Design Framework for Evolution

I'm with the others on this one. What are these mechanisms? It seems very vague and not concrete at all.

I accept your admonishment on the use f the term improvements. That usage is quite sloppy. 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. You have some reason to believe that this cannot occur simply with a genome vulnerable to copying errors. Edited by NoNukes, : No reason given.

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Taq: Quite frankly, software does not have a lot in common with DNA.

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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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NoNukes: 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.

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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.

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NoNukes: You have some reason to believe that this cannot occur simply with a genome vulnerable to copying errors

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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.

I understand that, but I think what you are saying is nonsense. What would be the equivalent thing you would say about Brownian motion? 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? Right, but who is trying to do the latter? Edited by NoNukes, : No reason given.

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.

Your motorcycle is not designed to do so. But your motorcycle will convert gasoline into usable energy "all on its own." 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." 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? 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 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.

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. 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): 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.

Hi Genomicus, 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 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:

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In the Krebs cycle problem the intermediary stages were also useful, but for different purposes, and, therefore, its complete design was a very clear case of opportunism.

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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.

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.

Hi Panda, 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.

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.

I agree - but that simply means their statement is not relevant to AZPaul3's question: 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.

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?