szostak's group has shown that vesicles can grow and divide. An alternative method would be excrusion through porous rocks"

    Neal Tedford:
    "With RNA molecules intact in both the parent and new vesicle?"
    ===

    Well you actually should read that 2004 research paper IT was referencing. It's loaded with personification fallacies and their flavourite euphemism called "emergence" which is meant to replace more accurate wordings like 'magic', 'luck', 'chance' or even more accurately 'miracle'. Then they sneak in Darwinian Natural Selection when the entire experiment was deliberately engineered from the start as the readily admit in the beginning of the paper. But seriously, if nothing else it is entertaining.
    -----

    Neal Tedford:

    "Sure bubbles can grow and divide, Mr. Bubble bath can do that! But what of the RNA in all the new bubbles?"
    ===

    There may be another way to view this article Neal. Take a look at another beautiful gem found in that paper:

    "Our laboratory has engineered a system of vesicle replication
    with discrete growth and division steps as
    depicted in model." (they then proceed to explain the step by step manipulation processes they employed for the desired outcome)

    What that means is that they then seeded those miracle bubbles with made made engineered functional RNA, something again they assumed already existed in the wild, but hey after all, it's just imaginationary as they admit at the start.

    Now consider Zachy's reference to montmorillonite (clay) which is actually similar to something I use called Bentonite clay. I've used it for health purposes and environmental alternative to creating ponds or lakes and eliminating the use of plastic , rubber or concrete lining of a pond. Well Drillers use it to line wells. why ??? Because the properties of such clay have a porosity of almost nill. That's why it is used in ponds because water won't percolate out of it.

    Now in the interest of the O.P. one has to wonder how such mud membranes allow food materials for the mechanism in for it to survive. It doesn't. But doesn't the thing have to eat ??? Of course! But rather than a lucky manufacturing plant, it's stuck in a mud prison. No doubt would die after the food is used up and then there is the problem with all those error correction mechanisms missing. Actually the questions just get more and more complicated, but hey, a fairytale doesn't have to be complex. They actually bank on the fact that the average poor slob is ignorant and will take it on faith the the genius actually knows what he's talking about. Attempt at any asking of hard questions and you're immediately attacked and demonized as a heretic to the faith.

    ReplyDelete
  51. Blas:

    "You need an internl concentration of nucleotides before they can be incorported in the polymers, so you need the gradient before the polymerization starts."
    ===

    Let's consider something even more fun here. There are a few familiar components of this very story Zach is telling that seem familiar. At least from a Biblical standpoint. Let's see if you agree.

    Zach referenced a paper that admitted intelligence was used thru and thru. The use of clay(finely powdered when dry) was mentioned. Then there is the brilliant informational library contained in the manufactured functional RNA. Let's compare some things now.
    ---

    Genesis 2:7

    Young's Literal Translation (YLT)

    7 And Jehovah God formeth the man -- dust from the ground, and breatheth into his nostrils breath of life, and the man becometh a living creature.

    Genesis 3:19

    Young's Literal Translation (YLT)

    19 "by the sweat of thy face thou dost eat bread till thy return unto the ground, for out of it hast thou been taken, for dust thou [art], and unto dust thou turnest back."

    So an intelligence is used to manipulate and engineered with purpose and intent and clay(dust) which are elements from the Earth are used as the building blocks. Then there is that deliberately inserted informational library into that bubble. Let's see.

    Psalm 139:16 (Darby Translation)

    16 "Thine eyes did see my unformed substance, and in thy book all [my members] were written; [during many] days were they fashioned, when [as yet] there was none of them."

    That's funny. Does this look oddly familiar to that 2004 experiment ??? You can almost see and feel the gnashing of teeth by some of the more dogmatic political pimping shills here.

    ReplyDelete
  52. Pedant said: Some mothers have healthy babies, some mothers have babies with fatal genetic disorders. Design or luck?

    I'm not sure how the above pertains.

    By analogy - some manufacture devices work, some fail and injure their intended users.... That failure doesn't preclude design, or even indicate bad design. Such failure could be resultant of entropy.

    The referenced statement seems to typify the metaphysical assumptions Dr. Hunter is trying to address in many of his essays regarding opposition to design in the sciences, especially in biology, a science that is rapidly uncovering massive evidence for exquisite design.

    ReplyDelete
  53. Eocene: I believe you hit the proverbial nail on the head here with the word IMAGINATION. Take a good look at an opening line in the link above that IT referenced:

    "Introduction: Several distinct pathways can be imagined for the replication of primitive vesicles"

    What more needs to be said. Any further attempt at dialogue on this subject is nothing more than debating science fiction.


    What more needs to be said it that you quote-mined the article. Imagining hypotheses is an important step of the scientific method. They go on to say,

    "In this review, we discuss the experimental evidence (or lack thereof) in support of these models for vesicle replication, and discuss the plausibility of these pathways in pre-biotic scenarios."

    So, they compare each model to the evidence in order to test for plausibility.

    ReplyDelete
  54. Blas: You need an internl concentration of nucleotides before they can be incorported in the polymers, so you need the gradient before the polymerization starts.

    You need some source of nucleosides, but we were discussing only the original contention that there was a chicken and egg problem with regards to the cellular membrane. There's not.

    ReplyDelete
  55. Eocene: What that means is that they then seeded those miracle bubbles with made made engineered functional RNA, something again they assumed already existed in the wild, but hey after all, it's just imaginationary as they admit at the start.

    These statements are experimentally demonstrable.

    "Fatty acid vesicles grow spontaneously when alkaline micelles are added to buffered vesicles."

    "a dispersion of montmorillonite clay in buffer can accelerate the assembly of vesicles from fatty acid micelles"

    That is was done in a laboratory is irrelevant.

    ReplyDelete
  56. Eocene: Zach{riel} referenced a paper that admitted intelligence was used thru and thru.

    That's sorta what we mean by "experiment". An example of an experiment is dropping stones from the Leaning Tower of Pisa. No, the stones didn't climb the stairs naturally. They were carried to the top and dropped. In the case of abiogenetics, researchers attempt to recreate part of the process based on plausible primordial conditions.

    ReplyDelete
  57. Zachriel:"You need some source of nucleosides, but we were discussing only the original contention that there was a chicken and egg problem with regards to the cellular membrane. There's not."

    But you solved the chicken and egg problem saying saying that "nucleotides" can cross the membrane by passive diffusion, scenario that is impossible because of the external concentrations of nucleotides needed. So you are again in the chicken and egg problem. May be you are now suggesting that "nucleosides" cross easier the mambrane and then the external concentration neede is not so impossible, but then you need to fosforilate the nucleosides and you have a new chicken and egg problem.

    ReplyDelete
  58. Zachriel,

    How an experiment was conducted is very relevant. Engineering RNA and seeding the Fatty acid vesicles is intelligent intervention. You did not mention that, Eocene did that. Was it on purpose that you avoided this? So the vesicles were seeded. That is much different than the vesicle dividing on its own with a replicated copy in the child vesicles.

    But after all this the question still remains, what came first the chicken or the egg, the DNA/RNA or the cellular membrane. You have intelligent agents creating a simple RNA molecule and then seeding the fatty acid vesicles under lab created conditions with the just right temperature, purity of water, etc.

    What I wanted to know was if the vesicles were dividing on their own with copies of parent RNA intact in the child vesicles. Apparently not without the lab tech seeding the vesicles. Correct?

    ReplyDelete
  59. Zachriel:"In the case of abiogenetics, researchers attempt to recreate part of the process based on plausible primordial conditions."

    LOL!

    ReplyDelete
  60. Blas: But you solved the chicken and egg problem saying saying that "nucleotides" can cross the membrane by passive diffusion, scenario that is impossible because of the external concentrations of nucleotides needed. So you are again in the chicken and egg problem.

    Of course there has to be a source of materials, including fatty acids and RNA components. The problem stated above was that the membrane couldn't form without being constructed by a complex mechanism and the complex mechanism couldn't exist without the membrane. But that's simply not the case. A protocell could be formed from simple RNA replicases and a fatty acid vesicle. There are other papers that deal with the prebiotic synthesis of nucleotides and nucleosides.

    You've shifted the goal post.

    Blas: LOL!

    Let's see. On the one hand, we have Jack Szostak, winner of the Nobel Prize for his work with telomeres, and on the other hand, we have "LOL!".
    http://genetics.mgh.harvard.edu/szostakweb/

    ReplyDelete
  61. Zachriel said, "That's sorta what we mean by "experiment". An example of an experiment is dropping stones from the Leaning Tower of Pisa. No, the stones didn't climb the stairs naturally. They were carried to the top and dropped."

    If your theory said that stones can ascend a tower on their own power, then yes, your experiment would be flawed. That wasn't the purpose.

    ReplyDelete
  62. Neal Tedford: Engineering RNA and seeding the Fatty acid vesicles is intelligent intervention.

    In this case, we are only concerned with the spontaneous formation of a semipermeable membrane.

    Neal Tedford: So the vesicles were seeded.

    Fatty acids can be formed by mineral catalysts from H2 and CO. The fatty acids will then form vesicles either under the proper pH, or catalyzed by montmorillonites.

    Neal Tedford: What I wanted to know was if the vesicles were dividing on their own with copies of parent RNA intact in the child vesicles.

    The contents of the vesicles are randomly divided between the daughter cells. Assuming large numbers of copies, daughter cells each inherit the replicases.

    ReplyDelete
  63. Tedford the Idiot said...

    Zachriel said, "That's sorta what we mean by "experiment". An example of an experiment is dropping stones from the Leaning Tower of Pisa. No, the stones didn't climb the stairs naturally. They were carried to the top and dropped."

    If your theory said that stones can ascend a tower on their own power, then yes, your experiment would be flawed. That wasn't the purpose.


    Tedford the Idiot's latest mangling of logic:

    "I DEMAND EXPERIMENTAL PROOF OF EVOLUTION!!'

    "OK, here's an experiment that clearly shows the processes in action."

    "THAT DOESN'T COUNT BECAUSE HUMANS SET UP THE EXPERIMENT!!"

    See Tedford, that's exactly why you get laughed at so loudly and so often.

    ReplyDelete
  64. Neal Tedford: If your theory said that stones can ascend a tower on their own power, then yes, your experiment would be flawed.

    We can devise and experiment to test how a stone will fall from a cliff face by carrying stones up a cliff. We can devise an experiment to show that fatty acids will form vesicles in the presence of a naturally occurring catalyst by putting fatty acids in contact with the catalyst.

    ReplyDelete
  65. arkady967 said...

    Pedant said: Some mothers have healthy babies, some mothers have babies with fatal genetic disorders. Design or luck?

    I'm not sure how the above pertains.


    It was a response to Hunter's statement:

    Random mutations must have luckily assembled molecular mechanisms...

    IF you want to deride the creative power of random mutation and natural selection in order to substitute a creative deity or demiurge who purposely brought about those molecular mechanisms...

    THEN, where do you draw the line that limits the responsibility of that creative deity or demiurge for any and all aspects of nature, such as the case of a baby born with a genetic defect?

    By analogy - some manufacture devices work, some fail and injure their intended users.... That failure doesn't preclude design, or even indicate bad design. Such failure could be resultant of entropy.

    You have presented three possibilities. How, by analogy, does one go about determining which possibility pertains to the design of a congenitally crippled baby?

    ReplyDelete
  66. Zachirel:"Let's see. On the one hand, we have Jack Szostak, winner of the Nobel Prize for his work with telomeres, and on the other hand, we have "LOL!".
    http://genetics.mgh.harvard.edu/szostakweb/"

    Winning a Nobel Prize not make less funny the "attempt to recreate part of the process based on plausible primordial conditions."

    ReplyDelete
  67. Eocene: Back in reality world however, bubbles couldn’t give a tinker's damn if they win the race or pop, but "IT" apparently figures you're dumb enough to be taken in by the fairytale given enough intellect speak loaded into the storyline.

    That's quite a non-sequitur you've got there, Eocene. Exactly how is "giving a tinker's damn" necessary for the formation of pro-cells?

    It's right up there with the non-sequitur Cornelius made, which was pointed out in numerous comments above. I'm sure you'll both get extra points from the big guy in the sky for arguing against the evils of evolution even when you lack a logical argument. That's true dedication.

    ReplyDelete
  68. Zachy:

    Eocene: Zach{riel} referenced a paper that admitted intelligence was used thru and thru.

    "That's sorta what we mean by "experiment". An example of an experiment is dropping stones from the Leaning Tower of Pisa. No, the stones didn't climb the stairs naturally. They were carried to the top and dropped. In the case of abiogenetics, researchers attempt to recreate part of the process based on plausible primordial conditions."
    ===

    This is so hilarious. Your own Church's dogma and articles of faith demand "NO INTELLIGENCE ALLOWED". Yet you become infuriated when it's pointed out to you. Don't provide your side's hijacking of "INTELLIGENT DESIGN" principles and guidelines and shove it down my throat as proof of evolution. Perhaps you should stick to the political debate forums since that appears to be your expertise anyway.

    As Cornelius points out. You just cannot make this stuff up.

    ReplyDelete
  69. Blas: Winning a Nobel Prize not make less funny the "attempt to recreate part of the process based on plausible primordial conditions."

    It does make Szostak more credible than your handwaving laugh.

    ReplyDelete
  70. Neal Tedford:

    "Zachriel,

    How an experiment was conducted is very relevant. Engineering RNA and seeding the Fatty acid vesicles is intelligent intervention. You did not mention that, Eocene did that. Was it on purpose that you avoided this? So the vesicles were seeded. That is much different than the vesicle dividing on its own with a replicated copy in the child vesicles."
    ===

    And basically that is the point. Anytime you ask these religious leaders to actually answer the question: "What role does the scientist in the experiment play, unguided blind forces or intelligent design ? , they deflect and bluff their way along and all the while hoping other trolls will come along and heave insults to get them out of trouble. Right Thort ???
    ---

    Neal Tedford:

    But after all this the question still remains, what came first the chicken or the egg, the DNA/RNA or the cellular membrane. You have intelligent agents creating a simple RNA molecule and then seeding the fatty acid vesicles under lab created conditions with the just right temperature, purity of water, etc.
    ===

    Well this is the single most important information they will always avoid. why ??? Because a materialist is incapable[at least publicly in front of full viewing of their PEERS] that life is about the information that drives it and not the material substrate it occupies. Don't ever expect an admission on any of this ever. At least in this universe. Virtual world, well that's another story.
    ---

    Neal Tedford:

    What I wanted to know was if the vesicles were dividing on their own with copies of parent RNA intact in the child vesicles. Apparently not without the lab tech seeding the vesicles. Correct?
    ===

    Forget the Lab. In the wild, where did the correction mechanisms come from. Healthy positive replication for life to continue without errors is a must, yet in their RNA world wet dream, such mechanisms haven't evolved yet. As time goes on it just gets more and more complex with scientific findings and the best they can come up with is bitterness, anger, insults and foul language. Patience tho. It's almost finished. For the moment as time permits, they are allowed to prove their Father's line of argumentation in this court trial. I believe we are in closing arguments as we speak.

    ReplyDelete
  71. Zacriel:"It does make Szostak more credible than your handwaving laugh."

    Yes? Why? Because she works on that subject? But that makes him and his co-workers need to be published, found significative results in agreement to the mainstream of the correctors.
    So all the abiogenesis investigators starts with a theory, averyone can choose one of the ten in wikipedia make his own variants immagine what you need for your starting point and say " four thousand million years ago the earth has this caracteristics" and then the so story begans. Chicken and eggs problems, solved with more chicken and egg problems, chemistry problems, not at all we are talking about biology, there is no prove how different was the earth who cares was so long ago.

    ReplyDelete
  72. Zachriel said, " In this case, we are only concerned with the spontaneous formation of a semipermeable membrane....

    The contents of the vesicles are randomly divided between the daughter cells. Assuming large numbers of copies, daughter cells each inherit the replicases. "

    ---

    So we really only have random chunks of repetitive RNA scattered in daughter vesicles. The vesicle are not truly integrated with the RNA. By integration I mean that there is not attachment of the RNA to the vesicle (like in prokaryote fisson) or signaling or any kind of internal control of the vesicle. The vesicle is really just an independent bubble of fatty acids. It is not integrated into the RNA any more than your shirt is integrated into your body and genetic code. In living cells, the membrane is a dynamic and integrated part of the whole cell.

    You said, "The problem stated above was that the membrane couldn't form without being constructed by a complex mechanism and the complex mechanism couldn't exist without the membrane. But that's simply not the case. A protocell could be formed from simple RNA replicases and a fatty acid vesicle. "

    No the problem was that living cellular membranes need the cellular DNA/RNA and organelles and vice versa. First off, what you described is not a protocell, as fission or mitosis is not taking place. You have an independent bubble of fatty acids. The formation of your bubble is not how a living cellular membrane is formed. Living cells form their new membranes from inside, not by adding fatty acids from the outside like applying siding to house. So you have something fundamentally different because your components are too basic, incomplete and non-integrated. To put it in everyday language, your fatty acid bubble is not "talking to" or "wired" to your primitive RNA molecule. Furthermore, without the internal controls of the membrane your bubble is only marginally held together and certainly not practical in the real world for very long.

    So you can't redefine the chicken and the egg and then demonstrate your case properly.

    ReplyDelete
  73. Eocene: Healthy positive replication for life to continue without errors is a must, yet in their RNA world wet dream, such mechanisms haven't evolved yet.

    We weren't addressing RNA replication, but the so-called chicken and egg problem with respect to the cell membrane.

    Blas: Yes? Why?

    Because evidence is more persuasive than handwaving.

    Neal Tedford: No the problem was that living cellular membranes need the cellular DNA/RNA and organelles and vice versa.

    Yes, the argument is that you need one for the other. And with modern cells, that is certainly the case. However, plausible membranes can form naturally. That answers the chicken and egg problem.

    ReplyDelete
  74. Neal Tedford: To put it in everyday language, your fatty acid bubble is not "talking to" or "wired" to your primitive RNA molecule.

    It doesn't have to be. Those structures can evolve as improvements to the basic design. Would have thought you understood the basics fo evolutionary theory, even if you disagree.

    Neal Tedford: Furthermore, without the internal controls of the membrane your bubble is only marginally held together and certainly not practical in the real world for very long.

    Vesicles can be quite stable. And it only has to be practical enough to start the evolutionary process.

    ReplyDelete
  75. Zachriel:"Because evidence is more persuasive than handwaving."

    You are confusing good speech with evidence.

    ReplyDelete
  76. Zachriel said, "Vesicles can be quite stable. And it only has to be practical enough to start the evolutionary process."

    Vesicles are only stable for a narrow range of temperature and water conditions.

    The formation process of the fatty acid bubble in your scenario is fundamentally different than how a living cell membrane is constructed. So your evolutionary gain in your example is really zero.

    This points to a fundamental failing of evolution on a more general level (prokaryotes or whatever evolving into eukaryotes), though some of the construction materials may be local and even in contact you still haven't explained how the genetic information actually begins to code for the construction. There's a big disconnect in your process. Real cells are information constructed entities. Hammering siding on a house does not automatically update the blueprint and the machines that manufacture the siding. Sticking prokaryote cells together does not update the genetic information to begin forming daughter eukaryote cells.

    In your example, other than locality, your fatty acid bubble is logically disconnected from the RNA molecule just as the shirt you are wearing is not part of your genome. How do you get your genome to start growing shirts on top of your skin?

    Remember the case where the handicapped person became fused to their couch? Do you think if they later were able to have children, the children would be born with little couches attached to them? Crazy? Yes, but so are evolutionary scenarios.

    ReplyDelete
  77. Zachriel:"Those structures can evolve as improvements to the basic design."

    You have moved to the ID side?

    ReplyDelete
  78. Neal Tedford: The formation process of the fatty acid bubble in your scenario is fundamentally different than how a living cell membrane is constructed.

    Well, duh. That's the whole point.

    Neal Tedford: you still haven't explained how the genetic information actually begins to code for the construction.

    That's a separate issue. A claim was made concerning membranes, and that is what we responded to.

    ReplyDelete
  79. Zachriel, the original question concerned the cell membrane in CH's article. You redefined the criteria and so your answer does not answer the question.

    ReplyDelete
  80. Neal,

    The comment Zachriel addressed was your own. You're the one who defined the criteria.

    Neal: What came first, the DNA that codes for the proteins of the cell membrane or the cell membrane?

    Had Zachriel not addressed your question, you'd be whining about that instead.

    Don't you realize this sort of behavior is obvious and transparent? What kind of example are you setting as a Christian and a pastor no less?

    ReplyDelete
  81. Scott,

    Zachriel gave an example of a self-assemblying fatty acid bubble, not a living cellular membrane. He gave an example of an engineered RNA molecule, not DNA. He gave an example of the fatty acid bubble being seeded with the RNA molecule by lab techs.

    His illustration is more suited for MR Bubble Bath meets MR Clean, not what came first, the chicken or the egg.

    ReplyDelete
  82. Neal Tedford: Zachriel gave an example of a self-assemblying fatty acid bubble, not a living cellular membrane.

    Well, duh. We're discussing the chicken and egg problem you brought up. We showed that there is a simple membrane that could have sufficed for a protocell, resolving the chicken and egg problem.

    ReplyDelete
  83. Zachriel, you have no protocell in your example.

    ReplyDelete
  84. Neal Tedford: you have no protocell in your example.

    You suggested a protocell *could not* form because of the chicken and egg problem. The contrary position is that it *could*. It isn't necessary to use a time machine to reject your claim, but just provide a plausible alternative.

    If you want to argue about something else, that's fine, but you should acknowledge the point.

    ReplyDelete
  85. Zachriel:"You suggested a protocell *could not* form because of the chicken and egg problem. The contrary position is that it *could*. It isn't necessary to use a time machine to reject your claim, but just provide a plausible alternative.

    If you want to argue about something else, that's fine, but you should acknowledge the point."

    No, you do didn´t solve the chicken and egg, you moved to another chiken and egg because the permeability of your membrane is not enough to allow the start of life.

    ReplyDelete
  86. Blas: No, you do didn´t solve the chicken and egg, you moved to another chiken and egg because the permeability of your membrane is not enough to allow the start of life.

    The fatty acids in a vesicle flip, which allows small molecules, such as nucleotides to pass, but not macromolecules, such as replicases.

    ReplyDelete
  87. Zachriel:"The fatty acids in a vesicle flip, which allows small molecules, such as nucleotides to pass, but not macromolecules, such as replicases."

    The pass of nucleotides trough your membrane will never reach flux enouch to sustain replication of any molecule. You are describing scenarios that do not occur in the real world as all the abiogenesis studies starting with Oparin and Miller -Urey.

    ReplyDelete
  88. Blas: The pass of nucleotides trough your membrane will never reach flux enouch to sustain replication of any molecule. You are describing scenarios that do not occur in the real world as all the abiogenesis studies starting with Oparin and Miller -Urey.

    "Flux enough"? Do you mean concentration? If so, then that is a different objection. There has to be a source of nucleotides for an RNA replicase. We can look at other studies, but in the meantime, that is irrelevant to the original objection.

    ReplyDelete
  89. Zachriel:" that is irrelevant to the original objection."

    No that is not irrelevant, is the core of the objection, you do not solved the chicken-egg problem, because your membrane is not functional enough to sustain the life. You are handwaging and moving from one chicken-egg problem to other as abiogenesi studies ar doing since they started just to not say "we do not have idea" and lose their grants.

    ReplyDelete
  90. Blas: No that is not irrelevant, is the core of the objection, you do not solved the chicken-egg problem, because your membrane is not functional enough to sustain the life.

    The chicken and egg problem stated above was that a membrane couldn't form without a complex mechanism, and the complex mechanism requires a membrane. It turns out that a primitive, semipermeable membrane can form fairly easily in plausible prebiotic conditions.

    You then argued that there was no sufficient source of nucleotides. You've moved the goal posts.

    ReplyDelete
  91. Zachriel:"The chicken and egg problem stated above was that a membrane couldn't form without a complex mechanism, and the complex mechanism requires a membrane. It turns out that a primitive, semipermeable membrane can form fairly easily in plausible prebiotic conditions."

    You are using a particular concept of membrane, a cellulare membrane is a specific thing different of your lipids bilayer.
    The first require a complex mechanism, the second isn`t good enough to allow the complex mechanism "arise", for example because nucleotides can not pass trough at a usefull rate.
    Is the same goal.

    ReplyDelete
  92. Blas,

    You're moved the goalpost by requiring the functionality be identical to modern day cells, use the same implementation, be just as efficient, etc. This was not part of the original criteria. Nor is it a claim of evolution or abiogenesis.

    ReplyDelete
  93. Blas: nucleotides can not pass trough at a usefull rate.

    "Our results show that membranes made from simple amphiphiles can form vesicles that are stable enough to retain encapsulated RNAs in the presence of divalent cations, yet dynamic enough to grow spontaneously and allow the passage of Mg2+ and mononucleotides without specific macromolecular transporters."

    Chen, Salehi-Ashtiani & Szostak, RNA Catalysis in Model Protocell Vesicles, Journal of the American Chemical Society 2005.

    ReplyDelete
  94. Zachriel, here's more of the quotation:

    "WE are engaged in a long-term EFFORT to SYNTHESIZE chemical systems capable of Darwinian evolution, based on the encapsulation of self-replicating nucleic acids in self-replicating membrane vesicles. Here, we address the issue of the compatibility of these two replicating systems.

    ******
    Fatty acids form vesicles that are able to grow and divide, BUT vesicles composed solely of fatty acids are incompatible with the folding and activity of most ribozymes, because low concentrations of divalent cations (e.g., Mg(2+)) cause fatty acids to precipitate. Furthermore, vesicles that grow and divide MUST be permeable to the cations and substrates required for internal metabolism. WE used a mixture of myristoleic acid and its glycerol monoester to CONSTRUCT vesicles that were Mg(2+)-tolerant and found that Mg(2+) cations can permeate the membrane and equilibrate within a few minutes. In vesicles encapsulating a hammerhead ribozyme, the addition of external Mg(2+) led to the activation and self-cleavage of the ribozyme molecules. Vesicles composed of these amphiphiles grew spontaneously through osmotically driven competition between vesicles, and further MODIFICATION of the membrane composition allowed growth following mixed micelle ADDITION. Our results show that membranes made from simple amphiphiles can form vesicles that are stable enough to retain encapsulated RNAs in the presence of divalent cations, yet dynamic enough to grow spontaneously and allow the passage of Mg(2+) and mononucleotides without specific macromolecular transporters. This combination of stability and dynamics is critical for BUIDLING model protocells in the laboratory and MAY have been important for early cellular evolution."

    CAPS added for emphasize. Looks like much intelligent effort went into creating a more complex primitive bubble around engineered RNA.


    Myristoleic acid, is an omega-5 fatty acid. It is biosynthesized from myristic acid by the enzyme delta-9 desaturase, but it is uncommon in nature.[1] One of the major sources of this fatty acid is the seed oil from plants of the genus Myristicaceae, comprising up to 30 per cent of the oil in some species.

    There's a patent on making glycerol monoesters...

    "Described is a method of producing compositions comprising a high concentration of glycerol monoesters. The method entails reacting a mixture of glycerol, a fatty acid source, and water, in the absence of catalysts, at a temperature preferably from about 180° C. to about 300° C., a pressure preferably from about 15 psig to 400 psig, and for a time sufficient to yield an acid value of preferably from about 2.0 to about 7.0 in the mixture, and a hydroxyl value preferably of from about 260 to about 460 in the mixture. The method can be used to make lipid mixtures comprising 90 wt % or more of glycerol monoesters. The method does not require molecular distillation"

    Read more: http://www.faqs.org/patents/app/20100148117#ixzz1Ot8M4Eyd


    With all these high tech engineering and manufacturing feats, they still do not have a living cell and it certainly is not demonstrating the evolution of the cell. If anything it shows how much intelligent effort is needed to create a primitive non-living lab model.

    ReplyDelete
  95. Zachriel:"Chen, Salehi-Ashtiani & Szostak, RNA Catalysis in Model Protocell Vesicles, Journal of the American Chemical Society 2005."

    I´m not going to pay for read that paper. Hope for you in a few do not became a new flaw as Oparin or Miller-Urey.

    ReplyDelete
  96. Neal Tedford: CAPS added for emphasize. Looks like much intelligent effort went into creating a more complex primitive bubble around engineered RNA.

    Lipids are synthesized in a number of plausible prebiotic conditions.

    McCollom, Ritter & Simoneit, Lipid synthesis under hydrothermal conditions by Fischer-Tropsch-type reactions, Origins of life and evolution of the biosphere 1999.

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  97. Blas: Hope for you in a few do not became a new flaw as Oparin or Miller-Urey.

    Miller-Urey showed that complex molecules can form under relatively simple conditions.

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  98. Zachriel:"Miller-Urey showed that complex molecules can form under relatively simple conditions."

    And all the scientific community, for years, said that is the way the life started. And they knew that wasn´t true.

    ReplyDelete
  99. Blas: And all the scientific community, for years, said that is the way the life started. And they knew that wasn´t true.

    Miller-Urey showed how complex organic compounds can form. Other experiments have demonstrated how they can form under a variety of plausibly prebiotic conditions, and even in extant nature.

    ReplyDelete
  100. Zachriel, from your article "Fatty acids form vesicles that are able to grow and divide, BUT vesicles composed solely of fatty acids are incompatible with the folding and activity of most ribozymes, because low concentrations of divalent cations (e.g., Mg(2+)) cause fatty acids to precipitate. Furthermore, vesicles that grow and divide MUST be permeable to the cations and substrates required for internal metabolism. WE used a mixture of myristoleic acid and its glycerol monoester to CONSTRUCT vesicles ..."

    Sources of myristoleic acid include chicken fat. So the chicken did come before the egg!
    Perhaps a dead chicken fell into a hydrothermal vent to make your prebiotic soup. That's also the origin of the original crispy KFC receipe. LOL. Have a good weekend.

    ReplyDelete
  101. Neal Tedford: Sources of myristoleic acid include chicken fat.

    Myristoleic acid is a fatty acid. They also used its glycerol monoester.

    Neal Tedford: ... CONSTRUCT ...

    Yes, they are testing theories of abiogenesis, so they constructed it based on what might be plausible from a prebiotic environment.

    But just as a sidenote, that's the fundamental difference between science and ID, the former actually do, like, stuff, to test their hypotheses.

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  102. Zachriel, myristoleic acid and glycerol monoester would not be found in a supposed prebiotic soup. Where would they come from? Testing a hypothesis is a good thing. Even better, is to be open to what the results indicate. That you can't see the obvious means that you too are driven by something other than science.

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  103. Tedford the Idiot said...

    Zachriel, myristoleic acid and glycerol monoester would not be found in a supposed prebiotic soup. Where would they come from? Testing a hypothesis is a good thing. Even better, is to be open to what the results indicate. That you can't see the obvious means that you too are driven by something other than science.


    Tedford, feel free to provide the scientific description of the detailed mechanisms for how the 'intelligent design' was implemented. Please let us know when, and where, and from what raw materials, in what order, and by what physical processes everything was assembled.

    Anytime idiot.

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  104. achriel:""Our results show that membranes made from simple amphiphiles can form vesicles that are stable enough to retain encapsulated RNAs in the presence of divalent cations, yet dynamic enough to grow spontaneously and allow the passage of Mg2+ and mononucleotides without specific macromolecular transporters."

    Chen, Salehi-Ashtiani & Szostak, RNA Catalysis in Model Protocell Vesicles, Journal of the American Chemical Society 2005."

    As I told you I´m not going to pay for that paper, but I could check my bibliography. The permeability coefficient of a lipid bilayer for glucose is about 10-7 , as a nucleotide is bigger and charged its permeability coefficient should be lower by at least one order of magnitude. ¿How could the authors obtain a replications inside the vescicles? They needed an insane gradient of concentration of nucleotides or maybe what they obtained were not stable vescicles able to compartimentalize.

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  105. Neal Tedford: myristoleic acid and glycerol monoester would not be found in a supposed prebiotic soup.

    Simple spark experiments yield fatty acids with length up to C12. Simulating hydrothermal vents yields chains of up to C33. Even meteorites can have chains up to C12. Myristoleic acid is C14.

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  106. Zachriel:"Simple spark experiments yield fatty acids with length up to C12. Simulating hydrothermal vents yields chains of up to C33. Even meteorites can have chains up to C12. Myristoleic acid is C14."

    You can found fatty acids in hydrotermal vents at a level of concentration of ...?
    The amount of fatty acids per Kg of meteroite is...?

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  107. Blas: You can found fatty acids in hydrotermal vents at a level of concentration of ...?

    Are you suggesting that compounds can't be concentrated naturally?

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  108. Zachriel:"Are you suggesting that compounds can't be concentrated naturally?"

    Yes, I´m curios to know how organics compounds can concentrate in hydrotermal vents. I´m sure you have a quote that prove how that happened.

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  109. Blas: Yes, I´m curios to know how organics compounds can concentrate in hydrotermal vents.

    Are you unaware of any mechanism by which compounds can be naturally concentrated? Do you think only intelligent design can implement such a process?

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  110. Zachriel said, "Simple spark experiments yield fatty acids with length up to C12. Simulating hydrothermal vents yields chains of up to C33. Even meteorites can have chains up to C12. Myristoleic acid is C14."

    ----

    "Spark experiments yield.. up to C12".

    Where's the myristoleic acid and glycerol monoester?

    "Simulating hydrothermal vents... up to C33."

    Back to the intelligently designed lab conditions... There are real vents in the world, how much of myristoleic acid have they found? Don't forget the glycerol monoester.

    "Even meteorites can have chains up to C12."

    No myristoleic acid and glycerol monoester found there either.

    Your scenario again comes up a dollar short.

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  111. Tedford the Idiot said...

    Your scenario again comes up a dollar short.


    Remind us again of all the details of your ID scenario Tedford.

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  112. Don't simulations have to be checked against real life to make sure they are accurate? Were the simulated hydrothermal vent results checked against real hydrothermal vents?

    And how was the replication of the replicator and the splitting of the fatty acid vesicle coordinated? Or did the just happily happen at right time?

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  113. natschuster said...

    Don't simulations have to be checked against real life to make sure they are accurate? Were the simulated hydrothermal vent results checked against real hydrothermal vents?

    And how was the replication of the replicator and the splitting of the fatty acid vesicle coordinated? Or did the just happily happen at right time?


    Why don't you quit being such a lazy jerk for once in your trolling life and RTFP.

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  114. I looked at the vidoe linked above. I didn't see nay mention of how the replicator's replicating and the vesicle dividing was coordinated. That's why I'm asking.

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  115. Zachriel:"Are you unaware of any mechanism by which compounds can be naturally concentrated? Do you think only intelligent design can implement such a process?"

    No, I can´t immagine a concentration of fatty acids in a thermal vent and I am not an ID supporter.

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  116. natschuster said...

    I looked at the vidoe linked above. I didn't see nay mention of how the replicator's replicating and the vesicle dividing was coordinated. That's why I'm asking.


    Why don't you quit being such a lazy jerk for once in your trolling life and READ THE F****** PAPERS.

    You'll never learn a damn thing by demanding to be spoon fed bits and pieces like a baby bird. But I suppose willful ignorance is your stated goal.

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  117. Blas said...

    I am not an ID supporter.


    Right. You reject abiogenesis and you're not an ID supporter.

    What else is left?

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  118. I read the abstract of the article linked. It mentioned that vesicles grow and divide. I didn't see anything about coordination.

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  119. Thorton:"Right. You reject abiogenesis and you're not an ID supporter."

    Why do you think I reject abiogenesis?

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  120. natschuster said...

    I read the abstract of the article linked.


    Why don't you quit being such a lazy jerk for once in your trolling life and READ THE F****** PAPERS.

    THE PAPERS. Not the abstracts.

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  121. Blas said...

    Thorton:"Right. You reject abiogenesis and you're not an ID supporter."

    Why do you think I reject abiogenesis?


    That wasn't the question.

    If you reject abiogenesis and you're not an ID supporter, what else is left?

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  122. Thorton:"If you reject abiogenesis and you're not an ID supporter, what else is left?"

    Aknoledge that science has not all the answers.

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  123. The papers are behind a paywall, and I'm a little embarrased financially now. That's why I'm asking. I guess it will just have to wait.

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  124. I did a google search on protocells. I couldn't find anyone discussing how replication and the division of the vesicle could be co-ordinated. I guess it is another case of us just being really, really lucky.

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  125. Blas said...

    Thorton:"If you reject abiogenesis and you're not an ID supporter, what else is left?"

    Aknoledge that science has not all the answers.


    That still didn't answer the question. Why is it so hard to get a straight answer from you?

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  126. This comment has been removed by the author.

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  127. Thorton:"Blas said...

    Thorton:"If you reject abiogenesis and you're not an ID supporter, what else is left?"

    Aknoledge that science has not all the answers.

    That still didn't answer the question. Why is it so hard to get a straight answer from you?


    You want a scientific answer or a metaphisical one?

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  128. Neal Tedford: Where's the myristoleic acid and glycerol monoester?

    Myristoleic acid is a C14 chain, so is well-within plausibility for hydrothermal vents. In any case, the stability of the vesicle is dependent on chain length and concentration, so it doesn't have to be a myristoleic acid. The ester is derived from the fatty acid.

    natschuster: And how was the replication of the replicator and the splitting of the fatty acid vesicle coordinated?

    They don't have to be directly coordinated. As long as there are large numbers scattered within each vesicle, then each daughter will inherit some. Also, the incorporation of nucleotides will tend to swell the vesicle. But it might have been a more continuous process, such as the vent forcing excrusion through mineral pores.

    Blas: No, I can´t immagine a concentration of fatty acids in a thermal vent and I am not an ID supporter.

    There are all sorts of natural mechanisms for concentrating compounds. A salt flat is a concentration of salt. How did all that salt end up in one place?
    http://www.rutaverdebolivia.com/Uyuni%20Salt%20Lake%202.jpg

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  129. Blas said...

    Thorton:"Blas said...

    Thorton:"If you reject abiogenesis and you're not an ID supporter, what else is left?"

    Aknoledge that science has not all the answers.

    That still didn't answer the question. Why is it so hard to get a straight answer from you?


    You want a scientific answer or a metaphisical one?


    Why don't you break with tradition and give a straight one.

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  130. Zachriel:"There are all sorts of natural mechanisms for concentrating compounds. A salt flat is a concentration of salt. How did all that salt end up in one place?
    http://www.rutaverdebolivia.com/Uyuni%20Salt%20Lake%202.jpg"

    And there the hydrothermal vents are ...
    in the place the actual abiogenesis theory needs.

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  131. Thorton:"Why don't you break with tradition and give a straight one."

    I give you one, but you do not understand by science the same I do.

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  132. Blas said...

    Thorton:"Why don't you break with tradition and give a straight one."

    I give you one, but you do not understand by science the same I do.


    LOL! Why don't you audition for Dancing With The Stars? The IDiot evasion tap dance you do would certainly take a prize.

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  133. Thorton:

    Thanks for the freebee. I didn't see anything on the paper about co-ordinating cleavage. I guess its just another case of us getting lucky.

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  134. natschuster said...

    Thorton:

    Thanks for the freebee. I didn't see anything on the paper about co-ordinating cleavage. I guess its just another case of us getting lucky.


    You're welcome.

    Interesting that you claim to have read and understood the paper in the less than one hour since I posted the link to it.

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  135. Blas: And there the hydrothermal vents are ...
    in the place the actual abiogenesis theory needs.


    Your point isn't clear. Hydrothermal vents can be found in many geologically active areas.

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  136. And in primordial times, there was far more geological activity.

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  137. Thorton:

    I scanned the article. I was looking for mention of how the cleavage of the vesicle would be co-ordinated with replication. I didn't see any mention.

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  138. natschuster said...

    Thorton:

    I scanned the article. I was looking for mention of how the cleavage of the vesicle would be co-ordinated with replication. I didn't see any mention.


    Right, just like all creationists. Instead of actually reading the article and trying to understand the work you skimmed for buzzwords and snippets to quote-mine.

    That's why you'll stay an ignorant fool your whole life.

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  139. I"m not looking for buzzwords. I'm not intersting in quote mining. I'm looking for a mechanism to co-ordinate cleavage. The cleavage of a membrane and the replication of the replicator has to co-ordinate somehow. In cells it is done by a complex system of proteins and such. But those didn't exist in proto-cells.

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  140. natschuster said...

    I"m not looking for buzzwords. I'm not intersting in quote mining. I'm looking for a mechanism to co-ordinate cleavage.


    Right. That's why you didn't bother to read the whole paper, and why you never noticed / didn't research the 50 or so references to other papers including work on vesicle division. Because you're looking for DA TRUTH!

    You and Tedford make quite the pair.

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  141. natschuster: And how was the replication of the replicator and the splitting of the fatty acid vesicle coordinated?

    They don't have to be directly coordinated. As long as there are large numbers of replicators scattered within each vesicle, then each daughter will inherit some. Also, the incorporation of nucleotides will tend to swell the vesicle leading to instability. But it might have been a more continuous process, such as the vent forcing excrusion through mineral pores.

    ReplyDelete