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Author | Topic: Design Framework for Evolution | |||||||||||||||||||||||||||||||||
Taq Member Posts: 10085 Joined: Member Rating: 5.1 |
Because my framework gives actual molecular mechanisms for evolution . . . I'm with the others on this one. What are these mechanisms?
Because I present a concrete (design) framework, it is also up for discussion. It seems very vague and not concrete at all.
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NoNukes Inactive Member |
I accept your admonishment on the use f the term improvements. That usage is quite sloppy.
Brownian motion is random, but can be used to give a direction to a molecule. I also assume a selection process, but they do not have to be natural. Brownian motion can give an unpredictable motion to a molecule. It would seem vain to me to reject Brownian motion or to call it unscientific on that basis. But it seems that you reject natural selection/random mutation on exactly that basis.
Wings and fins would have evolved not because there was some fitness advantage, but due to an intrinsic recombination process in which all possible kinds of extremities (wings, fins, legs) are continuously explored. You have some reason to believe that this cannot occur simply with a genome vulnerable to copying errors. Edited by NoNukes, : No reason given.Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846) I would say here something that was heard from an ecclesiastic of the most eminent degree; ‘That the intention of the Holy Ghost is to teach us how one goes to heaven, not how the heaven goes.’ Galileo Galilei 1615. If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass
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Albert de Roos Junior Member (Idle past 3999 days) Posts: 25 Joined: |
quote: Do not confuse the implementation of a design with the design itself. Like a blueprint is not a building and a model is not the real thing. Molecules are not balls with sticks and a 3D image of an animal on the screen is not the animal itself. Life is a molecular machine (or a system of machines if you like), and the entire system can be represented by a model or a design. The underlying design of both molecular machine (Life) and software (virtual machines) can still be the same.
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Albert de Roos Junior Member (Idle past 3999 days) Posts: 25 Joined: |
quote: What I try to say is that although random process may be involved, these would not help us to explain evolution. I do not reject NS+RM at all, but they cannot provide a framework for unraveling evolution. I know that an engine can run on gasoline as the enrgy source. It doesn't tell me however how the engine works or where the car is going. Same for evolution, RM+NS only says that Life evolved, but if you ask further they don't know say how evolution works or what path it has taken.
quote: We need mechanisms beyond RM+NS to explain evolution. I think that in order to grow in complexity there needs to be an intrinsic driving force, not an extrinsic force. I do think that it is possible to create a genome that can actively recombine into a more complex genome (exon shuffling, crossing over etc.) by initial copying errors. But to understand the active 'recombination machine'that has evolved, you need to look at the functions of the machine. The function of a house is not explained by timber, nails and a hammer.
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NoNukes Inactive Member |
What I try to say is that although random process may be involved, these would not help us to explain evolution. I do not reject NS+RM at all, but they cannot provide a framework for unraveling evolution. I understand that, but I think what you are saying is nonsense. What would be the equivalent thing you would say about Brownian motion?
We need mechanisms beyond RM+NS to explain evolution. I think that in order to grow in complexity there needs to be an intrinsic driving force, not an extrinsic force. And what is your reason for such a belief? Why are RM+NS so clearly insufficient? Are you familiar with software programs that attempt to model evolution using RM+NS?
But to understand the active 'recombination machine'that has evolved, you need to look at the functions of the machine. The function of a house is not explained by timber, nails and a hammer. Right, but who is trying to do the latter? Edited by NoNukes, : No reason given.Under a government which imprisons any unjustly, the true place for a just man is also in prison. Thoreau: Civil Disobedience (1846) I would say here something that was heard from an ecclesiastic of the most eminent degree; ‘That the intention of the Holy Ghost is to teach us how one goes to heaven, not how the heaven goes.’ Galileo Galilei 1615. If there is no struggle, there is no progress. Those who profess to favor freedom, and deprecate agitation, are men who want crops without plowing up the ground, they want rain without thunder and lightning. Frederick Douglass
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Taq Member Posts: 10085 Joined: Member Rating: 5.1 |
The underlying design of both molecular machine (Life) and software (virtual machines) can still be the same. But it isn't the same, as I already discussed. First, DNA between species falls into a nested hierarchy. Software does not. Second, it is the physical interactions between bases on the DNA molecule that produce the information. This is not how software works or is designed. Those are two major differences bewteen the two.
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
By that argument, then at the heart of all of technologies is simple chemistry. My motorcycle can't ride itself. Your motorcycle is not designed to do so. But your motorcycle will convert gasoline into usable energy "all on its own."
Salt crystals will just grow spontaneously, but my Legos don't put themselves together. But salt crystals are not considered life, and the discussion here is whether life is "just simple chemistry." It is, but only in the sense that a gasoline engine is "simple chemistry."
This is indeed true, but it misses the point. From the perspective of the genome - that is, when we consider the core features of the genomes of various taxa - life is not "illogical" from an engineering standpoint. But from that perspective its just chemistry. You're looking at salt crystals, not Legos. From the perspective of the genome, we are not looking at salt crystals, since the genome encodes the information needed to construct molecular machinery. When I say "genome," I do not mean merely the nucleic acids, but the information as well. So, when we consider the core features of the genome - that is, the features of the genome that are found in virtually all taxa (e.g., the Krebs cycle) - where do we find "illogical" or "irrational" design?
And that's because all the one's that didn't work that well were selected against, or not selected for. Then why do we have a system like the recurrent laryngeal nerve? Why wasn't it selected against, since there's obviously a more optimal way to produce the same function? Now, I'm pretty sure we both know the answer to that: the recurrent laryngeal nerve is the result of evolution from an aquatic ancestor that possessed a different anatomy. In other words, stages in evolution constrain the nature of possible adaptations. However, we must still wonder why there are no "recurrent laryngeal nerves" in the core machinery of life, while there are such things in the anatomy of multicellular organisms.
But you're looking at it in hind-sight and getting tricked into thinking there's more there than there is. Let me paing an analogy. I'm working in a grocery store and go to the apple bin. It full of all kinds of qualities of apples. I go through them one by one and keep all the really nice looking apples and then throw away all the bad looking ones. Then you come into the store and see the bin of apples and go: "Holy cow, the guy who buys the fruit for this store an amazingly logical purchaser. Look how he bought only the best looking apples and not one shitty one!" Little did you realize, he bought all kinds of shitty ones but they just didn't get selected to stay in the bin. But that's not a completely accurate picture of how evolution works. If something works, then evolution will not throw it out. Even clumsy function is better than no function. Thus, I don't see how your response addresses the problem of why the core structure of the bacterial flagellum displays no "irrational design," when it could have very probably displayed this on evolutionary grounds. Edited by Genomicus, : No reason given.
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
I would be interested on hearing your thoughts on where exactly the Krebs Cycle is the molecular equivalent of the recurrent laryngeal nerve. Which step in the Krebs Cycle should be eliminated? How would you design a system that performed the same function as the Krebs Cycle? No proof of anything, just conjecture. The only evidence to offer is the Krebs cycle itself. The Krebs Cycle takes glucose and extracts ATP which is used all throughout the cell to power reactions. For instance, ATP sparks the attachment of the various aminos to their tRNAs and then another to dislodge the amino once in position on the mRNA template and then another, maybe two depending, to attach the amino to the growing protein chain. Lots of other uses including RNA and DNA building. We see in the present Krebs Cycle, which is an aerobic process, the initial primitive anaerobic processes. Not to difficult to figure why since free oxygen wasn't much available for the first 2 billion years of cell evolution. Going further back we see the malate-fumarate-succinate steps which, the speculation goes, may be holdovers from when glucose wasn't so readily available thus relying on simpler compounds to power metabolism. When the abundance of glucose as the food of choice for cells developed these steps provided some advantage for reoxidizing an NADH molecule that came out of the glucose structure and so were retained. In essence glucose became this food of choice because there were processes already in place from simpler molecules. There is even the thought that since glucose is a plant sugar the photosynthetic processes were "geared" to its manufacture because a mechanism for its use was pretty much already in place. Who knows. From where I'm reading, your argument above is that the Krebs Cycle appears to use proteins that would make sense from the perspective of evolutionary history. But this is not what is at issue. We may discuss the arguments from homology, etc., but at present the issue is whether the Krebs Cycle is the molecular equivalent of the recurrent laryngeal nerve.
Is this the most efficient and effective way to break glucose into ATPs? With the evolutionary holdovers from pre-glucose and anaerobic processes I wouldn't think so, but then I'm not a biochemist. From a paper discussing the evolution of the Krebs Cycle (again, the discussion of the evolution of the Krebs Cycle is just a bit different than the issue of whether it is the molecular equivalent of something like the recurrent laryngeal nerve):
"The most novel result of our analysis is seeing how, with minimal new material, evolution created the most important pathway of metabolism, achieving the best chemically possible design. In this case, a chemical engineer who was looking for the best design of the process [Krebs Cycle process] could not have found a better design than the cycle which works in living cells." Source: The Puzzle of the Krebs Citric Acid Cycle: Assembling the Pieces of Chemically Feasible Reactions, and Opportunism in the Design of Metabolic Pathways During Evolution, 1996. Edited by Genomicus, : No reason given. Edited by Genomicus, : No reason given.
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Panda Member (Idle past 3741 days) Posts: 2688 From: UK Joined: |
Hi Genomicus,
Genomicus writes:
After reading that paper, I am unable to see how they justify the claim that a chemical engineer "could not have found a better design". "The most novel result of our analysis is seeing how, with minimal new material, evolution created the most important pathway of metabolism, achieving the best chemically possible design. In this case, a chemical engineer who was looking for the best design of the process [Krebs Cycle process] could not have found a better design than the cycle which works in living cells." Source: The Puzzle of the Krebs Citric Acid Cycle: Assembling the Pieces of Chemically Feasible Reactions, and Opportunism in the Design of Metabolic Pathways During Evolution, 1996. Could you maybe point me towards where they support that claim? I suspect that it is in fact their wording that is confusing.I think they perhaps would have been better writing "could not have found a better design using the material available." Because the quote you provided seems to contradict their previous statement: quote: "There is no great invention, from fire to flying, which has not been hailed as an insult to some god." J. B. S. Haldane
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AZPaul3 Member Posts: 8563 From: Phoenix Joined: Member Rating: 4.7
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Panda: I think they perhaps would have been better writing "could not have found a better design using the material available." Genomicus: We may discuss the arguments from homology, etc., but at present the issue is whether the Krebs Cycle is the molecular equivalent of the recurrent laryngeal nerve. Actually, I think you're both right. The present Krebs cycle may be as efficient as it can be considering its evolution but not as efficient as a deliberate re-design might achieve. But thinking on what Genomicus was asking for I now am reticent to put Krebs forward as such an example. You both win. And some say these discussions never achieve anything.
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Taq Member Posts: 10085 Joined: Member Rating: 5.1 |
From the perspective of the genome, we are not looking at salt crystals, since the genome encodes the information needed to construct molecular machinery. The genome IS a molecular machine, as you are defining it. The physical and chemical interactions that DNA participates in are no different than the physical and chemical interactions that proteins participate in. DNA folds around histones, forms stem-loop structures, binds to proteins and RNA's, recombines, and contorts. Nicks in DNA serve as triggers for apoptosis. DNA is as much of the machinery as any protein or any other cellular structure.
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
Hi Panda,
After reading that paper, I am unable to see how they justify the claim that a chemical engineer "could not have found a better design". Could you maybe point me towards where they support that claim? I agree that they do not explicitly defend the claim that "a chemical engineer could not have found a better design." The paper clearly explains how the Krebs Cycle is an optimal design based on the materials at hand, yet there is no reason to suppose the Krebs Cycle is not also optimal from an engineering standpoint. In other words, the statement that its design is a "very clear case of opportunism," does not, in itself, suggest that an engineer could construct a better Krebs Cycle. While one might argue that the signatures of opportunism are indicative of evolution, this does not show how the Krebs Cycle is a poor engineer solution. This is an another issue, IMHO.
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
The genome IS a molecular machine, as you are defining it. I'd say the genome is not a machine, but part of a machine; namely, the machine that is the cell. But that's just me. Others could argue that the various genomic interactions (e.g., DNA methylation) suggest that the genome is a molecular machine.
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Panda Member (Idle past 3741 days) Posts: 2688 From: UK Joined: |
Genomicus writes:
I agree - but that simply means their statement is not relevant to AZPaul3's question:
The paper clearly explains how the Krebs Cycle is an optimal design based on the materials at hand, yet there is no reason to suppose the Krebs Cycle is not also optimal from an engineering standpoint. In other words, the statement that its design is a "very clear case of opportunism," does not, in itself, suggest that an engineer could construct a better Krebs Cycle.AZPaul3 writes: Is this the most efficient and effective way to break glucose into ATPs? With the evolutionary holdovers from pre-glucose and anaerobic processes I wouldn't think so, but then I'm not a biochemist. Q: "Is this the most efficient and effective way to break glucose into ATPs?"A: "It is the most efficient and effective way to break glucose into ATPs given the material to hand. Do you see? It doesn't actually answer the question being asked.(It is instead answering the question: "Is this the most efficient and effective way to break glucose into ATPs given the materials to hand?".) As AZPaul3 says, there are inefficiencies in the Krebs Cycle.But your quote doesn't address those inefficiencies. "There is no great invention, from fire to flying, which has not been hailed as an insult to some god." J. B. S. Haldane
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Genomicus Member (Idle past 1970 days) Posts: 852 Joined: |
Do you see? It doesn't actually answer the question being asked. (It is instead answering the question: "Is this the most efficient and effective way to break glucose into ATPs given the materials to hand?".) On second thought, you're right. The provided quote doesn't address AZPaul's argument. Yet I still do not see where exactly the inefficiencies lie. Merely because the Krebs Cycle uses parts in other systems does not make it inefficient. What part of the Krebs Cycle is inefficient, or a sub-optimal design?
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